Literature DB >> 21666668

CREST maps somatic structural variation in cancer genomes with base-pair resolution.

Jianmin Wang1, Charles G Mullighan, John Easton, Stefan Roberts, Sue L Heatley, Jing Ma, Michael C Rusch, Ken Chen, Christopher C Harris, Li Ding, Linda Holmfeldt, Debbie Payne-Turner, Xian Fan, Lei Wei, David Zhao, John C Obenauer, Clayton Naeve, Elaine R Mardis, Richard K Wilson, James R Downing, Jinghui Zhang.   

Abstract

We developed 'clipping reveals structure' (CREST), an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution. Application of CREST to whole-genome sequencing data from five pediatric T-lineage acute lymphoblastic leukemias (T-ALLs) and a human melanoma cell line, COLO-829, identified 160 somatic structural variations. Experimental validation exceeded 80%, demonstrating that CREST had a high predictive accuracy.

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Year:  2011        PMID： 21666668      PMCID： PMC3527068          DOI： 10.1038/nmeth.1628

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  20 in total

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Authors:  Lars Feuk; Andrew R Carson; Stephen W Scherer
Journal:  Nat Rev Genet       Date:  2006-02       Impact factor: 53.242

3.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

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4.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Authors:  Peter J Campbell; Philip J Stephens; Erin D Pleasance; Sarah O'Meara; Heng Li; Thomas Santarius; Lucy A Stebbings; Catherine Leroy; Sarah Edkins; Claire Hardy; Jon W Teague; Andrew Menzies; Ian Goodhead; Daniel J Turner; Christopher M Clee; Michael A Quail; Antony Cox; Clive Brown; Richard Durbin; Matthew E Hurles; Paul A W Edwards; Graham R Bignell; Michael R Stratton; P Andrew Futreal
Journal:  Nat Genet       Date:  2008-04-27       Impact factor: 38.330

5.  A geometric approach for classification and comparison of structural variants.

Authors:  Suzanne Sindi; Elena Helman; Ali Bashir; Benjamin J Raphael
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

6.  Paired-end mapping reveals extensive structural variation in the human genome.

Authors:  Jan O Korbel; Alexander Eckehart Urban; Jason P Affourtit; Brian Godwin; Fabian Grubert; Jan Fredrik Simons; Philip M Kim; Dean Palejev; Nicholas J Carriero; Lei Du; Bruce E Taillon; Zhoutao Chen; Andrea Tanzer; A C Eugenia Saunders; Jianxiang Chi; Fengtang Yang; Nigel P Carter; Matthew E Hurles; Sherman M Weissman; Timothy T Harkins; Mark B Gerstein; Michael Egholm; Michael Snyder
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7.  Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.

Authors:  Robert E Handsaker; Joshua M Korn; James Nemesh; Steven A McCarroll
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8.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Authors: 
Journal:  Nature       Date:  2008-09-04       Impact factor: 49.962

9.  Transcriptome sequencing to detect gene fusions in cancer.

Authors:  Christopher A Maher; Chandan Kumar-Sinha; Xuhong Cao; Shanker Kalyana-Sundaram; Bo Han; Xiaojun Jing; Lee Sam; Terrence Barrette; Nallasivam Palanisamy; Arul M Chinnaiyan
Journal:  Nature       Date:  2009-01-11       Impact factor: 49.962

10.  Mapping and sequencing of structural variation from eight human genomes.

Authors:  Jeffrey M Kidd; Gregory M Cooper; William F Donahue; Hillary S Hayden; Nick Sampas; Tina Graves; Nancy Hansen; Brian Teague; Can Alkan; Francesca Antonacci; Eric Haugen; Troy Zerr; N Alice Yamada; Peter Tsang; Tera L Newman; Eray Tüzün; Ze Cheng; Heather M Ebling; Nadeem Tusneem; Robert David; Will Gillett; Karen A Phelps; Molly Weaver; David Saranga; Adrianne Brand; Wei Tao; Erik Gustafson; Kevin McKernan; Lin Chen; Maika Malig; Joshua D Smith; Joshua M Korn; Steven A McCarroll; David A Altshuler; Daniel A Peiffer; Michael Dorschner; John Stamatoyannopoulos; David Schwartz; Deborah A Nickerson; James C Mullikin; Richard K Wilson; Laurakay Bruhn; Maynard V Olson; Rajinder Kaul; Douglas R Smith; Evan E Eichler
Journal:  Nature       Date:  2008-05-01       Impact factor: 49.962
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  277 in total

