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Improving the Power of Structural Variation Detection by Augmenting the Reference.

ABSTRACT: The uses of the Genome Reference Consortium's human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.

SUBMITTER: Schroder J

PROVIDER: S-EPMC4556445 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Improving the Power of Structural Variation Detection by Augmenting the Reference.

Schröder Jan J Girirajan Santhosh S Papenfuss Anthony T AT Medvedev Paul P

PloS one 20150831 8

The uses of the Genome Reference Consortium's human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and li ...[more]

PMID: 26322511

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