The single-cell eQTLGen consortium.

ELife
Mgp van der WijstL Franke

Abstract

In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression quantitative trait locus (eQTL) analysis. Single-cell RNA-sequencing creates enormous opportunities for mapping eQTLs across different cell types and in dynamic processes, many of which are obscured when using bulk methods. Rapid increase in throughput and reduction in cost per cell now allow this technology to be applied to large-scale population genetics studies. To fully leverage these emerging data resources, we have founded the single-cell eQTLGen consortium (sc-eQTLGen), aimed at pinpointing the cellular contexts in which disease-causing genetic variants affect gene expression. Here, we outline the goals, approach and potential utility of the sc-eQTLGen consortium. We also provide a set of study design considerations for future single-cell eQTL studies.

References

Jun 22, 2002·Progress in Cardiovascular Diseases·Debabrata Mukherjee, Eric J Topol
Dec 20, 2005·PLoS Genetics·Barbara E StrangerEmmanouil T Dermitzakis
Oct 20, 2006·PLoS Biology·Arjun RajSanjay Tyagi
Sep 18, 2007·Nature Genetics·Barbara E StrangerEmmanouil T Dermitzakis
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Jan 9, 2009·BMC Medical Genomics·Graham A HeapLude Franke
Mar 24, 2009·Methods : a Companion to Methods in Enzymology·Jacob J MichaelsonAndreas Beyer
Mar 2, 2010·BMC Bioinformatics·Ching-Lin HsiaoCathy Sj Fann
Jun 3, 2010·Nature Reviews. Genetics·Jonathan Marchini, Bryan Howie
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Simon GravelCarlos D Bustamante
Dec 7, 2011·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Melissa D JohnsonMihai G Netea
Jun 19, 2012·Nature Genetics·Xiang Zhou, Matthew Stephens
Sep 24, 2013·Nature Methods·Philip BrenneckeMarcus G Heisler
Nov 5, 2014·Frontiers in Cell and Developmental Biology·Claudia Angelini, Valerio Costa
Feb 11, 2015·Nature Biotechnology·Victoria MoignardBerthold Göttgens
May 1, 2015·Nature·Nicholas J Schork
May 9, 2015·PLoS Genetics·Harm-Jan WestraLude Franke
Jun 18, 2015·Nature·Jason D BuenrostroWilliam J Greenleaf
Nov 17, 2015·Bioinformatics·S M Minhaz Ud-Dean, Rudiyanto Gunawan
Nov 22, 2015·BMC Systems Biology·Mahsa GhanbariMartin Vingron
Feb 9, 2016·Nature Genetics·Alexander GusevBogdan Pasaniuc
Jun 23, 2016·BMC Bioinformatics·Dongdong LinYu-Ping Wang
Aug 23, 2016·Nature Genetics·Shane McCarthyUNKNOWN Haplotype Reference Consortium
Oct 27, 2016·Scientific Reports·G V RoshchupkinW J Niessen
Dec 3, 2016·Nucleic Acids Research·Alireza F Siahpirani, Sushmita Roy
Dec 6, 2016·Nature Genetics·Daria V ZhernakovaLude Franke
Jan 10, 2017·American Journal of Human Genetics·Luke R Lloyd-JonesJoseph E Powell
Apr 4, 2017·American Journal of Human Genetics·Alicia R MartinEimear E Kenny
Apr 12, 2017·Genome Biology·Christof AngermuellerOliver Stegle
Apr 19, 2017·Nature Methods·Rhonda BacherChristina Kendziorski
May 30, 2017·Nature Genetics·Kazuyoshi IshigakiKazuhiko Yamamoto

❮ Previous
Next ❯

Citations

Sep 12, 2020·Science·Sarah Kim-HellmuthTuuli Lappalainen
May 13, 2020·Genome Biology·Ramon Massoni-BadosaHolger Heyn
Aug 28, 2020·Frontiers in Bioengineering and Biotechnology·Siwen XuYunlong Liu
Sep 20, 2020·Journal of Human Genetics·Masato Akiyama
Nov 28, 2020·Experimental & Molecular Medicine·Junha Cha, Insuk Lee
Dec 10, 2020·Nature Communications·Florence Lichou, Gosia Trynka
Jan 9, 2021·Cell Stem Cell·Patrick CahanChristine A Wells
Sep 12, 2020·Trends in Genetics : TIG·Benjamin D UmansYoav Gilad
Feb 10, 2021·Inflammation and Regeneration·Yuya Shirai, Yukinori Okada
Mar 6, 2021·Trends in Cardiovascular Medicine·Irene V van BloklandPim van der Harst
Mar 9, 2021·Frontiers in Immunology·Zaarour NancyChen Liye
Apr 13, 2021·Frontiers in Medicine·Atiyeh M Abdallah, Marawan Abu-Madi
Aug 21, 2020·Cold Spring Harbor Perspectives in Medicine·Eleonora PorcuZoltán Kutalik
May 5, 2021·Nature Biotechnology·Ricard ArgelaguetJohn C Marioni
May 11, 2021·Briefings in Functional Genomics·Xianjun DongMikhail Dozmorov
May 16, 2021·Nature Communications·Lieke MichielsenAhmed Mahfouz
Jun 15, 2021·Current Osteoporosis Reports·Abdullah Abood, Charles R Farber
Jul 1, 2021·Nature Reviews. Rheumatology·Yuriy BaglaenkoSoumya Raychaudhuri
Jul 3, 2021·International Journal of Molecular Sciences·Arina O DegtyarevaTatiana I Merkulova
Sep 24, 2021·BMC Genomics·N M PrashantAnelia Horvath
Sep 24, 2021·Science·Tuuli Lappalainen, Daniel G MacArthur
Oct 5, 2021·Seminars in Immunopathology·Kazuyoshi Ishigaki

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
scRNA-seq
single-cell sequencing

Software Mentioned

seqFISH
CAGE
MERFISH
HCA
ENCODE
BLUEPRINT
ImmVar
eQTLGen
sc
PsychENCODE

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Clinical Chemistry
Carmela PaolilloPaolo Fortina
Current Oncology Reports
Eli JohnsonMelanie Hayden Gephart
© 2021 Meta ULC. All rights reserved