JSM 2011 Online Program

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Abstract Details

Activity Number: 220
Type: Topic Contributed
Date/Time: Monday, August 1, 2011 : 2:00 PM to 3:50 PM
Sponsor: Section on Statistical Consulting
Abstract - #302497
Title: Notes on Algorithms for Detection of Amplicon Variants in Next-Generation Sequencing
Author(s): Wei-min Liu*+ and Yan Li and Julie Tsai and Mari Christensen and Wei Wen
Companies: Roche Molecular Systems, Inc. and Roche Molecular Systems, Inc. and Roche Molecular Systems, Inc. and Roche Molecular Systems, Inc. and Roche Molecular Systems, Inc.
Address: 4300 Hacienda Drive, Pleasanton, CA, 94588,
Keywords: complex variant ; sequencing ; simple variant ; equivalence test ; sample size estimation ; semi-global alignment
Abstract:

We remark on several issues in algorithm development and statistical analysis for detection of amplicon variants in next-generation sequencing. First, parameters of the semi-global alignment can be adjusted for various purposes. Second, compliance with the common nomenclature of mutations is helpful. Third, we propose the concept of simple variants and explain how it helps define unique simple or complex variants. Fourth, we propose and utilize a special file format that can significantly save storage space and reduce RAM usage. Fifth, we propose an approach to estimate the required counts for reliability of variant detection. In addition, we suggest the equivalence tests for read counts and mutation proportions to assess the effects of sequencing software version changes and different software packages, or to compare different platforms.


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