ORCID Profile
0000-0002-4791-2467
Current Organisations
The University of Texas at Austin
,
The University of Texas Health Science Center at Houston School of Public Health
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Publications
Testcrosses are an efficient strategy for identifying cis-regulatory variation: Bayesian analysis of allele-specific expression (BayesASE)
Publisher: Oxford University Press (OUP)
Date: 27-03-2021
DOI: 10.1093/G3JOURNAL/JKAB096
Abstract: Allelic imbalance (AI) occurs when alleles in a diploid in idual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? The approach described applies to any technology generating allele-specific sequence counts, for ex le for chromatin accessibility and can be applied generally including to comparisons between tissues or environments for the same genotype. Tests of allelic effect are generally performed by crossing in iduals and comparing expression between alleles directly in the F1. However, a crossing scheme that compares alleles pairwise is a prohibitive cost for more than a handful of alleles as the number of crosses is at least (n2-n)/2 where n is the number of alleles. We show here that a testcross design followed by a hypothesis test of AI between testcrosses can be used to infer differences between nontester alleles, allowing n alleles to be compared with n crosses. Using a mouse data set where both testcrosses and direct comparisons have been performed, we show that the predicted differences between nontester alleles are validated at levels of over 90% when a parent-of-origin effect is present and of 60%−80% overall. Power considerations for a testcross, are similar to those in a reciprocal cross. In all applications, the testing for AI involves several complex bioinformatics steps. BayesASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions. The modular structure of BayesASE has been packaged in Galaxy, made available in Nextflow and as a collection of scripts for the SLURM workload manager on github (github.com/McIntyre-Lab/BayesASE).
History and masculinity
Publisher: Routledge
Date: 19-12-2016
Related Organisations
Instituto De Investigaciones En Matematicas Aplicadas Y Sistemas
Location: Mexico
University Of Louisiana At Lafayette
Location: United States of America
The University Of Texas Health Science Center At Houston School Of Public Health
Location: United States of America
Related Funding Activities
No related grants have been discovered for Pauline Strong.