rnafoundry.com/yash, manufactured at the RNA Foundry.
In January 2025, 32-year-old Yashdeep Bindal was diagnosed with stage IV pancreatic cancer. He had just returned to work after the birth of his daughter, Maya.
At the RNA Foundry, we are developing a personalized cancer vaccine for Yash. We’re sharing his tumour DNA, tumour RNA, matched-normal DNA and vaccine designs so that other researchers can help refine the work.
Get the data · See the lead design · Run the code · Contribute
Data
| Dataset | When collected | Collected by | Files | Size |
|---|---|---|---|---|
| Tumour DNA | 15 Jan 2025 | Caris | BAM · index · Caris VCF | 13.26 GB BAM |
| Tumour RNA | 15 Jan 2025 | Caris | FASTQ R1 · FASTQ R2 · BAM · index | 1.38 GB FASTQ pair; 1.32 GB BAM |
| Matched-normal DNA | 30 Oct 2026 | BAM · index | 143.29 GB BAM | |
| Gene expression | 15 Jan 2025 | Caris | Supplied expression values | 461.10 kB |
| HLA typing | 15 Jan 2025 | Caris | Six class-I alleles used in our analyses | 727 B |
The data guide describes each dataset, sample and reference scope. The file catalog lists locations, sizes and SHA-256 checksums.
Clinical reports
Clinical timeline — diagnosis, treatments, scan findings and specimen collection.
- Stanford pathology and IHC — January 2025.
- Stanford STAMP — 31 January 2025.
- Caris tissue profiling — 22 February 2025.
- Guardant360 liquid biopsy — 21 October 2025.
See the lead design
Design #2 is the lead design, generated using matched-normal white-blood-cell DNA alongside tumour DNA and RNA. It contains 24 antigen regions in a 724-aa protein: 12 mutation, 5 splice, 5 CTA/self and 2 fusion regions.
- Selected antigens · protein · antigen order.
- RNA segment · coding DNA · annotated DNA segment.
- Methods · antigen-by-antigen review.
PolyA and any downstream extension are unspecified; nucleotide files contain the known segments. Design #1, generated without matched-normal DNA, is retained for comparison.
Verify and reproduce
With Python 3.11 or 3.12, run from the repository root:
python3.11 -m venv .venv source .venv/bin/activate python -m pip install -e '.[mrna]' yash-vaccine verify yash-vaccine reproduce --output work/design-2-replay
These commands check and replay the lead design using bundled evidence and recorded predictions. They need no sequencing downloads or cloud account. The usage guide explains replay and alternative designs; the pipeline guide covers new raw-read processing and inference.
Make another candidate
Fork the repository, add your work under designs/your-design/, and submit a pull request. Include your rationale, data sources, code, commands and useful results. Annotated protein or RNA sequences are welcome; label unspecified components explicitly. An analysis or antigen list can be contributed before a complete construct is assembled.
See CONTRIBUTING.md. Questions and ideas are welcome as GitHub issues or at yash@rnafoundry.com.
Other directions to explore
This is one approach to vaccine design. Alternatives could examine MHC class II targets, immunogenicity, antigen trafficking, or linker optimization for processing and presentation.
Shared data are in data/, designs in designs/, maintained helpers in src/, and upstream jobs in workflow/. See the agent guide, reference acquisition guide, provenance records, required credits and retained-source notices for details.