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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...to differ significantly from the reference, we adjusted QUAST's parameters to detect only large-scale genomic differences (Methods). Although the HiCanu assembly reported three more structural discrepancies than Canu (seven vs. four), it maintained the highest NG50 and alternate contig BUSCO completeness...
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Research: Accelerated rates of large-scale mutations in the presence of copper and nickel
- Frédéric J.J. Chain,
- Jullien M. Flynn,
- James K. Bull,
- and Melania E. Cristescu
Genome Res. January 2019 29: 64-73; Published in Advance November 28, 2018, doi:10.1101/gr.234724.118
...rates and influence the genetic load of populations. Moreover, most studies on stressors have focused on unicellular organisms and point mutations rather than large-scale deletions and duplications (copy number variations [CNVs]). We estimated mutation rates in Daphnia pulex exposed to low levels...
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Method: HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
- Jia Lv,
- Wenqian Jiao,
- Haobing Guo,
- Pingping Liu,
- Ruijia Wang,
- Lingling Zhang,
- Qifan Zeng,
- Xiaoli Hu,
- Zhenmin Bao,
- and Shi Wang
Genome Res. December 2018 28: 1919-1930; Published in Advance November 8, 2018, doi:10.1101/gr.235820.118
...a large set of gene-related markers can now be readily achieved through transcriptome sequencing (Ekblom and Galindo 2011; De Wit et al. 2015), targeted genotyping of these markers on a large scale (e.g., thousands to tens of thousands of markers) and in a cost-effective manner remains a major challenge...
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Research: Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency
- Linghua Wang,
- Shuichi Tsutsumi,
- Tokuichi Kawaguchi,
- Koichi Nagasaki,
- Kenji Tatsuno,
- Shogo Yamamoto,
- Fei Sang,
- Kohtaro Sonoda,
- Minoru Sugawara,
- Akio Saiura,
- Seiko Hirono,
- Hiroki Yamaue,
- Yoshio Miki,
- Minoru Isomura,
- Yasushi Totoki,
- Genta Nagae,
- Takayuki Isagawa,
- Hiroki Ueda,
- Satsuki Murayama-Hosokawa,
- Tatsuhiro Shibata,
- Hiromi Sakamoto,
- Yae Kanai,
- Atsushi Kaneda,
- Tetsuo Noda,
- and Hiroyuki Aburatani
Genome Res. February 2012 22: 208-219; Published in Advance December 7, 2011, doi:10.1101/gr.123109.111
...; Maitra and Hruban 2008). However, because Sanger sequencing is performed on single amplicons, its throughput is limited, and large-scale sequencing projects are expensive and laborious (Schuster 2008;Metzker 2010). Moreover, it has been reported that it has a limited sensitivity to recognize the mutant...
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Method: A generic, cost-effective, and scalable cell lineage analysis platform
- Tamir Biezuner,
- Adam Spiro,
- Ofir Raz,
- Shiran Amir,
- Lilach Milo,
- Rivka Adar,
- Noa Chapal-Ilani,
- Veronika Berman,
- Yael Fried,
- Elena Ainbinder,
- Galit Cohen,
- Haim M. Barr,
- Ruth Halaban,
- and Ehud Shapiro
Genome Res. November 2016 26: 1588-1599; Published in Advance August 24, 2016, doi:10.1101/gr.202903.115
...reduction in sequencing costs, sequencing whole s or even whole exomes from multiple cells is not a scalable approach for studying the lineage of hundreds of cells or more (Hou et al. 2012; Xu et al. 2012). Moreover, available commercial methods for targeted enrichment are not cost-efficient for large-scale...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, s hort t andem r epeat profiling using f lank-based m apping, a computational pipeline that can detect...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
..., Haikou, Hainan 571101, China Corresponding authors: sergey.koren@nih.gov, adam.phillippy@nih.govAbstractThe combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human...
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Research: Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication
- Eve Shinbrot,
- Erin E. Henninger,
- Nils Weinhold,
- Kyle R. Covington,
- A. Yasemin Göksenin,
- Nikolaus Schultz,
- Hsu Chao,
- HarshaVardhan Doddapaneni,
- Donna M. Muzny,
- Richard A. Gibbs,
- Chris Sander,
- Zachary F. Pursell,
- and David A. Wheeler
Genome Res. November 2014 24: 1740-1750; Published in Advance September 16, 2014, doi:10.1101/gr.174789.114
..., ranging from 10 to 100 mutations per Mb. MSI tumors also feature reduced chromosome instability compared to MSS tumors from the same organ (Ciriello et al. 2013). Recently, large-scale genetic and genomic studies have revealed tumors mutated in the exonuclease (proofreading) domain of DNA polymerase...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...of inbred mouse strains (Quinlan et al. 2010), and we found 20–110 copies in wild mice (Fig. 5; Supplemental Table S4). Hjurp mediates the centromere-specific assembly of CENP-A nucleosomes, contributing to high-fidelity chromosome segregation during cell division (Stellfox et al. 2013). The misregulation...
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Methods: DNA amplification method tolerant to sample degradation
- Gang Wang,
- Elizabeth Maher,
- Cameron Brennan,
- Lynda Chin,
- Christopher Leo,
- Manjit Kaur,
- Penny Zhu,
- Martha Rook,
- Jia Liu Wolfe,
- and G. Mike Makrigiorgos
Genome Res. November 2004 14: 2357-2366; doi:10.1101/gr.2813404
...and is widely used for genomic profiling and large-scale genotyping ( Lovmar et al. 2003 ; Paez et al. 2004 ; Rook et al. 2004 ; Wong et al. 2004 ). However, the amplification efficiency of MDA rapidly diminishes as the molecular weight of the starting material decreases, thus making it unsuitable...

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