# Alexander Young: early onset metastatic rectal cancer case Canonical website: https://youngcrc.com/ Release 1.16 · 8 October 2026. This Markdown view includes source-page text and the records loaded by the website. Full records and provenance remain in the linked JSON. My case and shared research data # Alexander Young: early onset metastatic rectal cancer case Two years ago, at the age of 35, I was diagnosed with metastatic rectal cancer. Unfortunately, I am still fighting it. I am sharing my treatment history, imaging, tissue and molecular data to help others study my case. Outside of being a cancer patient, I’m a statistical geneticist and an assistant professor in Human Genetics at UCLA:  [My personal website ](https://alextisyoung.com/). [Download my curated data ZIP ](https://youngcrc.com/downloads/curated-data.zip)[](https://alextisyoung.com/) ## My case at a glance Curated release Diagnosis Rectal adenocarcinoma Metastatic disease Mismatch repair pMMR / MSS Historical tissue testing Treatment biomarkers RAS / BRAF wild type Historical tissue testing Record period 2023–2026 Last curated 7 October 2026 Latest documented imaging ### Nodal progression on 28 September 2026 My PET-CT showed progression in multiple lymph-node regions after botensilimab / balstilimab. The report and treatment history are available; the latest scan images are not. [Explore the clinical record ](https://youngcrc.com/#timeline) This is my research record, not treatment advice. What I’ve shared ### Data for research Clinical events, imaging and pathology summaries 2,114 laboratory measurements, with assay-specific source records Specimens, assays and molecular findings Research evidence for vaccine targets Reviewed tumour and germline variant-call files Caris tumour DNA, Caris and Tempus RNA reads and alignments; matched-normal DNA My April 2026 PET-CT images and source reports CEA, TROP2 and cMET whole-slide pathology images from the liver metastasis [Browse my sequencing data ](https://youngcrc.com/#sequencing) Available and pending data Separate downloads total 35.38 GB across 35 files: six RNA FASTQs, six BAMs with indexes (including Natera matched-normal DNA), a Caris VCF with its index, 12 April PET-CT DICOM series, and CEA, TROP2 and cMET slides. Reports includes 24 PDFs and the JLF and Invoke HTML designs. Pending: additional Caris DNA reads, Natera tumour sequencing and the HER2 slide. June/September scan images are unavailable; April imaging includes selected series. [Full release status ](https://youngcrc.com/data/release_status.json). Plans and therapeutic evidence ### Treatment plans and options My plans and source-linked treatment evidence. Established options reviewed 8 October 2026; experimental candidates 7 October 2026. [Treatment evidence JSON ](https://youngcrc.com/data/clinical/treatment_options.json) Clinical record ## Treatment and disease timeline Evidence labels distinguish my reported plans from documented care. [Timeline JSON ](https://youngcrc.com/data/clinical/timeline.json) [Curated data and source documentation ](https://youngcrc.com/#research). Longitudinal results ## Laboratory measurements My UCLA and City of Hope results, with source dates, units and methods. Assays remain separate. Coverage is incomplete, and some original reports are unavailable. [Laboratory JSON ](https://youngcrc.com/data/clinical/laboratory_observations.json) Date precision matches the source; missing fields mean “not recorded.” Check original units and methods in the full record before comparing results. [Curated data and source documentation ](https://youngcrc.com/#research). Original evidence & research outputs ## Reports Key findings from my reports and research designs, grouped by type and provider. Each summary includes the specimen, date, limitations and original report. [Report catalogue JSON ](https://youngcrc.com/data/reports.json) Tumour profile & vaccine targets ## My molecular evidence My tumour findings, their evidence and connections to therapies. I preserve each report’s classification and distinguish clinical results from research predictions. [Summary JSON ](https://youngcrc.com/data/molecular/summary.json) Browse molecular source files Provider files by type and provider. [Reports ](https://youngcrc.com/#reports) contains the original documents; [Research & documentation ](https://youngcrc.com/#research) contains my detailed cross-provider audits. ### Molecular source inventory Files by subtype and provider. Download links appear only for verified public files. My sequencing and expression data ## Sequencing My DNA and RNA reads and alignments, with specimen, date, assay and reference details. Processed calls and expression tables are in [Molecular evidence ](https://youngcrc.com/#molecular). [All curated data ZIP ](https://youngcrc.com/downloads/curated-data.zip) ### Sequencing source inventory Files by subtype and provider. Download links appear only for verified public files. ### Sequencing source inventory Files by subtype and provider. Download links appear only for verified public files. My data by modality ## Pathology My whole-slide IHC images, downloaded separately from the curated ZIP. [Pathology summaries and documentation ](https://youngcrc.com/#research). [All curated data ZIP ](https://youngcrc.com/downloads/curated-data.zip) ### Sequencing source inventory Files by subtype and provider. Download links appear only for verified public files. My data by modality ## Imaging My CT and PET images, with dates and source details. Large files download separately from the curated ZIP. [Study summaries and documentation ](https://youngcrc.com/#research). [All curated data ZIP ](https://youngcrc.com/downloads/curated-data.zip) ### Sequencing source inventory Files by subtype and provider. Download links appear only for verified public files. My research and curated records ## Cross-provider research & documentation My research and cross-provider summaries, with sources, specimen links and evidence status. [All curated data ZIP ](https://youngcrc.com/downloads/curated-data.zip) Read before analysis ## Use, provenance and limitations [Website & tooling source ZIP ](https://youngcrc.com/downloads/source.zip) ### An identified, patient-led dataset I share these data under my own name for research and reanalysis. Sequencing, processed calls and native images are freely downloadable; some files remain pending. Genomic data can identify me and reveal inherited information. ### Evidence has a source and a status Stable identifiers link datasets to sources and specimens. I keep originals privately and publish reviewed copies with provider attribution and preparation notes. Findings are labelled clinical, research-derived, patient-reported or unresolved. Missing data do not mean a negative result. Older tissue may not represent a current node. Check specimens, collection/report dates and reference genomes before combining assays. Do not combine GRCh37/GRCh38 coordinates without documented conversion. ### Reuse and attribution My curated tables and explanatory text use [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/); website and release-tool code use MIT. Third-party reports, assay outputs and vaccine designs retain their own rights. Sharing vendor-processed VCFs, expression and alignments grants no license to proprietary methods. Research candidates do not establish a final manufactured product. Cite: Alexander Young. Open Cancer Data, release 1.16, 8 October 2026. Include the dataset filename and SHA-256 from the manifest in analyses. A DOI has not been assigned. ### Reproducibility The [manifest ](https://youngcrc.com/manifest.json) and [SHA-256 checksums ](https://youngcrc.com/checksums.sha256) document the [data archive ](https://youngcrc.com/downloads/curated-data.zip). The [source ZIP ](https://youngcrc.com/downloads/source.zip) contains the website, structured data, HTML report assets and release tools; PDFs download separately. Serve the extracted Invoke report through a local static server for offline use. Large files are outside both ZIPs. Find them in the manifest’s external_files and the [sequencing ](https://youngcrc.com/data/molecular/raw_release_catalog.json), [imaging ](https://youngcrc.com/data/imaging_release_catalog.json) and [pathology ](https://youngcrc.com/data/pathology_release_catalog.json) catalogues, with [checksums ](https://youngcrc.com/external-checksums.sha256). Downloads require no account. For large files, use curl -L -C - -O URL to resume downloads, then verify the published SHA-256 checksum. ### Known gaps ### Inspiration This independent project was inspired by [osteosarc.com ](https://osteosarc.com/). ## Clinical timeline ### 2024-03-18 — Initial rectosigmoid biopsy Superficial biopsy showed at least high-grade dysplasia in a tubulovillous adenoma, suspicious for invasion. Evidence: documented. Sources: CL-SRC-001. ### 2024-03-20 — Baseline CT staging Approximately 6 cm proximal rectal mass and indeterminate liver lesions; no definite intrathoracic metastatic disease. Evidence: documented. Sources: CL-SRC-003; CL-SRC-004. ### 2024-03-25 — Pelvic MRI staging Rectal MRI reported T3dN2Mx disease with involved circumferential resection margin and no sphincter involvement. Evidence: documented. Sources: CL-SRC-005. ### 2024-03-27 — Adenocarcinoma confirmed on repeat biopsy Moderately differentiated rectal adenocarcinoma; MLH1, MSH2, MSH6 and PMS2 nuclear expression retained. Evidence: documented. Sources: CL-SRC-002. ### 2024-03-27 — Liver MRI report Reported 23 mm left hepatic lesion, highly concerning for metastasis. Evidence: documented. Sources: CL-SRC-006. ### 2024-04-08 — Pelvic chemoradiotherapy Clinical history: capecitabine with 45 Gy in 25 fractions to pelvis/rectum, then a rectal boost to 50.4 Gy in 28 fractions total. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2024-05-20 — CT response after chemoradiation Decreased primary rectal mass size and enhancement, stable 22 mm segment 3 liver lesion, and no new lesions or progression. Evidence: documented. Sources: CL-SRC-253. ### 2024-06-04 — Six CAPOX cycles recorded Clinical history: six capecitabine/oxaliplatin cycles, June–September 2024. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2024-08-02 — CT response Primary CT reports: slight further decrease in rectal mass size and enhancement, unchanged 20 mm segment 3 liver lesion, no new lesions or intrathoracic metastases. Evidence: documented. Sources: CL-SRC-008; CL-SRC-251; CL-SRC-252. ### 2024-10-04 — Abdominal MRI response Segment 3 liver lesion slightly decreased to 17 mm with decreased diffusion restriction, remaining suspicious for metastasis; no new lesions. Evidence: documented. Sources: CL-SRC-250. ### 2024-10-11 — Pelvic MRI response Pelvic MRI: smaller rectal mass with residual tumor and incomplete response; suspicious extramesorectal nodes resolved and suspicious mesorectal nodes decreased. Evidence: documented. Sources: CL-SRC-008; CL-SRC-249. ### 2024-10-22 — Rectal and liver resection Rectal and left lateral liver resections: residual rectal adenocarcinoma and liver metastasis, negative margins; pathology stage ypT3N1aM1a. Evidence: documented. Sources: CL-SRC-008; CL-SRC-009. ### 2025-01-23 — Ileostomy reversal recorded Ileostomy takedown specimen collected January 23, 2025; January 28 pathology showed no dysplasia or malignancy. Evidence: documented. Sources: CL-SRC-007; CL-SRC-008; CL-SRC-239. ### 2025-03-31 — CT without recurrent or metastatic disease Primary CT reports: no recurrent disease or new metastases in abdomen/pelvis; no radiographic intrathoracic metastatic disease. Evidence: documented. Sources: CL-SRC-008; CL-SRC-245; CL-SRC-246. ### 2025-04-28 — Abdominal MRI without metastatic disease Primary abdominal MRI report: no abdominal metastatic disease after liver resection. Evidence: documented. Sources: CL-SRC-008; CL-SRC-244. ### 2025-07-03 — FDG-avid periportal/periceliac soft tissue New FDG-avid periportal/periceliac soft tissue concerning for metastatic disease; pelvic soft-tissue thickening was non-FDG avid and favored postsurgical change. Evidence: documented. Sources: CL-SRC-007; CL-SRC-008; CL-SRC-234. ### 2025-07-17 — Irinotecan and panitumumab started Clinical history: first irinotecan/panitumumab cycle. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2025-08-01 — Panitumumab held for rash Clinical history: irinotecan alone because of panitumumab-associated rash. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2025-09-08 — PET/CT suggests response Slightly decreased periportal/periceliac soft tissue size and decreased mild FDG uptake since July 3, suggesting treatment response. No definite new lesions or FDG-avid local rectal recurrence. Evidence: documented. Sources: CL-SRC-235. ### 2025-09-30 — Adaptive abdominal SBRT Clinical history: MR-guided upper-abdominal stereotactic radiotherapy, 50 Gy in five fractions, with daily adaptation. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2025-11-28 — City of Hope resection-slide review Outside review agreed with rectal and liver resection diagnoses; tissue collected October 22, 2024. Evidence: documented. Sources: CL-SRC-237. ### 2025-12 — Irinotecan and panitumumab resumed Clinical history: irinotecan/panitumumab restarted after radiation. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2025-12-23 — PET/CT with reduced uptake and an indeterminate finding Stable-size periportal/periceliac soft tissue with decreased mild uptake. New soft tissue and increased uptake around the proper hepatic and pancreaticoduodenal arteries favored post-radiation change, with follow-up requested to exclude recurrent disease. No definite FDG-avid local rectal recurrence. Evidence: documented. Sources: CL-SRC-236. ### 2026-01-22 — Partial resection-slide review Massachusetts General Hospital reviewed ten of thirty-nine rectal slides and one liver slide, confirming residual rectal adenocarcinoma and colorectal liver metastasis. Evidence: documented. Sources: CL-SRC-238. ### 2026-02-10 — Panitumumab alone recorded; irinotecan held Complete June oncology note: cycle 7 panitumumab alone; irinotecan held for abdominal pain. Assessment dates the hold to February 10, 2026. Evidence: clinician_reported_delivered. Sources: CL-SRC-008. ### 2026-03-06 — Hospital admission for upper gastrointestinal bleeding Clinical history: hospitalization for bleeding attributed to a duodenal ulcer. Evidence: clinician_reported_completed. Sources: CL-SRC-007; CL-SRC-008. ### 2026-03-10 — Chemotherapy hold recorded Complete June oncology chronology: chemotherapy held for abdominal pain on March 10, 2026. Evidence: clinician_reported_treatment_hold. Sources: CL-SRC-008. ### 2026-04-08 — New metabolically active periaortic nodes PET/CT showed new FDG-avid periaortic lymph nodes concerning for metastases, with no definite FDG-avid local rectal recurrence. Evidence: documented. Sources: CL-SRC-010. ### 2026-04-16 — Surveillance biopsies and colon-polyp pathology Peptic duodenitis, minimal chronic gastric inflammation and sessile serrated adenoma/polyp without cytologic dysplasia. Evidence: documented. Sources: CL-SRC-240. ### 2026-04-21 — Irinotecan and panitumumab resumed Clinical history: irinotecan/panitumumab resumed after progression. Evidence: clinician_reported_delivered. Sources: CL-SRC-007; CL-SRC-008. ### 2026-04-29 — HER2-negative result on archived liver tissue HER2 immunohistochemistry negative (HERACLES score 0) on liver tissue collected in October 2024. Evidence: documented. Sources: CL-SRC-009. ### 2026-05-06 — Irinotecan alone; panitumumab held Clinical history: irinotecan alone; panitumumab held for rash. Evidence: clinician_reported_delivered. Sources: CL-SRC-008. ### 2026-05-19 — Irinotecan and panitumumab recorded Clinical note: combination treatment recorded. Evidence: clinician_reported_delivered. Sources: CL-SRC-008. ### 2026-06-02 — Irinotecan recorded Clinical note: irinotecan cycle recorded; panitumumab administration unconfirmed. Evidence: clinician_reported_delivered. Sources: CL-SRC-008. ### 2026-06-11 — FDG avidity resolved in previously hypermetabolic nodes Primary June 11 PET/CT report: resolved FDG avidity in previously hypermetabolic retroperitoneal nodes; no new lesions or evidence of tumor progression. Evidence: documented. Sources: CL-SRC-008; CL-SRC-233. ### 2026-06-16 — Treatment hold and July BOT/BAL start planned June oncology plan: hold irinotecan/panitumumab and begin BOT/BAL in the UK on July 3, 2026. Subsequent dosing and actual start date unconfirmed. Evidence: clinician_reported_plan. Sources: CL-SRC-008. ### 2026-07-02 — Botensilimab and balstilimab course reported I report two cycles between July 2 and September 17, 2026. Evidence: patient_reported_administered. Sources: CL-SRC-012. ### 2026-09-28 — Progressive nodal disease on PET/CT PET/CT: progression in supraclavicular, mediastinal, retrocrural and retroperitoneal nodes. No suspicious liver lesion or focal osseous disease described; small subpleural lung nodules remained nonspecific. Evidence: documented. Sources: CL-SRC-011. ### Date unconfirmed — Rising circulating tumor DNA reported I report Signatera rising from 1.7 before botensilimab/balstilimab to 100 MTM/mL before the September 2026 PET/CT; exact collection dates are unconfirmed. Evidence: patient_reported_result. Sources: CL-SRC-012. ### Date unconfirmed — Recent clavicular-node biopsy reported I report a clavicular-node biopsy, with some material reserved for diagnostic pathology