Posts Tagged ‘eqtl’

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Quantitative GWAS & QTL studies

February 25, 2023

Primer
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:

https://www.nature.com/articles/s43586-022-00188-6

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.

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science

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).
https://doi.org/10.1038/s41588-021-00987-9

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

July 17, 2021

https://www.cell.com/ajhg/fulltext/S0002-9297(19)30505-1

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metabrain QTL

July 17, 2021

https://www.metabrain.nl/

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.

doi:
https://doi.org/10.1101/2021.03.01.433439

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

October 29, 2019

https://www.sciencedirect.com/science/article/pii/S0092867419310724?dgcid=author

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,

Cell,

Volume 179, Issue 3,
2019,
Pages 750-771.e22,
ISSN 0092-8674,
https://doi.org/10.1016/j.cell.2019.09.021

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

June 15, 2019

https://www.ncbi.nlm.nih.gov/pubmed/30612741

crisprQTL

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
doi: https://doi.org/10.1101/314344

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

December 25, 2018

seems to be better for eQTLs
https://www.nature.com/articles/s41588-018-0268-8

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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
https://GenomeMedicine.biomedcentral.com/articles/10.1186/s13073-015-0152-4 Validation w/ #Geuvadis

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Jclub paper

January 16, 2017

The impact of #SVs on…gene expression
http://biorxiv.org/content/early/2016/06/09/055962 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
doi: https://doi.org/10.1101/055962

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new CommonMind paper

December 22, 2016

Gene expr. elucidates functional impact of…risk for SCZ
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4399.html CMC resource contains >2.1M #eQTLs involving ~1.6M SNPs

NATURE NEUROSCIENCE | ARTICLE

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

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