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Dealing with the GC-content bias in second-generation DNA sequence data

by

Professor Terry Speed


Location: Room change: Horace Lamb lecture theatre

Date: Friday, 12 August

Time: 15:10

Abstract: The field of genomics is currently dealing with an explosion of data from so-called second-generation DNA sequencing machines. This is creating many challenges and opportunities for statisticians interested in the area. In this talk I will outline the technology and the data flood, and move on to one particular problem where the technology is used: copy-number analysis. There we find a novel bias, which, if not dealt with properly, can dominate the signal of interest. I will describe how we think about and summarize it, and go on to identify a plausible source of this bias, leading up to a way of removing it. Our approach makes use of the total variation metric on discrete measures, but apart from this, is largely descriptive.

The Colloquium will be followed by a reception for our speaker in the Staff Tea Room with wine and nibbles to which all are invited.

Terry's web-page

Slides of his talk

Tech report #804 of the UC Berkeley for more details