Computing Research Institute

Bioinformatics Seminar

September 10 @ 4:30 PM - 5:30 PM - Rawls (RAWL) Hall, 1086

Title: "Mutation Detection for Dene Function Discovery"
Speaker: Charles Addo-Quaye, Department of Horticulture and Landscape Architecture, Purdue University

Place: Rawls (RAWL) Hall 1086
Date: September 10, 2013; Tuesday
Time: 4:30pm

Abstract:

Discovering genes responsible for variation in specific traits is an important research goal in biology. In induced-mutation populations, single nucleotide polymorphisms (SNPs) present in the coding sequences of genes are often recovered as the cause of changes in gene function. Current computational methods available for SNP detection in next generation sequencing data have varying degree of accuracy. Although numerous techniques have been proposed to improve the accuracy of these methods, the results of SNP calling often contain false positives. The chemical mutagen ethyl methanesulfonate (EMS) results in G to A or C to T base substitutions. Knowledge of the expected mutation types can greatly reduce the false positive rate in SNP detection. In this talk, I will present a computational method and pipeline for detecting SNPs with high confidence in plant genomes, by analyzing DNA sequences derived from EMS-mutagenized populations. I will demonstrate the utility of this meth!
 od in detecting genes with mutations that have phenotypic consequences, in a variety of plant species.

Associated reading:
Nielsen, R., Paul, J. S., Albrechtsen, A. & Song, Y. S. Genotype and SNP calling from next-generation sequencing data. Nature reviews. Genetics 12, 443-51 (2011).
 

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