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Shirley in Garden
Shirley

Metastatic Ovarian Cancer​

Collaborative Bioinformatics

Multiple leading groups from industry and academia have come together to generate cutting edge genetic and multi-omic data for Shirley. We are inviting researchers with established pipelines to analyze the data with the hope of finding new targets or therapy options.

Shirley

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Introduction

Winter 2022. Shirley is a computational biologist and physicist who has worked at iconic institutions such as NASA and Caltech, where solving difficult science and engineering problems was a part of daily life. She was diagnosed with ovarian cancer stage IIIc in September, 2013 and is highly motivated to survive to raise her children, aged 3 and 9 years old at the time of diagnosis. As a scientist, she pursued getting her tumor DNA and RNA sequenced under a research protocol at a translational genomics institute, and conducting her own research on the data. In the seven plus years since diagnosis, she has continued to pursue out of the box treatment options based upon her tumor’s molecular characteristics and helped others do the same. Unfortunately, in the fall of 2020, the disease entered a new and more aggressive phase.

​We invite all scientists, researchers and medical professionals with intermediate to advanced experience to participate in Shirley'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.

Apply to Join

or, please email us at researchtothepeople@stanford.edu.

Options Under Consideration

IMPORTTANT

Available to registered participants

Shirley's treatment history and options under consideration. 

Case Brief

Multiple leading groups from industry and academia have come together to generate cutting edge genetic and multi-omic data for Shirely's case. We are inviting highly skilled researchers with established pipelines to run the analyses listed below with the hope of finding new targets or therapy options to improve patients' health and symptoms in real time. Please apply to join or email us directly at researchtothepeople@stanford.edu to join this case.

We’re specifically looking for:

  1. Bioinformaticians with cancer or complex diseases background. 
  2. Oncologists familiar with NGS application and multi-omics studies, particularly related to ovarian cancer.
  3. Immunologist, particularly related to cancer, and ovarian cancer.
  4. Pharmacist/pharmacologist for in silico drug screening based on drugable targets.

Data Sharing

Data will be shared via Google shared drives - Stanford University and will be available after ​obtaining written consent on data sharing agreement

Short and Long Term Goals

  1. Finding action items that can improve patients' health and symptoms in real time. 
  2. Better understanding of the molecular basis of ovarian cancer
  3. Sharing our findings with patients, scientific and pharma communities via publications. 

Case Schedule Plan

1st Meeting

January 28 event is a kick off where the data sets for Shirley are introduced and people who have the skills to do the analyses requested above will discuss the data and the analysis. We will recruit highly skilled scientists for their immediate help with the case. 

Agenda

  • 16:00 - 16:10 Intro to Research to the People at Stanford Program by Pete Kane, Director. Background, Format, Agenda, Overview of who’s involved.
  • 16:10 - 16:30 Case Definition by Shirley, computational biologist and physicist: background and treatments  
  • 16:30 - 16:40 Case Definition by ovarian cancer oncologist Dr. Gottfried Konecny 
  • 16:40 - 17:05 Study design, collaborative multidisciplinary teamwork plan, on analyzing longitudinal multi-omics data and preliminary result by Fereshteh Jahanbani, PhramD, PhD, Director/CSO at RTTP@stanford 
  • 17:05 -17:10 5-min Break 
  • 17:10 - 17:30 Single Cell Data and preliminary analysis led by Dr. Boris Winterhoff, MD, MS from University of Minnesota Medical School.
  • 17:30 - 17:50  Immune cell phenotyping analyses using Cytof by Justin Jarrell, PhD - Senior Scientist, Medical Strategy from Teiko.Bio  
  • 17:50 - 18:20 Group Discussion 
  • 18:20 - 18:30 Closing Ideas and next steps 

2nd Meeting

Analysis reports will be shafted with scientists and researchers participating in the case. This will help us all to move to the next step of data analyses, focused on integrative analyses to identify targeted pathways/genes to stop the current tumor growth. 

Feb 11th 16.00-18.00

Agenda

 

3rd Meeting

Focus on further integrating all analyses, thoughts, and suggestions to identify best targetable candidate pathways/genes and use public databases to find available drugs.

4th Meeting

Meet with the patient's main oncologists and share the findings with them, in the form of a clinical report, which summarizes key findings and action items, followed by discussion.

5th Meeting

Sync with the oncology team after their review of the final integrated clinical report. Get an update on how advanced data and bioinformatics was able to help the patient with an effective treatment.

Analyses Needed

  • Transcriptomics analyses 
  • Whole exome seq analyses for SNPs, CNVs / Ins / Del and Translocations, and short tandem repeats calling
  • Extrachromosomal circular DNA analyses from DNA and RNA seq data
  • T-Cell Repertoire Analysis from bulk RNA seq
  • Neoantigens detection and analyses from DNA and RNA seq
  • Phenotype and genotype integration using longitudinal multi-omics and clinical data
  • Integrating longitudinal ovarian cancer multi omics data and clinical data for clinical interpretation
  • Pathway Analysis
  • CyTOF Analysis for PBMC

Please review our detailed data analysis agenda here.