Thrilled to share our work to analyze insurance claim datasets to dissect genetic and environmental contributions to 1083 human diseases. We developed a spatial linear mixed model SMILE, using geolocations as a proxy for the environment. nature.com/articles/s4146…

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All of Us diversity and scale improve polygenic prediction contextually with greatest improvements for underrepresented populations biorxiv.org/cgi/content/sh… #biorxiv_genomic

I passed!!! 🥹🥹🥹 Thanks a lot to my great advisors Arslan Zaidi Mark Shriver and my amazing committed members George (PJ) Perry Joan Richtsmeier Zachary Szpiech

Interesting paper from 23andMe showing "the minimal contribution of non-additivity in the genetic architecture of adult human height." based on a GWAS of height in 3.6 million individuals. One caveat to note that is here the authors tested epistasis between only a ~1000 common

Polygenic scores explained in two slides 🧬

One of my favorite talks from TAGC last spring, by Aaron Ragsdale; excited to see the paper!

Excited to share my 1st-author work from the Arbel Harpak Lab! We examine the accuracy of polygenic score (PGS) predictions across individuals in the UK Biobank. We make 3 observations that expose gaps in our understanding of PGS “portability”. biorxiv.org/content/10.110… (1/28)

We know that DNA introgressed from one population into another is often deleterious, but why? Carl Veller and I show that stabilizing selection, by itself, can induce selection against introgressed ancestry. doi.org/10.1101/2024.0…

I wrote about some recent studies identifying widespread gene-environment interactions (GxE) acting on common traits, but through an unexpected mechanism. A few highlights 🧵:

Very happy to share that my first first-author paper on signatures of positive selection in Papua New Guinean populations, supervised by Andres Moreno-Estrada, is out on GBE (Genome Biology and Evolution)! academic.oup.com/gbe/article/16… 🧵📢

Really cool work from Juehan Wang and Steven Gazal providing evidence that genes differentially expressed across continental ancestries are enriched for GxE.

Nick Bailey Arvid Ågren Zach B. Hancock I have no idea how I have this, but here is a translation of Wahlund 1928! drive.google.com/file/d/1WHNUcR…

Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB arxiv.org/abs/2409.00613

Our paper on the evolution of structural variation at the amylase locus is out today in Nature! nature.com/articles/s4158… congrats to co-first authors Joana L. Rocha Nicolas Lou Davide Bolognini Alessandro Raveane & Alma Halgren, co-corresponding author Erik Garrison

The Li + Durbin 2011 paper showing that you can infer an entire population history from just a single genome is still one of the most mind-blowing results in genetics I have ever seen. nature.com/articles/natur…

Excited to share this new preprint with jeffrey spence and Doc Edge in which we developed a method to infer demographic history and mutation rates from millions of genomes, and applied it to gnomAD v4 data. Read on for a brief thread! biorxiv.org/content/10.110…

Two new chapters from my free online book in human genetics out this weekend! These complete Part 3 of the book, on human population structure and history: 3.3: Human prehistory [separate thread] 3.4: Ancient DNA: a genetic time capsule [this thread] web.stanford.edu/group/pritchar…

Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets biorxiv.org/cgi/content/sh… #biorxiv_genetic