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Stanford Internal
Genetics and Personalized Medicine Hackathon

Fall 2021

Date: Sept. 18th 2021
Time: 10.00am - 6.00pm
Location: Stanford Biomedical Innovation Building (BMI)

This event has ended and Vanessa's case remains active online. Please apply to join.

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

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.

Lab Opportunity

We're seeking a Stanford student with Cell Culture for Vanessa's case. This position is volunteer based. Our goal is to test drug screening to validate a possible therapy. You will be working directly with Fereshteh Jahanbani PharmD, PhD in the Snyder Lab. 

Goals

 

On September 18th, we want to establish foundational working knowledge of Vanessa's case across Stanford to help guide future work, data generation and collaborations. 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

Generated by Lan

  • Tumor Normal BAM files from WGS

  • Microbial 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.

Nebula Genomics:

  • 100x WGS Saliva - Vanessa

  • 100x WGS Saliva - Brother

  • 100x WGS Saliva - Mother

  • 100x WGS Saliva - Father

 

Upcoming

University of Louisville:

  • PacBio Long Read RNA and DNA-seq on blood cells & tumor sample

TBD:

  • T cell and B cell sequencing

  • Single cell RNA-seq

  • More...

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Setup​

 

Data Access: Data will be available locally to all Stanford participants.

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

Github: Presentations and Code will be pushed to 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!

Agenda

 

  1. Brunch and Dinner are provided.

  2. All talks will be recorded.

 

Morning Session

9.45: Doors Open

10.00 - 10.20: Get Food - Brunch & Social

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10.20 - 10.25: Pete and Organizers - Welcome. Talks will start Promptly at 10.20! 

10.25 - 10.50: Vanessa - Journey, Medical Summary and Q&A

10.50 - 11.00: Michael Snyder, PhD - Chair, Stanford Genetics and Personalized Medicine

11.00 - 11.10: Bill Paseman - RTTP Advisor and Patient #2: The importance of young talent.

11.10 - 11.25: Xiaowei Zhu, PhD - Pre-analysis presentation

11.25 - 11.40: Lan Zhao, PhD - Pre-analysis presentation

11.40 - 12.00: Fereshteh Jahanbani PharmD, PhD - Case Lead

Afternoon Session

12.15 - 16.30: Work and brainstorm session in smaller groups.

16.30: Regroup: Share new ideas, future objectives.

17.00: Dinner and Social in outdoor courtyard

18.00: Official End of Event

People​

COVID-19

Based on Santa Clara and San Mateo County orders and CDC guidance, face coverings are required indoors for all individuals regardless of COVID-19 vaccination status. Campus community members who are fully vaccinated for COVID are not required to wear face coverings in other outdoor settings. We want everyone to feel comfortable at this event, and have selected spaces on campus that will allow us to be more spread out.

Food Menu

Brunch:

Cafe Borrone

  • Quiche Lorraine, sliced in 16 (contains pork, dairy, eggs, onions, & gluten)

  • Spinach & Mushroom Quiche (vegetarian, contains dairy, eggs, onions, & gluten)

  • Steel Cut Oats (cooked in water, vegan), with side of brown sugar and milk selection

  • Housemade Granola with almonds & dried cherries (contains honey, nuts, & flax but otherwise vegan) with side of yogurt, milk, or oat milk

  • Breakfast Potatoes with onions & thyme (vegan, gluten free, dairy free)

  • Seasonal Salad-- mixed greens with peaches, walnuts, avocado, & dried cranberries, with gorgonzola cheese & balsamic vinaigrette on the side

  • French Toast with vanilla bean butter (contains gluten, dairy, eggs)

  • Fruit Salad 

  • Coffee Boxes with side of sweetener (stevia & sugar) & milk (half n half or oat milk)

Dinner:

True Food Kitchen

  • Teriyaki Bowls

  • Ancient Grains Bowls

  • Chop Salads

  • Ingredient Salads

  • Lasagna

  • Tofu / Chicken / Steak protein options

  • Cookies

  • Grape Lemonade

  • Passionfruit Limeade