Posts Tagged ‘eqtl’

Quantitative GWAS & QTL studies

February 25, 2023

Published: 25 January 2023

Molecular quantitative trait loci

François Aguet, Kaur Alasoo, Yang I. Li, Alexis Battle, Hae Kyung Im, Stephen B. Montgomery & Tuuli Lappalainen

Nature Reviews Methods Primers volume 3, Article number: 4 (2023)

Related to the discussion about quantitative GWAS and QTL, this primer review (and in particular box 1) is helpful in clarifying the (non) difference between the two types of studies:

The statistics behind quantitative GWAS and QTL studies is the same, the only main difference might be the multiple testing correction procedure.
In general, it’s more a nomenclature distinction, as the term “QTL” is often used specifically for molecular traits.


January 29, 2022

eQTLs paper is out in Nature Genetics:

Zeng, B., Bendl, J., Kosoy, R. et al. [Panos R] Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits. Nat Genet (2022).

Allele-Specific QTL Fine Mapping with PLASMA: The American Journal of Human Genetics

July 17, 2021

metabrain QTL

July 17, 2021

Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases by N. de Klein et al., bioRxiv, 2021.


Second fetal brain article…splciing and expression QTL and integration with single cell with WGCNA networks

October 29, 2019

Rebecca L. Walker, Gokul Ramaswami, Christopher Hartl, Nicholas Mancuso, Michael J. Gandal, Luis de la Torre-Ubieta, Bogdan Pasaniuc, Jason L. Stein, Daniel H. Geschwind,

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms,


Volume 179, Issue 3,
Pages 750-771.e22,
ISSN 0092-8674,

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. – PubMed – NCBI

June 15, 2019


crisprQTL mapping as a genome-wide association framework for cellular genetic screens
Molly Gasperini, Andrew J. Hill, José L. McFaline-Figueroa, Beth Martin, Cole Trapnell, Nadav Ahituv, Jay Shendure

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

December 25, 2018

seems to be better for eQTLs

paper on geuvadis rna-seq variant calling

February 11, 2017

Calling genotypes from public RNA-sequencing data enables
identification of genetic variants that affect gene-expression levels

Patrick Deelen†,
Daria V Zhernakova†,
Mark de Haan,
Marijke van der Sijde,
Marc Jan Bonder,
Juha Karjalainen,
K Joeri van der Velde,
Kristin M Abbott,
Jingyuan Fu,
Cisca Wijmenga,
Richard J Sinke,
Morris A Swertz† and
Lude Franke†

Genotypes from…#RNAseq…enables identification of…variants, related to ASE & eQTLs Validation w/ #Geuvadis

Jclub paper

January 16, 2017

The impact of #SVs on…gene expression 24k in 147 people in GTEx pilot act as causal variants in 3-7% of ~25k eQTLs

The impact of structural variation on human gene expression

Colby Chiang, Alexandra J Scott, Joe R Davis, Emily
K Tsang, Xin Li, Yungil Kim, Farhan N Damani, Liron Ganel, GTEx Consortium, Stephen B Montgomery, Alexis Battle, Donald F Conrad, Ira M Hall

new CommonMind paper

December 22, 2016

Gene expr. elucidates functional impact of…risk for SCZ CMC resource contains >2.1M #eQTLs involving ~1.6M SNPs


Gene expression elucidates functional impact of polygenic risk for schizophrenia

Menachem Fromer,
Panos Roussos,
Solveig K Sieberts,
Jessica S Johnson,
David H Kavanagh,
Thanneer M Perumal,
Douglas M Ruderfer,
Eric E Schadt,
Keisuke Hirai,
Kathryn Roeder,
Kristen J Brennand,
Nicholas Katsanis,
Enrico Domenici,
Bernie Devlin
& Pamela Sklar