We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️
www.nature.com/articles/s41...
✅ The UK Government has today granted access to half a million UK Biobank participants' coded GP data for health research.
This change will dramatically increase the power of UK Biobank's dataset to advance the diagnosis, treatment and management of conditions handled by GPs.
What We Inherit: How New Technologies and Old Myths Are Shaping Our Genomic Future by Sam Trejo and Daphne O. Martschenko
In What We Inherit, Sam Trejo and @daphmarts.bsky.social debate the use of genomic tools and their societal impact.
Now available (31 March UK pub).
Learn more about this fascinating book: press.princeton.edu/books/hardco...
#Biology #ReadUP
Perturbation Catalogue home page showing key metrics
The Perturbation Catalogue is live! 🧬🔎🖥️
It aims to bring genetic perturbation data into one curated, harmonised, and discoverable platform.
Take a look! www.ebi.ac.uk/perturbation...
Why 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...
How do the metabolic waste products get cleared from our brain? And how does this process intersect with the brain's immune system?
An exceptional review by
@jonykipnis.bsky.social
and colleagues
cell.com/neuron/fullt...
Excited to welcome @nmancuso.bsky.social! Join us tomorrow to learn about cutting edge methods for investigating regulatory genetic effects in diverse cell types and populations! 🧬🤩
@dbdsstanford.bsky.social @stanfordeph.bsky.social
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Genomic superstar @chundru.bsky.social taking on fake-news genotypes in >900k individuals. He shows allele-level filtering is rarely suffifient, and makes the brave choice to properly tackle chrX!
We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space
Presentations for Taylor Head (Room 205ABC Level 2 at 11:15 am on 10/15), Sean Bresnahan (Room 253ABC Level 2 at 8:45 am), and poster for Yung-Han Chang (Board 1108T, 2:30-4:30 pm on 10/16)
A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!
Samples of DNA collected from thousands of Ukrainians are part of a study probing the genetics of type 1 diabetes. https://scim.ag/4nabr6B
Can anyone recommend a good immigration lawyer?
Happy to see this online!
Having an extra sex chromosome really challenge the binary definition of sex based on XX and XY. So it is not only a medical, but also an important societal question.
Grateful for this terrific commentary by @tomonroe.bsky.social in @jclinical-invest.bsky.social on our paper that is out in final print format today: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Our new AJHG paper is online. We develop a new TWAS tool that uses local-ancestry information to improve power of gene mapping in admixed samples. Lead author Taylor Head (now at MD Anderson) did a phenomenal job spearheading this work!
A final point about trust. Herasight has apparently partnered with Heliospect Genomics, founded by self-described eugenicist Jonathan Anomaly (a member of both companies). Anomaly and Heliospect were profiled last year by Hope Not Hate:
investigations.hopenothate.org.uk/superbaby-fa...
We have 2-3 group leader positions opening @fimm-uh.bsky.social !!
We are looking for outstanding candidates in human genetics and precision medicine.
This time we have a focus on population health data science. E.g. AI for EHR/health data
Generous starting package 💰
shorturl.at/FAk6n
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
IDH mutations are some of the most informative prognostic markers for #glioma. Our small, proof-of-concept study shows that #multimodal classifiers that include #polygenic risk scores can improve pre-operative molecular subtyping: www.nature.com/articles/s41... 🧠🧬
@stanford-cancer.bsky.social
Our paper on the theoretical properties of SNP heritability in admixed populations is out in Genetics:
academic.oup.com/genetics/adv...
with @jinguohuang.bsky.social, @nicole-kleman.bsky.social , Saonli Basu, and Mark Shriver
It's that time of the year again: ASHG Abstracts!
ASHG has always provided an excellent avenue to present novel methods in StatGen and GenEpi, get early feedback, and meet your colleagues! Deadline is June 9th, so still plenty of time :D
Link below 👇
www.ashg.org/meetings/202...
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
I'm excited to share our latest work, now out in #PLOSGenetics! If you feel limited by linear models in TWAS or PWAS but don't think you can switch to nonlinear methods due to a lack of individual-level phenotype data, this paper is for you.
🔗 journals.plos.org/plosgenetics...
Thread below 👇 (1/6)
Hating on “Big Pharma”? Cool, it’s a $1.6 trillion regulated industry. But hang on…the $6.3 trillion wellness industry sells you mushroom tea, dewormers, crash diets, and alkaline water—no regulations, no oversight. But hey, it’s ‘natural,’ right?
3/n
Genetic correlation is straightforward but remember HLA - largely impacting T1D & other AIDs - is excluded by LDSC.
If genetic correlation is a genome-wide non-HLA measurement, how can we get HLA back into the game?
We built a within-sample HLA PGS with weighted ridge classifiers in FinnGen.
🚨 New paper 🚨
Do known genetic factors for obesity and type 2 diabetes affect weight loss from GLP1-RA (Ozempic) or bariatric surgery?
🔍 10,960 people, 9 biobanks, 6 countries
🧬 Minimal genetic impact on GLP1-RA response
📉 Modest effect after surgery
www.nature.com/articles/s41...
I started a newsletter.
My first post is going to be a deeper dive into insider trading on Wednesday.
I’ll be writing about tech, San Francisco, politics, and AI. With kindness.
I’d be grateful for any boosts as I’m excited and nervous for this.
data-and-politics.ghost.io
Accurately describes the phenomenon of Bureaucratic Capture, where a bureaucracy is set up to serve an organization, but everyone ends up serving the bureaucracy instead (not confined to universities, of course)
5 relative abundance plots arranged to have increasing compositional variability (variability across relative abundance samples, here vertical bars)
1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...
