Jack Kosmicki
@jakphd.bsky.social
Statistical geneticist @ Regeneron tweets are my own | he/him/his
New GWAS of Fibromyalgia identified 26 loci and found an HTT inframe indel (same gene as Huntington's disease [HD]). Howevere, the Fibromyalgia variant isn't associated with HD, the HD CAG repeat isn't associated with Fibromyalgia, and they aren't in LD. www.nature.com/articles/s41...
Former president Biden is still taking Amtrak - not flying on a private jet.
5 months after the UK Biobank breach, access will finally be restored in September.
After 4 years, it's rather nice to finally present our work on genetic's model trait, height, in >1.4M WES/WGS samples (826k discovery; led by Adam Locke & Goncalo Abecasis where we found (amongst many other things) 207 genes (P<1.75e-9). A thread of findings below⬇️ www.medrxiv.org/content/10.6...
A unique job opportunity to work on some of the most exciting genomic datasets in the world!
Institute for Molecular Medicine Finland (FIMM)@fimm-uh.bsky.social · 2mo agoThe Computational and Statistical Genomics Group led by @srubinacci.bsky.social at FIMM, together with @finngen.bsky.social project, is looking for a Genomics Data Analyst with skills to ensure that our WGS and WES data are harmonized & analysis-ready. Apply here: 🔗 jobs.helsinki.fi/job/Helsinki...
The Computational and Statistical Genomics Group led by @srubinacci.bsky.social at FIMM, together with @finngen.bsky.social project, is looking for a Genomics Data Analyst with skills to ensure that our WGS and WES data are harmonized & analysis-ready. Apply here: 🔗 jobs.helsinki.fi/job/Helsinki...
🎉It's always a great day when FinnGen releases new summary statistics!
FinnGen@finngen.bsky.social · 2mo agoWe are pleased to announce the release of FinnGen DF13 results! 🧬 While the number of participants remains unchanged, DF13 incorporates updated health register data, increasing the number of cases across most disease endpoints. Browsing & download instructions here: www.finngen.fi/en/access_re...
It's pretty amusing to see companies pivot in just a few months from "use AI" to "don't use AI" when they realize humans cost less $$$.😂 finance.yahoo.com/sectors/tech...
Microsoft data suggests using AI is more expensive than hiring people
"For my team, the cost of compute is far beyond the costs of the employees."
finance.yahoo.com
Sleep and step count are inversely correlated (e.g., sleep peaks while step count bottoms during winter) from AllofUs wearable devices in Nature Medicine. BUT, the Spring 2020 #COVID outbreak unsurprisingly caused real outliers compared to same month / dif year www.nature.com/articles/s41...
Someone tried to sell access to the genetic and health records of 500k voluntary participants in the UK Biobank on Alibaba. Thankfully, authorities stopped this before any harm was done. www.ukbiobank.ac.uk/news/a-messa...
A message to our participants: UK Biobank data security update
We would like to inform you about an incident involving UK Biobank data. We apologise to our participants for the concern this will cause, and we hope to provide reassurance by outlining the serious a...
ukbiobank.ac.uk
Can you believe that until now there were more genomes sequenced for the woolly mammoth than for living African elephants? Today, we bring you the first genomic, continent-scale analyses of 232 high-quality genomes of both species, the savanna and forest elephant. www.nature.com/articles/s41...
Eugenics has really back into mainstream fashion (with an impressive PR rebranding as 'genetic optimization'🙄). Even Tucker Carlson is debating it. open.spotify.com/episode/6SRl...
Tucker Debates Biotech CEO on Baby Customization, Eugenics, and God’s Existence
Spotify video
open.spotify.com
🤯 Wow, 3 Nature Genetics papers came out on Monday all covering another snRNA gene, RNU2-2, causing developmental disorders and epileptic encephalopathies. www.nature.com/articles/s41... www.nature.com/articles/s41... www.nature.com/articles/s41...
Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies - Nature Genetics
Analyses of snRNA genes in a French cohort of people with rare disorders, with validation through international collaboration, identify monoallelic and biallelic variants in RNU2-2 as frequent causes ...
nature.com
At long last, one's constraint analyses no longer have to be restricted to the autosomes🙏🏼🤩 Now to revise some reviewer responses in light of this . . . 😅
Kaitlin Samocha@ksamocha.bsky.social · 4mo agoWe are excited to share our gnomAD v4.1.1 release gnomad.broadinstitute.org/news/2026-03... Major changes: * Constraint scores on X and Y * Improved coverage correction * LOFTEE fix * Guidance on constraint cut-offs * New quality flag for low coverage/mappability genes @gnomad-project.bsky.social
Project Hail Mary is a beautiful brilliant film. But molecular biologists be warned there's a deeply disturbing scene midway through when Ryan Gosling's scientist places two eppendorfs directly next to each other in an otherwise empty unbalanced microcentrifuge & sets it spinning with wild abandon.
