Shirley Pepke's hackathon

Join the quest to find the best treatment options for Shirley Pepke

This patient-focused research effort is bringing together researchers, patients, scientists, bioinformaticians, and medical professionals to explore what is driving Shirley Pepke’s ovarian cancer and the best treatment options to stop it.

Shirley Pepke headshot
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To participate, click the button to apply. You will then be invited to the weekly chats and online discussion forum.

Research to the People is a framework for patients, researchers and physicians to collaborate on personalized medicine cases. Multiple leading groups from industry and academia have come together to generate cutting edge genetic and multi-omic data for Shirley.

We are inviting highly skilled researchers in cancer bioinformatics with established pipelines on DNA-seq, RNA-seq (bulk and single cell) and microbiome to join us to analyze the data 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.

Attn: We are in great need to find a bioinformatcian, who is heavily skilled on single cell RNA seq analyses, and can generate in-silco bulk RNA seq from single cell data.

Shirley hackathon

Are you (or someone you might know) interested and qualified to help Shirley Pepke make sense of her advanced ovarian cancer and guide her to a treatment strategy?

The late stage of Shirley Pepke’s cancer means that she needs insights that are well beyond the standard of care or even clinical trials. She is reaching into research labs and hoping that novel tests and bioinformatics can yield personalized “out of the box” treatments.

Sorry for the short notice, but Shirley needs answers fast = experts who can contribute insights within a week after the first meeting on Jan 28th.

This “hackathon” is hosted by Research to the People at Stanford Medicine and my friends Pete Kane and Fereshteh Jahanbani.

This is the planned schedule of (weekly?) virtual meetings:

  • There will a virtual symposium kicking things off this Friday, January 28, at 4:00pm (Pacific).
  • The next meeting will discuss and integrate the analyses, sharing the integrated reports with those actively participating in data analyses, and reporting their findings. This will help us all to move to the next step of data analyses which is focused mostly on integrative analyses to identify targeted pathways/genes to stop the current tumor growth.
  • The third meeting to further integrate all analyses, thoughts, and suggestions to identify the best targetable candidate pathways/genes and use public databases to find available drugs.
  • The fourth meeting we will meet with Shirley’s main oncologists and share the findings with them, in a form of easy clinical report, which summarizes all key findings and action items and let them brainstorm.
  • At the fifth meeting, we will hear from the oncologist’s team after their review of the final integrated clinical report and if they can begin helping the patient with an effective treatment.

I hope you can help.

Best,
Brad

I am a computational biologist, Girl Scout Troop Leader, and mother of two human children and four furry ones. I love learning, reading, spending time with friends and family, and getting out into nature. I have loved stargazing since I was a child. The wonder of looking out at the planets and our beautiful, dynamic galaxy strikes me with awe every time.

I was diagnosed with advanced ovarian cancer in 2013. Upon my diagnosis, I pivoted to researching ovarian cancer and advocating for personalized medicine and testing. I even applied my research to my own data early on and used it to choose my treatments. I did well, despite recurrences until December 2020, when my disease entered a very aggressive phase, infiltrating my organs.

Despite widespread disease, attempts to obtain adequate biopsies for testing failed. Standard chemo helped quite a bit, but did not eradicate the disease, which has rebounded quickly this year and become imminently life-threatening. However, this also provided an opportunity to obtain fresh sample for single cell and other assays, opening up hope for the discovery of more effective, personalized treatments.

  • Determine more effective short-term treatments from my tumor profiling
  • Discover better treatments for long term control of my tumor
  • Understand what changes in the tumor and/or microenvironment occurred to drive the sudden, rapid progression
  • Demonstrate the successful use of cutting-edge profiling for choosing personalized
    treatment for ovarian cancer
  • Bring together and expand the community of researchers interested in moving the bar
    for ovarian cancer treatment

Shirley will make her extensive inventory of medical data available to a crowd of participants for analysis and insights.

Weekly video chats will update participants on progress and specific questions that will help channel the research. An online discussion forum (via Slack) will enable asynchronous review of progress and opportunities for comments. A recorded version of the weekly updates will be posted shortly after for those who are unable to attend. Insights and recommendations will funnel into a global virtual “molecular tumor board” of leading rare and sarcoma cancer research oncologists and other experts.

This exercise will take about 2-3 months. The plan is to launch on January 28th. We will then proceed with additional insights on ways to make this exceptional research, analysis, and community of leaders available to more people.

We are engaging many people, representing multiple disciplines across institutions globally and bending the healthcare system to address the unique needs of one patient.

If you participate you should expect a culture of open participation, open data, and open results. You will be welcome to join weekly lightning update calls of 15 minutes on (day & time TBD), and an online discussion forum.

If you have analytical tools, you are encouraged to apply them and share your analysis. If you have specialist knowledge, you may participate in smaller discussions or may be asked to be on the molecular tumor board.

Right now we are especially encouraging bioinformaticians (any level), computational biologists, cancer scientists, AI/ML experts, and biohackers to apply to analyze the data. Any group accessing the data is required to submit a report on the outcome of their analysis.

More generally, patients, patient advocates and advocacy groups, and other interested parties are welcome to apply to participate in seminars and discussions.

Because you would like to help bridge the gap between cancer translational research and clinical applications for ovarian cancer, with the goal of speeding new treatment strategies from the lab to the clinic. You would like to help ovarian cancer patients, whose disease is relatively underfunded in terms of research dollars, gain access to more targeted treatment options. You would like to connect with researchers and advocates in cancer research. Because we will all be patients someday.

Contact Brad Power at bradfordpower@gmail.com for process, administration or organization questions.

Please see other info on this page and visit researchtothepeople.org/shirley