Literature DB >> 22743227

PurityEst: estimating purity of human tumor samples using next-generation sequencing data.

Xiaoping Su1, Li Zhang, Jianping Zhang, Funda Meric-Bernstam, John N Weinstein.   

Abstract

UNLABELLED: We developed a novel algorithm, PurityEst, to infer the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data. We applied our tool to a whole cancer genome sequencing datasets and demonstrated the accuracy of PurityEst compared with DNA copy number-based estimation. AVAILABILITY: PurityEst has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/~xsu1/PurityEst.html.

Entities:  

Mesh：

Year:  2012        PMID： 22743227      PMCID： PMC3426843          DOI： 10.1093/bioinformatics/bts365

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  A general approach to single-nucleotide polymorphism discovery.

Authors:  G T Marth; I Korf; M D Yandell; R T Yeh; Z Gu; H Zakeri; N O Stitziel; L Hillier; P Y Kwok; W R Gish
Journal:  Nat Genet       Date:  1999-12       Impact factor: 38.330

2.  BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.

Authors:  Guoqiang Yu; Bai Zhang; G Steven Bova; Jianfeng Xu; Ie-Ming Shih; Yue Wang
Journal:  Bioinformatics       Date:  2011-04-15       Impact factor: 6.937

3.  Whole-genome sequencing and variant discovery in C. elegans.

Authors:  LaDeana W Hillier; Gabor T Marth; Aaron R Quinlan; David Dooling; Ginger Fewell; Derek Barnett; Paul Fox; Jarret I Glasscock; Matthew Hickenbotham; Weichun Huang; Vincent J Magrini; Ryan J Richt; Sacha N Sander; Donald A Stewart; Michael Stromberg; Eric F Tsung; Todd Wylie; Tim Schedl; Richard K Wilson; Elaine R Mardis
Journal:  Nat Methods       Date:  2008-01-20       Impact factor: 28.547

4.  Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.

Authors:  Arief Gusnanto; Henry M Wood; Yudi Pawitan; Pamela Rabbitts; Stefano Berri
Journal:  Bioinformatics       Date:  2011-10-28       Impact factor: 6.937

5.  Allele-specific copy number analysis of tumors.

Authors:  Peter Van Loo; Silje H Nordgard; Ole Christian Lingjærde; Hege G Russnes; Inga H Rye; Wei Sun; Victor J Weigman; Peter Marynen; Anders Zetterberg; Bjørn Naume; Charles M Perou; Anne-Lise Børresen-Dale; Vessela N Kristensen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-13       Impact factor: 11.205

6.  TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.

Authors:  Henrik Bengtsson; Pierre Neuvial; Terence P Speed
Journal:  BMC Bioinformatics       Date:  2010-05-12       Impact factor: 3.169

7.  The genomic complexity of primary human prostate cancer.

Authors:  Michael F Berger; Michael S Lawrence; Francesca Demichelis; Yotam Drier; Kristian Cibulskis; Andrey Y Sivachenko; Andrea Sboner; Raquel Esgueva; Dorothee Pflueger; Carrie Sougnez; Robert Onofrio; Scott L Carter; Kyung Park; Lukas Habegger; Lauren Ambrogio; Timothy Fennell; Melissa Parkin; Gordon Saksena; Douglas Voet; Alex H Ramos; Trevor J Pugh; Jane Wilkinson; Sheila Fisher; Wendy Winckler; Scott Mahan; Kristin Ardlie; Jennifer Baldwin; Jonathan W Simons; Naoki Kitabayashi; Theresa Y MacDonald; Philip W Kantoff; Lynda Chin; Stacey B Gabriel; Mark B Gerstein; Todd R Golub; Matthew Meyerson; Ashutosh Tewari; Eric S Lander; Gad Getz; Mark A Rubin; Levi A Garraway
Journal:  Nature       Date:  2011-02-10       Impact factor: 49.962

