Spatial smoothing and hot spot detection for CGH data using the fused lasso

被引：249

作者：

Tibshirani, Robert ^{[1
,2
]}

Wang, Pei ^{[3
]}

机构：

[1] Stanford Univ, Dept Hlth Res & Policy, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Biostat, Stanford, CA 94305 USA

[3] Fred Hutchinson Canc Res Ctr, Seattle, WA 98109 USA

来源：

BIOSTATISTICS | 2008年 / 9卷 / 01期

关键词：

DNA copy number; Signal detection;

D O I：

10.1093/biostatistics/kxm013

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We apply the "fused lasso" regression method of Tibshirani and others (2004) to the problem of "hotspot detection", in particular, detection of regions of gain or loss in comparative genomic hybridization (CGH) data. The fused lasso criterion leads to a convex optimization problem, and we provide a fast algorithm for its solution. Estimates of false-discovery rate are also provided. Our studies show that the new method generally outperforms competing methods for calling gains and losses in CGH data.

引用

页码：18 / 29

页数：12

共 19 条

[11] Accurate detection of aneuploidies in array CGH and gene expression microarray data [J].

Myers, CL ;

Dunham, MJ ;

Kung, SY ;

Troyanskaya, OG .

BIOINFORMATICS, 2004, 20 (18) :3533-3543

[12] 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

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

Picard, F ;

Robin, S ;

Lavielle, M ;

Vaisse, C ;

Daudin, JJ .

BMC BIOINFORMATICS, 2005, 6 (1)

[14] Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors [J].

Pollack, JR ;

Sorlie, T ;

Perou, CM ;

Rees, CA ;

Jeffrey, SS ;

Lonning, PE ;

Tibshirani, R ;

Botstein, D ;

Borresen-Dale, AL ;

Brown, PO .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (20) :12963-12968

[15]

Ruppert D., 2003, Semiparametric regression

[16] A direct approach to false discovery rates [J].

Storey, JD .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 2002, 64 :479-498

[17] Sparsity and smoothness via the fused lasso [J].

Tibshirani, R ;

Saunders, M ;

Rosset, S ;

Zhu, J ;

Knight, K .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 2005, 67 :91-108

[18] Regression shrinkage and selection via the Lasso [J].

Tibshirani, R .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1996, 58 (01) :267-288

[19] A method for calling gains and losses in array CGH data [J].

Wang, P ;

Kim, Y ;

Pollack, J ;

Narasimhan, B ;

Tibshirani, R .

BIOSTATISTICS, 2005, 6 (01) :45-58

← 1 2 →