Blog Post
December 23, 2020

2020 Yearend p1RCC Hackathon Update

Assuming money is no object, your medical care is a function of your clinician's medical knowledge.  If you have a common, well understood condition, your clinician will treat you using a "Standard of Care", a written procedure that tells them exactly what to do and how to repeat it with great success.  Effective "Standards of Care" are usually straightforward.   For example, few people die of broken arms or common bacterial infections, because clinicians have a Standard of Care that explains how to set a broken arm and when to prescribe what antibiotic for which infection.

Kidney cancer "Standard of Care" is often neither effective nor straightforward and sits at the outer boundary of clinical care.  At this outer boundary, patients typically participate in multiple "Clinical Trials", experiments on human subjects usually sponsored by pharma companies looking for new markets for their drugs.  Oncology (Cancer) trials typically have a 3.4% success rate if they bother to report results at all.  The situation is even less promising for rare cancers, which typically have no standard of care and no meaningful clinical trials.

So what does one do in cases like mine, where Overall Survival has not increased in 14 years? (slide 5 footnote)  What sits past the "Clinical Trial" boundary of clinical care?

The answer is research: both diagnostic (What exactly do you have) and therapeutic (How do you treat it).  I have held "hackathons", salons[1] for rare cancer research organized by Research to the People, which has recently become affiliated with the Stanford Snyder lab.  The hackathon's purpose is to try and help patients with rare types of cancer who do not fit into regular cancer trials and existing treatment regimens.  It starts by gathering research grade data on the patient.  Whereas clinical grade data is great for making decisions within the Standard of Care, research grade data is typically broader, more detailed and lends itself to more novel insights.  Next, Bioinformaticians, Cancer Biologists, Doctors, Data Scientists and a range of other researchers are invited to participate.   One draw for them is the ability to access this state of the art research data.  Another draw is that the "salon" atmosphere of the hackathon allows them to freely discuss novel diagnostic and therapeutic theories.  This group then applies advanced algorithmic analysis to the patient's DNA, RNA, and other specialized sequencing data.  The ultimate goal is to try and provide these patients with effective treatment paths that fit their unique versions of cancer.  I have held two hackathons, one in 2018 and one in 2020.  Typically, hackathon analysis involves comparing the patient's situation to that of others in the four ways listed below.  So far, the most progress for my case has been made using Pan Cancer analysis and verified by Familial analysis.

  • Cohort Analysis - Lump RCC into broad histological types (clear cell, papillary...) and analyze their members.  This is the preponderance of most current RCC research. 
  • Pan Cancer Analysis - Look for common factors in multiple cancer types often by leveraging TCGA data.  For example, QuantumInsights approach to clustering Clemson University's filtering of my p1RCC RNA-seq data indicates that it is "most similar" to thyroid cancer.
  • Familial Analysis - Unbeknowst to both Clemson and QuantumInsights, one of my siblings was recently diagnosed with both thyroid cancer and a lung carcinoid (The patient underwent an operation and is doing fine.).  Do my sibling and I share a common gene/pathway that explains both maladies?
  • Comorbidities - I was also diagnosed with a meningioma.  Do I have a gene/pathway that explains both my meningioma and kidney cancer?

Links between (Papillary) thyroid cancer and papillary kidney cancer have been described previously (e.g. 1, 2).  My hope is that there is biology behind my particular associations.  My next step then, is to enable discovery of a hard genetic link with a known oncogene or tumor suppressor.  Therapeutic research on my case is also in progress. 

Hackathons might be something other rare cancer patients want to explore if, like me, research on their type of cancer has stalled.  

None of the progress to date would have been possible without the generous help of many, many people.  Special thanks to:

[1] In the 19th century, many elements of French philosophy were created or discussed in salons, gatherings of people held by an inspiring host. During the gathering they amuse one another and increase their knowledge through conversation.  RTTP's host is typically the patient.

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