Comprehensive Detection of Genes Causing a Phenotype Using Phenotype Sequencing and Pathway Analysis

Harper, Marc; Gronenberg, Luisa; Liao, James; Lee, Christopher

doi:10.1371/journal.pone.0088072

Title: Comprehensive Detection of Genes Causing a Phenotype Using Phenotype Sequencing and Pathway Analysis

Journal Article · Wed Feb 26 00:00:00 EST 2014 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0088072· OSTI ID:1904727

Harper, Marc ^[1]; Gronenberg, Luisa ^[1]; Liao, James ^[1]; Lee, Christopher ^[1]

University of California, Los Angeles, CA (United States)

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. We combine an experimental design for detecting independent genetic causes of a phenotype with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome.

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Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FC02-02ER63421

OSTI ID:: 1904727

Journal Information:: PLoS ONE, Vol. 9, Issue 2; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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