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Thanks for pushing back on their paper Hutan. The grouping looks even tighter in chillier's random data.

I think the rsids that have a "P" (for proxy) refer to another variant in LD with the DecodeME SNP that they tested in the other cohorts if the other cohorts didn't have the variant in question. The ones you named: 1. GRCh38 variant 13:53194927-GT-G rs35306732 2. GRCh37 variant 13:53750354:A:G...

I'm just learning about this, but I think technically these 13 genes weren't necessarily enriched in brain tissue. I'm having ChatGPT explain MAGMA to me, and it says it's basically two different analyses. The 13 highest scoring genes from the first part are likely to play a role in the brain...

On the topic of the brain expression, I don't remember much discussion about this yet. While all 13 brain tissues had enrichment of ME/CFS genes, there is an ordering of most to least significant that might give some clues. Written out and grouped: I added pituitary gland even though it...

On the topic of "what does DecodeME" show, my feeling is that it's really early for anyone to be saying with much confidence that the genes they found point to any specific pathway. From the DecodeME blog and paper respectively: Here are the candidate genes suggested by DecodeME: Is it...

Just adding the context from Wikipedia for why they say candidate gene studies don't replicate:

TLDR: They didn't do the replication with a second cohort properly, and the significant SNPs don't replicate in DecodeME. Fukuda criteria. They found significantly more participants had the T allele in the TNF-857 SNP. Also fewer had the A allele in the IFN-γ-874 SNP, but this was much less...

A first study of cytokine genomic polymorphisms in CFS: Positive association of TNF-857 and IFNgamma 874 rare alleles N Carlo-Stella, C Badulli, A De Silvestri, L Bazzichi, M Martinetti, L Lorusso, S Bombardieri, L Salvaneschi, M Cuccia Published: 2006 [Line breaks added] Objective In the...

Clinically Meaningful Improvements in Long COVID Symptoms Following Ketogenic Metabolic Therapy Combined with Lifestyle Interventions—A Clinical Case Report and Review of the Literature Dana Dharmakaya Colgan, Diane D. Stadler, Aluko A. Hope, Heather Zwickey, Todd E. Davenport, Thomas Weimbs...

Association of TLR9-rs352140 Polymorphism and Serum Levels of CRP, IL-6, and Anti-RBD IgG with the Chance of Developing Long COVID-19 Syndrome Zeynab Alavitabar, Hamed Fouladseresht, Amaneh Javid, Ensiye Torki, Majid Hosseinzadeh Background Long COVID-19 syndrome (LCS) is characterized by a...

Thread for the above study: A Pilot Study on the Effects of Exercise Training on Cardiorespiratory Performance, Quality of Life, and Immunologic Variables in [LC], 2024, Abbasi+ Another study from this group: Two-Day Cardiopulmonary Exercise Testing in Long COVID Post-Exertional Malaise...

Prospective associations between major depressive disorder, generalized anxiety disorder, fibromyalgia, and myalgic encephalomyelitis/chronic fatigue syndrome Nathaniel Stembridge Thomas, Michael C. Neale, Kenneth S. Kendler, Hanna M. van Loo, Nathan A. Gillespie Background Functional...

Circulating cell-free RNA signatures for the characterization and diagnosis of myalgic encephalomyelitis/chronic fatigue syndrome Anne E. Gardella, Daniel Eweis-LaBolle, Conor J. Loy, Emma D. Belcher, Joan S. Lenz, Carl J. Franconi, Sally Y. Scofield, Andrew Grimson, Maureen R. Hanson, Iwijn De...

I don't see one. I'll make a thread. Edit: https://www.s4me.info/threads/circulating-cell-free-rna-signatures-for-the-characterization-and-diagnosis-of-myalgic-encephalomyelitis-chronic-fatigue-syndrome-2025-gardella.45605/

Yeah, good point. Still good information one way or another.

Yeah, I realized after posting that with a small heritability it might still not be very useful.

Unrelated to above discussion: The individual variants aren't going to be diagnostically useful from this study. But I wonder if there might be an attempt to make a polygenic risk score from the DecodeME data and then see how well it classifies patients in other databases.

This is interesting. But I don't see the preprint talk about the data source for looking for shared intervals with all these other assorted traits like Parkinson's and arthritis. Only depression, pain, and anxiety. @Chris Ponting, is it that all traits in the UK BioBank were checked for similar...

Oh, when you click on that reassigned identifier, it goes to a page on an "Archive" Ensembl website, which I assumed was like an archive for genes that are no longer active. I couldn't find that new identifier on the regular Ensembl.

Oh, snoZ178 actually is/was a gene in humans that looks like it's closer to the DecodeME locus than CA10: LocusZoom But the Ensembl website says it was retired, which I think might mean that it was predicted to be there, but then that turned out not to be the case. So I'm guessing it's not...