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Title: Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Authors: Reumers, Joke *
De Rijk, Peter *
Zhao, Hui
Liekens, Anthony
Smeets, Dominiek
Cleary, John
Van Loo, Peter
Van Den Bossche, Maarten
Catthoor, Kirsten
Sabbe, Bernard
Despierre, Evelyn
Vergote, Ignace
Hilbush, Brian
Lambrechts, Diether ×
Del-Favero, Jurgen #
Issue Date: Jan-2012
Publisher: Gale Group Inc.
Series Title: Nature Biotechnology vol:30 issue:1 pages:61-68
Article number: 10.1038/nbt.2053
Abstract: Distinguishing single-nucleotide variants (SNVs) from errors in whole-genome sequences remains challenging. Here we describe a set of filters, together with a freely accessible software tool, that selectively reduce error rates and thereby facilitate variant detection in data from two short-read sequencing technologies, Complete Genomics and Illumina. By sequencing the nearly identical genomes from monozygotic twins and considering shared SNVs as 'true variants' and discordant SNVs as 'errors', we optimized thresholds for 12 individual filters and assessed which of the 1,048 filter combinations were effective in terms of sensitivity and specificity. Cumulative application of all effective filters reduced the error rate by 290-fold, facilitating the identification of genetic differences between monozygotic twins. We also applied an adapted, less stringent set of filters to reliably identify somatic mutations in a highly rearranged tumor and to identify variants in the NA19240 HapMap genome relative to a reference set of SNVs.
ISSN: 1087-0156
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Translational Genetics (Vesalius Research Center) (+)
Human Genome Laboratory
Gynaecological Oncology
Vesalius Research Centre (-)
* (joint) first author
× corresponding author
# (joint) last author

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