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My memory of the webinar discussion between Eric Topol and Kevin Tracey was that those with the vagus nerve stimulator switched on were equally likely to report sensations (e.g. tingles in the neck) as those in the control group.

I will think about whether their results and DecodeME's are concordant only when the EpiSwitch test is applied to (i) samples from cases and controls when they are taken, and are stored, in exactly the same way, (ii) when they more precisely match for age and sex, (iii) when they include cases...

I'd love for the company/authors to tell me that I'm wrong, but here is my critique up at everyone's favourite Science Media Centre: “The authors claim a ‘revolutionary blood test’ for ME/CFS based on a technology, EpiSwitch®, developed by Oxford BioDynamics Plc who co-authored and funded this...

No timeframe for completion of the HLA analysis. The Manhattan plot in the preprint includes all variants including those in the HLA. But note that in the HLA analyses we do not test each DNA variant, rather we test combinations of variants that are commonly coinherited, i.e. "HLA alleles". So...

Hi. Yes, we needed to LiftOver DNA variants from human genome build 38 (hg38) to the previous version (GRCh37 (hg19)) which FUMA uses for, e.g., MAGMA analysis. You're correct that some SNPs are lost in the LiftOver, but only a few. More variants are lost because FUMA's reference panel of...

Thank you. Table S4 genes are from the gene based analysis. And then these genes were tested against the tissue types in Fig 3, which found significant association to 13 brain tissues.

Hi. There were lots of SNPs (approximately half) that were discarded in the initial QC steps (see Supplemental Methods). Then there were lots of SNPs that were imputed (>8 million), and we only look at those with INFO>0.9. So discard all those with INFO<0.9.

My apologies. This is indeed the wrong citation. We'll fix for the next version.

Hi. I've posted this elsewhere on Science for ME, but think it's important to leave here too. About the "only a 1% difference between [the frequencies of] those with ME and controls". This small "effect size" does not matter if you're focused on drug discovery. This is because the success rate...

My guess is that this variant is absent from the dbSNP Release used by GeneAtlas at the time, but present in the reference panel that we used for imputation (namely, UK Biobank Whole Genome Sequencing variants). Not all variants are listed in all resources unfortunately.

Hi. First, I should say that we didn't complete in time for the preprint a second DecodeME analysis that uses all cases passing quality control. We're going to keep going on this. But in answer to your question about "European ancestry", this is genetics short-hand for people whose DNA variation...

To help, we wrote a document on candidate genes: https://www.pure.ed.ac.uk/ws/portalfiles/portal/533352484/Candidate_Genes.pdf

Sorry to be late in responding. The analysis for Figure 5 considered the association of 80 symptoms as well as age and sex in the same model. The important thing to say is that 62 of these symptoms are significantly female-biased, so these tend to favour greater severity in the model; being male...

Every human on earth carries deleterious changes to their genes. This person has several such changes, and the authors focus on only 1, to ADCK1, and to only one of their two copies of the ADCK1 gene. Notably, there is not evidence for deleterious changes to the ADCK1 gene being linked to any...

Yes - please email me if/when funding is announced for SequenceME.

Also: "Oxford Nanopore’s breakthrough genetic sequencing tech to analyse 50,000 samples from UK Biobank, to create a world-first ‘epigenetic map’." https://www.gov.uk/government/news/landmark-genetics-partnership-to-probe-causes-of-cancer-and-dementia

Right on cue, a preprint came out today that spells out the benefits of applying both GWAS and Whole Genome Sequencing: https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1.full.pdf “GWAS and LoF burden [whole genome sequencing] tests reveal distinct but complementary aspects of trait...

With one voice we ask the UK Govt (and other governments), and their funding agencies, to strategically prioritise ME/CFS research funding. If not forthcoming, then the obvious next question is: "Why not, given the huge disease burden and cost to the economy?" There will be a cost benefit from...

In no particular order here are a dozen: (i) rare DNA differences causing disease (found using whole genome sequencing), rather than the common ones investigated in DecodeME/GWAS, (ii) "stratifying" pwME based on more rigorous clinical investigation and/or clustering of electronic health...

Thank you, Simon. But what you don't say is how you came to my rescue a decade before. This is what friends do - when they can - and Simon did this first!