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A bright, bright light is about to shine on the most severely ill among us. The first part of the ME/CFS Severely Ill Big Data Study has been fully funded. It didn’t take long. The Davis’s kicked off a funding drive for the Severely Ill project about a month ago at their home. A couple of days later they received a $500,000 donation in the mail. (Imagine opening THAT letter….How does a $500,000 donation come? In the form of $500,000 check.). The Open Medicine Foundation just announced that that, plus other donations, plus a check for $350,000 dollars gave a green light to the ambitious, million dollar project.

big data medicine

The Davis Group will be digging deep, deep, deep into the biology of severely ill patients.

The project will undertake an exhaustive search for molecular biomarkers in home and/or bedbound patients with ME/CFS.  Each patient will receive approximately $25,000 worth of tests. By the time this study is done it’s likely that no patients in any other disease will have received the amount of study these patients will have.

I asked Stanford’s top immunologist, Mark Davis, about  this big search  effort for biomarkers. He said that the NIH – a hypothesis driven institution – doesn’t get the idea of a big open-ended search effort like this, but that he thought this was the way to go in an under-researched field like ME/CFS.

A study like this – if successful – could cut years, decades even, off the search for the cause of ME/CFS. It could uncover factors never contemplated before, or it could highlight areas we know about, or both.  It faces some challenges – lots of measures in a small group of patients, and sorting out the confounding issue of immobility- but then again it has Ron Davis and his group of top researchers.  Mark Davis said – when Ron asks you to do something – you do it :).

Davis recently developed the first way to cheaply and accurately assess the HLA part of our genome, and he’ll be developing other ways to do tests in these homebound patients.

It’s a bold effort and that boldness, plus the strength of the Davis team and Linda Tanenbaum’s work to get the message out have succeeded – and quickly. That’s good news for the ME/CFS Community.

This is just the beginning thrust of the End ME/CFS search effort. Davis has proposed the federal government adopt a strategic approach to ME/CFS – something along the lines of what happened with the Human Genome Project. This consortium based effort to understand ME/CFS  would cost around $5 million/year.

Janet Dafoe, Ron Davis’s wife, recently tweeted that Davis is committed to apply at every NIH session for funds to study this illness.

The ME/CFS Stigma Project

Davis’s inability to get funding for the severely ill project turned out to be a head-cringingly, embarrassing moment for the NIH.  That episode, which suggested the reviewers hardly took the time to read the grant, suggested the stigma surrounding ME/CFS is alive and well in some parts of the NIH.

John Kim, a marketing and advertising professional (and friend of Whitney Dafoe, Ron and Janet’s severely ill son) wants to help out. He’s asking people with ME/CFS to talk about the stigma’s they face at home, in the workplace, in doctor’s offices in order to help him produce more effective awareness and fundraising campaigns.

You help him out with this project by telling him about the stigma’s you may have encountered here.

The Big Biomarker Search

Genomic Biomarker Search

  • Whole Genome sequence  – Exome DNA sequence, Mitochondrial DNA sequence, Cell free RNA and DNA, DNA methylation of all immune cells
  • Metabolomics  – Saliva, Urine and Feces
  • Saliva – Whole Genome sequence
  • Feces –  DNA sequence of microbes Metabolomics

Immune Biomarker Search

Blood: Isolation of individual immune cell types. Especially NK cells,  Cy-TOF of many immune cell types, Karyotype of immune cells,  measure cytokine levels, NK cell  activity and gene expression

Novel Biomarker  Search

Ultimately the biomarkers – should they appear – could include findings from several different systems ( e.g. proteins in the blood, metabolites in the urine, DNA polymorphisms, epigentic changes) which put together spell ME/CFS. In a recent talk Ron Davis noted that some of the results from his son Whitney’s metabolomics tests were off the charts. That’s the kind the thing they hope will pop out.

Blood: HLA DNA sequence, KIR DNA sequence, Immune repertoire of all immune cells, Gene expression of a mix of all immune cells on Affymetrix exon array, Gene expression on individual immune cell types. Especially NK cells, Gene expression on individual cells by molecular bar coding and sequencing, Evaluation of alternative splicing from exon array, Magnetic levitation profile of all immune cells DNA sequence all particles (virus, bacteria, fungus,& parasites), PCR assay for common viruses (EBV, HHV6, CMV, enterovirus), MS/antibody assay for mycotoxins, Cu concentration and other metals, Development of software for Hypothesis Generator using our data and all literature

Saliva: DNA sequence all particles (virus, bacteria, fungus, & parasites) PCR assay for common viruses (EBV, HHV6, CMV, enterovirus), MS/antibody assay for mycotoxins

Sweat: In real time, remotely by wearable electronics Na, K, glucose, lactate and cytokines

Urine: DNA sequence all particles (virus, bacteria, fungus, & parasites) PCR assay for common viruses (EBV, HHV6, CMV, Enterovirus) MS/antibody assay for mycotoxins Cu concentration and other metals

Feces: DNA sequence all particles (virus, bacteria, fungus, & parasites) PCR assay for common viruses (EBV, HHV6, CMV, enterovirus) MS/antibody assay for mycotoxins

 

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