8.  Absolute quantification of somatic DNA alterations in human cancer.

Authors:  Scott L Carter; Kristian Cibulskis; Elena Helman; Aaron McKenna; Hui Shen; Travis Zack; Peter W Laird; Robert C Onofrio; Wendy Winckler; Barbara A Weir; Rameen Beroukhim; David Pellman; Douglas A Levine; Eric S Lander; Matthew Meyerson; Gad Getz
Journal:  Nat Biotechnol       Date:  2012-05       Impact factor: 54.908

9.  Integrated study of copy number states and genotype calls using high-density SNP arrays.

Authors:  Wei Sun; Fred A Wright; Zhengzheng Tang; Silje H Nordgard; Peter Van Loo; Tianwei Yu; Vessela N Kristensen; Charles M Perou
Journal:  Nucleic Acids Res       Date:  2009-07-06       Impact factor: 16.971
  9 in total
  33 in total

Review 1.  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

2.  PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.

Authors:  Nicholas B Larson; Brooke L Fridley
Journal:  Bioinformatics       Date:  2013-06-06       Impact factor: 6.937

Review 3.  An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples.

Authors:  Vinod Kumar Yadav; Subhajyoti De
Journal:  Brief Bioinform       Date:  2014-02-20       Impact factor: 11.622

4.  Comparison of custom capture for targeted next-generation DNA sequencing.

Authors:  Eric Samorodnitsky; Jharna Datta; Benjamin M Jewell; Raffi Hagopian; Jharna Miya; Michele R Wing; Senthilkumar Damodaran; Juliana M Lippus; Julie W Reeser; Darshna Bhatt; Cynthia D Timmers; Sameek Roychowdhury
Journal:  J Mol Diagn       Date:  2015-01       Impact factor: 5.568

5.  Power and sample size calculations for high-throughput sequencing-based experiments.

Authors:  Chung-I Li; David C Samuels; Ying-Yong Zhao; Yu Shyr; Yan Guo
Journal:  Brief Bioinform       Date:  2018-11-27       Impact factor: 11.622

6.  DNA methylation marker to estimate the breast cancer cell fraction in DNA samples.

Authors:  Hiroki Ishihara; Satoshi Yamashita; Satoshi Fujii; Kazunari Tanabe; Hirofumi Mukai; Toshikazu Ushijima
Journal:  Med Oncol       Date:  2018-09-14       Impact factor: 3.064

7.  AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.

Authors:  Lei Bao; Minya Pu; Karen Messer
Journal:  Bioinformatics       Date:  2014-01-02       Impact factor: 6.937

8.  Mutational dynamics between primary and relapse neuroblastomas.

Authors:  Alexander Schramm; Johannes Köster; Yassen Assenov; Kristina Althoff; Martin Peifer; Ellen Mahlow; Andrea Odersky; Daniela Beisser; Corinna Ernst; Anton G Henssen; Harald Stephan; Christopher Schröder; Lukas Heukamp; Anne Engesser; Yvonne Kahlert; Jessica Theissen; Barbara Hero; Frederik Roels; Janine Altmüller; Peter Nürnberg; Kathy Astrahantseff; Christian Gloeckner; Katleen De Preter; Christoph Plass; Sangkyun Lee; Holger N Lode; Kai-Oliver Henrich; Moritz Gartlgruber; Frank Speleman; Peter Schmezer; Frank Westermann; Sven Rahmann; Matthias Fischer; Angelika Eggert; Johannes H Schulte
Journal:  Nat Genet       Date:  2015-06-29       Impact factor: 38.330

9.  MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.

Authors:  Xiaoqi Zheng; Qian Zhao; Hua-Jun Wu; Wei Li; Haiyun Wang; Clifford A Meyer; Qian Alvin Qin; Han Xu; Chongzhi Zang; Peng Jiang; Fuqiang Li; Yong Hou; Jianxing He; Jun Wang; Jun Wang; Peng Zhang; Yong Zhang; Xiaole Shirley Liu
Journal:  Genome Biol       Date:  2014-08-07       Impact factor: 13.583

10.  SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Authors:  Yi Qiao; Aaron R Quinlan; Amir A Jazaeri; Roeland Gw Verhaak; David A Wheeler; Gabor T Marth
Journal:  Genome Biol       Date:  2014-08-26       Impact factor: 13.583
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