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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...) technologies continue to make whole- sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...-read high-throughput sequencing (HTS) technologies, studies have revealed that somatic SVs can drive malignant phenotypes by altering the expression or function of oncogenes (The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020; Cosenza et al. 2022). Additionally, certain somatic SVs within...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...years has revolutionized our ability to catalog cancer risk variants and understand the genomic landscape of cancer. Early studies relied on targeted sequencing and microarrays to detect genomic and transcriptomic variations enriched in cancer patients, revealing, for example, the prevalence...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
.... Mol Neurodegener 8: 12. ChenX, Schulz-Trieglaff O, ShawR, Barnes B, Schlesinger F, KällbergM, Cox AJ, Kruglyak S, Saunders CT. 2016. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32: 1220–1222. Church DM, Schneider VA...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...NG50, the numbers of errors, and other statistical information of scaffolds ($500 bp) obtained by each assembler tested are shown. The corrected scaffold NG50 was computed after breaking assembled sequences at eachmisassembled (structural difference) point detected by the...
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Research: The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
- Thomas E. Hughes,
- Jane A. Langdale,
- and Steven Kelly
Genome Res. August 2014 24: 1348-1355; Published in Advance April 30, 2014, doi:10.1101/gr.172684.114
...of the sequence regions that are putative targets of these transcription factors are difficult to define, and we were unable to find direct evidence on a -wide scale of a link betweenR-NF transcription factors and the presence or absence of motifs in the promoter regions of differentially expressed genes. Sub-1...
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Research: Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
- Hoon Kim,
- Siyuan Zheng,
- Seyed S. Amini,
- Selene M. Virk,
- Tom Mikkelsen,
- Daniel J. Brat,
- Jonna Grimsby,
- Carrie Sougnez,
- Florian Muller,
- Jian Hu,
- Andrew E. Sloan,
- Mark L. Cohen,
- Erwin G. Van Meir,
- Lisa Scarpace,
- Peter W. Laird,
- John N. Weinstein,
- Eric S. Lander,
- Stacey Gabriel,
- Gad Getz,
- Matthew Meyerson,
- Lynda Chin,
- Jill S. Barnholtz-Sloan,
- and Roel G.W. Verhaak
Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114
...Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution Hoon Kim 1 , 12 , Siyuan Zheng 1 , 2 , 12 , Seyed S. Amini 1 , Selene M. Virk 3 , Tom Mikkelsen 4...
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Research: Whole genome sequencing of matched primary and metastatic acral melanomas
- Samra Turajlic,
- Simon J. Furney,
- Maryou B. Lambros,
- Costas Mitsopoulos,
- Iwanka Kozarewa,
- Felipe C. Geyer,
- Alan MacKay,
- Jarle Hakas,
- Marketa Zvelebil,
- Christopher J. Lord,
- Alan Ashworth,
- Meirion Thomas,
- Gordon Stamp,
- James Larkin,
- Jorge S. Reis-Filho,
- and Richard Marais
Genome Res. February 2012 22: 196-207; Published in Advance December 19, 2011, doi:10.1101/gr.125591.111
...Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational...
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Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
...representing the number of shipments between 1991 and 2022 of strains containing each balancer.Using srWGS to detect known and unexpected high complexity in genomic variationWe first sequenced five balancer strains with well-defined and structurally complicated intrachromosomal rearrangements to reassess our...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
...Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance Tim Downing 1 , 10 , Hideo Imamura 2 , 10 , Saskia Decuypere 2 , Taane G. Clark 3...
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