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

被引：52

作者：

Su, Xiaoping ^{[1
]}

Zhang, Li ^{[1
]}

Zhang, Jianping ^{[1
]}

Meric-Bernstam, Funda ^{[2
]}

Weinstein, John N. ^{[1
]}

机构：

[1] Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA

[2] Univ Texas MD Anderson Canc Ctr, Dept Surg Oncol, Houston, TX 77030 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 17期

关键词：

D O I：

10.1093/bioinformatics/bts365

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2265 / 2266

页数：2

共 10 条

[1] TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays [J].

Bengtsson, Henrik ;

Neuvial, Pierre ;

Speed, Terence P. .

BMC BIOINFORMATICS, 2010, 11

[2] The genomic complexity of primary human prostate cancer [J].

Berger, Michael F. ;

Lawrence, Michael S. ;

Demichelis, Francesca ;

Drier, Yotam ;

Cibulskis, Kristian ;

Sivachenko, Andrey Y. ;

Sboner, Andrea ;

Esgueva, Raquel ;

Pflueger, Dorothee ;

Sougnez, Carrie ;

Onofrio, Robert ;

Carter, Scott L. ;

Park, Kyung ;

Habegger, Lukas ;

Ambrogio, Lauren ;

Fennell, Timothy ;

Parkin, Melissa ;

Saksena, Gordon ;

Voet, Douglas ;

Ramos, Alex H. ;

Pugh, Trevor J. ;

Wilkinson, Jane ;

Fisher, Sheila ;

Winckler, Wendy ;

Mahan, Scott ;

Ardlie, Kristin ;

Baldwin, Jennifer ;

Simons, Jonathan W. ;

Kitabayashi, Naoki ;

MacDonald, Theresa Y. ;

Kantoff, Philip W. ;

Chin, Lynda ;

Gabriel, Stacey B. ;

Gerstein, Mark B. ;

Golub, Todd R. ;

Meyerson, Matthew ;

Tewari, Ashutosh ;

Lander, Eric S. ;

Getz, Gad ;

Rubin, Mark A. ;

Garraway, Levi A. .

NATURE, 2011, 470 (7333) :214-220

[3] Absolute quantification of somatic DNA alterations in human cancer [J].

Carter, Scott L. ;

Cibulskis, Kristian ;

Helman, Elena ;

McKenna, Aaron ;

Shen, Hui ;

Zack, Travis ;

Laird, Peter W. ;

Onofrio, Robert C. ;

Winckler, Wendy ;

Weir, Barbara A. ;

Beroukhim, Rameen ;

Pellman, David ;

Levine, Douglas A. ;

Lander, Eric S. ;

Meyerson, Matthew ;

Getz, Gad .

NATURE BIOTECHNOLOGY, 2012, 30 (05) :413-+

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

Gusnanto, Arief ;

Wood, Henry M. ;

Pawitan, Yudi ;

Rabbitts, Pamela ;

Berri, Stefano .

BIOINFORMATICS, 2012, 28 (01) :40-47

[5] Whole-genome sequencing and variant discovery in C-elegans [J].

Hillier, LaDeana W. ;

Marth, Gabor T. ;

Quinlan, Aaron R. ;

Dooling, David ;

Fewell, Ginger ;

Barnett, Derek ;

Fox, Paul ;

Glasscock, Jarret I. ;

Hickenbotham, Matthew ;

Huang, Weichun ;

Magrini, Vincent J. ;

Richt, Ryan J. ;

Sander, Sacha N. ;

Stewart, Donald A. ;

Stromberg, Michael ;

Tsung, Eric F. ;

Wylie, Todd ;

Schedl, Tim ;

Wilson, Richard K. ;

Mardis, Elaine R. .

NATURE METHODS, 2008, 5 (02) :183-188

[6] A general approach to single-nucleotide polymorphism discovery [J].

Marth, GT ;

Korf, I ;

Yandell, MD ;

Yeh, RT ;

Gu, ZJ ;

Zakeri, H ;

Stitziel, NO ;

Hillier, L ;

Kwok, PY ;

Gish, WR .

NATURE GENETICS, 1999, 23 (04) :452-456

[7] PERCENTAGE POINTS FOR A GENERALIZED ESD MANY-OUTLIER PROCEDURE [J].

ROSNER, B .

TECHNOMETRICS, 1983, 25 (02) :165-172

[8] Integrated study of copy number states and genotype calls using high-density SNP arrays [J].

Sun, Wei ;

Wright, Fred A. ;

Tang, Zhengzheng ;

Nordgard, Silje H. ;

Van Loo, Peter ;

Yu, Tianwei ;

Kristensen, Vessela N. ;

Perou, Charles M. .

NUCLEIC ACIDS RESEARCH, 2009, 37 (16) :5365-5377

[9] Allele-specific copy number analysis of tumors [J].

Van Loo, Peter ;

Nordgard, Silje H. ;

Lingjaerde, Ole Christian ;

Russnes, Hege G. ;

Rye, Inga H. ;

Sun, Wei ;

Weigman, Victor J. ;

Marynen, Peter ;

Zetterberg, Anders ;

Naume, Bjorn ;

Perou, Charles M. ;

Borresen-Dale, Anne-Lise ;

Kristensen, Vessela N. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (39) :16910-16915

[10] BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data [J].

Yu, Guoqiang ;

Zhang, Bai ;

Bova, G. Steven ;

Xu, Jianfeng ;

Shih, Ie-Ming ;

Wang, Yue .

BIOINFORMATICS, 2011, 27 (11) :1473-1480

← 1 →