Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation.

doi:10.1038/s41467-025-64336-8

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Article

Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation.

Nature communications - 22 Nov 2025

Liu Chunyu, Joehanes Roby, Ma Jiantao, Xie Jiuyong, Yang Jian, Wang Mengyao, Huan Tianxiao, Hwang Shih-Jen, Wen Jia, Sun Quan, Demirkale Cumhur Y, Heard-Costa Nancy L, Orchard Peter, Carson April P, Haessler Jeffrey W, Raffield Laura M, Reiner Alex P, Franceschini Nora, Auer Paul L, Kooperberg Charles, Li Yun, O'Connor George, Murabito Joanne M, Munson Peter, Levy Daniel

Abstract excerpt

We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10-8) across 4,971 genes. Among 11,425 sentinel cis-irQTLs, 72% replicate (P < 1 × 10-4) in the...

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PMID: 41274869
DOI: 10.1038/s41467-025-64336-8
PMCID: PMC12660940

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