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Method: De novo discovery of mutated driver pathways in cancer
- Fabio Vandin,
- Eli Upfal,
- and Benjamin J. Raphael
Genome Res. February 2012 22: 375-385; Published in Advance June 7, 2011, doi:10.1101/gr.120477.111
...sequencing technologies, whole- or whole-exome measurements of the somatic mutations in large numbers of cancer s are now a reality (Mardis and Wilson 2009; International Cancer Genome Consortium 2010; Meyerson et al. 2010). A major challenge for these studies is to distinguish the functional “driver...
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Research: Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
- Elena Helman,
- Michael S. Lawrence,
- Chip Stewart,
- Carrie Sougnez,
- Gad Getz,
- and Matthew Meyerson
Genome Res. July 2014 24: 1053-1063; Published in Advance May 13, 2014, doi:10.1101/gr.163659.113
.....org Genome Research 1053 www..org in cancer progression. We expand our search to exome data using a modified tool and find additional somatic insertions into exons in endometrial carcinoma. Results Whole- sequencing reveals numerous nonreference retrotransposon insertions To identify nonreference somatic...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...of canine lymphoma and human cancer. The figure shows a single-amino-acid site, R470, which accounts for 41% of all FBXW7 somatic mutations in a cohort of whole-exome-sequenced lymphoma samples. Data obtained from UCSC, originally provided by Elvers et al. (2015).Disease gene studies in modern dogs...
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Research: A comprehensive characterization of cis-acting splicing-associated variants in human cancer
- Yuichi Shiraishi,
- Keisuke Kataoka,
- Kenichi Chiba,
- Ai Okada,
- Yasunori Kogure,
- Hiroko Tanaka,
- Seishi Ogawa,
- and Satoru Miyano
Genome Res. August 2018 28: 1111-1125; Published in Advance July 16, 2018, doi:10.1101/gr.231951.117
...creating splice site motifs and applied it to matched whole-exome and transcriptome sequencing data from 8976 samples across 31 cancer types, generating a catalog of 14,438 SAVs. Such a large collection of SAVs enabled us to characterize their genomic features, underlying mutational processes...
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Research: Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma
- Winnie S. Liang,
- William Hendricks,
- Jeffrey Kiefer,
- Jessica Schmidt,
- Shobana Sekar,
- John Carpten,
- David W. Craig,
- Jonathan Adkins,
- Lori Cuyugan,
- Zarko Manojlovic,
- Rebecca F. Halperin,
- Adrienne Helland,
- Sara Nasser,
- Christophe Legendre,
- Laurence H. Hurley,
- Karthigayini Sivaprakasam,
- Douglas B. Johnson,
- Holly Crandall,
- Klaus J. Busam,
- Victoria Zismann,
- Valerie Deluca,
- Jeeyun Lee,
- Aleksandar Sekulic,
- Charlotte E. Ariyan,
- Jeffrey Sosman,
- and Jeffrey Trent
Genome Res. April 2017 27: 524-532; doi:10.1101/gr.213348.116
...is available for this article.] Comprehensive sequencing of large cancer cohorts has revealed genomic landscapes of common malignant diseases, enabling deduction of tumorigenic pathways and clinically actionable information. Such genomic analyses of more than 600 cutaneous melanomas (CM), the most common...
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Research: Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans
- Maria Zhivagui,
- Alvin W.T. Ng,
- Maude Ardin,
- Mona I. Churchwell,
- Manuraj Pandey,
- Claire Renard,
- Stephanie Villar,
- Vincent Cahais,
- Alexis Robitaille,
- Liacine Bouaoun,
- Adriana Heguy,
- Kathryn Z. Guyton,
- Martha R. Stampfer,
- James McKay,
- Monica Hollstein,
- Magali Olivier,
- Steven G. Rozen,
- Frederick A. Beland,
- Michael Korenjak,
- and Jiri Zavadil
Genome Res. April 2019 29: 521-531; Published in Advance March 7, 2019, doi:10.1101/gr.242453.118
...a sound rationale for extended sequencing at the exome scale.View this table: In this window In a new window Table 1. Summary of cell lines, treatment conditions, and TP53 mutation statusAnalysis of mutation spectraWhole-exome sequencing (WES) of all Spont as well as exposed clones revealed that the total...
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Perspective: From human genome to cancer genome: The first decade
- David A. Wheeler and
- Linghua Wang
Genome Res. July 2013 23: 1054-1062; doi:10.1101/gr.157602.113
...,000 genes, defined by the human sequence, in 11 each of breast and colorectal tumors (Wood et al. 2007). This brute force whole-exome sequencing (WES) approach afforded for the first time a comprehensive view of themutation profile of each patient, which, when summed across patients, revealed the ‘‘cancer...
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Research: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
- Yumeng Wang,
- Xiaoyan Xu,
- Shuangxing Yu,
- Kang Jin Jeong,
- Zhicheng Zhou,
- Leng Han,
- Yiu Huen Tsang,
- Jun Li,
- Hu Chen,
- Lingegowda S. Mangala,
- Yuan Yuan,
- A. Karina Eterovic,
- Yiling Lu,
- Anil K. Sood,
- Kenneth L. Scott,
- Gordon B. Mills,
- and Han Liang
Genome Res. July 2017 27: 1112-1125; Published in Advance April 14, 2017, doi:10.1101/gr.219741.116
..., we assessed the ICGC whole- sequencing data and TCGA whole-exome sequencing data at the identified miRNA editing hotspots and removedsiteswithpotentialDNAmutational signals. This analysis yielded 20 uniquemiRNA editing sites with strong Ato-I editing signals. The editing site in miR-4510 was removed...
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Research: Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand
- Maria A. Andrianova,
- Georgii A. Bazykin,
- Sergey I. Nikolaev,
- and Vladimir B. Seplyarskiy
Genome Res. August 2017 27: 1336-1343; Published in Advance May 16, 2017, doi:10.1101/gr.219915.116
...repair system Genome Research 1341 www..org introduction and repair of mismatches helps reduce the genomic mutation rate and prevent accumulation of local strand biases in nucleotide composition. Methods Mutation data We used the following previously published data: (1) somatic mutations for whole-exome...

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