Literature DB >> 25030933

Computational methods for DNA copy-number analysis of tumors.

Jude Kendall1, Alexander Krasnitz.   

Abstract

Study of DNA copy-number variation is a key part of cancer genomics. With the help of a comprehensive multistep computational procedure described here, copy-number profiles of tumor tissues or individual tumor cells may be generated and interpreted, starting with data acquired by next-generation sequencing. Several of the methods presented are specifically designed to handle cancer-related copy-number profiles. These include accounting for variation of ploidy and distilling somatic copy number alterations from the inherited background.

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Mesh：

Year:  2014        PMID： 25030933      PMCID： PMC5136461          DOI： 10.1007/978-1-4939-0992-6_20

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  13 in total

1.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

Authors:  Yee Hwa Yang; Sandrine Dudoit; Percy Luu; David M Lin; Vivian Peng; John Ngai; Terence P Speed
Journal:  Nucleic Acids Res       Date:  2002-02-15       Impact factor: 16.971

2.  Target inference from collections of genomic intervals.

Authors:  Alexander Krasnitz; Guoli Sun; Peter Andrews; Michael Wigler
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-06       Impact factor: 11.205

3.  Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors:  B Ewing; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

4.  Novel patterns of genome rearrangement and their association with survival in breast cancer.

Authors:  James Hicks; Alexander Krasnitz; B Lakshmi; Nicholas E Navin; Michael Riggs; Evan Leibu; Diane Esposito; Joan Alexander; Jen Troge; Vladimir Grubor; Seungtai Yoon; Michael Wigler; Kenny Ye; Anne-Lise Børresen-Dale; Bjørn Naume; Ellen Schlicting; Larry Norton; Torsten Hägerström; Lambert Skoog; Gert Auer; Susanne Månér; Pär Lundin; Anders Zetterberg
Journal:  Genome Res       Date:  2006-12       Impact factor: 9.043

5.  Genome-wide copy number analysis of single cells.

Authors:  Timour Baslan; Jude Kendall; Linda Rodgers; Hilary Cox; Mike Riggs; Asya Stepansky; Jennifer Troge; Kandasamy Ravi; Diane Esposito; B Lakshmi; Michael Wigler; Nicholas Navin; James Hicks
Journal:  Nat Protoc       Date:  2012-05-03       Impact factor: 13.491

6.  Tumour evolution inferred by single-cell sequencing.

Authors:  Nicholas Navin; Jude Kendall; Jennifer Troge; Peter Andrews; Linda Rodgers; Jeanne McIndoo; Kerry Cook; Asya Stepansky; Dan Levy; Diane Esposito; Lakshmi Muthuswamy; Alex Krasnitz; W Richard McCombie; James Hicks; Michael Wigler
Journal:  Nature       Date:  2011-03-13       Impact factor: 49.962

7.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

8.  DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma.

Authors:  Wen Xue; Alexander Krasnitz; Robert Lucito; Raffaella Sordella; Linda Vanaelst; Carlos Cordon-Cardo; Stephan Singer; Florian Kuehnel; Michael Wigler; Scott Powers; Lars Zender; Scott W Lowe
Journal:  Genes Dev       Date:  2008-06-01       Impact factor: 11.361

9.  Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model.

Authors:  Anka Bric; Cornelius Miething; Carl Uli Bialucha; Claudio Scuoppo; Lars Zender; Alexander Krasnitz; Zhenyu Xuan; Johannes Zuber; Michael Wigler; James Hicks; Richard W McCombie; Michael T Hemann; Gregory J Hannon; Scott Powers; Scott W Lowe
Journal:  Cancer Cell       Date:  2009-10-06       Impact factor: 31.743

