Improving the Power of Structural Variation Detection by Augmenting the Reference

PloS One
Jan SchröderPaul Medvedev

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.

References

Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Sep 7, 2007·PLoS Biology·Samuel LevyJ Craig Venter
Dec 10, 2009·Nature Biotechnology·Ruiqiang LiJian Wang
Feb 5, 2011·Nature·Ryan E MillsUNKNOWN 1000 Genomes Project
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
May 10, 2013·Nucleic Acids Research·Sangwoo KimVineet Bafna
Jul 3, 2013·Bioinformatics·Lin HuangSerafim Batzoglou
Oct 18, 2013·BioData Mining·Daniel WolfeSarah A Pendergrass
Aug 16, 2014·Bioinformatics·Guillaume RizkClaire Lemaitre
Mar 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jouni SirénVeli Mäkinen

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Citations

May 17, 2018·BMC Genomics·Daniel ValenzuelaVeli Mäkinen
Jul 22, 2017·BMC Bioinformatics·Jan SchröderAnthony T Papenfuss
Jan 24, 2021·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Murukarthick JayakodiMartin Mascher
Jul 15, 2021·Bioinformatics·Tuukka NorriVeli Mäkinen

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Methods Mentioned

BETA
454 sequencing
genotyping
Illumina sequencing

Software Mentioned

GRC
bowtie2
RepeatMasker
Delly
PhenoGram
SV
ref

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