and some sent for tissue banking. Evidence: patient_reported_completed. Sources: CL-SRC-012. ### Date unconfirmed — Chemotherapy restart plan reported My plan is to restart irinotecan/panitumumab and potentially add capecitabine. Evidence: patient_reported_plan. Sources: CL-SRC-012; CL-SRC-254. ## My reported context and treatment plans I was 35 when diagnosed and am now 37. I have had no prior anti-VEGF treatment. Capecitabine may potentially be added; this is not confirmed treatment. These are patient-reported facts, reported 2026-10-07; sources: CL-SRC-254. ### Irinotecan + panitumumab, potentially adding capecitabine Status: My reported treatment plan. I plan to restart irinotecan and panitumumab, potentially adding capecitabine (Xeloda), to regain disease control. Previous treatment is documented; the restart date, final regimen and delivered doses remain unconfirmed. Rationale: Historical rectal-tumour reports describe RAS/BRAF wild-type disease, supporting consideration of EGFR-directed treatment. Current resistance testing matters after prior panitumumab. Evidence summary: Randomized evidence supports irinotecan–panitumumab activity in selected colorectal cancer. Observational CAPIRI–panitumumab evidence does not establish the benefit of adding capecitabine here. Timing: Disease-control treatment is planned soon; start date unconfirmed. Vaccine production can proceed alongside clinician-directed systemic care. Evidence needed: Confirm the delivered regimen and current resistance profile; older negative, low-tumour-fraction plasma tests cannot establish present sensitivity. Public caveat: Treatment delivery and benefit are not established by a plan. Source: [Tempus molecular and pharmacogenetic reports](reports/tempus/tempus.pdf) Source: [September 2026 PET/CT](reports/clinical/clinical_september_pet.pdf) Source: [PICCOLO: panitumumab plus irinotecan versus irinotecan](https://pmc.ncbi.nlm.nih.gov/articles/PMC3699713/) Source: [Effectiveness and safety of capecitabine, irinotecan and panitumumab in advanced colorectal cancer](https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2023.1138357/full) Source: [CHRONOS: ctDNA-guided panitumumab rechallenge](https://www.nature.com/articles/s41591-022-01886-0) ### JLF personalized peptide vaccine Status: Manufacturing reported; administration unconfirmed. My personalized peptide vaccine is designed; I understand manufacturing is underway. The JLF list records proposed precursors, HLA restrictions and epitopes. Final manufactured peptides and administration remain undocumented here. Rationale: Candidates aim to direct T cells against tumour-associated mutations. The recent node could help check that prioritized mutations and expressed sequences persist in current disease. Evidence summary: Small MSS colorectal-cancer studies show personalized peptides can induce T-cell responses. Clinical activity varies; survival benefit for this JLF design is unestablished. Timing: Manufacturing completion and first dose need confirmation; no delivery date is verified. Evidence needed: Reconcile final peptide sequences with the design laboratory and check retention and expression in current disease before locking the product. Public caveat: Candidate precursors are not a final batch-release specification, and immune responses are not equivalent to tumour control. Source: [JLF peptide candidate list](reports/jlf/peptide_candidate_list.html) Source: [Independent sequence questions and read evidence](data/molecular/vaccine_evidence.json) Source: [Preliminary clinical study of personalized neoantigen vaccine therapy for MSS advanced colorectal cancer](https://pubmed.ncbi.nlm.nih.gov/36795124/) Source: [Personalized neoantigen vaccine with or without pembrolizumab in MSS metastatic colorectal cancer — AACR 2025 CT012](https://aacrjournals.org/cancerres/article/85/8_Supplement_2/CT012/761393/Abstract-CT012-Personalized-neoantigen-vaccine) ### Invoke Bio / Aureon mRNA vaccine project Status: Research design available; update under consideration. The Invoke/Aureon report lists candidate rankings, peptide sequences and DNA/RNA evidence. I plan an mRNA vaccine and am considering updating targets from my recent nodal biopsy. A final construct, manufacturing release and administration remain undocumented. Rationale: An update could prioritize mutations expressed in the current metastasis while retaining useful candidates supported by earlier specimens. Evidence summary: Early clinical studies of other personalized mRNA vaccines show neoantigen-specific T-cell responses, including in MSS colorectal cancer. They support the biological rationale; this design and its individual clinical benefit remain unvalidated. Timing: Design and manufacturing milestones need confirmation; no first-dose date is verified. Evidence needed: Current-node DNA and bulk RNA can establish retained mutations and expressed sequences. If viable tissue permits, single-cell RNA/TCR profiling can add tumour and immune heterogeneity data, complementing bulk sequence evidence. Public caveat: The research report ranks targets; it does not establish current-node retention, HLA presentation or a manufactured mRNA product. Source: [Invoke Bio / Aureon vaccine target report](reports/invoke/aureon_vaccine_target_report.html) Source: [Independent sequence questions and read evidence](data/molecular/vaccine_evidence.json) Source: [Autogene cevumeran with or without atezolizumab in advanced solid tumors: phase 1 trial](https://www.nature.com/articles/s41591-024-03334-7) Full timeline: https://youngcrc.com/data/clinical/timeline.json ## Reports: pertinent results ### Caris molecular profiling of the initial rectal biopsy Type: DNA and RNA molecular profiling. Provider: Caris. Complete 23-page report: molecular findings, expression, methods and specimen limitations. - KRAS, NRAS and BRAF mutations not detected; microsatellite stable; low tumour mutational burden, 5 mutations/Mb. - Pathogenic APC p.S1411fs and p.V450fs, PTEN p.R335* and SOX9 c.432-2A>T; likely pathogenic SMARCA4 p.D1177Y. - ERBB2/HER2 and EGFR amplification and NTRK1/2/3, BRAF and RET fusions not detected. Low genomic loss of heterozygosity, 5%. - Predicted HLA-A A*02:01 / A*02:01; HLA-B B*07:02 / B*44:02; HLA-C C*03:04 / C*05:01. HLA-A loss of heterozygosity not detected. - FOLFIRSTai reported increased relative benefit for first-line FOLFOX plus bevacizumab in metastatic colorectal cancer. The superficial biopsy was predominantly intramucosal carcinoma and may not represent invasive or metastatic disease. FOLFIRSTai is a signature result, not evidence I received bevacizumab. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2; 3; 5 Report id: RPT-CARIS Collection date: 2024-03-27 Report date: 2026-06-03 Evidence class: clinical_laboratory_report Specimens: sample id: M-SAMPLE-001; label: Initial rectal primary biopsy; anatomical site: rectum; role: primary_tumour; collection date: 2024-03-27; provenance status: primary_Caris_report_confirmed Assay ids: M-ASSAY-001; M-ASSAY-002 Provenance summary: Rectal FFPE biopsy collected 27 March 2024. Report: https://youngcrc.com/reports/caris/caris.pdf ### Tempus xT, xR, DPYD and UGT1A1 reports Type: DNA and RNA molecular profiling. Provider: Tempus. Complete 17-page packet: 648-gene DNA panel, RNA analysis, HLA typing and pharmacogenetics. - Rectal resection: APC p.V450fs loss-of-function frameshift at 8.6% variant allele fraction; no reported pathogenic KRAS, NRAS or BRAF variant or copy-number change. - Microsatellite stable; low tumour mutational burden, 4.2 mutations/Mb. No reportable RNA rearrangement or altered splicing. - HLA-A A*02:01 / A*02:01; HLA-B B*07:02 / B*44:02; HLA-C C*03:04 / C*05:01. - No potential germline variant reported within the limited gene set. Somatic variants of unknown significance included CCDC6, ELF3, SMARCA4 and SOX9. - DPYD: none of five targeted variants detected. UGT1A1 *1/*28: predicted intermediate metabolizer; insufficient evidence for a dose change based on this genotype alone. Results concern historical rectal resection and matched-normal blood. Limited germline analysis does not exclude hereditary cancer risk. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2; 3; 9; 12; 14 Report id: RPT-TEMPUS Collection date: 2024-10-22 Report date: 2025-02-21 Evidence class: clinical_laboratory_report Specimens: sample id: M-SAMPLE-002; label: Rectal resection specimen; anatomical site: rectum; role: primary_tumour_resection; collection date: 2024-10-22; provenance status: primary_Tempus_and_BostonGene_reports_confirmed; sample id: M-SAMPLE-004; label: Tempus matched-normal blood; anatomical site: blood; role: matched_normal; collection date: 2025-01-28; provenance status: primary_Tempus_report_confirmed Assay ids: M-ASSAY-003; M-ASSAY-004 Provenance summary: Rectal resection collected 22 October 2024; matched-normal blood, 28 January 2025. Summary and RNA report dated 21 February 2025; DNA and pharmacogenetic reports, 15 February 2025. Report: https://youngcrc.com/reports/tempus/tempus.pdf ### BostonGene Tumor Portrait through Valius Type: DNA and RNA molecular profiling. Provider: Valius / Kandinsky / BostonGene. 25-page genomic/transcriptomic profile with tumour microenvironment analysis and methods. - October 2024 rectal resection: estimated tumour content 15%; tumour mutational burden 0.42 mutations/Mb. Copy-number alterations and MSI unreported because tumour content was low. - No oncogenic NTRK1/2/3 or RET fusion or pathogenic/likely pathogenic germline variant in the limited reportable set. No biomarker-based treatment option suggested. - RNA microenvironment classification: fibrotic, immune non-inflamed; low MHC-I and medium PD-L1 expression signatures; enriched fibroblasts and endothelial cells. - HLA-A*02:01 identified for trial matching; confirmation of predicted HLA typing recommended. Residual rectal tumour after chemoradiation, with 15% tumour content. Low purity limits mutation detection and interpretation of TMB. Bulk-RNA microenvironment signatures include stromal and immune cells and do not establish tumour-cell MHC-I loss or the immune state of current metastases. Historical external HER2/MMR entries are not new tests of this specimen. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2; 3; 4 Report id: RPT-VALIUS-PORTRAIT Collection date: 2024-10-22 Report date: 2026-09-30 Evidence class: clinical_laboratory_report Specimens: sample id: M-SAMPLE-002; label: Rectal resection specimen; anatomical site: rectum; role: primary_tumour_resection; collection date: 2024-10-22; provenance status: primary_Tempus_and_BostonGene_reports_confirmed; sample id: M-SAMPLE-011; label: BostonGene matched-normal saliva; anatomical site: saliva; role: matched_normal; collection date: 2026-05-13; provenance status: primary_BostonGene_report_confirmed Assay ids: M-ASSAY-019 Provenance summary: BostonGene: rectal FFPE resection collected 22 October 2024; saliva normal, 13 May 2026. Distinct from liver tissue used for Valius single-cell/IHC reports. Report: https://youngcrc.com/reports/valius/valius_portrait.pdf ### Baseline CT abdomen and pelvis report Type: Imaging · CT. Provider: Clinical records & imaging. March 2024 CT: rectal mass and indeterminate liver lesions. - Proximal rectal mass approximately 5.9 × 3.5 × 5 cm; adjacent 2.2 cm pelvic nodule could be part of the mass or a node. - Indeterminate liver lesions, including a 23 × 20 mm left-lobe lesion not clearly a cyst. - Hepatic and pelvic MRI recommended to clarify liver lesions and pelvic nodal involvement. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-BASELINE-CT-ABDOMEN Report date: 2024-03-20 Evidence class: clinical_imaging_report Provenance summary: Study/report 20 March 2024; three-page portal print. Report: https://youngcrc.com/reports/clinical/clinical_baseline_ct_abdomen.pdf ### Baseline CT chest report Type: Imaging · CT. Provider: Clinical records & imaging. March 2024 CT chest findings and acquisition details. - No definite intrathoracic metastatic disease or thoracic lymphadenopathy. - Left-upper-lobe micronodule, 1 mm: most likely a mucus plug, not a definite metastasis. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-BASELINE-CT-CHEST Report date: 2024-03-20 Evidence class: clinical_imaging_report Provenance summary: Study/report 20 March 2024; three-page portal print. Report: https://youngcrc.com/reports/clinical/clinical_baseline_ct_chest.pdf ### Baseline MRI abdomen report Type: Imaging · MRI. Provider: Clinical records & imaging. March 2024 MRI: suspected hepatic metastasis. - Left hepatic lesion, 23 × 22 mm, with restricted diffusion: highly concerning for metastasis. - Additional subcentimetre right-lobe focus too small to characterize. - Itching and hives documented after Eovist contrast. Source discrepancy retained: the main lesion is labelled segment 3 in the body and segment 2 in the impression. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-BASELINE-MRI-LIVER Report date: 2024-03-27 Evidence class: clinical_imaging_report Provenance summary: Signed 27 March 2024; ordered 26 March. Acquisition date unverified. Report: https://youngcrc.com/reports/clinical/clinical_baseline_mri_liver.pdf ### Baseline MRI pelvis report Type: Imaging · MRI. Provider: Clinical records & imaging. March 2024 rectal MRI: stage, nodes and margins. - Upper rectal tumour approximately 5.5 cm long; MRI stage T3dN2Mx; extramural invasion 26 mm. - Circumferential resection margin involved; sphincter uninvolved. Extramural venous invasion/tumour deposits and suspicious regional nodes described. - Possible invasion into an adjacent sigmoid loop remained uncertain; abutment/scan technique could explain the appearance. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-BASELINE-MRI-PELVIS Report date: 2024-03-25 Evidence class: clinical_imaging_report Provenance summary: Study/signed report 25 March 2024; three-page portal print. Report: https://youngcrc.com/reports/clinical/clinical_baseline_mri_pelvis.pdf ### April 2026 FDG PET/CT report Type: Imaging · PET/CT. Provider: Clinical records & imaging. Four-page portal report with imaging measurements and impression. - New FDG-avid periaortic nodes concerning for metastases: right para-aortic 7 × 15 mm, SUVmax 4.3; left para-aortic 8 × 12 mm, SUVmax 3.6. - Periportal/periceliac soft tissue remained about 16 mm, with a small uptake increase to SUVmax 2.1. - Postoperative rectal changes without definite FDG-avid local recurrence. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 2; 3 Report id: RPT-CLINICAL-APRIL-PET Report date: 2026-04-08 Evidence class: clinical_imaging_report Provenance summary: Study 8 April 2026. Portal navigation links removed; findings and acquisition details retained. Report: https://youngcrc.com/reports/clinical/clinical_april_pet.pdf ### June 2026 FDG PET/CT report Type: Imaging · PET/CT. Provider: Clinical records & imaging. Complete three-page report: response of previously hypermetabolic retroperitoneal nodes. - FDG avidity resolved in previously hypermetabolic retroperitoneal nodes; no new lesions or evidence of progression. - Residual nodes mildly prominent: right para-aortic 8 × 14 mm, SUVmax 1.8; left para-aortic 8 × 12 mm, SUVmax 1.5. - Periportal/periceliac soft tissue stable in size, with low uptake, SUVmax 1.6. Comparison dates are inconsistent; no missing comparison measurement is inferred. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 2; 3 Report id: RPT-CLINICAL-JUNE-PET Report date: 2026-06-11 Evidence class: clinical_imaging_report Provenance summary: Study/final signatures 11 June 2026. Original comparison-date inconsistencies and clinical history retained; neither establishes procedure or administration dates. Source ids: CL-SRC-233 Report: https://youngcrc.com/reports/clinical/portal_ucla_pet_2026_06_11.pdf ### September 2026 FDG PET/CT report Type: Imaging · PET/CT. Provider: Clinical records & imaging. Two-page signed report: nodal progression above and below the diaphragm. - Metabolically active nodal progression above and below the diaphragm: new supraclavicular, posterior mediastinal and retrocrural nodes; recurrent/more numerous retroperitoneal nodes. - Examples: left supraclavicular cluster 14 mm, SUVmax 3.2; aortocaval cluster 14 mm, SUVmax 8.2; left para-aortic cluster 13 mm, SUVmax 7.9. - No suspicious liver lesion or focal suspicious bone lesion described. Nonspecific small subpleural lung nodules; monitoring recommended. - Left supraclavicular nodes accessible for ultrasound-guided biopsy. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-SEPTEMBER-PET Report date: 2026-09-28 Evidence class: clinical_imaging_report Provenance summary: Study and sign-out 28 September 2026. Original wording and historical indication dates retained without correction. Report: https://youngcrc.com/reports/clinical/clinical_september_pet.pdf ### Valius cell surface target report Type: Integrated cell-surface target analysis. Provider: Valius / Kandinsky / BostonGene. Complete 33-page report: single-cell expression, target staining and therapeutic hypotheses. - Archived liver single-cell analysis: 92,897 cells, including 1,018 classified as tumour cells. - Single-cell expression: MET 41%, CEACAM5 40%, TROP-2 55%, EPCAM 68% and EPHA2 71% of tumour cells. - Protein staining: CEACAM5 H-score 300, 100% strong; MET H-score 160, 60% moderate and 40% weak cytoplasmic; TROP-2 H-score 20, 10% moderate membranous. - HER2 protein staining negative despite RNA expression in some tumour cells. MET and CEACAM5 prioritized as therapeutic research hypotheses. October 2024 liver tissue. Whole-exome and whole-transcriptome sequencing had failed quality control at the time; single-cell profiling and therapeutic hypotheses are investigational. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 4; 5; 9; 11; 13; 15; 20; 33 Report id: RPT-VALIUS Collection date: 2024-10-22 Report date: 2026-09 Evidence class: investigational_integrated_report Specimens: sample id: M-SAMPLE-003; label: Liver metastasis resection specimen; anatomical site: liver; role: metastasis; collection date: 2024-10-22; provenance status: previous_report_review Assay ids: M-ASSAY-010; M-ASSAY-011 Provenance summary: Liver FFPE tissue collected 22 October 2024; 10x Genomics Flex v2. Exact single-cell aliquot-to-block linkage not supplied. Report: https://youngcrc.com/reports/valius/valius.pdf ### Caris Assure blood report, January 2026 Type: Liquid biopsy · ctDNA and plasma profiling. Provider: Caris. Complete four-page report and two-page technical appendix. - Estimated tumour fraction 0.0%; no pathogenic tumour-derived somatic variant or therapy-associated biomarker detected. - Blood tumour mutational burden and microsatellite instability indeterminate—not low TMB or confirmed microsatellite stability. - No incidental pathogenic germline or clonal-haematopoiesis variant detected within the reportable set. DPYD: no detected variant, activity score 2.0, normal-metabolizer phenotype. - Predicted HLA-A A*02:01 / A*02:01; HLA-B B*44:02 / B*07:02; HLA-C C*05:01 / C*03:04. Low tumour fraction can cause false negatives. Limited incidental germline screening does not exclude hereditary risk. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CARIS-ASSURE Collection date: 2026-01-27 Report date: 2026-02-06 Evidence class: clinical_laboratory_report Provenance summary: Blood collected 27 January 2026. Alternate portal copies represent the same specimen. Source ids: CL-SRC-243 Report: https://youngcrc.com/reports/caris/portal_caris_assure_2026_02_06.pdf ### Guardant360 Liquid report, December 2025 Type: Liquid biopsy · ctDNA and plasma profiling. Provider: Guardant Health. Complete seven-page report: somatic, epigenetic and pharmacogenomic findings; methods. - No reportable somatic alteration with an associated therapy; estimated tumour fraction <0.05%, biomarker-negative confidence <90%. - Blood tumour mutational burden not evaluable; MSI-High not detected. TRAF2 T113I at 1.7%: variant of uncertain significance. - UGT1A1 *1/*28 and CYP2D6 *1/*4: intermediate-metabolizer genotypes. No abnormal DPYD variant detected among reportable alleles. - HLA-A A*02:01 / A*02:01; HLA-B B*07:02 / B*44:02; HLA-C C*03:04 / C*05:01. Essentially undetectable tumour DNA (<0.05% estimated tumour fraction) limits negative findings. TRAF2 at 1.7% cfDNA allele fraction is not confirmed tumour-derived; allele fraction and tumour fraction are different measurements. This assay does not establish current tumour genotype or absence of disease. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2; 3 Report id: RPT-GUARDANT360-LIQUID Collection date: 2025-12-18 Report date: 2025-12-24 Evidence class: clinical_laboratory_report Provenance summary: Low-fraction plasma profile: tumour fraction <0.05%, biomarker-negative confidence <90%; blood TMB not evaluable, MSI-High not detected; TRAF2 T113I VUS. Source ids: CL-SRC-242 Report: https://youngcrc.com/reports/guardant/portal_guardant_2025_12_24.pdf ### Natera Signatera report and historical ctDNA results Type: Liquid biopsy · ctDNA and plasma profiling. Provider: Natera. Two-page report: positive 1.69 MTM/mL on 16 June 2026, 12 historical results and full assay limitations. - 16 June 2026 plasma: ctDNA positive, 1.69 mean tumour molecules/mL (MTM/mL). - Historical values: 68.63 MTM/mL on 31 March 2026, 13.31 on 17 March, 0.00 on 27 January; 12 dated draws listed. - A full panel of 16 bespoke assays could not be designed from the tumour section, potentially reducing sensitivity. Tumour-informed monitoring, not broad resistance genotyping. Negative results do not exclude cancer; single MTM/mL values should not be compared across patients. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-NATERA-SIGNATERA Collection date: 2026-06-16 Report date: 2026-06-23 Evidence class: clinical_laboratory_report Specimens: sample id: M-SAMPLE-010; label: Rectal resection block B7 — Natera assay design; anatomical site: rectum; role: primary_tumour_resection; collection date: 2024-10-22; provenance status: primary_Signatera_report_confirmed; sample id: M-SAMPLE-012; label: Natera Signatera plasma — 16 June 2026; anatomical site: blood_plasma; role: ctDNA_monitoring; collection date: 2026-06-16; provenance status: primary_Signatera_report_confirmed Assay ids: M-ASSAY-018 Provenance summary: Plasma collected 16 June 2026. Assay-design tissue: rectal resection section collected 22 October 2024, distinct from liver material. Exact sequencing BAM IDs absent from the report. Report: https://youngcrc.com/reports/natera/natera_signatera.pdf ### Tempus xM / Personalis amended ctDNA report Type: Liquid biopsy · ctDNA and plasma profiling. Provider: Tempus. Two amended pages from a five-page packet; blank and superseded pages omitted. - Tumour-informed ctDNA detected: 245 parts per million (PPM), plasma collected 18 December 2025. - Collection date amended from 19 to 18 December; one specimen/result, not a second draw. PPM differs from Signatera MTM/mL. The amendment sentence conflicts with the February 2026 header/signature. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-TEMPUS-PERSONALIS-AMENDED Collection date: 2025-12-18 Report date: 2026-02-27 Evidence class: clinical_laboratory_report Provenance summary: One specimen/result: 245 PPM. Collection corrected from 19 to 18 December 2025. Header/signature dated 27 February 2026; amendment sentence prints 2025-02-27. Source ids: CL-SRC-241 Report: https://youngcrc.com/reports/tempus/portal_personalis_amended_2026_02_27.pdf ### City of Hope review of rectal and liver resection slides Type: Pathology · Histology and slide reviews. Provider: Clinical records & imaging. Complete two-page outside review of four resection slides. - Review agreed with residual moderately differentiated colorectal adenocarcinoma with mucinous features invading pericolorectal fat; liver slides showed metastatic adenocarcinoma consistent with colorectal origin. - Stage ypT3 pN1a pM1a; partial treatment response, score 2; multiple tumour deposits; 1 of 12 regional nodes positive. - Negative rectal/liver margins and lymphovascular/perineural invasion recorded from the original resection report. Four-slide review of archived tissue; several findings are by report, not a new complete specimen examination. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-CITY-OF-HOPE-PATHOLOGY Collection date: 2024-10-22 Report date: 2025-11-28 Evidence class: clinical_pathology_review Provenance summary: Archived tissue collected 22 October 2024; four slides reviewed 28 November 2025. Several measurements, margins and 1-of-12 node count are from the original report. Source ids: CL-SRC-237 Report: https://youngcrc.com/reports/clinical/portal_city_of_hope_pathology_2025_11_28.pdf ### Initial rectosigmoid biopsy pathology Type: Pathology · Histology and slide reviews. Provider: Clinical records & imaging. Two-page biopsy report: MMR immunohistochemistry and sampling limitations. - At least high-grade dysplasia in a tubulovillous adenoma; suspicious for invasive adenocarcinoma. - MLH1, MSH2, MSH6 and PMS2 nuclear expression retained; no mismatch-repair protein loss. The superficial biopsy could not establish definite invasion; the report cautions against overinterpreting MMR in this sampling context. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-INITIAL-BIOPSY Collection date: 2024-03-18 Report date: 2024-03-21 Evidence class: clinical_pathology_report Provenance summary: Collected 18 March 2024; histology signed 20 March; MMR addendum 21 March 2024. Report: https://youngcrc.com/reports/clinical/clinical_initial_biopsy.pdf ### Repeat rectal biopsy pathology Type: Pathology · Histology and slide reviews. Provider: Clinical records & imaging. Two-page report: moderately differentiated adenocarcinoma and intact MMR proteins. - Repeat rectal biopsy confirmed moderately differentiated adenocarcinoma arising in a tubulovillous adenoma with high-grade dysplasia. - MLH1, MSH2, MSH6 and PMS2 nuclear expression retained; no mismatch-repair protein loss. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2 Report id: RPT-CLINICAL-REPEAT-BIOPSY Collection date: 2024-03-27 Report date: 2024-03-29 Evidence class: clinical_pathology_report Specimens: sample id: M-SAMPLE-001; label: Initial rectal primary biopsy; anatomical site: rectum; role: primary_tumour; collection date: 2024-03-27; provenance status: primary_Caris_report_confirmed Provenance summary: Collected 27 March 2024; signed 29 March 2024. Corresponds to the initial-primary material profiled by Caris. Report: https://youngcrc.com/reports/clinical/clinical_repeat_biopsy.pdf ### Liver HER2 add-on and original resection pathology Type: Pathology · Immunohistochemistry. Provider: Clinical records & imaging. Six-page packet: HER2 staining, rectal/liver resection pathology, stage and margins. - Archived liver HER2: IHC 0, negative by HERACLES criteria. - Rectal resection: residual moderately differentiated adenocarcinoma with treatment-associated mucinous features; partial treatment response, score 2. - Pathologic stage ypT3N1aM1a; 1 of 12 regional nodes positive, numerous tumour deposits, extramural venous and perineural invasion. - Negative rectal and liver margins; closest rectal circumferential margin 2 mm. Liver resection confirmed metastatic colorectal adenocarcinoma. The April 2026 HER2 add-on used October 2024 tissue; reaccession was not a new collection. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2; 3; 4; 6 Report id: RPT-CLINICAL-HER2-PATHOLOGY Collection date: 2024-10-22 Report date: 2026-04-29 Evidence class: clinical_pathology_report Specimens: sample id: M-SAMPLE-002; label: Rectal resection specimen; anatomical site: rectum; role: primary_tumour_resection; collection date: 2024-10-22; provenance status: primary_Tempus_and_BostonGene_reports_confirmed; sample id: M-SAMPLE-003; label: Liver metastasis resection specimen; anatomical site: liver; role: metastasis; collection date: 2024-10-22; provenance status: previous_report_review Provenance summary: HER2 add-on reported 29 April 2026 on archived liver tissue. Includes pathology from 22 October 2024 surgery, signed 28 October 2024. Report: https://youngcrc.com/reports/clinical/clinical_her2_pathology.pdf ### Valius / Peninsula Pathologists CEA staining Type: Pathology · Immunohistochemistry. Provider: Valius / Kandinsky / BostonGene. CEA IHC: H-score 300; 100% strong cytoplasmic/membranous tumour staining. - CEA/CEACAM5 tumour H-score 300: 100% strong (3+) cytoplasmic and membranous staining. - Stroma negative. Archived liver block C4 adequate for IHC; approximately 5% viable tumour in a predominantly acellular mucinous lesion. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1 Report id: RPT-VALIUS-CEA Collection date: 2024-10-22 Evidence class: clinical_pathology_report Specimens: sample id: M-SAMPLE-003; label: Liver metastasis resection specimen; anatomical site: liver; role: metastasis; collection date: 2024-10-22; provenance status: previous_report_review Assay ids: M-ASSAY-011 Provenance summary: Liver left lateral segment FFPE; estimated viable tumour 5%. Collected 22 October 2024 per resection pathology; reaccessioned 28 April 2026. Issue date absent. Report: https://youngcrc.com/reports/valius/valius_cea.pdf ### Valius / Peninsula Pathologists HER2 staining Type: Pathology · Immunohistochemistry. Provider: Valius / Kandinsky / BostonGene. HER2 IHC 0, H-score 0; assay and scoring details. - HER2 IHC 0, tumour H-score 0: no tumour or stromal staining; negative by colorectal HERACLES criteria. - Archived liver block C4: approximately 5% viable tumour; pathologist considered it adequate for IHC. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1 Report id: RPT-VALIUS-HER2 Collection date: 2024-10-22 Evidence class: clinical_pathology_report Specimens: sample id: M-SAMPLE-003; label: Liver metastasis resection specimen; anatomical site: liver; role: metastasis; collection date: 2024-10-22; provenance status: previous_report_review Assay ids: M-ASSAY-011 Provenance summary: Liver left lateral segment FFPE; estimated viable tumour 5%. Collected 22 October 2024; 28 April 2026 is the reaccession date, not new surgery. Report: https://youngcrc.com/reports/valius/valius_her2.pdf ### Valius / Peninsula Pathologists TROP-2 staining Type: Pathology · Immunohistochemistry. Provider: Valius / Kandinsky / BostonGene. TROP-2 H-score 20; moderate membranous staining in 10% of tumour cells. - TROP-2 tumour H-score 20: 10% moderate (2+) membranous staining; 90% negative. - Weak cytoplasmic staining in about 10% excluded from scoring. Stroma negative. The report states that TROP-2 staining has no established relationship with treatment response in colorectal cancer. Archived liver tissue, not a current-node assay. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1 Report id: RPT-VALIUS-TROP2 Collection date: 2024-10-22 Evidence class: clinical_pathology_report Specimens: sample id: M-SAMPLE-003; label: Liver metastasis resection specimen; anatomical site: liver; role: metastasis; collection date: 2024-10-22; provenance status: previous_report_review Assay ids: M-ASSAY-011 Provenance summary: Liver left lateral segment FFPE; estimated viable tumour 5%. Collected 22 October 2024; reaccessioned 28 April 2026. Report: https://youngcrc.com/reports/valius/valius_trop2.pdf ### Valius / Peninsula Pathologists cMET staining Type: Pathology · Immunohistochemistry. Provider: Valius / Kandinsky / BostonGene. cMET H-score 160; 60% 2+, 40% 1+, 0% 3+; cytoplasmic tumour staining. - cMET tumour H-score 160: 60% moderate (2+), 40% weak (1+), no strong (3+) staining. - Cytoplasmic staining; stroma negative. Archived liver block C4: about 5% viable tumour; adequate for IHC. The report cautions that IHC does not reliably establish MET exon-14 alteration or amplification. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1 Report id: RPT-VALIUS-MET Collection date: 2024-10-22 Evidence class: clinical_pathology_report Specimens: sample id: M-SAMPLE-003; label: Liver metastasis resection specimen; anatomical site: liver; role: metastasis; collection date: 2024-10-22; provenance status: previous_report_review Assay ids: M-ASSAY-011 Provenance summary: Liver left lateral segment FFPE; estimated viable tumour 5%. Collected 22 October 2024; reaccessioned 28 April 2026. Staining location/intensity retained as reported. Report: https://youngcrc.com/reports/valius/valius_met.pdf ### TrufflePig exploratory expression analysis Type: RNA expression analysis. Provider: TrufflePig. 