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:

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1. Tumor Elimination: Stabilization and Reduction

2. Wound Closure

3. Long-Term Suppression

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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.

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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

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Memorial Sloan Kettering Cancer Center

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

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Medical Reports​

• Summary of Medical History

• UCSF Reports

• Kaiser Reports

• OSU Reports

• MSK Reports

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Imaging

• March 2021 MRI

• June 2021 MRI

• June 2021 CT 

• Photographs of wound.

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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)

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Generated by Egor

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

• VCF files

• Microsatellite instability (MSI) analysis

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Generated by Lan

• Tumor Normal BAM files from WGS

• Microbial Analysis

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In Progress

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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

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Stanford University:

• Plasma Metabolomics;

• Plasma Proteomics;

• Plasma Cytokine Profiling.

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Nebula Genomics:

• 100x WGS Saliva - Vanessa

• 100x WGS Saliva - Brother

• 100x WGS Saliva - Mother

• 100x WGS Saliva - Father

 

Upcoming

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University of Louisville:

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

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TBD:

• T cell and B cell sequencing

• Single cell RNA-seq

• More...