The Dissection of Expression Quantitative Trait Locus Hotspots

Genetics
Jianan TianKarl W Broman

Abstract

Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effects on gene expression: expression quantitative trait locus hotspots. We describe a set of exploratory graphical methods as well as a formal likelihood-based test for assessing whether a given hotspot is due to one or multiple polymorphisms. We first look at the pattern of effects of the locus on the expression traits that map to the locus: the direction of the effects and the degree of dominance. A second technique is to focus on the individuals that exhibit no recombination event in the region, apply dimensionality reduction (e.g., with linear discriminant analysis), and compare the phenotype distribution in the nonrecombinant individuals to that in the recombinant individuals: if the recombinant individuals display a different expression pattern than the nonrecombinant individuals, this indicates the presence of multiple causal polymorphisms. In the formal likelihood-based test, we compare a two-locus model, with each expression trait affected by one or the other locus, to a single-locus model. We apply our methods to a large mouse intercross with gene expression microarray data on six tissues.

References

Aug 10, 2000·Nature Genetics·J H Nadeau, W N Frankel
Oct 3, 2000·Genetics·S A Knott, C S Haley
Jun 22, 2001·Trends in Genetics : TIG·R C Jansen, J P Nap
Mar 30, 2002·Science·Rachel B BremLeonid Kruglyak
Mar 21, 2003·Nature·Eric E SchadtStephen H Friend
May 2, 2003·Bioinformatics·Karl W BromanGary A Churchill
Oct 3, 2007·PLoS Genetics·Jeffrey T Leek, John D Storey
Oct 25, 2008·PLoS Genetics·Rainer BreitlingRitsert C Jansen
Sep 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jennifer ListgartenDavid Heckerman
Nov 22, 2011·Biostatistics·Johann A Gagnon-Bartsch, Terence P Speed
Jan 1, 1951·Journal of Genetics·T C CARTER, D S FALCONER
Feb 25, 2015·Nature Reviews. Genetics·Frank W Albert, Leonid Kruglyak

❮ Previous
Next ❯

Citations

Jul 18, 2018·ELife·Frank Wolfgang AlbertLeonid Kruglyak
Dec 30, 2018·Genetics·Christopher L BakerKenneth Paigen
May 17, 2019·G3 : Genes - Genomes - Genetics·Frederick J BoehmKarl W Broman
May 5, 2017·Proceedings. Biological Sciences·Emma I K VitikainenMichael A Cant
Mar 24, 2018·Genetics·Mark P KellerAlan D Attie
Dec 13, 2018·Nature Communications·John T LovellThomas E Juenger
Oct 4, 2016·Genetics·Michelle D ParmenterBret A Payseur
Jan 1, 2019·Journal of Open Source Software·Frederick BoehmKarl W Broman
Feb 20, 2021·G3 : Genes - Genomes - Genetics·Quoc Tran, Karl W Broman
Jul 1, 2019·G3 : Genes - Genomes - Genetics·Frederick J BoehmKarl W Broman
Sep 18, 2021·Nature Communications·Andrew J Conith, R Craig Albertson

❮ Previous
Next ❯

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.