30-page research analysis: sample composition, expression, candidate targets and reference-tissue expression. - Expression classification most strongly supported rectal adenocarcinoma (READ). Estimated composition: 45% tumour, 30% stroma, 25% immune cells; tumour-purity estimates ranged from 26% to 71%. - Stromal and immune signals enriched 8.29-fold and 1.43-fold, respectively, versus TCGA READ. - Hypoxia-associated expression 3.21 times the cohort median; interferon response nearer baseline at 1.39-fold. - Research targets included CEACAM5, CD46, IGF1R, FGFR2 and EGFR, compared with colorectal cancer and healthy-tissue expression references. Bulk-RNA model estimates, not measured tumour-cell counts or confirmed protein targets. Source specimen and inputs remain unverified. Summary basis: Report summary; no cross-provider interpretation. Summary pages: 1; 2; 6; 7; 9; 10; 30 Report id: RPT-TRUFFLEPIG Evidence class: exploratory_research_report Provenance summary: Exploratory analysis; exact specimen, processing date and input manifest absent from the supplied PDF. Report: https://youngcrc.com/reports/trufflepig/trufflepig.pdf ### Invoke Bio / Aureon multi-sample vaccine target report Type: Vaccine designs. Provider: Invoke Bio / Aureon. Interactive research report: candidate rankings, sequences, expression and immunogenicity figures. All 250 embedded IGV sessions omitted; cells labelled “Snapshot omitted”. - Tier-ranked multi-sample neoantigen candidates with DNA/RNA allele fractions, expression, proposed 25-mer sequences and predicted CD8/CD4 epitopes. - Leading candidates include STAG3 p.D893Y, KLHL26 p.V126M and PRKDC stop-loss; epitope tables list HLA restrictions and candidate probabilities. - CD8/CD4 probabilities and immunogenicity figures are model predictions, not measured immune recognition. Historical research design with unresolved input mapping; candidates do not establish current-node retention, antigen presentation or a final manufactured vaccine. Public copy omits alignment snapshots. Summary basis: Report summary; no cross-provider interpretation. Summary section: Integrated candidate and epitope tables; expression and immunogenicity figures Report id: RPT-INVOKE Report date: 2026-09-28 Evidence class: Research vaccine-design report Specimens: sample id: M-SAMPLE-001; label: Initial rectal primary biopsy; anatomical site: rectum; role: primary_tumour; collection date: 2024-03-27; provenance status: primary_Caris_report_confirmed; sample id: M-SAMPLE-008; label: Normal material used in Invoke embedded tracks; anatomical site: not_confirmed; role: normal_label_in_research_report; collection date: Not recorded; provenance status: provider_confirmation_requested Assay ids: M-ASSAY-012; M-ASSAY-013; M-ASSAY-014; M-ASSAY-017 Provenance summary: Earlier read audits support selected primary-biopsy input linkage. Complete input manifest and normal-sample identity remain unresolved. Report: https://youngcrc.com/reports/invoke/aureon_vaccine_target_report.html ### JLF peptide candidate list Type: Vaccine designs. Provider: JLF. 20 precursor candidates, HLA restrictions and source notes. HTML preserves red class-I epitopes, bold class-II epitopes, underlined variant residues and green driver-gene fills. - 20 proposed peptide precursors with flanking amino-acid sequences and HLA restrictions. - Candidates include APC, SMAD4, CCDC6, SMARCA4 and ELF3. Online tables retain class-I/class-II epitope and variant-residue annotations. - Class-I restrictions include A*02:01, B*07:02, B*44:02, C*03:04 and C*05:01. Some rows specify class-II DPA1*01:03-DPB1*02:01 or DQA1*01:02-DQB1*06:02. Historical, undated candidate design; does not identify final manufactured peptides or confirm vaccination. Summary basis: Report summary; no cross-provider interpretation. Summary section: Candidate table and source notes Report id: RPT-JLF Evidence class: Research peptide-design workbook rendering Specimens: sample id: M-SAMPLE-001; label: Initial rectal primary biopsy; anatomical site: rectum; role: primary_tumour; collection date: 2024-03-27; provenance status: primary_Caris_report_confirmed Assay ids: M-ASSAY-016 Provenance summary: Undated, patient-supplied design workbook based on historical tumour sequencing. Report: https://youngcrc.com/reports/jlf/peptide_candidate_list.html Full report metadata: https://youngcrc.com/data/reports.json ## Molecular evidence ```json { "finding_id": "M-FINDING-001", "sample_id": "M-SAMPLE-001", "assay_id": "M-ASSAY-001", "feature": "Microsatellite status", "value": "MSS", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-001", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Historical primary specimen; not a new metastatic assay." } ``` ```json { "finding_id": "M-FINDING-002", "sample_id": "M-SAMPLE-001", "assay_id": "M-ASSAY-001", "feature": "Tumour mutational burden", "value": 5, "unit": "mutations/Mb", "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-001", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Assay-specific value; not directly interchangeable with another platform." } ``` ```json { "finding_id": "M-FINDING-003", "sample_id": "M-SAMPLE-002", "assay_id": "M-ASSAY-003", "feature": "Tumour mutational burden", "value": 4.2, "unit": "mutations/Mb", "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-002", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Assay-specific value from resection profiling." } ``` ```json { "finding_id": "M-FINDING-004", "sample_id": "M-SAMPLE-001", "assay_id": "M-ASSAY-001", "feature": "KRAS/NRAS/BRAF clinical status", "value": "wild_type_reported", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-001", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Does not exclude acquired resistance after subsequent anti-EGFR exposure." } ``` ```json { "finding_id": "M-FINDING-005", "sample_id": "M-SAMPLE-001", "assay_id": "M-ASSAY-001", "feature": "ERBB2 amplification", "value": "not_detected_reported", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-001", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "RNA expression alone must not be labelled gene amplification." } ``` ```json { "finding_id": "M-FINDING-006", "sample_id": "M-SAMPLE-001", "assay_id": "M-ASSAY-001", "feature": "HLA-A loss of heterozygosity", "value": "negative_reported", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-001", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Does not establish intact class-I/class-II antigen processing across all tumour sites." } ``` ```json { "finding_id": "M-FINDING-007", "sample_id": "M-SAMPLE-003", "assay_id": "M-ASSAY-011", "feature": "CEACAM5 IHC H-score", "value": 300, "unit": "H-score", "evidence_class": "previous_research_report_extraction", "source_ids": [ "M-SOURCE-003" ], "current_node_status": "not_assessed_here", "notes": "Prior review described 100% 3+ staining. Current-node confirmation and trial-specific assay criteria remain separate." } ``` ```json { "finding_id": "M-FINDING-008", "sample_id": "M-SAMPLE-003", "assay_id": "M-ASSAY-011", "feature": "MET IHC H-score", "value": 160, "unit": "H-score", "evidence_class": "previous_research_report_extraction", "source_ids": [ "M-SOURCE-003" ], "current_node_status": "not_assessed_here", "notes": "Prior review described 60% 2+ and 40% 1+, no 3+, with cytoplasmic staining. This does not establish MET amplification or a particular ADC eligibility score." } ``` ```json { "finding_id": "M-FINDING-009", "sample_id": "M-SAMPLE-003", "assay_id": "M-ASSAY-011", "feature": "TROP2 IHC H-score", "value": 20, "unit": "H-score", "evidence_class": "previous_research_report_extraction", "source_ids": [ "M-SOURCE-003" ], "current_node_status": "not_assessed_here", "notes": "Historical metastatic specimen; staining details should be verified against original assay/images." } ``` ```json { "finding_id": "M-FINDING-010", "sample_id": "M-SAMPLE-003", "assay_id": "M-ASSAY-011", "feature": "HER2 IHC score", "value": 0, "unit": "IHC category", "evidence_class": "previous_research_report_extraction", "source_ids": [ "M-SOURCE-003" ], "current_node_status": "not_assessed_here", "notes": "Do not infer HER2 positivity from bulk RNA expression." } ``` ```json { "finding_id": "M-FINDING-011", "sample_id": "M-SAMPLE-002", "assay_id": "M-ASSAY-003", "feature": "HLA-A", "value": "A*02:01 / A*02:01", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-002", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Concordant in previous Caris/Tempus report review. Full clinical class-II typing is not supplied here." } ``` ```json { "finding_id": "M-FINDING-012", "sample_id": "M-SAMPLE-002", "assay_id": "M-ASSAY-003", "feature": "HLA-B", "value": "B*07:02 / B*44:02", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-002", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Concordant in previous Caris/Tempus report review. Full clinical class-II typing is not supplied here." } ``` ```json { "finding_id": "M-FINDING-013", "sample_id": "M-SAMPLE-002", "assay_id": "M-ASSAY-003", "feature": "HLA-C", "value": "C*03:04 / C*05:01", "unit": null, "evidence_class": "previous_clinical_report_extraction", "source_ids": [ "M-SOURCE-002", "M-SOURCE-007" ], "current_node_status": "not_assessed_here", "notes": "Concordant in previous Caris/Tempus report review. Full clinical class-II typing is not supplied here." } ``` ## My molecular profile and vaccine targets These results concern my historical tissue and plasma; my current lymph node has no published molecular profile. The March 2024 rectal biopsy was superficial and predominantly intramucosal. The October 2024 resections sampled residual disease after treatment. Different specimens and assays limit comparisons; VAF is the fraction of sequenced alleles, not tumour fraction. ### Pathogenic variants Caris-reported pathogenic variants from my March 2024 rectal biopsy, with October 2024 Tempus results alongside. SOX9 has a conflicting Tempus VUS classification. Not listed does not mean absent. #### APC p.S1411fs c.4233delT Caris: Pathogenic variant; 23% VAF. Initial rectal primary biopsy, collected 2024-03-27. Caris matched the investigational β-catenin/TCF inhibitor FOG-001. APC also appears in the vaccine designs; exact mutant transcripts and peptides need separate assessment. Neither match establishes benefit or eligibility. Not listed in the Tempus clinical report; omission is not proof of absence. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0096; M-READ-0098. Therapy evidence: [Caris historical biomarker trial matches, page 6](https://youngcrc.com/reports/caris/caris.pdf#page=6) Therapy evidence: [FOG-001 β-catenin/TCF mechanism, primary AACR research abstract](https://aacrjournals.org/mct/article/24/10_Supplement/C133/766281/Abstract-C133-Distinct-aspects-of-catenin-biology) #### APC p.V450fs c.1349delT (Caris); c.1349del (Tempus) Caris: Pathogenic variant; 28% VAF. Initial rectal primary biopsy, collected 2024-03-27. Tempus: Biologically relevant; loss-of-function frameshift; 8.6% VAF. Rectal resection, block B4, collected 2024-10-22. Caris matched the investigational β-catenin/TCF inhibitor FOG-001. APC is also a vaccine candidate. The reports do not establish a mutation-selected standard treatment or individual benefit. Tempus uses biologically relevant / loss-of-function wording, rather than the Caris pathogenic category. Clinical VAF 8.6% and research count 66/790 are distinct source values. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0058; M-READ-0061; M-READ-0062; M-READ-0064. Therapy evidence: [Caris historical biomarker trial matches, page 6](https://youngcrc.com/reports/caris/caris.pdf#page=6) Therapy evidence: [FOG-001 β-catenin/TCF mechanism, primary AACR research abstract](https://aacrjournals.org/mct/article/24/10_Supplement/C133/766281/Abstract-C133-Distinct-aspects-of-catenin-biology) #### PTEN p.R335* c.1003C>T Caris: Pathogenic variant; 34% VAF. Initial rectal primary biopsy, collected 2024-03-27. Caris supplied investigational biomarker trial matches. This does not establish an approved colorectal-cancer treatment biomarker or trial eligibility. Not listed in the Tempus clinical report. Do not infer absence or suitability for every automatic Caris trial match. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0102. Therapy evidence: [Caris historical biomarker trial matches, page 6](https://youngcrc.com/reports/caris/caris.pdf#page=6) #### SOX9 c.432-2A>T c.432-2A>T Caris: Pathogenic variant; 78% VAF. Initial rectal primary biopsy, collected 2024-03-27. Tempus: Variant of unknown significance; splice-region variant; 29.1% VAF. Rectal resection, block B4, collected 2024-10-22. No established variant-selected treatment connection is supplied by these reports. This splice variant is distinct from Invoke’s SOX9 missense candidates. Caris and Tempus classifications differ; preserve both. RNA overlap at a splice-region locus does not itself establish the exact aberrant transcript. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0033; M-READ-0036. ### Likely pathogenic variants Caris reported SMARCA4 as likely pathogenic; Tempus reported the same alteration as a VUS. This is a provider disagreement, not a consensus classification. A missense call alone does not establish loss of protein function. #### SMARCA4 p.D1177Y c.3529G>T Caris: Likely pathogenic variant; 29% VAF. Initial rectal primary biopsy, collected 2024-03-27. Tempus: Variant of unknown significance; 13.7% VAF. Rectal resection, block B4, collected 2024-10-22. Caris matched LY4050784, an investigational SMARCA2 inhibitor. Trial cohorts use different SMARCA4 criteria; this missense call does not establish protein loss or eligibility. Caris: likely pathogenic; Tempus: VUS. Neither call alone proves SMARCA4 protein loss. JLF and Invoke also nominated this variant as a vaccine target. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0039; M-READ-0042; M-READ-0043; M-READ-0045. Therapy evidence: [Caris historical biomarker trial matches, page 6](https://youngcrc.com/reports/caris/caris.pdf#page=6) Therapy evidence: [Lilly LY4050784 / SMARCA2 trial and SMARCA4 cohort requirements](https://www.lillyoncologypipeline.com/molecule/smarca2-brm/clinical-trial/NCT06561685) ### Variants of uncertain significance VUS are not established treatment-selection biomarkers. Tempus also called SOX9 and SMARCA4 VUS; those calls are shown once in the tables above. #### BRCA2 p.W194R c.580T>C Caris: Variant of uncertain significance; 34% VAF. Initial rectal primary biopsy, collected 2024-03-27. Tempus: Variant of unknown significance; 14.3% VAF. Rectal resection, block B4, collected 2024-10-22. JLF and Invoke nominated p.W194R as a vaccine target. Its VUS classification does not establish a PARP-treatment indication. A BRCA2 VUS does not establish a PARP-treatment indication. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0021; M-READ-0024. #### KIT p.I403V c.1207A>G Caris: Variant of uncertain significance; 46% VAF. Initial rectal primary biopsy, collected 2024-03-27. No established variant-selected treatment connection is reported for this VUS. Source: https://youngcrc.com/reports/caris/caris.pdf#page=3; IDs: M-SOURCE-001; specimen: M-SAMPLE-001; assay: M-ASSAY-001; audit records: Not recorded. #### FOXL2 p.A234E c.701C>A Tempus: Variant of unknown significance; 30.2% VAF. Rectal resection, block B4, collected 2024-10-22. Invoke nominated p.A234E as a vaccine target (rank 4). This prediction does not establish clinical actionability. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. #### CCDC6 p.E311fs c.931del Tempus: Variant of unknown significance; frameshift; 14.3% VAF. Rectal resection, block B4, collected 2024-10-22. JLF and Invoke nominated this frameshift as a vaccine target. The conflicting displayed RNA value is addressed in the vaccine table. A frameshift remains a VUS when that is the provider classification. Vaccine design and read evidence are separate. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0012; M-READ-0015; M-READ-0016; M-READ-0018. #### HGF p.C149F c.446G>T Tempus: Variant of unknown significance; 12.4% VAF. Rectal resection, block B4, collected 2024-10-22. Invoke nominated p.C149F as a vaccine target (rank 21). No established variant-selected drug connection is reported. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. #### ELF3 p.Q151H c.453G>C Tempus: Variant of unknown significance; 10% VAF. Rectal resection, block B4, collected 2024-10-22. JLF and Invoke nominated p.Q151H as a vaccine target. The patient-specific precursor sequence needs adjudication, as noted below. Variant phase and peptide flank questions are documented separately in vaccine evidence. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. Source: https://youngcrc.com/data/molecular/target_read_evidence.json; IDs: M-SOURCE-006; specimen: See source; assay: See source; audit records: M-READ-0003; M-READ-0006; M-READ-0007; M-READ-0009. #### PRKDC p.*4128Gext*? c.12382T>G Tempus: Variant of unknown significance; stop loss; 8.7% VAF. Rectal resection, block B4, collected 2024-10-22. Invoke nominated a stop-loss extension as a vaccine target (rank 3). Transcript-dependent numbering and current retention remain unresolved. Protein position/extension representation is transcript-dependent; do not silently merge p.*4097 and p.*4128 annotations. Source: https://youngcrc.com/reports/tempus/tempus.pdf#page=3; IDs: M-SOURCE-002; specimen: M-SAMPLE-002; assay: M-ASSAY-003; audit records: Not recorded. #### TRAF2 p.T113I Guardant360: VUS at 1.7% cfDNA allele fraction. Blood collected 18 December 2025; estimated tumour fraction <0.05%, biomarker-negative confidence <90%. Invoke also lists p.T113I as a vaccine candidate (rank 77). Its link to this low-tumour-fraction plasma result remains unestablished; no variant-selected drug benefit is shown. With essentially undetectable tumour DNA in this plasma sample, tumour origin is unconfirmed. The 1.7% cfDNA allele fraction is a different measurement from tumour fraction; this is not a confirmed tumour variant. Source: https://youngcrc.com/reports/guardant/portal_guardant_2025_12_24.pdf#page=2; IDs: CL-SRC-242; specimen: None; assay: None; audit records: Not recorded. ### Treatment and immune biomarkers #### MMR protein expression MLH1, MSH2, MSH6 and PMS2 nuclear expression retained in March 2024 rectal biopsies. The published pathology supports historical proficient mismatch repair; it is not a new assay of current metastatic disease. #### Microsatellite status and TMB Caris March 2024 biopsy: MSS, TMB 5 mutations/Mb. Tempus October 2024 resection: MSS, TMB 4.2 mutations/Mb. BostonGene: TMB 0.42 mutations/Mb in residual rectal tumour after chemoradiation (October 2024; 15% tumour content); MSI and copy number were not reported. BostonGene’s low tumour content limits detection sensitivity; its TMB estimate and negative mutation findings need caution. Keep assay-specific values separate: the lower estimate does not establish a change over time. Historical MSS/low TMB do not provide an MSI-high/TMB-high treatment biomarker. #### KRAS / NRAS / BRAF and kinase biomarkers Caris reported KRAS, NRAS and BRAF mutations not detected; ERBB2/HER2 and EGFR amplification and NTRK1/2/3, BRAF and RET fusions not detected. Tempus reported no pathogenic KRAS/NRAS/BRAF variant or copy-number change, and no reportable RNA rearrangement or altered splicing. Historical RAS/BRAF wild-type findings support the rationale for EGFR-directed treatment. They do not exclude acquired resistance after prior panitumumab; current resistance is unassessed. #### HLA and antigen presentation Predicted HLA-A A*02:01/A*02:01; HLA-B B*07:02/B*44:02; HLA-C C*03:04/C*05:01. Caris reported HLA-A loss of heterozygosity not detected. BostonGene’s low MHC-I bulk-RNA signature came from residual rectal tissue after chemoradiation, with 15% tumour content. Relevant to vaccine and HLA-restricted cell-therapy research. Predicted HLA needs clinical confirmation; full clinical class-II typing is absent. Negative HLA-A LOH and a low-purity bulk-RNA signature establish neither intact presentation nor tumour-cell MHC-I loss at current tumour sites. #### Historical Guardant360 plasma profiling Blood collected 18 December 2025: tumour fraction <0.05%; biomarker-negative confidence <90%; no reportable somatic alteration with an associated therapy. Blood TMB not evaluable; MSI-high not detected. TRAF2 p.T113I at 1.7% cfDNA classified VUS. Essentially undetectable tumour DNA makes negative plasma findings uninformative about absence of disease or current RAS/RAF genotype. TRAF2’s tumour origin is unconfirmed; its 1.7% cfDNA allele fraction is separate from the <0.05% tumour-fraction estimate. #### Historical Caris Assure plasma profiling Blood collected 27 January 2026: estimated tumour fraction 0.0%; no pathogenic tumour-derived somatic variant or therapy-associated biomarker detected. Blood TMB and MSI indeterminate. Do not call this plasma assay MSS or low TMB. A negative result with 0.0% reported tumour fraction cannot rule out disease or current resistance. ### Expression and pathology My archived liver resection contained residual disease after treatment. RNA percentages are calculated within cells classified as tumour, not all cells or surface protein. Target IHC used liver block C4 with about 5% viable tumour; the exact link to the single-cell aliquot remains unresolved. These historical results do not establish expression in my current metastases. The expression and target-IHC evidence comes from liver metastasis resected 22 October 2024, not the recent lymph node. Valius single-cell profiling used FFPE 10x Flex v2: 92,897 cells, including 1,018 classified as tumour; exact single-cell aliquot-to-block linkage remains unresolved. The IHC reports identify liver block C4, about 5% viable tumour in a predominantly acellular mucinous lesion, adequate for IHC. 28 April 2026 is reaccession, not tissue collection. Detectable RNA percentages are not measurements of surface protein or evidence of amplification. #### CEACAM5 / CEA RNA: Detectable RNA in 39.49% of classified tumour cells and 0% of stromal cells. Protein: H-score 300; 100% strong (3+) cytoplasmic and membranous staining. Stroma negative. Strong historical target staining supports investigating CEACAM5-directed research therapies; current-node expression, trial eligibility and benefit remain unconfirmed. