Modernizing Reference Genome Assemblies

Church, Deanna M.; Schneider, Valérie; Graves, Tina; Auger, Katherine A.; Cunningham, Fiona; Bouk, Nathan; Chen, Hsiu Chuan; Agarwala, Richa; McLaren, William; Ritchie, Graham R. S.; Albracht, Derek; Kremitzki, Milinn; Rock, Susan M.; Kotkiewicz, Holland; Kremitzki, Colin; Wollam, Aye; Trani, Lee; Fulton, Lucinda A.; Fulton, Robert S.; Matthews, Lucy; Whitehead, Siobhan; Chow, William; Torrance, James; Dunn, Matthew; Harden, Glenn; Threadgold, Glen; Wood, Jonathan; Collins, Joanna; Heath, P. D.; Griffiths, Guy; Pelan, Sarah; Grafham, Darren; Eichler, Evan E.; Weinstock, George M.; Mardis, Elaine R.; Wilson, Richard K.; Howe, Kerstin; Flicek, Paul; Hubbard, Tim

doi:10.1371/journal.pbio.1001091

Cited by 469 publications

(364 citation statements)

References 23 publications

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“…Analysis of the mouse and human genomes suggests that these typically correspond to 300-500 regions (;140-150 Mbp) per genome, including in some cases almost entire chromosomes, such as the Y chromosome (Hughes et al 2012). The approach we have described provides a strategy to resolve these more structurally complex regions during the final stages of assembly, ensuring that the 1000-2000 genes mapping therein become incorporated within future mammalian genome assemblies (Alkan et al 2011b;Church et al 2011). …”

Section: Discussionmentioning

confidence: 99%

“…Complete high-quality sequence assembly remains a difficult problem for the de novo assembly of genomes (Alkan et al 2011b;Church et al 2011;Salzberg et al 2012). Finishing of the human and mouse genomes involved selecting large-insert BAC clones and subjecting them to capillary-based shotgun sequence and assembly (English et al 2012).…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

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Reconstructing complex regions of genomes using long-read sequencing technology

et al. 2014

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Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state.

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Section: Discussionmentioning

confidence: 99%

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Reconstructing complex regions of genomes using long-read sequencing technology

et al. 2014

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“…The sequences of the complete human genome, version GRC37.1 from the Genome Reference Commission (41), and the yeast genome (Saccharomyces cerevisiae, S288c-NCBI) were scanned using regular expressions representing the plus and minus strand versions of ERSE-26. The promoters of all human genes were searched.…”

Section: Methodsmentioning

confidence: 99%

Identification of a Novel Endoplasmic Reticulum Stress Response Element Regulated by XBP1

Misiewicz

Déry

Foveau

et al. 2013

Journal of Biological Chemistry

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Background: Endoplasmic reticulum (ER) stress maintains cellular protein homeostasis. Results: A novel ER stress-responsive element, ERSE-26, identified in 38 genes, is regulated by sXBP1 during ER stress. Conclusion: ER stress increases levels of prion and other proteins not previously known to be involved in the ER stress response. Significance: ERSE-26 implicates novel genes regulated by the ER stress response.

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“…A revision to the assembly model, first used in the previous version of the reference, GRCh37 (GCA_000001405.1), expanded the ability of the reference assembly to represent the extent of structural variation and population genomic diversity whose discovery it facilitated (The International HapMap Consortium 2005; Kidd et al 2008;Sudmant et al 2010;Church et al 2011; The 1000 Genomes Project Consortium 2015). The introduction of alternate loci scaffolds enabled GRCh37 to include additional sequence representations for the highly variant MHC region, as well as the divergent haplotypes of the MAPT and UGT2B loci, while retaining the linear chromosome representations familiar and intuitive to most users (Horton et al 2008;Xue et al 2008;Zody et al 2008).…”

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confidence: 99%

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Graves-Lindsay²,

et al. 2017

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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.

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Modernizing Reference Genome Assemblies

Cited by 469 publications

References 23 publications

Reconstructing complex regions of genomes using long-read sequencing technology

Reconstructing complex regions of genomes using long-read sequencing technology

Identification of a Novel Endoplasmic Reticulum Stress Response Element Regulated by XBP1

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

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