scholarly journals Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain

Neuron ◽  
2017 ◽  
Vol 93 (5) ◽  
pp. 1094-1109.e7 ◽  
Author(s):  
Wei-Chao Huang ◽  
Elliott Ferris ◽  
Tong Cheng ◽  
Cornelia Stacher Hörndli ◽  
Kelly Gleason ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Cellular Level ◽  
Mammalian Brain ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Allele-specific expression reveals interactions between genetic variation and environment

2015 ◽  
Author(s):  
David A Knowles ◽  
Joe R Davis ◽  
Anil Raj ◽  
Xiaowei Zhu ◽  
James B Potash ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cellular Level ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Sequencing Studies ◽  
Allele Specific ◽  
Gxe Interactions ◽  
Over Dispersion ◽  
The Impact

The impact of environment on human health is dramatic, with major risk factors including substance use, diet and exercise. However, identifying interactions between the environment and an individual's genetic background (GxE) has been hampered by statistical and computational challenges. By combining RNA sequencing of whole blood and extensive environmental annotations collected from 922 individuals, we have evaluated GxE interactions at a cellular level. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on association between environment and allele-specific expression (ASE). EAGLE increases power by leveraging the controlled, within-sample comparison of environmental impact on different genetic backgrounds provided by ASE, while also taking into account technical covariates and over-dispersion of sequencing read counts. EAGLE identifies 35 GxE interactions, a substantial increase over standard GxE testing. Among EAGLE hits are variants that modulate response to smoking, exercise and blood pressure medication. Further, application of EAGLE identifies GxE interactions to infection response that replicate results reported in vitro, demonstrating the power of EAGLE to accurately identify GxE candidates from large RNA sequencing studies.

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

scholarly journals Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

Genetics ◽  
2013 ◽  
Vol 195 (3) ◽  
pp. 1157-1166 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Lisa Martin ◽  
Farhad Hormozdiari ◽  
Pierre-François Roux ◽  
Calvin Pan ◽  
...  
Keyword(s):  
Mouse Liver ◽  
Genetic Linkage ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Allele-specific expression elucidates cis-regulatory logic

PLoS Genetics ◽  
2018 ◽  
Vol 14 (11) ◽  
pp. e1007690
Author(s):  
Sofie Y. N. Delbare ◽  
Andrew G. Clark
Keyword(s):  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Germline Allele-Specific Expression of DAPK1 in Chronic Lymphocytic Leukemia

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e55261 ◽  
Author(s):  
Quan-Xiang Wei ◽  
Rainer Claus ◽  
Thomas Hielscher ◽  
Daniel Mertens ◽  
Aparna Raval ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Lymphocytic Leukemia ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific
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