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius_cea.pdf; IDs: M-SOURCE-003. #### MET / cMET RNA: Detectable RNA in 41.36% of classified tumour cells and 9.7% of stromal cells. Protein: H-score 160: 60% moderate (2+), 40% weak (1+), no strong (3+) staining. Cytoplasmic staining; stroma negative. Supports a MET-directed research hypothesis. IHC does not establish MET amplification, exon-14 alteration or a trial-specific membrane-expression score. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius_met.pdf; IDs: M-SOURCE-003. #### TROP-2 RNA: Detectable RNA in 54.91% of classified tumour cells and 0.02% of stromal cells. Protein: H-score 20: 10% moderate (2+) membranous staining, 90% negative. Weak cytoplasmic staining in about 10% excluded from scoring; stroma negative. RNA and protein results differ. The source states no established relationship between TROP-2 staining and treatment response in colorectal cancer. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius_trop2.pdf; IDs: M-SOURCE-003. #### HER2 RNA: Detectable RNA in 46.07% of classified tumour cells and 4.61% of stromal cells. Protein: IHC 0; H-score 0; no tumour or stromal staining. Negative by colorectal HERACLES criteria. Tumour-cell RNA expression does not establish HER2 positivity or amplification. Caris also reported ERBB2 amplification not detected. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius_her2.pdf; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/caris/caris.pdf; IDs: M-SOURCE-001. #### EpCAM RNA: Detectable RNA in 68.07% of classified tumour cells and 0% of stromal cells. Protein: No target-specific IHC result in the released evidence. Provides an RNA-level target hypothesis for EpCAM-directed research; protein availability and benefit are unestablished. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. #### EPHA2 RNA: Detectable RNA in 70.73% of classified tumour cells and 10.17% of stromal cells. Protein: No target-specific IHC result in the released evidence. Provides an RNA-level target hypothesis; no validated treatment-selection inference follows. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. #### PD-L1 RNA: Detectable RNA in 0% of classified tumour cells and 2.69% of stromal cells. Protein: No clinical PD-L1 IHC score in the released evidence. Keep separate from the medium PD-L1 RNA signature in BostonGene rectal tissue. RNA results do not establish checkpoint-treatment benefit. Source: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius.pdf; IDs: M-SOURCE-003. Source: https://youngcrc.com/reports/valius/valius_portrait.pdf; IDs: M-SOURCE-011. BostonGene analysed residual rectal tumour after chemoradiation, from block B4 collected 22 October 2024 (report 30 September 2026; estimated tumour content 15%). Low tumour content limits detection sensitivity; MSI and copy number were not reported. Bulk-RNA signatures were fibrotic, immune non-inflamed, low MHC-I and medium PD-L1. They describe a mixture of tumour, stromal and immune cells in previously treated tissue, not tumour-cell MHC-I loss, absent antigen presentation, a PD-L1 IHC score or the immune state of my current metastases. My rectal and liver resections confirmed moderately differentiated colorectal adenocarcinoma with treatment-associated mucinous features. Rectal stage: ypT3N1aM1a; 1/12 nodes positive, numerous tumour deposits, venous and perineural invasion. Margins were negative (closest 2 mm); treatment response was partial (score 2). Later review of 1/3 evaluable nodes does not replace the original 1/12 count. ### JLF and Invoke vaccine targets JLF proposed 20 peptide precursors. Invoke ranked 250 candidate targets, including the same targets and additional candidates. These are historical research designs; RNA support and prediction scores do not establish antigen presentation, immune recognition or retention in my current metastases. All 20 JLF targets appear in Invoke’s ranked 250-candidate report. Thirteen class-I windows match; seven differ. Target overlap does not mean identical peptide designs. Invoke allele fractions and TPM are maxima across available samples; they are not a single specimen’s unified measurements. HLA restrictions below come from JLF designs; Invoke supplies no candidate-specific HLA allele columns. | Target | JLF HLA / class I core | Invoke tier / rank | RNA AF / TPM | Invoke peptide | |---|---|---|---|---| | SMAD4 p.G359E | HLA-C*05:01 / YVDPSGEDRF | 2 / 35 | 0.460 / 572.9 | CPIVTVDGYVDPSGEDRFCLGQLSN | | KIF1C p.Q227L | HLA-A*02:01 / AVFTIVFTL | 3 / 116 | 0.320 / 251.1 | SHAVFTIVFTLRCHDQLTGLDSEKV | | GALK2 p.G450D | HLA-C*03:04 / FATKPGDGAL | 1 / 9 | 0.600 / 45.4 | LAPEKQSLFATKPGDGALVLLEA | | KMT2E p.T897P | HLA-C*03:04 / YAPPTHTDI | 1 / 23 | 0.250 / 110.3 | TSTPTPSPYAPPTHTDITPMDPSFA | | SLC39A10 p.M740I | HLA-A*02:01 / LLSAIMAYI | 1 / 14 | 0.570 / 17.2 | MTVKQAIVYNLLSAIMAYIGMLIGT | | PRRC2C p.Y392N | HLA-B*07:02 / VPNGKGPSF | 2 / 28 | 0.430 / 141.0 | SSQIPAQPSVAKVPNGKGPSFNQER | | TLN2 p.E2148Q | HLA-A*02:01 / ALQATIECI | 1 / 18 | 0.640 / 63.3 | KAVEDEATRGTRALQATIECIKQEL | | BRCA2 p.W194R | HLA-B*07:02 / DPDMSRSSSL | 2 / 53 | 0.480 / 315.7 | LGAEVDPDMSRSSSLATPPTLSSTV | | HNF4G p.L195F | HLA-A*02:01/DPA1*01:03-DPB1*02:01 / SMKQQLFVLV | 2 / 39 | 0.680 / 28.1 | DVCESMKQQLFVLVEWAKYIPAFCE | | LRCH4 p.A109V | HLA-B*07:02 / NPVLGNLTAL | 2 / 38 | 0.320 / 13.3 | YHNCLRCLNPVLGNLTALTYLNLSR | | CCDC6 p.E311Rfs*19 | HLA-C*05:01 / SVDSSPRVS | 2 / 49 | 0.000 / 264.0 | LQRKLQRRWREEKPSVDSSPRVSPA | | NBPF15 p.R153K | HLA-A*02:01 / KLTQHLVQKL | 2 / 58 | 0.220 / 67.5 | DLQEQLAEGCKLTQHLVQKLSPEND | | FHIP2B p.D350N | HLA-C*05:01 / WFDYCNHLI | 2 / 57 | 0.280 / 32.9 | AAFLGWFDYCNHLITEAHTVVADAL | | WDFY1 p.V390I | HLA-A*02:01 / RIIKIWDMTPV | 1 / 22 | 0.270 / 40.1 | LMVTCGTDRIIKIWDMTPVVGCSLA | | AASS p.L88I | HLA-B*44:02/DQA1*01:02-DQB1*06:02 / SEACIILGV | 2 / 67 | 0.420 / 5.9 | AGGILQEDISEACIILGVKRPPEEK | | WWC1 p.D1064E | HLA-B*44:02 / GELQTEKMM | 1 / 16 | 0.590 / 32.1 | DRAEHKGELQTEKMMRAAAKDVHRL | | APC p.V450Gfs*4 | HLA-B*44:02 / VEHQICPAGVF | 3 / 128 | Not reported / 355.6 | NPMPAPVEHQICPAGVF | | SMARCA4 p.D1177Y | HLA-C*05:01 / SADTVIIFDSY | 1 / 17 | 0.370 / 3386.1 | LNLQSADTVIIFDSYWNPHQDLQA | | ELF3 p.Q151H | HLA-B*44:02 / HEALDPGPF | 2 / 65 | 0.370 / 481.0 | SWIIELLEKDGMAFHEALDPGPFD | | APC p.S1411Rfs*4 | HLA-B*44:02 / VQSEPCREW | 2 / 60 | Not reported / 355.6 | ESRSIASSVQSEPCREW | | STAG3 p.D893Y | Not in JLF list | 1 / 1 | 0.140 / 4.4 | YGVLEMDAASYVFKHYNKFYNDYGD | | KLHL26 p.V126M | Not in JLF list | 1 / 2 | 0.030 / 6.5 | RGLRHIIDFAYSAEMTLDLDCVQDV | | PRKDC p.*4129Gext*14 | Not in JLF list | 1 / 3 | 0.470 / 1846.0 | GRTWEGWEPWMGGLWESADRKHYIV | | FOXL2 p.A234E | Not in JLF list | 1 / 4 | 0.570 / 4.8 | AAAAAAAAAAAAAEGPGSPGAAAVV | | PKD1 p.R3130W | Not in JLF list | 1 / 5 | 0.600 / 49.9 | FKYEILVKTGWGWGSGTTAHVGIML | | CARF p.D455N | Not in JLF list | 1 / 6 | 0.250 / 5.1 | QLRKFVERELFKPNEVPERHNLSFF | | FNDC1 p.R336H | Not in JLF list | 1 / 7 | 0.200 / 6.7 | IENLIPDTVYEFAVHISQGERDGKW | | MYH7B p.A549D | Not in JLF list | 1 / 8 | 0.460 / 3.5 | EECMFPKASDDSFRAKLYDNHAGKS | | BCAS1 p.V461Gfs*28 | Not in JLF list | 1 / 10 | Not reported / 50.2 | STKEMLHLNPQKRNSKEKKANQEPL⚠ | | TRIM14 p.V68L | Not in JLF list | 1 / 11 | 0.170 / 29.3 | RGHPVGLALEAAVHLQKLSQECLK | | DAGLB p.V28G | Not in JLF list | 1 / 12 | 0.150 / 15.2 | ASDDLVFPGFFELVGRVLWWIGILT | | GPR157 p.P314A | Not in JLF list | 1 / 13 | 0.600 / 5.7 | PPTKSPAGTPKAAAPSKPGESQES | | HMCN1 p.V4127I | Not in JLF list | 1 / 15 | 0.170 / 3.1 | KDGRAIVESIRQRILSSGSLQIAFV | | PAN2 p.E602A | Not in JLF list | 1 / 19 | Not reported / 30.6 | EASALGLILADSDAASGKGNLARLI | | SSTR4 p.L351I | Not in JLF list | 1 / 20 | 1.000 / 1.4 | GGAEEEPLDYYATAIKSKGGAGCM | | HGF p.C149F | Not in JLF list | 1 / 21 | Not reported / 17.0 | GTVSITKSGIKFQPWSSMIPHEHSF | | ZNF704 p.S127G | Not in JLF list | 1 / 24 | 0.240 / 29.1 | GSWKEGGCVPSSTSGSGYWSWSAPS | | CASP10 p.N240K | Not in JLF list | 1 / 25 | 0.380 / 6.7 | PQESWQNKHAGSKGNRATNGAPSLV | | PLXNA4 p.I1045Lfs*45 | Not in JLF list | 2 / 26 | Not reported / 2.8 | LVFQYVEDPTIVRLSQNGALSVETH | | TTN p.D20524Y | Not in JLF list | 2 / 27 | Not reported / 1.9 | GKVLVREKRVYLIQDLPRVELQIKE | | PLEKHG2 p.R1293W | Not in JLF list | 2 / 29 | Not reported / 12.0 | ASYISQSLARWQGPGGGAPAASRGS | | ADPRHL1 p.R1805W | Not in JLF list | 2 / 30 | 0.920 / 4.5 | GAQERAWEQGWEQALTSGMAPRAWE | | DNASE1L2 p.L11F | Not in JLF list | 2 / 31 | Not reported / 1.3 | MGGPRALLAAFWALEAAGTAALRIG | | SLFN12L p.C535G | Not in JLF list | 2 / 32 | Not reported / 3.0 | AKIGGYTKKVGVMTKIFSLSPEGKT | | GAPDHS p.L174I | Not in JLF list | 2 / 33 | Not reported / 1.2 | PYVVESTGVYISIQAASDHISAGA | | ABCC12 p.T1251I | Not in JLF list | 2 / 34 | Not reported / 1.6 | TIMKLPEKLQAEVIENGENFSVGER | | RELN p.T1712M | Not in JLF list | 2 / 36 | Not reported / 4.2 | VPPTIGCLHYMESSIYTSERFQNWK | | VSIG10L p.A188T | Not in JLF list | 2 / 37 | 1.000 / 0.4 | ESKFSAETHSTASFPQQVGGPLAVL | | SELPLG p.Q135_T144del | Not in JLF list | 2 / 40 | Not reported / 10.0 | IQTTQPAATEAQTTPLAATEA | | GBX2 p.K140M | Not in JLF list | 2 / 41 | Not reported / 1.9 | APQPLPGGGNFDMAEALQADAEDGK | | E4F1 p.R740Q | Not in JLF list | 2 / 42 | Not reported / 11.0 | ASAISEGTVLAAQAGTSGTEQATVT | | GOLGA4 p.E744D | Not in JLF list | 2 / 43 | 0.010 / 114.0 | QQVDSIIKEHDVSIQRTEKALKDQI | | PTOV1 p.G15D | Not in JLF list | 2 / 44 | Not reported / 19.0 | VRPRRAPYRSGAGDPLGGRGRPPRP | | WASHC2A p.A12V | Not in JLF list | 2 / 45 | Not reported / 67.9 | MNRTTPDQELVPASEPVWERPWSVE | | LSM8 p.N66D | Not in JLF list | 2 / 46 | 0.090 / 269.0 | EQVVLGLYIVRGDDVAVIGEIDEET | | LAMC3 p.R344H | Not in JLF list | 2 / 47 | Not reported / 1.6 | SGRSEECTFDRELFHSTGHGGRCHH | | PTPRS p.V53M | Not in JLF list | 2 / 48 | 0.060 / 13.3 | PKDQIGVSGGVASFMCQATGDPKPR | | OLFML2B p.V604G | Not in JLF list | 2 / 50 | Not reported / 5.0 | YVAAWAMLHDGAYEEATPWRWQGHS | | LMO7 p.T153R | Not in JLF list | 2 / 51 | 0.540 / 530.7 | LNLKAFENLLGQALRKALEDSSFLK | | PCOLCE2 p.V124G | Not in JLF list | 2 / 52 | 1.000 / 0.5 | ALVSSGNKMMGQMISDANTAGNGFM | | DMRT1 p.A37V | Not in JLF list | 2 / 54 | 1.000 / 0.6 | GRAGGFGKASGVLVGAASGSSAGGS | | MTMR7 p.R650W | Not in JLF list | 2 / 55 | 0.420 / 4.0 | SGGEHAPSEDSGKDWDSDEAVFLTA | | RFX1 p.Q238H | Not in JLF list | 2 / 56 | 0.400 / 3.7 | VPQQLQVHGVHQSVPVTQERSVVQA | | GPD1 p.D103Y | Not in JLF list | 2 / 59 | 0.500 / 4.1 | LIFVVPHQFIGKICYQLKGHLKANA | | MYOCD p.V491G | Not in JLF list | 2 / 61 | 0.500 / 6.8 | DASPSFGLHPSPVHGCTEESLMSSL | | VGF p.H568N | Not in JLF list | 2 / 62 | 1.000 / 1.8 | PPSALRRRHYHNALPPSRHYPGREA | | ZNF646 p.M1243I | Not in JLF list | 2 / 63 | 0.290 / 7.9 | QACSKGFSNLISLKNHRRIHADPRR | | MTMR3 p.R541Q | Not in JLF list | 2 / 64 | 0.530 / 25.4 | ERTCSVWSLLQAGNKAFKNLLYSSQ | | RHBDF1 p.E494K | Not in JLF list | 2 / 66 | Not reported / 31.6 | RQDPQVHSFIRSARKREKHSACCVR | | GPSM3 p.Q117K | Not in JLF list | 2 / 68 | Not reported / 2.8 | DREQLYSTILSHQCKRMEAQRSEPP | | MDN1 p.R5381C | Not in JLF list | 2 / 69 | 0.330 / 22.6 | RKDKIWLRRTKPSKCQYQICLAIDD | | ZNF77 p.V455G | Not in JLF list | 2 / 70 | 0.250 / 5.5 | FSCHSSLREHGRTHSGEKPYECNQ | | BCLAF3 p.S6C | Not in JLF list | 2 / 71 | 0.880 / 25.1 | MARSRCRSPRWKHRSLSPVP | | PODXL p.Q350H | Not in JLF list | 2 / 72 | Not reported / 21.9 | AHESNWAKCEDLETHTQSEKQLVLN | | ZNF77 p.V455M | Not in JLF list | 2 / 73 | 0.250 / 5.5 | CGKAFSCHSSLREHMRTHSGEKPYE | | ZNF473 p.S434N | Not in JLF list | 2 / 74 | 0.640 / 5.7 | IHQRVHSGEKPYKCNECGKAFHRHT | | ZNF473 p.S434R | Not in JLF list | 2 / 75 | 0.640 / 5.7 | IHQRVHSGEKPYKCRECGKAFHRHT | | MED29 p.A123V | Not in JLF list | 2 / 76 | 0.750 / 5.7 | CDQLELCLRLVHECLSQSCDSAKHS | | TRAF2 p.T113I | Not in JLF list | 2 / 77 | 0.380 / 29.1 | LPAVCPSDGCIWKGTLKEYESCHEG | | THBS4 p.Y459C | Not in JLF list | 2 / 78 | 0.600 / 0.8 | VTCVCGVGWAGDGCICGKDVDIDSY | | ACOX1 p.H647D | Not in JLF list | 3 / 79 | 0.110 / 37.2 | EWAKNSPLNKAEVDESYKHLKSLQS | | EMP1 p.G148D | Not in JLF list | 3 / 80 | 0.050 / 50.5 | YILGWICFCFSFIIDVLYLVLRKK | | PUM2 p.Q874R | Not in JLF list | 3 / 81 | Not reported / 81.7 | LQFIIDAFKGRVFVLSTHPYGCRVI | | H2AC7 p.I80T | Not in JLF list | 3 / 82 | 0.100 / 496.7 | AARDNKKTRITPRHLQLAIRNDEEL | | SHANK1 p.P1668L | Not in JLF list | 3 / 83 | Not reported / 5.6 | AAPAPAAPQPGPDPLPGTDSGIEEV | | MITF p.M245T | Not in JLF list | 3 / 84 | 0.240 / 94.0 | SSYNEEILGLTDPALQMANTLPVSG | | SLC6A15 p.L631F | Not in JLF list | 3 / 85 | Not reported / 0.7 | VCVSLVVFAIFPVPVVFIVRRFNLI | | IGLV3-1 p.S70N | Not in JLF list | 3 / 86 | 0.100 / 14.1 | KPGQSPVLVIYQDNKRPSGIPERFS | | AMER1 p.V663L | Not in JLF list | 3 / 87 | 0.050 / 56.5 | EYQMRPLGPSLMGLAAGVSGTSQIS | | CPXCR1 p.L100F | Not in JLF list | 3 / 88 | Not reported / 0.0 | LLLQTPIPRKFVSHKPLNDRSRSHS | | RPL3 p.M216K | Not in JLF list | 3 / 89 | 0.060 / 1763.9 | PVNQVFGQDEKIDVIGVTKGKGYKG | | DNA2 p.H285R | Not in JLF list | 3 / 90 | 0.050 / 54.5 | LKGKIDVTVGVKIRRGYKTKYKIMP | | MSANTD4 p.N270D | Not in JLF list | 3 / 91 | Not reported / 10.7 | EREKLRLQIVDSEKPSLENELGQGE | | ASIC2 p.P17A | Not in JLF list | 3 / 92 | Not reported / 0.4 | AGLPAAALTGAGRFRMAREEPAPAA | | CPS1 p.T900I | Not in JLF list | 3 / 93 | Not reported / 1.4 | NMEKTLKGLNSESMIEETLKRAKEI | | CCDC30 p.S358R | Not in JLF list | 3 / 94 | Not reported / 5.7 | TMKPEEIVRLREELRHINQSLLQS | | TUBA4B p.T69P | Not in JLF list | 3 / 95 | 0.250 / 2.8 | DRIRKLADQCPGLQGFLVFHSLGRG | | PLEKHG3 p.A147T | Not in JLF list | 3 / 96 | 0.070 / 37.6 | QVSALFGNIENIYTLNSQLLRDLDS | | SOX9 p.S279N | Not in JLF list | 3 / 97 | 0.080 / 4311.5 | DFRDVDIGELNSDVISNIETFDVNE | | METTL1 p.V8L | Not in JLF list | 3 / 98 | Not reported / 9.7 | MAAETRNLAGAEAPPPQKRYYR | | RPL3 p.M216V | Not in JLF list | 3 / 99 | 0.060 / 1763.9 | PVNQVFGQDEVIDVIGVTKGKGYKG | | TBX3 p.P485L | Not in JLF list | 3 / 100 | 0.370 / 18.9 | QGPLPGLGFALGLAGQQFFNGHPLF | | ZFHX4 p.A569T | Not in JLF list | 3 / 101 | Not reported / 1.4 | FADASASKDSTTAAHPSEIARGDED | | PTPRD p.Q1601R | Not in JLF list | 3 / 102 | 0.090 / 262.0 | QRNYMVQTEDRYIFIHDALLEAVT | | KRT20 p.E377D | Not in JLF list | 3 / 103 | Not reported / 192.4 | IATYRRLLEGDDVKTTEYQLSTLEE | | SELENOP p.L13Sfs*24 | Not in JLF list | 3 / 104 | Not reported / 56.6 | LCSSHREEQRARTKAPYVSNPQPGA | | TRMT12 p.V23I | Not in JLF list | 3 / 105 | Not reported / 3.9 | RESGKPVAVVAIVTEPRFTQRYREY | | TCF15 p.R80W | Not in JLF list | 3 / 106 | 1.000 / 0.7 | GPVVVVRQRQAANAWERDRTQSVNT | | METTL1 p.V8W | Not in JLF list | 3 / 107 | Not reported / 9.7 | MAAETRNWAGAEAPPPQKRYYR | | PHF21B p.A138T | Not in JLF list | 3 / 108 | 0.670 / 1.6 | SQPQALAEPATLASPLSSAGVAYAI | | METTL1 p.V8G | Not in JLF list | 3 / 109 | Not reported / 9.7 | MAAETRNGAGAEAPPPQKRYYR | | DEF8 p.C390W | Not in JLF list | 3 / 110 | 0.440 / 15.2 | DCERCQAKGFVWELCREGDVLFPFD | | CLEC2L p.R68H | Not in JLF list | 3 / 111 | Not reported / 4.3 | TSWKAALEDTTTHLLLGAIAVLLFA | | DEF8 p.C390Y | Not in JLF list | 3 / 112 | 0.440 / 15.2 | DCERCQAKGFVYELCREGDVLFPFD | | GOLGB1 p.E1411D | Not in JLF list | 3 / 113 | Not reported / 61.7 | ELQKLISKKEDDVSYLSGQLSEKEA | | POLR2A p.S1808N | Not in JLF list | 3 / 114 | 0.050 / 66.1 | SYSPTSPSYSPSNPRYTPQSPTYTP | | MUC4 p.Q2605H | Not in JLF list | 3 / 115 | 0.050 / 30.1 | | | CUX1 p.Q571R | Not in JLF list | 3 / 117 | 0.060 / 294.5 | KEQLIKHNIGRRIFGHYVLGLSQGS | | MLXIPL p.E648K | Not in JLF list | 3 / 118 | 0.060 / 14.4 | SRGRPDSNKTKNRRITHISAEQKRR | | AGAP4 p.T306A | Not in JLF list | 3 / 119 | 0.070 / 39.7 | WLKTWKKKYVALCSNGVLTYYSSLG | | CAD p.I1587M | Not in JLF list | 3 / 120 | 0.500 / 39.5 | HFETWPSHLPMVAHAEQQTVAAVLM | | TMEM190 p.L56M | Not in JLF list | 3 / 121 | 0.800 / 1.3 | SCGGQAAIDSPNLCMRLRCCYRNGV | | PCDHGB1 p.R635H | Not in JLF list | 3 / 122 | 0.140 / 2.2 | ARALGDRDAAHQRLLVAVRDGGQPP | | SV2A p.R419H | Not in JLF list | 3 / 123 | Not reported / 1.1 | IQSDTGTWYQHWGVRALSLGGQVWG | | GUCY1A1 p.F288L | Not in JLF list | 3 / 124 | Not reported / 4.7 | SLVIPTSLFCKTFPLHFMFDKDMTI | | SPMIP6 p.V255L | Not in JLF list | 3 / 125 | Not reported / 2.2 | APARNAVCCYNSPALILPISEP | | TET1 p.N100D | Not in JLF list | 3 / 126 | Not reported / 3.7 | TEVLFQNPESLTCDGFTMALRSTSL | | TMEM207 p.P132L | Not in JLF list | 3 / 127 | 1.000 / 0.2 | QTPDLYPVPAPCFGLLGSPPPYEEI | | POMP p.F55S | Not in JLF list | 3 / 129 | 0.350 / 44.0 | LLPSHPLELSEKNSQLNQDKMNFST | | BICDL1 p.G161R | Not in JLF list | 3 / 130 | 0.710 / 18.8 | ELRRRFENREREWEGRVSELESDVK | | SALL1 p.T745M | Not in JLF list | 3 / 131 | Not reported / 7.5 | KCKICGRAFTMKGNLKTHYSVHRAM | | H2AC16 p.S123N | Not in JLF list | 3 / 132 | 0.500 / 342.5 | LPNIQAVLLPKKTENHHKAKGK | | DENND4A p.S167I | Not in JLF list | 3 / 133 | 0.340 / 26.8 | NTLAVTDICIIIPIKGESPPHTFCK | | PITPNM3 p.E520D | Not in JLF list | 3 / 134 | Not reported / 6.4 | ASRFQRPGRRMSDGSSHSESSESSD | | ZNF77 p.V455R | Not in JLF list | 3 / 135 | Not reported / 5.5 | CGKAFSCHSSLREHRRTHSGEKPYE | | POTEH p.S41I | Not in JLF list | 3 / 136 | 0.040 / 27.4 | HCFAWCRGSGKINVGTSGDHDDSAM | | ZNF880 p.Q406K | Not in JLF list | 3 / 137 | 0.060 / 9.3 | FCLTNHHRMHTGEKPYKCNECGKAF | | ZNF880 p.Q406R | Not in JLF list | 3 / 138 | 0.070 / 9.3 | FCLTNHHRMHTGERPYKCNECGKAF | | MAGI3 p.K3N | Not in JLF list | 3 / 139 | 0.330 / 11.8 | MSNTLKKKKHWLSKVQE | | FIP1L1 p.R532Q | Not in JLF list | 3 / 140 | 0.390 / 358.8 | REKEERHRERQHREKEETRHKSSRS | | FRAT2 p.G116Lfs*94 | Not in JLF list | 4 / 141 | Not reported / Not reported | RGGGRRRPQRAAGAVPARMAQGRGH⚠ | | MB21D2 p.D52V | Not in JLF list | 4 / 142 | Not reported / 4.1 | EFTKHDQREYVDQRALEIHTAKDFI | | TMEM271 p.G113Afs*120 | Not in JLF list | 4 / 143 | Not reported / 0.6 | EATPGESGAAAGAPAAAPGAGEQPE⚠ | | FOXK1 p.E371Afs*14 | Not in JLF list | 4 / 144 | Not reported / 9.9 | LSLNRYFIKVPRSQAWEGVLLANRP | | MAB21L1 p.C215W | Not in JLF list | 4 / 145 | Not reported / 0.8 | AEVKAEGFNLLSKEWHSLAGKQSSA | | IGKC p.Y79D | Not in JLF list | 4 / 146 | 0.000 / 3597.8 | SSTLTLSKADDEKHKVYACEVTHQG | | PRUNE2 p.D1080V | Not in JLF list | 4 / 147 | Not reported / 11.6 | EDDVGESSQSSYVDPSMMQLYNETN | | MKI67 p.T2380P | Not in JLF list | 4 / 148 | Not reported / 144.7 | EEEFLALRKRPPSAGKAMDTPKPAV | | TM9SF2 p.L484Rfs*60 | Not in JLF list | 4 / 149 | Not reported / 91.2 | ALWFCISVPRRLLVHTLVLRRMPLN⚠ | | KIF3B p.G285D | Not in JLF list | 4 / 150 | Not reported / 27.4 | SLSALGNVISALVDDKSTHIPYRDS | | CHD2 p.K344E | Not in JLF list | 4 / 151 | 0.000 / 1877.5 | GLKKLENFKKEEDEIKQWLGKVSPE | | H2AC6 p.G107D | Not in JLF list | 4 / 152 | 0.030 / 121.0 | NKLLGRVTIAQGDVLPNIQAVLLPK | | SOX9 p.A202D | Not in JLF list | 4 / 153 | 0.000 / 4311.5 | ATEQTHISPNDIFKALQADSPHSSS | | FOXK1 p.P373Lfs*11 | Not in JLF list | 4 / 154 | Not reported / 9.9 | LNRYFIKVPRSQEELLLGRGPFGE | | FAT1 p.S4259T | Not in JLF list | 4 / 155 | 0.000 / 7296.8 | PPQVPVRPISYTPTIPSDSRNNLDR | | PRKDC p.D2937V | Not in JLF list | 4 / 156 | 0.010 / 1846.0 | WVELAKLYRSIGEYVVLRGIFTSEI | | SSR2 p.D39H | Not in JLF list | 4 / 157 | Not reported / 52.5 | LLNRYAVEGRHLTLQYNIYNVGSSA | | CEACAM5 p.N610T | Not in JLF list | 4 / 158 | 0.020 / 3850.8 | ISPPDSSYLSGATLNLSCHSASNPS | | ADGRL3 p.E563F | Not in JLF list | 4 / 159 | Not reported / 4.3 | PSASSQIPALFESCEAVEAREIMWF | | MYO15B p.V2664T | Not in JLF list | 4 / 160 | Not reported / 171.8 | LSLSDDVSKLATASFLALMRFMGD | | SCIMP p.A105D | Not in JLF list | 4 / 161 | 0.120 / 0.8 | SPQEAPSQPPDTYSLVNKVKNKKTV | | SOX9 p.I203V | Not in JLF list | 4 / 162 | 0.000 / 4311.5 | TEQTHISPNAVFKALQADSPHSSSG | | SEM1 p.D16V | Not in JLF list | 4 / 163 | 0.000 / 1141.0 | QPVDLGLLEEVDEFEEFPAEDWAGL | | EXOC4 p.L69S | Not in JLF list | 4 / 164 | 0.010 / 145.3 | DELIVQHYTESTTAIRTYQSITERI | | STUM p.A16V | Not in JLF list | 4 / 165 | Not reported / Not reported | SHKDAETAAAAAVVAAADPRGASSS | | SF3B1 p.A861V | Not in JLF list | 4 / 166 | 0.000 / 2396.6 | SRIVDDLKDEVEQYRKMVMETIEKI | | ATP1A1 p.N754D | Not in JLF list | 4 / 167 | 0.000 / 560.1 | SKQAADMILLDDDFASIVTGVEEGR | | ELOB p.G76W | Not in JLF list | 4 / 168 | Not reported / 74.1 | FTSQTARPQAPATVWLAFRADDTFE | | NOS1 p.I87N | Not in JLF list | 4 / 169 | Not reported / 1.1 | SYDSALEVLRGNASETHVVLILRGP | | H1-5 p.K160T | Not in JLF list | 4 / 170 | 0.000 / 352.2 | KKAVKKTPKKATKPAAAGVKKVAKS | | WRN p.L161S | Not in JLF list | 4 / 171 | 0.040 / 604.3 | LRDFDIKLKNFVESTDVANKKLKCT | | KRT20 p.E377V | Not in JLF list | 4 / 172 | Not reported / 192.4 | IATYRRLLEGVDVKTTEYQLSTLEE | | HCN2 p.G805R | Not in JLF list | 4 / 173 | Not reported / 0.8 | RTSPYGGLPAAPLARPALPARRLSR | | CDH1 p.S635T | Not in JLF list | 4 / 174 | Not reported / 10186.8 | PNTSPFTAELTHGATANWTIQYNDP | | H1-4 p.K159T | Not in JLF list | 4 / 175 | Not reported / 231.2 | KKSAKKTPKKATKPAAAAGAKKAKS | | ACTB p.R116H | Not in JLF list | 4 / 176 | 0.000 / 1681.4 | TEAPLNPKANHEKMTQIMFETFNTP | | CGNL1 p.A109V | Not in JLF list | 4 / 177 | Not reported / 2.8 | EELQLPENPYVQPSPIRNLKQPLLH | | DSP p.H2363D | Not in JLF list | 4 / 178 | Not reported / 192.7 | AMNKELIEKGDGIRLLEAQIATGGI | | DNAH10 p.I3606V | Not in JLF list | 4 / 179 | Not reported / 3.9 | GTPFLFRDVDEYVDPVIDNVLEKNI | | NKX2-2 p.S11L | Not in JLF list | 4 / 180 | Not reported / 1.0 | MSLTNTKTGFLVKDILDLPDTNDEE | | TSPAN15 p.V71D | Not in JLF list | 4 / 181 | Not reported / 96.1 | APAIILILLGDVMFMVSFIGVLASL | | DDR1 p.G707D | Not in JLF list | 4 / 182 | 0.030 / 447.4 | LCMITDYMENDDLNQFLSAHQLEDK | | EEF2 p.E254D | Not in JLF list | 4 / 183 | 0.000 / 2507.1 | LGPAERAKKVDDMMKKLWGDRYFDP | | NKX2-1 p.G89V | Not in JLF list | 4 / 184 | Not reported / 2.1 | PPTAAMQQHAVVHHGAVTAAYHMTA | | SOX9 p.N201D | Not in JLF list | 4 / 185 | 0.000 / 4311.5 | EEATEQTHISPDAIFKALQADSPHS | | OPTN p.F226V | Not in JLF list | 4 / 186 | Not reported / 78.0 | RSRSADGAKNYVEHEELTVSQLLL | | IGHV3-72 p.A82V | Not in JLF list | 4 / 187 | Not reported / 11.6 | RTRNKANSYTTEYVASVKGRFTISR | | ACTB p.E117D | Not in JLF list | 4 / 188 | Not reported / 1681.4 | EAPLNPKANRDKMTQIMFETFNTPA | | PRR36 p.P756H | Not in JLF list | 4 / 189 | Not reported / 4.3 | PPPLQTASAPLTTPHLENLPSLAPP | | B2M p.C100R | Not in JLF list | 4 / 190 | 0.010 / 3207.6 | FTPTEKDEYARRVNHVTLSQPKIVK | | KIF13B p.E19Q | Not in JLF list | 4 / 191 | Not reported / 88.7 | AVRIRPMNRRQTDLHTKCVVDVDAN | | FAT1 p.E2921D | Not in JLF list | 4 / 192 | Not reported / 7296.8 | VNDSPPRFTADIYKGTVSEDDPQGG | | TRAPPC14 p.L79R | Not in JLF list | 4 / 193 | Not reported / 7.5 | RGAWAELATARAALASVSAGGGMPG | | CFAP65 p.P650T | Not in JLF list | 4 / 194 | Not reported / 1.6 | FFFDGTSDITIFPPTISVEPVEVDF | | KDM4B p.N173I | Not in JLF list | 4 / 195 | Not reported / 27.0 | RECGTIIEGVITPYLYFGMWKTTFA | | KDM4B p.N173Y | Not in JLF list | 4 / 196 | Not reported / 27.0 | RECGTIIEGVYTPYLYFGMWKTTFA | | CFL1 p.V64I | Not in JLF list | 4 / 197 | 0.010 / 585.0 | EEGKEILVGDVGQTIDDPYATFVKM | | TMEM176B p.I160V | Not in JLF list | 4 / 198 | Not reported / 87.1 | CVNSFIWQTEPFLYVDTVCDRSDPV | | SOX9 p.H197Y | Not in JLF list | 4 / 199 | 0.010 / 4311.5 | KNGQAEAEEATEQTYISPNAIFKAL | | NKX2-1 p.H90P | Not in JLF list | 4 / 200 | Not reported / 2.1 | TAAMQQHAVGPHGAVTAAYHMTAAG | | KCNT1 p.V984A | Not in JLF list | 4 / 201 | Not reported / 1.1 | SISMLDTLLYQSFAKDYMITITRLL | | RPL3 p.I217N | Not in JLF list | 4 / 202 | 0.000 / 1763.9 | VNQVFGQDEMNDVIGVTKGKGYKGV | | RIPOR3 p.R379W | Not in JLF list | 4 / 203 | Not reported / 8.2 | LQQPTQQALLLGGPWATSILSYLSD | | C1orf127 p.A765D | Not in JLF list | 4 / 204 | Not reported / 1.7 | SSPPSTQTLSLWDPTGVLLPSLVEL | | DICER1 p.S1896R | Not in JLF list | 4 / 205 | 0.000 / 1016.7 | GKGKFKGVGRRYRIAKSAAARRALR | | CLIC1 p.N171D | Not in JLF list | 4 / 206 | 0.030 / 197.5 | AEDEGVSQRKFLDGDELTLADCNLL | | ELOB p.T74P | Not in JLF list | 4 / 207 | Not reported / 74.1 | FTSQTARPQAPAPVGLAFRADDTFE | | CARD11 p.D415V | Not in JLF list | 4 / 208 | 0.000 / 134.1 | DKYRKQIRELEEKNVEMRIEMVRRE | | TPT1 p.Y88D | Not in JLF list | 4 / 209 | 0.000 / 2981.4 | MNHHLQETSFTKEADKKYIKDYMKS | | LBR p.S97P | Not in JLF list | 4 / 210 | Not reported / 194.8 | PGRPPKSARRPASASHQADIKEARR | | SOX9 p.Q195P | Not in JLF list | 4 / 211 | 0.000 / 4311.5 | SVKNGQAEAEEATEPTHISPNAIFK | | CEACAM5 p.T317A | Not in JLF list | 4 / 212 | 0.000 / 3850.8 | TGLNRTTVTTIAVYAEPPKPFITSN | | KDM4B p.N173F | Not in JLF list | 4 / 213 | Not reported / 27.0 | RECGTIIEGVFTPYLYFGMWKTTFA | | EWSR1 p.R506L | Not in JLF list | 4 / 214 | Not reported / 502.0 | DRGGFPPRGPRGSLGNPSGGGNVQH | | MITF p.L244S | Not in JLF list | 4 / 215 | Not reported / 94.0 | ESSYNEEILGSMDPALQMANTLPVS | | MAP7 p.M269T | Not in JLF list | 4 / 216 | 0.030 / 133.3 | PIIMPYKAAHSRNSTDRPKLFVTPP | | CACNA1G p.P1906L | Not in JLF list | 4 / 217 | Not reported / 1.8 | EGPDSPDSPKLGALHPAAHARSASH | | SF3B1 p.E870A | Not in JLF list | 4 / 218 | 0.000 / 2396.6 | DEAEQYRKMVMATIEKIMGNLGAAD | | ACTB p.N115D | Not in JLF list | 4 / 219 | 0.000 / 1681.4 | LTEAPLNPKADREKMTQIMFETFNT | | ADGRL3 p.C566W | Not in JLF list | 4 / 220 | Not reported / 4.3 | SSQIPALEESWEAVEAREIMWFKTR | | APCDD1 p.K162L | Not in JLF list | 4 / 221 | Not reported / 44.7 | QVICHTEAVAELLGQQVNRTCPGFL | | ATRX p.N365D | Not in JLF list | 4 / 222 | Not reported / 2947.2 | MIKKAKKLIETTADMNSSYVKFLK | | COPG2 p.C647R | Not in JLF list | 4 / 223 | Not reported / 10.5 | TEAETEYFVRRIKHMFTNHIVFQFD | | KCNT1 p.V984M | Not in JLF list | 4 / 224 | Not reported / 1.1 | SISMLDTLLYQSFMKDYMITITRLL | | SOX9 p.E134D | Not in JLF list | 4 / 225 | Not reported / 4311.5 | KLADQYPHLHNADLSKTLGKLWRLL | | NCOA5 p.P501S | Not in JLF list | 4 / 226 | Not reported / 91.3 | GGSAQNMGPRSGAPSQGLFGQPSSR | | BNC2 p.A650V | Not in JLF list | 4 / 227 | Not reported / 13.4 | MPVKIEKEIIDTVDEFDDEDDDPND | | COX4I1 p.E80D | Not in JLF list | 4 / 228 | Not reported / 451.5 | WSSLSMDEKVDLYRIKFKESFAEMN | | FMN2 p.S1536P | Not in JLF list | 4 / 229 | Not reported / 7.8 | KSSDNSRSLLPYIVSYYLRNFDEDA | | MTDH p.E500D | Not in JLF list | 4 / 230 | Not reported / 342.2 | LKTISTSDPADVLVKNSQPIKTLPP | | CEACAM5 p.K492T | Not in JLF list | 4 / 231 | 0.000 / 3850.8 | SASGHSRTTVTTITVSAELPKPSIS | | ELOB p.V75L | Not in JLF list | 4 / 232 | Not reported / 74.1 | FTSQTARPQAPATLGLAFRADDTFE | | FYB1 p.W648Sfs*14 | Not in JLF list | 4 / 233 | Not reported / 7.6 | GSTLQVQEKSNTSVLGDFEDVKGKR | | CEACAM5 p.S404N | Not in JLF list | 4 / 234 | 0.000 / 3850.8 | GIQNELSVDHNDPVILNVLYGPDDP | | SOX9 p.P433L | Not in JLF list | 4 / 235 | 0.010 / 4311.5 | PFNLPHYSPSYLPITRSQYDYTDH | | LINGO1 p.V571D | Not in JLF list | 4 / 236 | Not reported / 2.1 | LIIATTMGFISFLGDVLFCLVLLFL | | MUC17 p.N4116T | Not in JLF list | 4 / 237 | Not reported / 103.5 | TTSFPTVTTTAVPTTTTIKSNPTST | | CACNA1G p.K1905R | Not in JLF list | 4 / 238 | Not reported / 1.8 | VEGPDSPDSPRPGALHPAAHARSAS | | OSBPL7 p.L306M | Not in JLF list | 4 / 239 | Not reported / 22.6 | PPTDYAHLQRSFWAMAQKVHSSLSS | | TGM6 p.Y216D | Not in JLF list | 4 / 240 | 0.060 / 3.1 | TDVSCRHNPIDVTRVISAMVNSNND | | ACTG1 p.N115D | Not in JLF list | 4 / 241 | 0.000 / 920.2 | LTEAPLNPKADREKMTQIMFETFNT | | SOX9 p.Y84H | Not in JLF list | 4 / 242 | 0.000 / 4311.5 | IREAVSQVLKGHDWTLVPMPVRVNG | | MUC13 p.S118P | Not in JLF list | 4 / 243 | 0.010 / 130.1 | STTNVNSLATPDIITASSPNDGLIT | | FAT1 p.G2653D | Not in JLF list | 4 / 244 | 0.010 / 7296.8 | VKENLEINKLSDVITTKESLIGLEN | | ATXN2 p.A1078T | Not in JLF list | 4 / 245 | 0.010 / 134.1 | QQTVFTIHPSHVQPTYTNPPHMAHV | | PIK3CB p.Q207H | Not in JLF list | 4 / 246 | Not reported / 1001.7 | YGGKLIVAVHFENCHDVFSFQVSPN | | B4GALT5 p.L265R | Not in JLF list | 4 / 247 | Not reported / 15.3 | HFATKLDKYMYRLPYTEFFGGVSGL | | DNM2 p.F258Y | Not in JLF list | 4 / 248 | Not reported / 216.3 | GKKDIRAALAAERKYFLSHPAYRHM | | ZMYND8 p.G533D | Not in JLF list | 4 / 249 | 0.010 / 124.6 | TTKTDKTSTTDSILNLNLDRSKAEM | | OSBPL7 p.L306R | Not in JLF list | 4 / 250 | Not reported / 22.6 | PPTDYAHLQRSFWARAQKVHSSLSS | #### Vaccine sequence evidence: SMAD4 p.G359E JLF precursor: QVGETFKVPSSCPIVTVDGYVDPSGEDRFCLGQLSNVHRTEAIERARLHIG. Class I: YVDPSGEDRF. Class II: Not specified. M-VACCINE-008: Primary RNA 251/550; resection RNA 0/58; not listed in the resection VCF. Cross-specimen differences need assay/coverage and copy-number context. #### Vaccine sequence evidence: KIF1C p.Q227L JLF precursor: ARTVAATNMNETSSRSHAVFTIVFTLRCHDQLTGLDSEKVSKISLVDLAGS. Class I: AVFTIVFTL. Class II: Not specified. #### Vaccine sequence evidence: GALK2 p.G450D JLF precursor: TVSMVPADKLPSFLANVHKAYYQRSDGSLAPEKQSLFATKPGDGALVLLEA. Class I: FATKPGDGAL. Class II: Not specified. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. #### Vaccine sequence evidence: KMT2E p.T897P JLF precursor: KKRRFYQLLDSVYSETSTPTPSPYAPPTHTDITPMDPSFATPPRIKSDDET. Class I: YAPPTHTDI. Class II: Not specified. #### Vaccine sequence evidence: SLC39A10 p.M740I JLF precursor: LGDFAVLLKAGMTVKQAIVYNLLSAIMAYIGMLIGTAVGQYANNITLWIFA. Class I: LLSAIMAYI. Class II: Not specified. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. #### Vaccine sequence evidence: PRRC2C p.Y392N JLF precursor: KETDEVSNTKSSSQIPAQPSVAKVPNGKGPSFNQERGTSSHLPPPPKLLAQ. Class I: VPNGKGPSF. Class II: Not specified. #### Vaccine sequence evidence: TLN2 p.E2148Q JLF precursor: VTNVTSLLKTVKAVEDEATRGTRALQATIECIKQELTVFQSKDVPEKTSSP. Class I: ALQATIECI. Class II: Not specified. #### Vaccine sequence evidence: BRCA2 p.W194R JLF precursor: KFVKGRQTPKHISESLGAEVDPDMSRSSSLATPPTLSSTVLIVRNEEASET. Class I: DPDMSRSSSL. Class II: Not specified. #### Vaccine sequence evidence: HNF4G p.L195F JLF precursor: GSSTDINVKKIASIGDVCESMKQQLFVLVEWAKYIPAFCELPLDDQVALLR. Class I: SMKQQLFVLV. Class II: KQQLFVLVEWAKYIP. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. #### Vaccine sequence evidence: LRCH4 p.A109V JLF precursor: PEAACQLVSLEGLSLYHNCLRCLNPVLGNLTALTYLNLSRNQLSLLPPYIC. Class I: NPVLGNLTAL. Class II: Not specified. #### Vaccine sequence evidence: CCDC6 p.E311Rfs*19 JLF precursor: KMAQYLEEERHMREENLRLQRKLQRRWREEKPSVDSSPRVSPA. Class I: SVDSSPRVS. Class II: Not specified. Invoke displays RNA AF 0.000; the independent released audit counted 708 alternate / 1,681 informative primary-RNA fragments. The displayed zero conflicts with read evidence and must not imply absent mutant expression. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. M-VACCINE-002: Primary RNA audit counted 708 alternate among 1,681 informative fragments; the report display of zero is contradicted by the embedded reads. The junction-containing sequence had 437 supporting mutation-bearing fragments. #### Vaccine sequence evidence: NBPF15 p.R153K JLF precursor: QALLTPDEPDKSQGQDLQEQLAEGCKLTQHLVQKLSPENDNDDDEDVQVEV. Class I: KLTQHLVQKL. Class II: Not specified. Mutation-bearing reads support this sequence; locus/paralog and self-proteome specificity remain unresolved. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. M-VACCINE-006: Primary DNA 480/1,652; normal 0/1,758; RNA 67/287 high-quality informative fragments. Thirty-six mutation-bearing fragments support this sequence, but locus/paralog and self-proteome specificity remain unresolved. #### Vaccine sequence evidence: FHIP2B p.D350N JLF precursor: SAPSDEASFPGKEALAAFLGWFDYCNHLITEAHTVVADALAKAVAENFFVE. Class I: WFDYCNHLI. Class II: Not specified. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. #### Vaccine sequence evidence: WDFY1 p.V390I JLF precursor: ATFHEGKHNISHMSMDIARGLMVTCGTDRIIKIWDMTPVVGCSLATGFSPH. Class I: RIIKIWDMTPV. Class II: Not specified. JLF and Invoke select different class-I peptide windows for the same target; retain the provider-specific sequences. #### Vaccine sequence evidence: AASS p.L88I JLF precursor: NRRAIHDKDYVKAGGILQEDISEACIILGVKRPPEEKLMSRKTYAFFSHTI. Class I: SEACIILGV. Class II: LQEDISEACIILGVK. #### Vaccine sequence evidence: WWC1 p.D1064E JLF precursor: RFRLLLRMLEKRQMDRAEHKGELQTEKMMRAAAKDVHRLRGQSCKEPPEVQ. Class I: GELQTEKMM. Class II: Not specified. #### Vaccine sequence evidence: APC p.V450Gfs*4 JLF precursor: EAHEPGMDQDKNPMPAPVEHQICPAGVF. Class I: VEHQICPAGVF. Class II: Not specified. M-VACCINE-003: Primary RNA contains 53 alternate among 400 informative fragments. Mutation-bearing RNA supports the tail; this is not proof of protein presentation. #### Vaccine sequence evidence: SMARCA4 p.D1177Y JLF precursor: FLLSTRAGGLGLNLQSADTVIIFDSYWNPHQDLQAQDRAHRIGQQNEVRVL. Class I: SADTVIIFDSY. Class II: Not specified. M-VACCINE-005: Canonical mature-RNA flank had 83 supporting fragments versus 15 for the alternative unspliced context. A missense call does not establish functional SMARCA4 loss. #### Vaccine sequence evidence: ELF3 p.Q151H JLF precursor: RDLTSSSSDELSWIIELLEKDGMAFHEALDPGPFDQGSPFAQELLDDGQQA. Class I: HEALDPGPF. Class II: Not specified. The JLF precursor contains HEALDPGPFDQGSP; released patient-specific phasing supports HEALDPGPFDQDSP. The minimal HEALDPGPF core remains supported, but longer precursor context needs design-laboratory adjudication. M-VACCINE-001: Fifty-four high-quality fragments phase the somatic change with a downstream germline variant; no fragments supported the alternative proposed haplotype. Adjudicate the full patient-specific precursor with the design laboratory; the minimal mutant core remains supported. #### Vaccine sequence evidence: APC p.S1411Rfs*4 JLF precursor: RCTSVSSLDSFESRSIASSVQSEPCREW. Class I: VQSEPCREW. Class II: Not specified. M-VACCINE-004: Primary RNA contains 45 alternate among 132 informative fragments; the resection VCF did not list this change. Missing resection tumour DNA alignment prevents adjudication of absence; low RNA coverage is inconclusive. #### Vaccine sequence evidence: PRKDC p.