CNVDetector: locating copy number variations using array CGH data

被引：10

作者：

Chen, Peng-An ^{[1
]}

Liu, Hsiao-Fei ^{[1
]}

Chao, Kun-Mao ^{[1
,2
,3
]}

机构：

[1] Natl Taiwan Univ, Dept Comp Sci & Informat Engn, Taipei 10764, Taiwan

[2] Natl Taiwan Univ, Grad Inst Biomed Elect & Bioinformat, Taipei 10764, Taiwan

[3] Natl Taiwan Univ, Grad Inst Networking & Multimedia, Taipei 10764, Taiwan

来源：

BIOINFORMATICS | 2008年 / 24卷 / 23期

关键词：

D O I：

10.1093/bioinformatics/btn517

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

CNVDetector is a program for locating copy number variations (CNVs) in a single genome. CNVDetector has several merits: (i) it can deal with the array comparative genomic hybridization data even if the noise is not normally distributed; (ii) it has a linear time kernel; (iii) its parameters can be easily selected; (iv) it evaluates the statistical significance for each CNV calling.

引用

页码：2773 / 2775

页数：3

共 11 条

[1]

BERNHOLT T, 2007, P 23 ANN S COMP GEOM, P310

[2]

Hogg Robert V., 2006, Probability and Statistical Inference

[3] Analysis of array CGH data:: from signal ratio to gain and loss of DNA regions [J].

Hupé, P ;

Stransky, N ;

Thiery, JP ;

Radvanyi, F ;

Barillot, E .

BIOINFORMATICS, 2004, 20 (18) :3413-3422

[4] Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data [J].

Lai, WR ;

Johnson, MD ;

Kucherlapati, R ;

Park, PJ .

BIOINFORMATICS, 2005, 21 (19) :3763-3770

[5] Efficient calculation of interval scores for DNA copy number data analysis [J].

Lipson, D ;

Aumann, Y ;

Ben-Dor, A ;

Linial, N ;

Yakhini, Z .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13 (02) :215-228

[6] Circular binary segmentation for the analysis of array-based DNA copy number data [J].

Olshen, AB ;

Venkatraman, ES ;

Lucito, R ;

Wigler, M .

BIOSTATISTICS, 2004, 5 (04) :557-572

[7] A statistical approach for array CGH data analysis [J].

Picard, F ;

Robin, S ;

Lavielle, M ;

Vaisse, C ;

Daudin, JJ .

BMC BIOINFORMATICS, 2005, 6 (1)

[8] High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays [J].

Pinkel, D ;

Seagraves, R ;

Sudar, D ;

Clark, S ;

Poole, I ;

Kowbel, D ;

Collins, C ;

Kuo, WL ;

Chen, C ;

Zhai, Y ;

Dairkee, SH ;

Ljung, BM ;

Gray, JW ;

Albertson, DG .

NATURE GENETICS, 1998, 20 (02) :207-211

[9] Global variation in copy number in the human genome [J].

Redon, Richard ;

Ishikawa, Shumpei ;

Fitch, Karen R. ;

Feuk, Lars ;

Perry, George H. ;

Andrews, T. Daniel ;

Fiegler, Heike ;

Shapero, Michael H. ;

Carson, Andrew R. ;

Chen, Wenwei ;

Cho, Eun Kyung ;

Dallaire, Stephanie ;

Freeman, Jennifer L. ;

Gonzalez, Juan R. ;

Gratacos, Monica ;

Huang, Jing ;

Kalaitzopoulos, Dimitrios ;

Komura, Daisuke ;

MacDonald, Jeffrey R. ;

Marshall, Christian R. ;

Mei, Rui ;

Montgomery, Lyndal ;

Nishimura, Kunihiro ;

Okamura, Kohji ;

Shen, Fan ;

Somerville, Martin J. ;

Tchinda, Joelle ;

Valsesia, Armand ;

Woodwark, Cara ;

Yang, Fengtang ;

Zhang, Junjun ;

Zerjal, Tatiana ;

Zhang, Jane ;

Armengol, Lluis ;

Conrad, Donald F. ;

Estivill, Xavier ;

Tyler-Smith, Chris ;

Carter, Nigel P. ;

Aburatani, Hiroyuki ;

Lee, Charles ;

Jones, Keith W. ;

Scherer, Stephen W. ;

Hurles, Matthew E. .

NATURE, 2006, 444 (7118) :444-454

[10] A comparison study: applying segmentation to array CGH data for downstream analyses [J].

Willenbrock, H ;

Fridlyand, J .

BIOINFORMATICS, 2005, 21 (22) :4084-4091

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