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Evaluation of GRCh38and de novo haploidgenome assembliesdemonstrates theenduring quality ofthe referenceassembly Valérie SchneiderTina A. Graves-LindsayKerstin Howe2017 год

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
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Аннотация: The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.
Год издания: 2017
Авторы: Valérie Schneider, Tina A. Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul Kitts, Terence D. Murphy, Kim D. Pruitt, Françoise Thibaud‐Nissen, Derek Albracht, Robert S. Fulton, Milinn Kremitzki, Vincent Magrini, Chris Markovic, Sean McGrath, Karyn Meltz Steinberg, Kate Auger, William Chow, Joanna Collins, Glenn Harden, Tim Hubbard, Sarah Pelan, Jared T. Simpson, Glen Threadgold, James Torrance, Jonathan Wood, Laura Clarke, Sergey Koren, Matthew Boitano, Paul Peluso, Heng Li, Chen-Shan Chin, Adam M. Phillippy, Richard Durbin, Richard K. Wilson, Paul Flicek, Evan E. Eichler, Deanna M. Church
Издательство: Cold Spring Harbor Laboratory Press
Источник: Genome Research
Ключевые слова: Genomics and Phylogenetic Studies, Chromosomal and Genetic Variations, Genomic variations and chromosomal abnormalities
Другие ссылки: Genome Research (PDF)
Genome Research (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
PubMed Central (HTML)
bioRxiv (Cold Spring Harbor Laboratory) (HTML)
PubMed (HTML)