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
Nov 3, 2009·Nature Methods·Paul MedvedevMichael Brudno
Dec 10, 2009·Nature Biotechnology·Ruiqiang LiJian Wang
Apr 14, 2010·Bioinformatics·Iman HajirasoulihaS Cenk Sahinalp
Feb 5, 2011·Nature·Ryan E MillsUNKNOWN 1000 Genomes Project
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 11, 2012·Bioinformatics·Tobias RauschJan O Korbel
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Dec 12, 2012·Genome Research·Thomas ZichnerJan O Korbel
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
Citations
May 17, 2018·BMC Genomics·Daniel ValenzuelaVeli Mäkinen
Oct 24, 2018·Frontiers in Neuroscience·Xia-An BiZhigang Wang
Jul 22, 2017·BMC Bioinformatics·Jan SchröderAnthony T Papenfuss
Jan 6, 2021·Genes·Monika Cechova
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