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Vanessa's case ran from January 2021 to June 2022.

Vanessa

PATIENT CASE

Desmoid Tumor​

Fall 2021. 
Vanessa is a desmoid tumor patient who’s case remains unresolved. Since she was diagnosed in 2011, Vanessa has been on 9 drugs and/or treatments. Her case is unique because she still lacks a molecular diagnosis for desmoid tumor and has run out of known clinical options. As a public facing patient, Vanessa is making her personal health data open to the scientific community to help create new insights for her case. She documents her medical and spiritual journey on her blog, tiny healer. 

We invite all scientists, researchers and medical professionals with intermediate to advanced experience to participate in Vanessa's case. Research to the People's cases are Open Participation, Open Data and Open Results. Submitted analysis will remain accessible via GitHub and through this site.

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Vanessa

Goals

The primary and most important goal here is to help Vanessa ie:

  1. Tumor Elimination: Stabilization and Reduction

  2. Wound Closure

  3. Long-Term Suppression

Publication

 

Our scientific outputs will be geared towards publishing in the Journal of Molecular Case StudiesAll collaborators will be included on the paper. This is a new goal for our program and feedback on this process is welcome.

What to Expect

 

Collaborate, learn and build biomedicine skills with other leading researchers, engineers and medical professionals. Most of all, help a real patient.

Data

 

Available Now

Memorial Sloan Kettering Cancer Center

  • 100x WGS DNA Whole Blood and Tumor. [Wavier Required]

Medical Reports

  • Summary of Medical History

  • UCSF Reports

  • Kaiser Reports

  • OSU Reports

  • MSK Reports

Imaging

  • March 2021 MRI

  • June 2021 MRI

  • June 2021 CT 

  • Photographs of wound.

Generated by Xiaowei @ Stanford

  • Alignment files for the Tumor Normal WGS data, against hg38 (.bam)

  • Read depth file (.wig)

  • Germline SNV file (annotated .vcf)

  • Mobile element insertion (only 1 detected)

  • Planned: somatic SNV list (.vcf).

  • Planned: copy number variations (CNV) and structural variations (SV's)

Generated by Egor

  • Genotyping Repeats (Based on newly generated genome-wide repeat catalog.)

  • VCF files

  • Microsatellite instability (MSI) analysis

In Progress

Personalis ImmunoID NeXT DNA and RNA-seq

  • 2018 Whole Blood and Tumor;

  • 2021 Whole Blood and Drainage Sample. (Note: drainage is something new and we are proposing it as surrogate for biopsy, as desmoid tumor can become very aggressive due to biopsy).

  • ImmunoID NeXT covers:

    • T-cell receptor (TCR) alpha & beta repertoire

    • Neoantigen detection and neoantigen load

    • Tumor mutational burden (TMB)

    • Microsatellite instability (MSI) characterization

    • Human leukocyte antigens (HLA) typing, HLA and beta-2 microglobulin (B2M) somatic mutations, and HLA loss of heterozygosity (LOH)

    • Tumor escape and resistance mechanisms

    • Oncoviral detection

Stanford University:

  • Plasma Metabolomics;

  • Plasma Proteomics;

  • Plasma Cytokine Profiling.

 

Upcoming

  • Familial Sequencing

  • T cell and B cell sequencing

  • Single cell RNA-seq

  • More...

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Setup​

 

Data Access: Data is available locally and in the Cloud. If you are accessing MSK files, please sign this wavier.

Discord: Primary communications platform for Voice and Text: Download Discord | Join Vanessa Channel

Github: Please put Analysis, code and presenations on Github. Research to the People Github

Zoom: We'll use Zoom for follow ups and subsequent meetings.

The Plan

 

Pre-analysis for Vanessa's case was hosted over the summer at Hack4Rare, an annual Hackathon produced by Children's Tumor FoundationMIT Hacking Medicine and Sage Bionetworks. We hosted a track at this event where researchers collaborated on re-analyzing Vanessa's existing clinical data. Read their work here.

 

As more data comes online we will continue to organize collaborative analysis / mini hackathons.

 

We're excited for you to join us as we work on solving Vanessa's case!

People​

Fall

2021

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On September 18th 2021, we hosted a 1-day hackathon at Stanford to generate new ideas for Vanessa's case.

Summer 2021

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Hack for Rare hosted a collaborative Desmoid Tumor Track at their 2021 rare disease hackathon.