TY - JOUR
T1 - Improving the power of structural variation detection by augmenting the reference
AU - Schröder, Jan
AU - Girirajan, Santhosh
AU - Papenfuss, Anthony T.
AU - Medvedev, Paul
N1 - Funding Information:
We would like to acknowledge Thanh Le for helping with alignment, Tobias Marschall and Alexander Schönhuth for initial discussions and providing us with VNA annotations, and Yao Wang for help with the gene analysis. PM was funded in part by National Science Foundation ( nsf.gov ), grants DBI-1356529 and IIS-1453527 J.S. and A.T.P. were supported by an NHMRC Program Grant (1054618) ( www.nhmrc.gov.au/ ).
Publisher Copyright:
© 2015 Schröder et al.
PY - 2015/8/31
Y1 - 2015/8/31
N2 - 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 systemfor 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 polymorphismin a population.
AB - 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 systemfor 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 polymorphismin a population.
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U2 - 10.1371/journal.pone.0136771
DO - 10.1371/journal.pone.0136771
M3 - Article
C2 - 26322511
AN - SCOPUS:84943339647
SN - 1932-6203
VL - 10
JO - PLoS One
JF - PLoS One
IS - 8
M1 - e0136771
ER -