*4129Gext*14 Invoke labels this stop-loss p.*4129Gext*14; protein numbering varies across transcript annotations. Retain the exact peptide and distinguish it from PRKDC p.D2937V, a separate Invoke candidate. M-VACCINE-010: Somatic calls and RNA support span primary and resection; a 25-aa extension had 36 supporting primary fragments. Protein numbering varies across transcript annotations. Full source-linked molecular summary: https://youngcrc.com/data/molecular/summary.json JLF source: https://youngcrc.com/reports/jlf/peptide_candidate_list.html Invoke source: https://youngcrc.com/reports/invoke/aureon_vaccine_target_report.html Molecular evidence: https://youngcrc.com/data/molecular/findings.json ## Data catalogue ### Natera matched-normal exome — DNA alignment Modality: dna. Type: Matched-normal DNA alignments and indexes. Provider: Natera. Origin: provider_source. Sequencing role verified from retained analysis records; physical source and collection date unconfirmed. Normal input does not imply blood. Dictionary matches GRCh37/hs37d5; original reference MD5s unavailable. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-015_natera_normal_input_dna.bam ### Natera matched-normal exome — regenerated BAM index Modality: dna. Type: Matched-normal DNA alignments and indexes. Provider: Natera. Origin: provider_source. Sequencing role verified from retained analysis records; physical source and collection date unconfirmed. Normal input does not imply blood. Dictionary matches GRCh37/hs37d5; original reference MD5s unavailable. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-015_natera_normal_input_dna.bam.bai ### Tempus — Matched-normal targeted DNA alignment Modality: dna. Type: Matched-normal DNA alignments and indexes. Provider: Tempus. Origin: provider_source. Matched-normal targeted panel DNA alignment. Tempus reports matched-normal blood collected 28 January 2025, received 30 January 2025; preservation unspecified. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-003_matched_normal_dna_grch37.bam ### Tempus — Matched-normal DNA alignment index Modality: dna. Type: Matched-normal DNA alignments and indexes. Provider: Tempus. Origin: provider_source. Companion BAI; download with its matching released BAM. Tempus reports matched-normal blood collected 28 January 2025, received 30 January 2025; preservation unspecified. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-003_matched_normal_dna_grch37.bam.bai ### Caris primary rectal tumour DNA alignment Modality: dna. Type: Tumour DNA alignments and indexes. Provider: Caris. Origin: See full record. DNA alignment from the initial rectal biopsy; report collection date 27 March 2024. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-017_caris_primary_tumour_dna.bam ### Caris primary rectal tumour DNA alignment index Modality: dna. Type: Tumour DNA alignments and indexes. Provider: Caris. Origin: See full record. Regenerated index for the matching primary rectal tumour DNA BAM. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-017_caris_primary_tumour_dna.bam.bai ### PET-CT 8 April 2026 — CT Lung/ABD 2.0 MPR cor Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 139 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-002_ct.zip ### PET-CT 8 April 2026 — CT Lung/ABD 2.0 MPR sag Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 168 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-003_ct.zip ### PET-CT 8 April 2026 — SMALL FOV CT WB W/Contrast 2.0 Br38 Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 535 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-005_ct.zip ### PET-CT 8 April 2026 — CT ABD/PLVS W/Contrast 2.0 MPR cor Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 119 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-006_ct.zip ### PET-CT 8 April 2026 — CT ABD/PLVS W/Contrast 2.0 MPR sag Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 177 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-007_ct.zip ### PET-CT 8 April 2026 — CT Abd wo 3.0 Br38 Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 93 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-008_ct.zip ### PET-CT 8 April 2026 — AC CT WB Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 357 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-009_ct.zip ### PET-CT 8 April 2026 — CT WB W/Contrast 2.0 eFoV Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 535 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-010_ct.zip ### PET-CT 8 April 2026 — CT Lung 3.0 Br46 Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 122 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-015_ct.zip ### PET-CT 8 April 2026 — CT Lung 1.0 Br46 Modality: imaging. Type: CT images. Provider: Clinical records & imaging. Origin: provider_source. 339 DICOM instances; CT, units HU. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-016_ct.zip ### PET-CT 8 April 2026 — PET WB Modality: imaging. Type: PET images. Provider: Clinical records & imaging. Origin: provider_source. 357 DICOM instances; PT, units BQML. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-021_pt.zip ### PET-CT 8 April 2026 — PET WB Uncorrected Modality: imaging. Type: PET images. Provider: Clinical records & imaging. Origin: provider_source. 357 DICOM instances; PT, units PROPCPS. Original decoded pixels and scientific geometry preserved. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/img-012_dcm-series-022_pt.zip ### Kandinsky combined gene explorer Modality: molecular. Type: Combined gene expression and variants. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Combined portal table: BostonGene expression links to rectal resection block B4; Valius single-cell data to liver resected the same day. Per-column input-file mapping is incomplete: columns do not all measure one tissue. Cohort percentiles are not within-patient longitudinal changes. Download: https://youngcrc.com/data/valius/kandinsky_gene_explorer.csv ### Additional caris expression provenance unresolved Modality: molecular. Type: Expression summaries. Provider: Caris. Origin: provider_source. Bulk RNA expression; source tissue, collection date and fraction unresolved. Current tumour expression is unconfirmed. Download: https://youngcrc.com/data/expression/additional_caris_expression_provenance_unresolved.csv ### Liver valius celltype expression summary Modality: molecular. Type: Expression summaries. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Selected gene-by-cell-type aggregates, not a cell-by-gene matrix. Cell-type/malignancy assignment methods requested. Download: https://youngcrc.com/data/expression/liver_valius_celltype_expression_summary.csv ### Liver valius target expression summary Modality: molecular. Type: Expression summaries. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Selected gene-level aggregates, not raw or per-cell data. Units and normalization require full laboratory methods. Download: https://youngcrc.com/data/expression/liver_valius_target_expression_summary.csv ### Normal natera identity panel hs37d5 Modality: molecular. Type: Germline variant calls. Provider: Natera. Origin: provider_source. Matched-normal file role verified from retained analysis records; physical source and collection date unconfirmed. Selected identity/tracer SNPs, not a comprehensive germline catalogue or serial ctDNA result. Download: https://youngcrc.com/data/variants/normal_natera_identity_panel_hs37d5.vcf ### Resection tempus germline freebayes grch37 Modality: molecular. Type: Germline variant calls. Provider: Tempus. Origin: provider_source. Vendor-labelled germline FreeBayes calls with normal and tumour genotypes; no new interpretation. Tempus reports matched-normal blood collected 28 January 2025, received 30 January 2025; preservation unspecified. Download: https://youngcrc.com/data/variants/resection_tempus_germline_freebayes_grch37.vcf ### Resection tempus germline pindel grch37 Modality: molecular. Type: Germline variant calls. Provider: Tempus. Origin: provider_source. Vendor-labelled germline Pindel calls with normal and tumour genotypes; no new interpretation. Tempus reports matched-normal blood collected 28 January 2025, received 30 January 2025; preservation unspecified. Download: https://youngcrc.com/data/variants/resection_tempus_germline_pindel_grch37.vcf ### Kandinsky predicted HLA class I Modality: molecular. Type: HLA predictions. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Kandinsky-exported OptiType prediction; exact reads and tissue unidentified. Not independent clinical HLA typing; does not establish allele-specific tumour retention. Download: https://youngcrc.com/data/valius/kandinsky_predicted_hla_class_i.csv ### Kandinsky Arriba fusion candidates Modality: molecular. Type: RNA fusion candidates. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Arriba fusion candidates with read support, confidence and filters retained. Source filename identifies the BostonGene sample; exact alignment/reference provenance requested. Candidate presence does not establish a validated actionable fusion. Download: https://youngcrc.com/data/valius/kandinsky_rna_fusion_candidates.csv ### Primary caris vendor calls hg38 Modality: molecular. Type: Tumour variant calls. Provider: Caris. Origin: provider_source. Vendor tumour calls with all original filters; not a clean paired-normal somatic catalogue. Download: https://youngcrc.com/data/variants/primary_caris_vendor_calls_hg38.vcf ### Caris — Additional Caris DNA outputs — vendor variant calls Modality: molecular. Type: Tumour variant calls. Provider: Caris. Origin: provider_source. Additional Caris tumour-labelled calls; exact tissue/date and specimen provenance unresolved. Vendor-processed calls, not raw reads or a clinical mutation list. Original PASS/failed filters retained; many calls have failure annotations. Requires the exact custom masked reference; ordinary GRCh38 is not assumed equivalent. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/processed/m-release-010_caris_additional_specimen_vendor_calls.vcf.gz ### Caris — Additional Caris DNA outputs — variant call index Modality: molecular. Type: Tumour variant calls. Provider: Caris. Origin: provider_source. Additional Caris tumour-labelled calls; exact tissue/date and specimen provenance unresolved. Vendor-processed calls, not raw reads or a clinical mutation list. Original PASS/failed filters retained; many calls have failure annotations. Requires the exact custom masked reference; ordinary GRCh38 is not assumed equivalent. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/processed/m-release-010_caris_additional_specimen_vendor_calls.vcf.gz.tbi ### Resection tempus somatic freebayes grch37 Modality: molecular. Type: Tumour variant calls. Provider: Tempus. Origin: provider_source. Vendor-labelled somatic FreeBayes calls; original filters and genotypes retained. Tempus reports matched-normal blood collected 28 January 2025, received 30 January 2025; preservation unspecified. Download: https://youngcrc.com/data/variants/resection_tempus_somatic_freebayes_grch37.vcf ### Resection tempus somatic pindel grch37 Modality: molecular. Type: Tumour variant calls. Provider: Tempus. Origin: provider_source. Vendor-labelled somatic Pindel calls; original filters and genotypes retained. Tempus reports matched-normal blood collected 28 January 2025, received 30 January 2025; preservation unspecified. Download: https://youngcrc.com/data/variants/resection_tempus_somatic_pindel_grch37.vcf ### Kandinsky somatic variant candidates Modality: molecular. Type: Tumour variant candidates. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Fourteen candidate rows with tumour/normal counts and annotations. Exact BAM inputs and reference assembly unconfirmed; coordinate-based integration requires the pipeline manifest. Supplied research calls, not fresh clinical validation. Download: https://youngcrc.com/data/valius/kandinsky_somatic_variants.csv ### CEA whole-slide IHC image Modality: pathology. Type: Whole-slide IHC images. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Research copy: CEA-stained whole slide; all four tissue pyramid levels and native compressed tiles preserved. Original label, macro and thumbnail images omitted. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/ihc-wsi-003_cea.svs ### TROP2 whole-slide IHC image Modality: pathology. Type: Whole-slide IHC images. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Research copy: TROP2-stained whole slide; all four tissue pyramid levels and native compressed tiles preserved. Original label, macro and thumbnail images omitted. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/ihc-wsi-004_trop2.svs ### cMET whole-slide IHC image Modality: pathology. Type: Whole-slide IHC images. Provider: Valius / Kandinsky / BostonGene. Origin: provider_source. Research copy: cMET-stained whole slide; all four tissue pyramid levels and native compressed tiles preserved. Original label, macro and thumbnail images omitted. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/imaging/ihc-wsi-001_cmet.svs ### Clinical timeline Modality: research. Type: Clinical chronology. Provider: Clinical records & imaging. Origin: derived_summary. Treatment, imaging, procedures and patient reports with evidence labels. Download: https://youngcrc.com/data/clinical/timeline.json ### Variants Modality: research. Type: Curated variant evidence. Provider: Cross-provider research & documentation. Origin: derived_summary. Thirty research-audit loci with explicit mixed genome builds; not a newly validated somatic catalogue. Download: https://youngcrc.com/data/molecular/variants.csv ### Variants Modality: research. Type: Curated variant evidence. Provider: Cross-provider research & documentation. Origin: derived_summary. Thirty research-audit loci with explicit mixed genome builds; not a newly validated somatic catalogue. Download: https://youngcrc.com/data/molecular/variants.json ### Public imaging download catalogue Modality: research. Type: Imaging release documentation. Provider: Clinical records & imaging. Origin: research_documentation. Selected native PET-CT series, 8 April 2026. Read the preparation scope before analysis. Download: https://youngcrc.com/data/imaging_release_catalog.json ### April PET-CT series and preparation manifest Modality: research. Type: Imaging release documentation. Provider: Clinical records & imaging. Origin: research_documentation. Selected native PET-CT series, 8 April 2026. Read the preparation scope before analysis. Download: https://youngcrc.com/data/imaging/IMG-012/release_manifest.json ### April PET-CT instance checksums Modality: research. Type: Imaging release documentation. Provider: Clinical records & imaging. Origin: research_documentation. Selected native PET-CT series, 8 April 2026. Read the preparation scope before analysis. Download: https://youngcrc.com/data/imaging/IMG-012/instance_manifest.json ### April PET-CT series inventory Modality: research. Type: Imaging release documentation. Provider: Clinical records & imaging. Origin: research_documentation. Selected native PET-CT series, 8 April 2026. Read the preparation scope before analysis. Download: https://youngcrc.com/data/imaging/IMG-012/series_manifest.json ### April PET-CT preparation and viewer notes Modality: research. Type: Imaging release documentation. Provider: Clinical records & imaging. Origin: research_documentation. Selected native PET-CT series, 8 April 2026. Read the preparation scope before analysis. Download: https://youngcrc.com/data/imaging/IMG-012/README.txt ### Valius export provenance and limitations Modality: research. Type: Integrated analysis documentation. Provider: Valius / Kandinsky / BostonGene. Origin: research_documentation. Column-level specimen distinctions, assay limitations and missing input manifests. Download: https://youngcrc.com/data/valius/README.txt ### Findings Modality: research. Type: Integrated molecular findings. Provider: Cross-provider research & documentation. Origin: derived_summary. Selected report-derived molecular facts; labelled prior extractions are not fresh clinical validation. Download: https://youngcrc.com/data/molecular/findings.csv ### Findings Modality: research. Type: Integrated molecular findings. Provider: Cross-provider research & documentation. Origin: derived_summary. Selected report-derived molecular facts; labelled prior extractions are not fresh clinical validation. Download: https://youngcrc.com/data/molecular/findings.json ### My molecular profile and vaccine targets Modality: research. Type: Integrated molecular findings. Provider: Cross-provider research & documentation. Origin: derived_summary. Report-linked pathogenic, likely pathogenic and VUS variants; assay-specific biomarkers, target expression, pathology and JLF/Invoke vaccine candidates. Download: https://youngcrc.com/data/molecular/summary.json ### Laboratory observations Modality: research. Type: Laboratory