A “Metabolic Trap” for Chronic Fatigue Syndrome (ME/CFS)? Send in your genome to help research.

Yet another hypothesis on HealthRising.org

https://www.healthrising.org/blog/2018/04/03/a-metabolic-trap-for-chronic-fatigue-syndrome-me-cfs/

Researcher Robert Phair is seeking ME/CFS patients who have had their genomes sequenced and who would be willing to share their data for research purposes. That includes 23andme data as well.

Edit: Dr. Phair now now has enough 23andMe data but could still use whole exome or whole genome data

 

Speculative but very interesting (even if it reminds me of the Dynamics & Control module I did years back, *shudder*). I seem to recall another ME/CFS researcher (Klimas?) having a similar proposed mechanism of action and who believed a 'nudge' to the system could lead to a permanent reset. I imagine it also ties in with Naviaux's approach as well.

The proof of the pudding (to me) will be whether said hypothesis could explain PEM, specifically its delayed impact.

 

@Mattie, do you think it would be worth adding to your title, 'Robert Phair seeks data from ME/CFS patients who've had their genomes mapped'?

Personally, I'd like to know more about his project before I sent him anything but anyone who gets Ron Davis's attention is interesting.

Another one for your Q&A list, @Andy?

 

I see Cort is checking with Phair whether 23&Me data count (I thought it wasn't the full genome).

 

I added it at the beginning of the post, otherwise title will be very long.

 

I also asked Dr. Phair that same question
I have 23andme data in txt format, I’ve emailed him to ask if that format is usable for his research. Will post his reply here as soon as I get it.

 

He says specifically that he is looking for whole genome or exome sequences, not 23andme.

 

He prefers whole genome, but 23andme data is also useful.

E-mail from Dr. Phair:

Yes, the .txt format will work. 23andMe only covers three of the five genetic variants that are important for the metabolic trap theory, but I can say that even this limited information is useful.

The 23and Me file that I need has a filename like this: genome_firstName_lastName_Full_date_time_in_digits.txt
so if it was mine it would be something like
genome_Robert_Phair_Full_20180315085441.txt
.zip instead of .txt is also fine

If you can open the file in a text editor it should begin with a header that looks like this:
# This data file generated by 23andMe at: Wed Jun 14 12:04:30 2017
#
# This file contains raw genotype data, including data that is not used in 23andMe reports.

Regards,
Robert D Phair PhD | Chief Science Officer | Integrative Bioinformatics Inc
Mountain View, CA

Edit: Dr. Phair now now has enough 23andMe data but could still use whole exome or whole genome data

 

I see that Dr Phair has kindly answered comments from patients on Cort's article (I haven't read them yet):

https://www.healthrising.org/blog/2018/04/03/a-metabolic-trap-for-chronic-fatigue-syndrome-me-cfs/

 

Update: Dr. Phair now now has enough 23andMe data but could still use whole exome or whole genome data

 

what are the RSid's for the 3 genetic variants on 23andme?

 

Which cost effective genome or exome testing does this doctor recommend?

 

Illumina, 10xGenomics, Veritas, and Qiagen. As of 2016 a whole genome sequence from Illumina or Veritas costs about $1,000 but Illumina hopes to bring the price down to $100 in the next 3-10 years.

From the original article on healthrising.org:
https://www.healthrising.org/blog/2018/04/03/a-metabolic-trap-for-chronic-fatigue-syndrome-me-cfs/

 

Don’t know that.