Category: Publications
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Distance Indexing and Seed Clustering in Sequence Graphs
Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten Cold Spring Harbor Laboratory | Dec 23, 2019 Abstract Graph representations of genomes are capable of expressing more genetic variation and can therefore better represent a population than standard linear genomes. However, due to the greater complexity of genome graphs relative to linear genomes, some functions that are trivial on linear genomes become…
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A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
Article | BMC Genomics| Published: 27 Dec 2019 Christopher J. Troll, Joshua Kapp, Varsha Rao, Kelly M. Harkins, Charles Cole, Colin Naughton, Jessica M. Morgan, Beth Shapiro & Richard E. Green Abstract Background Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA,…
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One fly – one genome : Chromosome-scale genome assembly of a single outbred Drosophila melanogaster
Matthew Adams, Jakob McBroome, Nicholas Maurer, Evan Pepper-Tunick, Nedda Saremi, Richard E. Green, Christopher Vollmers, Russell B. Corbett-Detig Abstract A high quality genome assembly is a vital first step for the study of an organism. Recent advances in technology have made the creation of high quality chromosome scale assemblies feasible and low cost. However, the amount of input DNA needed for an assembly project can be a limiting factor for…
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A fully phased accurate assembly of an individual human genome
David Porubsky, Peter Ebert, Peter A. Audano, Mitchell R. Vollger, William T. Harvey, Katherine M. Munson, Melanie Sorensen, Arvis Sulovari, Marina Haukness, Maryam Ghareghani, Human Genome Structural Variation Consortium, Peter M. Lansdorp, Benedict Paten, Scott E. Devine, Ashley D. Sanders, Charles Lee, Mark J.P. Chaisson, Jan O. Korbel, Evan E. Eichler, Tobias Marschall Abstract The prevailing genome assembly paradigm is to produce consensus sequences that “collapse” parental haplotypes into a consensus sequence. Here, we…
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Nanopore native RNA sequencing of a human poly(A) transcriptome
Rachael E. Workman, Alison D. Tang, Paul S. Tang, Miten Jain, John R. Tyson, Roham Razaghi, Philip C. Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Goes de Jesus, Karen L. Jones, Cameron M. Soulette, Terrance P. Snutch, Nicholas Loman, Benedict Paten, Matthew Loose, Jared T. Simpson, Hugh E. Olsen, Angela…
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Telomere-to-telomere assembly of a complete human X chromosome
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon, Valerie A Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G Bouffard, Alexander M Chang, Nancy…
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Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
Present workflows for producing human genome assemblies from long-read technologies have cost and production time bottlenecks that prohibit efficient scaling to large cohorts. We demonstrate an optimized PromethION nanopore sequencing method for eleven human genomes. The sequencing, performed on one machine in nine days, achieved an average 63x coverage, 42 Kb read N50, 90% median…
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Barriers to accessing public cancer genomic data
Katrina Learned, ann Durbin, Robert Currie , Ellen towle Kephart, Holly C. Beale, Lauren M. Sanders, Jacob Pfeil, theodore C. Goldstein, Sofie R. Salama, David Haussler, Olena Morozova Vaske & Isabel M. Bjork. Although increasingly recognized as critical to genomic research, genomic data sharing is hindered by an absence of standards regarding timing, patient privacy,…
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BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.
Article | PLoS Genetics| Published: 26 Dec 2018 Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman…
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Article | Nature Biotechnology | Published: 29 Jan 2018 Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Tom Nieto, Justin O’Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron R Quinlan,…
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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
Article | Nature Genetics | Published: 01 October 2018 Jingtao Lilue, Anthony G. Doran, Ian T. Fiddes, Monica Abrudan, Joel Armstrong, Ruth Bennett, William Chow, Joanna Collins, Stephan Collins, Anne Czechanski, Petr Danecek, Mark Diekhans, Dirk-Dominik Dolle, Matt Dunn, Richard Durbin, Dent Earl, Anne Ferguson-Smith, Paul Flicek, Jonathan Flint, Adam Frankish, Beiyuan Fu, Mark Gerstein,…
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Historical Sketch: The Santa Cruz Workshop
Robert L. SinsheimerMay, 1985. | Genomics. Volume 5, Issue 4, November 1989, Pages 954-956. The Santa Cruz Workshop in May 1985 resulted from the convergence of several lines of thought.The first complete genome to be sequenced was that of the bacterial virus ¢Xl 74 (5400 nucleotides) by Fred Sanger in 1977. Before that, my laboratory…