AmpliVar: Mutation Detection in High-Throughput Sequence from Amplicon-Based Libraries
Arthur L Hsu, Olga Kondrashova, Sebastian Lunke, Clare J Love, Cliff Meldrum, Renate Marquis-Nicholson, Greg Corboy, Pham Kym, Matthew Wakefield, Paul M Waring, Graham R Taylor
HUMAN MUTATION | WILEY | Published : 2015
Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then call variants at each position. Here, we demonstrate an orthogonal means of identifying sequence variation by grouping the reads as amplicons prior to any alignment. We used AmpliVar to make key-value hashes of sequence reads and group reads as individual amplicons using a table of flanking sequences. Low-abundance reads were removed according to a selectable threshold, and reads above this threshold were aligned as groups, rather than as individual reads, permitting the use of sensitive alignment tools. We show that this approach is more sensitive, more specific, a..View full abstract
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Awarded by National Health and Medical Research Council (NHRMC)
Contract Grant Sponsors: the National Health and Medical Research Council (NHRMC, APP1025879 and APP1029974); the Victorian Cancer Agency; the Victorian Comprehensive Cancer Centre and the Education Investment Fund of the Australian Government's Super Science Initiative; the Herman Trust.