result summaries. Provider: Clinical records & imaging. Origin: derived_summary. Source-linked CEA, blood counts, chemistry and iron measurements from authenticated portal captures, plus PET preparation glucose. Download: https://youngcrc.com/data/clinical/laboratory_observations.json ### Public pathology-image download catalogue Modality: research. Type: Pathology release documentation. Provider: Valius / Kandinsky / BostonGene. Origin: research_documentation. Verified whole-slide files with specimen linkage and preparation scope. Download: https://youngcrc.com/data/pathology_release_catalog.json ### Pathology Modality: research. Type: Pathology summaries. Provider: Clinical records & imaging. Origin: derived_summary. Histology, staging and immunohistochemistry linked to tissue collection. Download: https://youngcrc.com/data/clinical/pathology.json ### Personalis liquid-biopsy observation (PPM) Modality: research. Type: Plasma molecular profiling summaries. Provider: Clinical records & imaging. Origin: derived_summary. One amended primary Personalis xM result in its original PPM unit; displayed separately from Signatera. Download: https://youngcrc.com/data/clinical/liquid_biopsy_observations.json ### Plasma profiling report findings Modality: research. Type: Plasma molecular profiling summaries. Provider: Clinical records & imaging. Origin: derived_summary. Guardant360 Liquid and Caris Assure findings with original comparators, indeterminate results and low-fraction limitations. Download: https://youngcrc.com/data/clinical/plasma_profiling_assays.json ### Missing data priorities Modality: research. Type: Release status and gaps. Provider: Cross-provider research & documentation. Origin: research_documentation. Important gaps and records needed for future releases. Download: https://youngcrc.com/data/gaps.json ### Sequencing and imaging release status Modality: research. Type: Release status and gaps. Provider: Cross-provider research & documentation. Origin: research_documentation. Verified public downloads, available files still in preparation, selected-series DICOM scope and missing later scan images; reviewed 7 October 2026. Download: https://youngcrc.com/data/release_status.json ### Index Modality: research. Type: Research dataset index. Provider: Cross-provider research & documentation. Origin: research_documentation. Molecular dataset overview and completeness. Download: https://youngcrc.com/data/molecular/index.json ### Processed release catalog Modality: research. Type: Sequencing inventories and release documentation. Provider: Cross-provider research & documentation. Origin: research_documentation. Released vendor-processed calls and expression summaries, not raw sequencing reads. Source originals unchanged. Download: https://youngcrc.com/data/molecular/processed_release_catalog.csv ### Processed release catalog Modality: research. Type: Sequencing inventories and release documentation. Provider: Cross-provider research & documentation. Origin: research_documentation. Released vendor-processed calls and expression summaries, not raw sequencing reads. Source originals unchanged. Download: https://youngcrc.com/data/molecular/processed_release_catalog.json ### Raw file inventory Modality: research. Type: Sequencing inventories and release documentation. Provider: Cross-provider research & documentation. Origin: research_documentation. Source-file inventory and preparation status. Only verified public files have download links; proposed public filenames differ from laboratory names. Download: https://youngcrc.com/data/molecular/raw_file_inventory.csv ### Raw file inventory Modality: research. Type: Sequencing inventories and release documentation. Provider: Cross-provider research & documentation. Origin: research_documentation. Source-file inventory and preparation status. Only verified public files have download links; proposed public filenames differ from laboratory names. Download: https://youngcrc.com/data/molecular/raw_file_inventory.json ### Alignment release catalogue (JSON) Modality: research. Type: Sequencing inventories and release documentation. Provider: Cross-provider research & documentation. Origin: research_documentation. Verified public alignment derivatives and regenerated indexes, hosted separately from the curated archive. URLs, sizes, SHA-256 hashes and lineage describe released objects, not original bytes. Download: https://youngcrc.com/data/molecular/raw_release_catalog.json ### Alignment release catalogue (CSV) Modality: research. Type: Sequencing inventories and release documentation. Provider: Cross-provider research & documentation. Origin: research_documentation. Verified public alignment derivatives and regenerated indexes, hosted separately from the curated archive. URLs, sizes, SHA-256 hashes and lineage describe released objects, not original bytes. Download: https://youngcrc.com/data/molecular/raw_release_catalog.csv ### Clinical data dictionary Modality: research. Type: Sources and data dictionaries. Provider: Clinical records & imaging. Origin: research_documentation. Evidence labels, date conventions and limitations. Download: https://youngcrc.com/data/clinical/dataset_info.json ### Clinical sources Modality: research. Type: Sources and data dictionaries. Provider: Clinical records & imaging. Origin: research_documentation. Source descriptions and document completeness. Download: https://youngcrc.com/data/clinical/sources.json ### Data dictionary Modality: research. Type: Sources and data dictionaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Identifiers, coordinates, filter and count conventions. Download: https://youngcrc.com/data/molecular/data_dictionary.json ### Sources Modality: research. Type: Sources and data dictionaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Provenance labels for extracted oncology facts; original documents excluded. Download: https://youngcrc.com/data/molecular/sources.csv ### Sources Modality: research. Type: Sources and data dictionaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Provenance labels for extracted oncology facts; original documents excluded. Download: https://youngcrc.com/data/molecular/sources.json ### Assays Modality: research. Type: Specimen and assay summaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Assays with genome build, source uncertainty and raw-versus-derived status. Download: https://youngcrc.com/data/molecular/assays.csv ### Assays Modality: research. Type: Specimen and assay summaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Assays with genome build, source uncertainty and raw-versus-derived status. Download: https://youngcrc.com/data/molecular/assays.json ### Sample links Modality: research. Type: Specimen and assay summaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Clinical–molecular specimen links; exact assay aliquot/block linkage is separately qualified. Download: https://youngcrc.com/data/molecular/sample_links.csv ### Sample links Modality: research. Type: Specimen and assay summaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Clinical–molecular specimen links; exact assay aliquot/block linkage is separately qualified. Download: https://youngcrc.com/data/molecular/sample_links.json ### Samples Modality: research. Type: Specimen and assay summaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Specimen map; unknowns are null or unresolved. Public IDs differ from laboratory identifiers. Download: https://youngcrc.com/data/molecular/samples.csv ### Samples Modality: research. Type: Specimen and assay summaries. Provider: Cross-provider research & documentation. Origin: research_documentation. Specimen map; unknowns are null or unresolved. Public IDs differ from laboratory identifiers. Download: https://youngcrc.com/data/molecular/samples.json ### Imaging studies Modality: research. Type: Study summaries. Provider: Clinical records & imaging. Origin: derived_summary. Dated radiology summaries; prepared April 2026 native DICOM series are separate downloads. Download: https://youngcrc.com/data/clinical/imaging.json ### Target read evidence Modality: research. Type: Target sequence evidence. Provider: Cross-provider research & documentation. Origin: derived_summary. Reformatted direct-read audit counts: unmapped/secondary/supplementary/QC-failed/duplicate records excluded; MAPQ >=30, locus BQ >=20 and exact CIGAR support for indels. Fragment names are not UMI-proven molecules. Download: https://youngcrc.com/data/molecular/target_read_evidence.csv ### Target read evidence Modality: research. Type: Target sequence evidence. Provider: Cross-provider research & documentation. Origin: derived_summary. Reformatted direct-read audit counts: unmapped/secondary/supplementary/QC-failed/duplicate records excluded; MAPQ >=30, locus BQ >=20 and exact CIGAR support for indels. Fragment names are not UMI-proven molecules. Download: https://youngcrc.com/data/molecular/target_read_evidence.json ### Treatment plans, vaccines and trial options Modality: research. Type: Treatment plans. Provider: Cross-provider research & documentation. Origin: derived_summary. Treatment/vaccine plans and experimental/conventional options with case relevance, primary evidence and UK access. Experimental evidence reviewed 7 October 2026; established/retreatment options refreshed 8 October 2026. Download: https://youngcrc.com/data/clinical/treatment_options.json ### Signatera ctDNA history (JSON) Modality: research. Type: Tumour-informed ctDNA summaries. Provider: Natera. Origin: derived_summary. Twelve report-documented blood draws and one separately labelled later patient-reported result. Download: https://youngcrc.com/data/clinical/ctdna.json ### Signatera ctDNA history (CSV) Modality: research. Type: Tumour-informed ctDNA summaries. Provider: Natera. Origin: derived_summary. Twelve report-documented blood draws and one separately labelled later patient-reported result. Download: https://youngcrc.com/data/clinical/ctdna.csv ### Vaccine evidence Modality: research. Type: Vaccine research evidence. Provider: Cross-provider research & documentation. Origin: derived_summary. Selected unresolved design questions and sequence evidence; research observations, not clinical or manufacturing instructions. Download: https://youngcrc.com/data/molecular/vaccine_evidence.csv ### Vaccine evidence Modality: research. Type: Vaccine research evidence. Provider: Cross-provider research & documentation. Origin: derived_summary. Selected unresolved design questions and sequence evidence; research observations, not clinical or manufacturing instructions. Download: https://youngcrc.com/data/molecular/vaccine_evidence.json ### Caris — Additional Caris RNA outputs — RNA alignment Modality: rna. Type: RNA alignments and indexes. Provider: Caris. Origin: provider_source. Additional Caris RNA; tissue, collection date and tumour fraction unconfirmed. No new biological analysis or clinical interpretation. Source sequence dictionary retained; verify exact reference FASTA/checksums before reanalysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-009_caris_specimen_unresolved_rna.bam ### Caris — Additional Caris RNA outputs — BAM index Modality: rna. Type: RNA alignments and indexes. Provider: Caris. Origin: provider_source. Additional Caris RNA; tissue, collection date and tumour fraction unconfirmed. No new biological analysis or clinical interpretation. Source sequence dictionary retained; verify exact reference FASTA/checksums before reanalysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-009_caris_specimen_unresolved_rna.bam.bai ### Caris primary RNA — RNA alignment Modality: rna. Type: RNA alignments and indexes. Provider: Caris. Origin: provider_source. Primary rectal tumour mapped at specimen level; exact block/aliquot and original pipeline checksum requested. No new biological analysis or clinical interpretation. Source sequence dictionary retained; verify exact reference FASTA/checksums before reanalysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-011_caris_primary_tumour_rna.bam ### Caris primary RNA — BAM index Modality: rna. Type: RNA alignments and indexes. Provider: Caris. Origin: provider_source. Primary rectal tumour mapped at specimen level; exact block/aliquot and original pipeline checksum requested. No new biological analysis or clinical interpretation. Source sequence dictionary retained; verify exact reference FASTA/checksums before reanalysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-011_caris_primary_tumour_rna.bam.bai ### Tempus — Tumour RNA alignment Modality: rna. Type: RNA alignments and indexes. Provider: Tempus. Origin: provider_source. Bulk tumour RNA alignment; exact GRCh37 dictionary retained. Original RNA header lacked reference MD5s. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-001_resection_tumour_rna_grch37.bam ### Tempus — Tumour RNA alignment index Modality: rna. Type: RNA alignments and indexes. Provider: Tempus. Origin: provider_source. Companion BAI; download with its matching released BAM. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-001_resection_tumour_rna_grch37.bam.bai ### Caris primary RNA — RNA reads R1 Modality: rna. Type: RNA reads. Provider: Caris. Origin: provider_source. Caris bulk RNA mapped to the primary rectal tumour at specimen level; not single-cell data. Exact block/aliquot, original pipeline metadata/checksum, reference checksum and library structure requested. Pair identity/order and biological bytes verified; no new alignment or variant analysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-007_caris_primary_tumour_rna_r1.fastq.gz ### Caris primary RNA — RNA reads R2 Modality: rna. Type: RNA reads. Provider: Caris. Origin: provider_source. Caris bulk RNA mapped to the primary rectal tumour at specimen level; not single-cell data. Exact block/aliquot, original pipeline metadata/checksum, reference checksum and library structure requested. Pair identity/order and biological bytes verified; no new alignment or variant analysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-008_caris_primary_tumour_rna_r2.fastq.gz ### Caris — Additional Caris RNA outputs — RNA reads R1 Modality: rna. Type: RNA reads. Provider: Caris. Origin: provider_source. Additional Caris bulk RNA; tissue, collection date and tumour fraction unconfirmed. Not single-cell data. Original pipeline/reference checksum and exact library structure requested. Pair identity/order and biological bytes verified; no new alignment or variant analysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-005_caris_specimen_unresolved_rna_r1.fastq.gz ### Caris — Additional Caris RNA outputs — RNA reads R2 Modality: rna. Type: RNA reads. Provider: Caris. Origin: provider_source. Additional Caris bulk RNA; tissue, collection date and tumour fraction unconfirmed. Not single-cell data. Original pipeline/reference checksum and exact library structure requested. Pair identity/order and biological bytes verified; no new alignment or variant analysis. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-006_caris_specimen_unresolved_rna_r2.fastq.gz ### Tempus resection RNA — RNA reads ordinal 1 Modality: rna. Type: RNA reads. Provider: Tempus. Origin: provider_source. Tempus rectal-resection bulk RNA, not single-cell data. Original read ordinals 1 and 3 retained; matching instrument/inline-sequence identifiers link corresponding records. Vendor chemistry/read structure and original pipeline/reference checksum requested; read 2 is not established as a missing mate or index. Pair identity/order and biological bytes verified; no new alignment or variant analysis. Released BAM: 13,970,734 unpaired SAM records; raw files: 13,837,280 matching records each. BAM read names include merged/pair processing suffixes; the undocumented transformation prevents direct count comparison. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-013_tempus_resection_tumour_rna_read1.fastq.gz ### Tempus resection RNA — RNA reads ordinal 3 Modality: rna. Type: RNA reads. Provider: Tempus. Origin: provider_source. Tempus rectal-resection bulk RNA, not single-cell data. Original read ordinals 1 and 3 retained; matching instrument/inline-sequence identifiers link corresponding records. Vendor chemistry/read structure and original pipeline/reference checksum requested; read 2 is not established as a missing mate or index. Pair identity/order and biological bytes verified; no new alignment or variant analysis. Released BAM: 13,970,734 unpaired SAM records; raw files: 13,837,280 matching records each. BAM read names include merged/pair processing suffixes; the undocumented transformation prevents direct count comparison. Download: https://alexander-young-cancer-data.alextisyoung.workers.dev/releases/2026-10-07/raw/m-raw-014_tempus_resection_tumour_rna_read3.fastq.gz ## Full structured records Treatment plans and evidence: https://youngcrc.com/data/clinical/treatment_options.json Laboratory measurements: https://youngcrc.com/data/clinical/laboratory_observations.json Clinical source metadata: https://youngcrc.com/data/clinical/sources.json Native sequencing: https://youngcrc.com/data/molecular/raw_release_catalog.json Native imaging: https://youngcrc.com/data/imaging_release_catalog.json Native pathology: https://youngcrc.com/data/pathology_release_catalog.json Availability and gaps: https://youngcrc.com/data/release_status.json and https://youngcrc.com/data/gaps.json Checksums: https://youngcrc.com/manifest.json and https://youngcrc.com/checksums.sha256