ACGHViewer: a Generic Visualization Tool for ACGH Data

Overview

Journal Cancer Inform

Publisher Sage Publications

Specialty Biomedical Engineering

Date 2007 Apr 4

PMID 17404607

Citations 5

Authors

Ganesh Shankar

Michael R Rossi

Devin E McQuaid

Jeffrey M Conroy

Daniel G Gaile

John K Cowell

Norma J Nowak

Ping Liang

Affiliations

Soon will be listed here.

Abstract

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/.

Citing Articles

Analysis of wilms tumors using SNP mapping array-based comparative genomic hybridization.

Hawthorn L, Cowell J PLoS One. 2011; 6(4):e18941.

PMID: 21544195 PMC: 3081321. DOI: 10.1371/journal.pone.0018941.

CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.

Lee M, Kim Y BMC Bioinformatics. 2009; 10:424.

PMID: 20003544 PMC: 2801522. DOI: 10.1186/1471-2105-10-424.

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

Gu J, Wei M, Rao P, Lau C, Behl S, Man T Gene Regul Syst Bio. 2009; 1:131-6.

PMID: 19936083 PMC: 2759124.

Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to perform comparisons of data derived from different microarray platforms.

Lo K, Shankar G, Turpaz Y, Bailey D, Rossi M, Burkhardt T Cancer Inform. 2009; 3:307-19.

PMID: 19455250 PMC: 2675835.

Computational methods for the analysis of array comparative genomic hybridization.

Chari R, Lockwood W, Lam W Cancer Inform. 2007; 2:48-58.

PMID: 17992253 PMC: 2067254.

References

Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K . arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics. 2005; 6:124. PMC: 1173083. DOI: 10.1186/1471-2105-6-124. View

Deeb G, Baer M, Gaile D, Jani Sait S, Barcos M, Wetzler M . Genomic profiling of myeloid sarcoma by array comparative genomic hybridization. Genes Chromosomes Cancer. 2005; 44(4):373-83. DOI: 10.1002/gcc.20239. View

Miliaras D, Grimbizis G, Conroy J, Psarra N, Miliaras S, Nowak N . Novel karyotypic changes detected by comparative genomic hybridization in a case of congenital cervical immature teratoma. Birth Defects Res A Clin Mol Teratol. 2005; 73(8):572-6. DOI: 10.1002/bdra.20152. View

Margolin A, Greshock J, Naylor T, Mosse Y, Maris J, Bignell G . CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics. 2005; 21(15):3308-11. DOI: 10.1093/bioinformatics/bti500. View

Locke D, Segraves R, Carbone L, Archidiacono N, Albertson D, Pinkel D . Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res. 2003; 13(3):347-57. PMC: 430292. DOI: 10.1101/gr.1003303. View

Pinkel D, Albertson D . Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005; 37 Suppl:S11-7. DOI: 10.1038/ng1569. View

Jong K, Marchiori E, Meijer G, Vaart A, Ylstra B . Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics. 2004; 20(18):3636-7. DOI: 10.1093/bioinformatics/bth355. View

Cowell J, Matsui S, Wang Y, LaDuca J, Conroy J, McQuaid D . Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme. Cancer Genet Cytogenet. 2004; 151(1):36-51. DOI: 10.1016/j.cancergencyto.2003.09.012. View

Daruwala R, Rudra A, Ostrer H, Lucito R, Wigler M, Mishra B . A versatile statistical analysis algorithm to detect genome copy number variation. Proc Natl Acad Sci U S A. 2004; 101(46):16292-7. PMC: 528962. DOI: 10.1073/pnas.0407247101. View

10.

Awad I, Rees C, Hernandez-Boussard T, Ball C, Sherlock G . Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics. 2004; 5:151. PMC: 528725. DOI: 10.1186/1471-2105-5-151. View

11.

Rossi M, La Duca J, Matsui S, Nowak N, Hawthorn L, Cowell J . Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme. Genes Chromosomes Cancer. 2005; 44(4):392-404. DOI: 10.1002/gcc.20256. View

12.

Ching T, Maunakea A, Jun P, Hong C, Zardo G, Pinkel D . Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet. 2005; 37(6):645-51. DOI: 10.1038/ng1563. View

13.

Nowak N, Gaile D, Conroy J, McQuaid D, Cowell J, Carter R . Genome-wide aberrations in pancreatic adenocarcinoma. Cancer Genet Cytogenet. 2005; 161(1):36-50. DOI: 10.1016/j.cancergencyto.2005.01.009. View

14.

Wang J, Meza-Zepeda L, Kresse S, Myklebost O . M-CGH: analysing microarray-based CGH experiments. BMC Bioinformatics. 2004; 5:74. PMC: 446184. DOI: 10.1186/1471-2105-5-74. View

15.

Myers C, Chen X, Troyanskaya O . Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinformatics. 2005; 6:146. PMC: 1181623. DOI: 10.1186/1471-2105-6-146. View

16.

Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N . TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003; 34(2):374-8. DOI: 10.2144/03342mt01. View

17.

Snijders A, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J . Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001; 29(3):263-4. DOI: 10.1038/ng754. View

18.

Wang P, Kim Y, Pollack J, Narasimhan B, Tibshirani R . A method for calling gains and losses in array CGH data. Biostatistics. 2004; 6(1):45-58. DOI: 10.1093/biostatistics/kxh017. View

19.

Hupe P, Stransky N, Thiery J, Radvanyi F, Barillot E . Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics. 2004; 20(18):3413-22. DOI: 10.1093/bioinformatics/bth418. View

20.

Eilers P, de Menezes R . Quantile smoothing of array CGH data. Bioinformatics. 2004; 21(7):1146-53. DOI: 10.1093/bioinformatics/bti148. View