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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...

So in the pain paper, it looks like it was significant in females, but not males or combined. In DecodeME this locus was genome-wide significant in females and combined, and p=~.01 in males. They also suggest something other than CA10, something called snoZ178, that this locus might be...

Looking at that paper, in table 1, they give the sex-stratified results. Here's the locus that I think is what matches with DecodeME (note the position is based on GRCh37 unlike DecodeME, so needs to be converted): Here's the zoomed in manhattan plot of the chromosome 17 "tower" from...

I think the wrong paper is cited for the matching locus with multisite chronic pain: 41. Harlow CE, Uzochukwu E, Fernando HA, Mordaunt CE, Hughey JM, Eicher JD, et al. GWAS of Extended Prescription Analgesic Use Identifies Novel Genetic Loci in Chronic Pain [Internet]. 2024 [cited 2025 Jul...

As far as I understand, that shouldn't really change anything. h19 and hg38 are just different ways to refer to a SNP and can be converted between each other.

To add to what jnmaciuch explained, I think you might be referring to a common convention. SNVs (single nucleotide variants) are used to describe any places where a single nucleotide/letter is changed in the DNA. SNP (single nucleotide polymorphism) can refer to an SNV that is present in at...