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Available now - https://www.rnz.co.nz/national/programmes/saturday/audio/2018992365/approaching-life-changing-diagnosis-for-missing-millions

I did 30x WGS and I've had WES done. WES didn't highlight the gene as far as I'm aware. Here is another very similar example. A few years ago I had a researcher ask me if I had any SERPINA1 variants (Alpha-1-Antitrypsin Deficiency related) in my WGS (they were reviewing their ME/CFS data) and I...

Is it worth forwarding the paper to Prof Cambridge as this is in her interest area? Another chance for tea and biscuits and a natter.

Comment about it on X "Frustrating the Radio 4 Today team consulted the Science Media Centre for the piece on a blood test for ME. The Science Media Centre’s behavioural beliefs about ME have been debunked so many times it is incredible anyone still talks to them."

I have P2RX7 (P2X7) variants and the first paper I found a number of years ago shows reduced levels for the variants I have. That paper focused on low bone density, but when I checked recently it's become associated with quite a few more diseases. Seems a bit of a leap what they claim as I'm...

CostPlus charges $61.24 for 30 x 2mg tablets plus $5 shipping. A fraction of the cost of a doctors visit to Kaufman. I suspect the labs were much more expensive, as quite a few of the tests they were ordering are only covered once per year only on Medicare insurance e.g. A1C, Lipid panel. So...

Thank you. The best p-value on the UK Biobank for these variants for CFS is 0.1 which is nothing close to the p-values reported in the paper of this thread. Link

All 4 were high impact frameshift or missense variants. I think the issue is clearer in the gene.iobio plot of the gene for my data. There are way too many missense (orange squares) and frameshift (red circles) variants. It's is obviously garbage data despite good sequencing depth for these.

I seem to remember the oxaloacetate trial paper promoted one of the physical function scales in the text of the paper vs the other which had null results (hope I'm remembering right). Sure would be nice to see Sf-36 data. Some of the same clinicians took part in the oxaloacetate and rapamycin...

Putrino's lab with funding from PolyBio is running another trial. I was really disappointed that Amy Proal/PolyBio are reposting success stories on X of people posting a good response to Rapamycin and no poor responses.

On top of what @forestglip explained about the plot you need to manually check variants that are higher in the plot that you are interested in to see if the MAF is too low. Low MAF values are not filtered out by the plot that would be filtered in a research study analysis. If you look at the...

That's a relief. I checked PTPRD in the UK Biobank data and nothing jumped out at me. Is it easy for you to do the other gene variants you list?

The control data in the study comes from a small subset of a genetic database, 1000 Genomes I think. The case data comes from the sequencing used in the study. gnomAD is saying the WGS data is not consistent across databases indicating a possible/probable issue with the data in the databases...

That's interesting. gnomAD doesn't list that and the Kaviar database can't find either rs1553120233 or rs112674709. Kaviar database search on location shows a T allele frequency of 13%, not far off the gnomAD of 18% but does NOT list an rsID (it normally does). OpenSNP has shutdown (end of...

Google AI interpretation: If the Broad Institute's GATK (Genome Analysis Toolkit) provides a warning about a genome's inbreeding coefficient, it likely indicates a higher than expected level of homozygosity at certain genetic locations (sites) . Meaning of Inbreeding Coefficient in this...

Here is Google AI Response: If the Broad Institute indicates that a genome (or variant) "failed random forest filter," it means the quality control process flagged it based on a random forest model . Here's a breakdown: Random Forest Model in Genome QC: In the context of genomics...

I don't understand the first 2 warnings but I assume they mean some sort of quality issue when Broad run their automated checks. My take is it means there is dodgy data reported in some WGS databases for this variant so be careful of using this data. EDIT : see following two posts for Google AI...

Two warnings on gnomAD. 1. Failed allele specific VSQR filter 2. Warning This variant is covered in fewer than 50% of individuals in gnomAD v3.1.2 genomes. This may indicate a low-quality site. 3 warnings on gnomAD. Same two as before + inbreeding coefficient warning. 2 warnings on gnomAD...

This paper looks to have serious quality issues. I took the first three variants in Table 1 (Top ranked genes) and all three have known quality issues noted on the Broad Institute gnomAD browser/database. NBPF1, rs3897177, SNV:1-16909052-C-T (GRCh37) Warning : Genomes failed random forest...

I took a quick look at some of the genes they highlighted and the UK Biobank is missing data for quite a number of variants that they highlighted.