Excited to share our new preprint on gnomAD v4! We present the full analysis of 730,947 exomes — new constraint metrics, improved LoF annotation (LOFTEE-2), LLM-based literature curation, and a unified framework for gene discovery and rare disease diagnosis. www.medrxiv.org/content/10.6...
Integrating 730,947 exome sequences with clinical literature improves gene discovery
Accurate estimates of allele frequencies aid in genetic discovery, including rare disease diagnosis, common disease investigations, and population genetics. Here, we present the Genome Aggregation Dat...
medrxiv.org
vibe reading papers with Claude is a game changer #vibereading
The No ICE in Minnesota is a fantastic deal. Lots of good video games and lots of physical games (TTRPG, etc) too! itch.io/b/3484/no-ic...
No ICE in Minnesota by jesthehuman and 651 others
No ICE in Minnesota: 1439 items for $10.00
itch.io
Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...
Population-scale sequencing resolves determinants of persistent EBV DNA - Nature
Population-scale WGS reveals genetic determinants of persistent EBV DNA, linking immune regulation—especially antigen processing and MHC class II variation—to EBV persistence and heterogeneous di...
nature.com
A new preprint from Peter Mchale and Michael Goldberg in my group on the latent biases inherent to current models of non-coding constraint. www.biorxiv.org/content/10.6...
The performance of genetic-constraint metrics varies significantly across the human noncoding genome
A longstanding goal in human genetics is to prioritize noncoding loci that, when disrupted, lead to developmental disorders and other Mendelian traits. In pursuit of this goal, multiple metrics have been developed to distinguish neutrally evolving sequences from those subjected to purifying selection. These metrics are commonly evaluated genome-wide, e.g., by computing a precision-recall curve on windows tiling the entire noncoding genome. Here, we identify parts of the noncoding genome where these metrics significantly underperform relative to their genome-wide performance due to "bias" in the underlying models of neutral genetic variation and/or a low "signal-to-noise ratio" in the genetic data. The most extreme effects are found for Gnocchi (Chen et al. 2024), the performance of which declines as GC content increases. We suggest annotating constraint scores of noncoding genomic intervals with robust measures of the bias of the corresponding model, allowing users to gauge confidence in those scores. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, R01HG012252
biorxiv.org
It's truly a sad state of affairs when it takes longer to pull GWAS sumstats out of the AllofUs research platform than it takes to generate them.
Really nice work by @nbaya.bsky.social and co. showing that, as expected, individuals whose observed phenotype deviates from their genetically predicted trait are enriched for rare damaging variants in associated genes with said trait. Now to see if embryo selection companies pick up on this 😉
Nik Baya@nbaya.bsky.social · 7mo agoWhy do some individuals defy their polygenic score? In the largest study of its kind (402k UKB individuals; 7 continuous traits + 3 diseases), we asked: If your phenotype deviates from common-variant polygenic score prediction, what's driving that difference? www.medrxiv.org/content/10.6...
I wrote about the bizarre case of Herasight, the embryo selection company going all in on eugenics.
Embryo selection company Herasight goes all in on eugenics
...
open.substack.com
You run a new command in #rlang #python #bash, and you don’t really know how long it should take. Will it be done in 30 seconds? 5 minutes? 45 minutes? Longer? 😫 An automatic notification might help to stay focused on #programming Let me introduce you to ntfy.sh slowkow.com/notes/ntfy/
Get notifications on desktop and mobile from long-running jobs in your terminal sessions
If you’re like me, you get tired of waiting for long-running jobs in the terminal. You run a new command, and you don’t really know how long it should take to finish. Will it be done in 30 seconds? 5 ...
slowkow.com
Another #aDNA preprint! We recovered DNA from 7,000 year old (!) goat leather from Cueva de los Murciélagos - and see a genetic link with Bermeya goats today! Credit to Francisco Martínez-Sevilla for seeing me on Youtube(?!) + reaching out to collaborate - there's still value in the internet.
Genetic analysis of 7,000 year old preserved goat leather from Cueva de los Murciélagos (Albuñol, Spain).
Advances in ancient DNA research have expanded the range of materials from which genetic information can be recovered, enabling the analysis of atypical materials. These often preserve both host and e...
biorxiv.org
Excited to share our new FinnGen single-nucleus multiome preprint! 🧬 We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇 🔗 Link: www.medrxiv.org/content/10.1...
