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Abstract Details

Activity Number: 668
Type: Contributed
Date/Time: Thursday, August 2, 2012 : 10:30 AM to 12:20 PM
Sponsor: Section on Statistics in Epidemiology
Abstract - #304467
Title: Comparison of Somatic Mutation-Calling Methods Based on DNA Sequence from Matched Tumor-Normal Pairs
Author(s): Su Yeon Kim*+ and Terry Speed
Companies: University of California at Berkeley and University of California at Berkeley
Address: 367 Evans Hall, Berkeley, CA, 94720, United States
Keywords: cancer genome ; next-generation sequencing ; somatic mutation-calling ; methods comparison ; gold standards ; validation
Abstract:

Somatic mutation-calling based on DNA from matched tumor-normal patient samples is one of the key tasks carried by many cancer genome projects. In particular, The Cancer Genome Atlas (TCGA) is now routinely compiling catalogs of somatic mutations for hundreds of patients for various tumor types. Due to its significance, benchmark studies have been performed to compare mutation-callers developed by major sequencing centers. Initial summaries of such studies show substantial discrepancies. Validation data is not yet available, and even when it will be, only a fraction of all candidate mutations are likely to be validated. To assess the performance of mutation callers, we made use of another caller to define pseudo-positives and pseudo-negatives in a whole set of variants compiled from outputs of all callers. This approach allowed us to give other visualizations of the discrepancies between the different mutation call sets, and to summarize each mutation-caller's performance in terms of pseudo-false-positive and pseudo-false-negative rates. Some insights were gained from observing consistent results from two other callers that are not expected to introduce the same biases.


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