Event info

La Trobe-Kyushu Joint Seminar on Mathematics for Industry (12)

Date & Time : Apr. 5 , 2016 13:00(Australian time) / 12:00(Japan time) Venue: IMI Australia Branch in La Trobe University / C503 Small Lecture Room, IMI, Kyushu University

Title: Assessing Impact of Batch Effects and Failed Conversion Rates in Whole-Genome Bisulfite Sequencing Data
Speaker: Dr. Agus Salim, Mathematics and Statistics, La Trobe University

Abstract:
DNA Methylation is an epigenetic mechanism where a methyl group (CH3) is added to the DNA. Over the last few years, microarray-based and sequencing-based technologies have allowed genome-wide interrogations of methylation profiles. There is evidence that array-based methylation data also suffers from batch effects. On the other hand, assessment of batch effects in whole-genome bisulfite sequencing (WGBS) data and its impact is scarce, despite the fact that batch effects have been observed in other sequencing-based data such as RNA-seq. Current software developed specifically for WGBS data do not incorporate systematic procedures for removing batch effects. Using simulated and real datasets, we assess the impact of batch effects and failed conversion on Epigenome-wide Association Studies (EWAS) and evaluate the performance of currently-available methods in the presence of these unwanted variations.