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Effective filtering strategies to improve data quality from population-based whole exome sequencing studies PDF available through Get Fulltext Research

Carson, Andrew R Smith, Erin N Matsui, Hiroko Brækkan, Sigrid K Jepsen, Kristen Hansen, John-Bjarne Frazer, Kelly A

Published in BMC Bioinformatics

BackgroundGenotypes generated in next generation sequencing studies contain errors which can significantly impact the power to detect signals in common and rare variant association tests. These genotyping errors are not explicitly filtered by the standard GATK Variant Quality Score Recalibration (VQSR) tool and thus remain a source of errors in who...

MiningABs: mining associated biomarkers across multi-connected gene expression datasets PDF available through Get Fulltext Research

Cheng, Chun-Pei DeBoever, Christopher Frazer, Kelly A Liu, Yu-Cheng Tseng, Vincent S

Published in BMC Bioinformatics

BackgroundHuman disease often arises as a consequence of alterations in a set of associated genes rather than alterations to a set of unassociated individual genes. Most previous microarray-based meta-analyses identified disease-associated genes or biomarkers independent of genetic interactions. Therefore, in this study, we present the first meta-a...

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