
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.

Vanessa
Vanessa writes a blog about her experience, Tiny Healer.
She was recently featured on Techtopia with Chitra Ragavan - Ep. 7 — How a patient with a rare tumor is taking personalized medicine to a new level through a unique non-profit biomedical research initiative.
Goals
The primary and most important goal here is to help Vanessa ie:
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Tumor Elimination: Stabilization and Reduction
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Wound Closure
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Long-Term Suppression
Publication
Our scientific outputs will be geared towards publishing in the Journal of Molecular Case Studies. All 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
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100x WGS DNA Whole Blood and Tumor. [Wavier Required]
Medical Reports
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Summary of Medical History
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UCSF Reports
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Kaiser Reports
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OSU Reports
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MSK Reports
Imaging
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March 2021 MRI
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June 2021 MRI
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June 2021 CT
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Photographs of wound.
Generated by Xiaowei @ Stanford
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Alignment files for the Tumor Normal WGS data, against hg38 (.bam)
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Read depth file (.wig)
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Germline SNV file (annotated .vcf)
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Mobile element insertion (only 1 detected)
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Planned: somatic SNV list (.vcf).
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Planned: copy number variations (CNV) and structural variations (SV's)
Generated by Egor
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Genotyping Repeats (Based on newly generated genome-wide repeat catalog.)
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VCF files
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Microsatellite instability (MSI) analysis
In Progress
Personalis ImmunoID NeXT DNA and RNA-seq
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2018 Whole Blood and Tumor;
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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).
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ImmunoID NeXT covers:
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T-cell receptor (TCR) alpha & beta repertoire
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Neoantigen detection and neoantigen load
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Tumor mutational burden (TMB)
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Microsatellite instability (MSI) characterization
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Human leukocyte antigens (HLA) typing, HLA and beta-2 microglobulin (B2M) somatic mutations, and HLA loss of heterozygosity (LOH)
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Tumor escape and resistance mechanisms
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Oncoviral detection
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Stanford University:
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Plasma Metabolomics;
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Plasma Proteomics;
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Plasma Cytokine Profiling.
Upcoming
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Familial Sequencing
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T cell and B cell sequencing
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Single cell RNA-seq
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More...

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 Foundation, MIT 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
Resources
The following resources and readings have been compiled by the Desmoid Tumor Research Foundation:
Recommended Readings
The following were determined to be relavent for Vanessa's case. Please feel free to send us addtional papers to include here!
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MedPacto suggests potential therapy for desmoid tumors at AACR 2021
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Intra-abdominal desmoid tumors mimicking gastrointestinal stromal tumors — 8 cases: A case report
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Comparison of CT volumetric measurement with RECIST response in patients with lung cancer
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Tumor Volume as an Alternative Response Measurement for Imatinib Treated GIST Patients