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