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Authors:  Olca Basturk; Michael F Berger; Hiroshi Yamaguchi; Volkan Adsay; Gokce Askan; Umesh K Bhanot; Ahmet Zehir; Fatima Carneiro; Seung-Mo Hong; Giuseppe Zamboni; Esra Dikoglu; Vaidehi Jobanputra; Kazimierz O Wrzeszczynski; Serdar Balci; Peter Allen; Naoki Ikari; Shoko Takeuchi; Hiroyuki Akagawa; Atsushi Kanno; Tooru Shimosegawa; Takanori Morikawa; Fuyuhiko Motoi; Michiaki Unno; Ryota Higuchi; Masakazu Yamamoto; Kyoko Shimizu; Toru Furukawa; David S Klimstra
Journal:  Mod Pathol       Date:  2017-08-04       Impact factor: 7.842

Review 2.  Genomic profiling of B-progenitor acute lymphoblastic leukemia.

Authors:  Charles G Mullighan
Journal:  Best Pract Res Clin Haematol       Date:  2011-11-06       Impact factor: 3.020

3.  The Pediatric Cancer Genome Project.

Authors:  James R Downing; Richard K Wilson; Jinghui Zhang; Elaine R Mardis; Ching-Hon Pui; Li Ding; Timothy J Ley; William E Evans
Journal:  Nat Genet       Date:  2012-05-29       Impact factor: 38.330

Review 4.  Detecting Somatic Mutations in Normal Cells.

Authors:  Yanmei Dou; Heather D Gold; Lovelace J Luquette; Peter J Park
Journal:  Trends Genet       Date:  2018-05-03       Impact factor: 11.639

5.  Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.

Authors:  David H Spencer; Jennifer K Sehn; Haley J Abel; Mark A Watson; John D Pfeifer; Eric J Duncavage
Journal:  J Mol Diagn       Date:  2013-06-26       Impact factor: 5.568

6.  A genomic random interval model for statistical analysis of genomic lesion data.

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Journal:  Bioinformatics       Date:  2013-07-10       Impact factor: 6.937

7.  CONSERTING: integrating copy-number analysis with structural-variation detection.

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Journal:  Nat Methods       Date:  2015-05-04       Impact factor: 28.547

8.  TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer.

Authors:  Jeremy Chien; Hugues Sicotte; Jian-Bing Fan; Sean Humphray; Julie M Cunningham; Kimberly R Kalli; Ann L Oberg; Steven N Hart; Ying Li; Jaime I Davila; Saurabh Baheti; Chen Wang; Sabine Dietmann; Elizabeth J Atkinson; Yan W Asmann; Debra A Bell; Takayo Ota; Yaman Tarabishy; Rui Kuang; Marina Bibikova; R Keira Cheetham; Russell J Grocock; Elizabeth M Swisher; John Peden; David Bentley; Jean-Pierre A Kocher; Scott H Kaufmann; Lynn C Hartmann; Viji Shridhar; Ellen L Goode
Journal:  Nucleic Acids Res       Date:  2015-04-27       Impact factor: 16.971

9.  Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells.

Authors:  Michael N Cornforth; Pavana Anur; Nicholas Wang; Erin Robinson; F Andrew Ray; Joel S Bedford; Bradford D Loucas; Eli S Williams; Myron Peto; Paul Spellman; Rahul Kollipara; Ralf Kittler; Joe W Gray; Susan M Bailey
Journal:  Radiat Res       Date:  2018-05-11       Impact factor: 2.841

10.  Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.

Authors:  Jiali Zhuang; Zhiping Weng
Journal:  Nucleic Acids Res       Date:  2015-08-17       Impact factor: 16.971
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