Posts Tagged ‘eqtl’

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

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

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

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay: Cell

August 18, 2016

Identification of…expr.-Modulating Variants using #MPRA, by @sabeti_lab http://www.cell.com/cell/fulltext/S0092-8674(16)30421-4 Some w. allelic skew related to PWM change

RNA splicing is a primary link between genetic variation and disease | Science

July 4, 2016

Splicing is a prim. link betw…variation & disease by @JKPritch, @Y_Gilad &co http://science.sciencemag.org/content/352/6285/600.long many chrom-QTLs effect protein levels

RNA splicing is a primary link between genetic variation and disease | Science

June 21, 2016

http://science.sciencemag.org/content/352/6285/600.long

Yang I. Li1,
Bryce van de Geijn2,
Anil Raj1,
David A. Knowles3,4,
Allegra A. Petti5,
David Golan1,
Yoav Gilad2,*,
Jonathan K. Pritchard1,6,7,*

RNA splicing is a primary link between genetic variation and disease | Science

June 15, 2016

http://science.sciencemag.org/content/352/6285/600.long

The role of regulatory variation in complex traits and disease : Nature Reviews Genetics : Nature Publishing Group

June 12, 2016

Reg. variation in cplx traits by @LeonidKruglyak
http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html nice teaching figure for #eQTLs, showing how mostly cis + hotspots http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html

pQTLs

July 21, 2015

Impact of regulatory variation from RNA to protein
http://www.sciencemag.org/content/347/6222/664.abstract pQTLs for prot levels less related to #eQTLs & rQTLs than expected

How genetics affect phenotypic variation
http://www.sciencemag.org/content/347/6222/664.abstract

Detection and replication of epistasis influencing transcription in humans : Nature : Nature Publishing Group

March 2, 2014

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13005.html