Thrilled to share our UCI TR-gnomAD published in Cell today: https://t.co/pzVrBoNTed. UCI TR-gnomAD is the first biobank-scale genetic reference for ~1.0M Tandem Repeat (TR) expansions across 340K humans, facilitating TR-based disease association studies and clinical diagnostics
Our new paper @NatureComms performed the first Alternative polyadenylation transcriptome-wide association study for 11 brain disorders with 17,300 RNA-seq samples. We identified 354 novel APA-linked risk genes including ATXN3 for ALS.
https://t.co/TnsqVkx0Dp
Ultimately, adjusting hidden covariates or not examines different DE effects (conditional vs marginal). But regardless of this difference, I still think no DE genes are expected be found (in the average sense) from permuted samples where conditional labels are randomly shuffled.
@borishej@mikelove @KasperDHansen @timtriche@andrewejaffe@lpachter@RodThiebaut@denis_agniel We thank @borishej et al for sending us the draft of their correspondence on May 3. Here is a threshold of key points in our reply sent on that day. 1/ The main message of our article is that using popular methods without a sanity check may lead to inflated FDR.
Study of false positives when calling differentially expressed genes, from @YM123411, @ge_xinzhou, @FanglueP, @superweili & @jsb_ucla. With population-scale sample sizes, common methods have inflated FDR. The authors suggest using Wilcoxon rank-sum test https://t.co/TrjCbGPwkZ
💥An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability | by Eric J. Wagner & Wei Li and colleagues
Find it here 👇@NatureGenet
https://t.co/3KbCYdms2n
Super excited to share our recent work on 3′UTR alternative polyadenylation (APA) quantitative trait loci (3′aQTLs), which can explain ~16.1% GWAS SNPs and are largely distinct from eQTLs. Wonderful collaborations with @Wagnerlab_RNA@LeiLi_bioinfo
https://t.co/j7nFyPt3pZ
Twenty years of Genome Biology. Quite honored that our MACS is one of the top papers published in the last two decades, together with Bowtie, DESeq, TopHat2, SCANPY, DAVID, and BioConductor!
https://t.co/deFxbGxh0h