New statistical method disentangles cis vs. trans effects in gene expression, published in Genetics
lpachter · x · 2026-09-16
Lior Pachter shares a thread on his team's new Genetics paper by Ingileif Hallgrímsdóttir and Maria Carilli on separating cis from trans contributions to gene expression differences.
- Classic idea: crosses of homozygotes testing whether parent-strain phenotype ratios are preserved across F1 haplotypes, previously explored by Eric Lander, Andy Clark, Patricia Wittkopp and others.
- New contributions: a simple linear transformation simplifies coordinate interpretation; GLM-based testing effectively uses replicates, demonstrated by reanalyzing data from the Nachman lab.
- Motivation: trans effects are hard to study in humans — GTEx found only dozens of trans variants versus tens of thousands of cis variants, mostly a statistical power problem; the method offers an existence-proof strategy.
- The method has already been applied by others to methylation studies.
Related event: New statistical method decomposes cis and trans gene expression effects(2 posts)→
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