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Computational methods for the analysis of array comparative genomic hybridization.

作者信息

Chari Raj, Lockwood William W, Lam Wan L

机构信息

Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3.

出版信息

Cancer Inform. 2007 Feb 10;2:48-58.

DOI:
PMID:17992253
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2067254/
Abstract

Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/dbb6b29bf93a/CIN-02-48-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/8fe117dae7b7/CIN-02-48-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/ba9aa1d92dd4/CIN-02-48-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/f44085081f7d/CIN-02-48-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/e13ffcc8bca6/CIN-02-48-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/5525d057cd4c/CIN-02-48-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/dbb6b29bf93a/CIN-02-48-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/8fe117dae7b7/CIN-02-48-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/ba9aa1d92dd4/CIN-02-48-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/f44085081f7d/CIN-02-48-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/e13ffcc8bca6/CIN-02-48-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/5525d057cd4c/CIN-02-48-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e693/2675507/dbb6b29bf93a/CIN-02-48-g006.jpg

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[1]
Computational methods for the analysis of array comparative genomic hybridization.

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引用本文的文献

[1]
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PLoS One. 2019-10-16

[2]
A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data.

Adv Bioinformatics. 2012

[3]
A meta-analysis of array-CGH studies implicates antiviral immunity pathways in the development of hepatocellular carcinoma.

PLoS One. 2011-12-12

[4]
aCGH.Spline--an R package for aCGH dye bias normalization.

Bioinformatics. 2011-2-25

[5]
Computational method for estimating DNA copy numbers in normal samples, cancer cell lines, and solid tumors using array comparative genomic hybridization.

J Biomed Biotechnol. 2010

[6]
A double-layered mixture model for the joint analysis of DNA copy number and gene expression data.

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[7]
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Cancer Metastasis Rev. 2010-3

[8]
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[9]
A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes.

BMC Genomics. 2008-1-29

[10]
ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

PLoS One. 2007-8-15

本文引用的文献

[1]
Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer.

Cancer Inform. 2007-2-5

[2]
aCGHViewer: a generic visualization tool for aCGH data.

Cancer Inform. 2006

[3]
Common deletion polymorphisms in the human genome.

Nat Genet. 2006-1

[4]
BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

Nucleic Acids Res. 2006-1-26

[5]
Common deletions and SNPs are in linkage disequilibrium in the human genome.

Nat Genet. 2006-1

[6]
A high-resolution survey of deletion polymorphism in the human genome.

Nat Genet. 2006-1

[7]
A stepwise framework for the normalization of array CGH data.

BMC Bioinformatics. 2005-11-18

[8]
Recent advances in array comparative genomic hybridization technologies and their applications in human genetics.

Eur J Hum Genet. 2006-2

[9]
Identification of disease genes by whole genome CGH arrays.

Hum Mol Genet. 2005-10-15

[10]
High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH.

Int J Cancer. 2006-3-15

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