10.  The landscape of somatic copy-number alteration across human cancers.

Authors:  Rameen Beroukhim; Craig H Mermel; Dale Porter; Guo Wei; Soumya Raychaudhuri; Jerry Donovan; Jordi Barretina; Jesse S Boehm; Jennifer Dobson; Mitsuyoshi Urashima; Kevin T Mc Henry; Reid M Pinchback; Azra H Ligon; Yoon-Jae Cho; Leila Haery; Heidi Greulich; Michael Reich; Wendy Winckler; Michael S Lawrence; Barbara A Weir; Kumiko E Tanaka; Derek Y Chiang; Adam J Bass; Alice Loo; Carter Hoffman; John Prensner; Ted Liefeld; Qing Gao; Derek Yecies; Sabina Signoretti; Elizabeth Maher; Frederic J Kaye; Hidefumi Sasaki; Joel E Tepper; Jonathan A Fletcher; Josep Tabernero; José Baselga; Ming-Sound Tsao; Francesca Demichelis; Mark A Rubin; Pasi A Janne; Mark J Daly; Carmelo Nucera; Ross L Levine; Benjamin L Ebert; Stacey Gabriel; Anil K Rustgi; Cristina R Antonescu; Marc Ladanyi; Anthony Letai; Levi A Garraway; Massimo Loda; David G Beer; Lawrence D True; Aikou Okamoto; Scott L Pomeroy; Samuel Singer; Todd R Golub; Eric S Lander; Gad Getz; William R Sellers; Matthew Meyerson
Journal:  Nature       Date:  2010-02-18       Impact factor: 49.962
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  6 in total

Review 1.  Patterns of Chromosomal Aberrations in Solid Tumors.

Authors:  Marian Grade; Michael J Difilippantonio; Jordi Camps
Journal:  Recent Results Cancer Res       Date:  2015

2.  Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer.

Authors:  Joan Alexander; Jude Kendall; Jean McIndoo; Linda Rodgers; Robert Aboukhalil; Dan Levy; Asya Stepansky; Guoli Sun; Lubomir Chobardjiev; Michael Riggs; Hilary Cox; Inessa Hakker; Dawid G Nowak; Juliana Laze; Elton Llukani; Abhishek Srivastava; Siobhan Gruschow; Shalini S Yadav; Brian Robinson; Gurinder Atwal; Lloyd C Trotman; Herbert Lepor; James Hicks; Michael Wigler; Alexander Krasnitz
Journal:  Cancer Res       Date:  2017-11-27       Impact factor: 12.701

3.  DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells.

Authors:  Ramya Viswanathan; Elsie Cheruba; Lih Feng Cheow
Journal:  Nucleic Acids Res       Date:  2019-11-04       Impact factor: 16.971

Review 4.  Early Detection of Cancer in Blood Using Single-Cell Analysis: A Proposal.

Authors:  Alexander Krasnitz; Jude Kendall; Joan Alexander; Dan Levy; Michael Wigler
Journal:  Trends Mol Med       Date:  2017-06-03       Impact factor: 11.951

5.  Integrated Computational Pipeline for Single-Cell Genomic Profiling.

Authors:  Lubomir Chorbadjiev; Jude Kendall; Joan Alexander; Viacheslav Zhygulin; Junyan Song; Michael Wigler; Alexander Krasnitz
Journal:  JCO Clin Cancer Inform       Date:  2020-05

6.  SOAT1 promotes mevalonate pathway dependency in pancreatic cancer.

Authors:  Tobiloba E Oni; Giulia Biffi; Lindsey A Baker; Yuan Hao; Claudia Tonelli; Tim D D Somerville; Astrid Deschênes; Pascal Belleau; Chang-Il Hwang; Francisco J Sánchez-Rivera; Hilary Cox; Erin Brosnan; Abhishek Doshi; Rebecca P Lumia; Kimia Khaledi; Youngkyu Park; Lloyd C Trotman; Scott W Lowe; Alexander Krasnitz; Christopher R Vakoc; David A Tuveson
Journal:  J Exp Med       Date:  2020-09-07       Impact factor: 14.307
  6 in total

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