Josh Weinstock

You can find PRSFNN code here: github.com/weinstockj/PRS . It takes in GWAS summary statistics + LD reference panel + annotations, and we compute the posterior using variational inference to make it fast.

A pleasure to build this with @aprilkim.bsky.social and @alexisbattle.bsky.social

We observed similar non-linear effects with AlphaMissense predictions, where low impact coding variants were prioritized, but highly pathogenic variants were not prioritized (presumably because these are so rare in real GWAS).

More compellingly, it also learns non-linear effects wrt to chromatin accessibility - variants in cCREs present in 10-50 cell types were more highly prioritized than variants in cCRE that are present in numerous (> 50) cell types, suggesting a preference for cell/tissue specificity.

In our annotation curation, we included lots of scATAC, cCREs from ENCODE, conservation from Zoonomia, pathogenicity from AlphaMissense, among others. Generally - PRSFNN "learns" that low-frequency SNPs in accessible chromatin are likely to have larger effect sizes (maybe not that surprising).

We connected the SNP annotations to the parameters of the prior distribution on the weights in a novel way with a neural network, so we're calling it Polygenic Risk Scores with Functional Neural Network (PRSFNN). We were excited to see that PRSFNN does well in benchmarks (at least in our hands).

Polygenic prediction of phenotypes with a neural empirical Bayes approach Polygenic risk scores (PRS) estimate the expected value of a phenotype based on individual genotypes. Although statistical approaches for calculating PRS have advanced considerably in recent years, fe...

Really excited to share our new PRS method, developed with @aprilkim.bsky.social and @alexisbattle.bsky.social ! Our approach is to use a lot of recently developed functional annotations to better estimate the weights of the SNPs.
www.medrxiv.org/content/10.1...

Congratulations!

Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...

Sharing some of our lecture slides on statistical genetics! 🧬

Co-taught with Mike Epstein, Dave Cutler, Karen Conneely, Jingjing Yang, Jian Hu.

Mendelian randomization: weinstocklab.org/lecture_slid...

Biobank scale GWAS methods: weinstocklab.org/lecture_slid...

Hope they're helpful!

We have multiple postdoc positions available in my group at NYU. Join us if you're interested in complex trait genetics and biology. More information about the lab on our website: mostafavilab.org

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1

Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures Popp et al. generate dozens of cell types from 53 human iPSC lines in order to characterize the dynamic genetic regulation of gene expression across early stages of cellular differentiation. Accessing...

Excited to see our study on genetic regulation in heterogeneous differentiating cultures out in final form!

www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6

I'm developing a pipeline to call CHIP mutations in UK Biobank using the DNA Nexus RAP that is fast/cheap/reproducible. Initial results are promising; calls looks reasonable and cost to do this across all of UKB is likely < 500$.

Feel free to DM if of interest.

Great talk from Zeyun Lu on integrating cis-eQTLs with perturb-seq to increase discovery in Mendelian randomization #ASHG2023 !