Genomics Inform.  2008 Sep;6(3):126-129.

CGHscape: A Software Framework for the Detection and Visualization of Copy Number Alterations

• Jeong YB
• Kim TM
• Chung YJ

Abstract

The robust identification and comprehensive profiling of copy number alterations (CNAs) is highly challenging. The amount of data obtained from high-throughput technologies such as array-based comparative genomic hybridization is often too large and it is required to develop a comprehensive and versatile tool for the detection and visualization of CNAs in a genome-wide scale. With this respective, we introduce a software framework, CGHscape that was originally developed to explore the CNAs for the study of copy number variation (CNV) or tumor biology. As a standalone program, CGHscape can be easily installed and run in Microsoft Windows platform. With a user-friendly interface, CGHscape provides a method for data smoothing to cope with the intrinsic noise of array data and CNA detection based on SW-ARRAY algorithm. The analysis results can be demonstrated as log2 plots for individual chromosomes or genomic distribution of identified CNAs. With extended applicability, CGHscape can be used for the initial screening and visualization of CNAs facilitating the cataloguing and characterizing chromosomal alterations of a cohort of samples.

Keyword

array-CGH; copy number alteration (CNA); copy number variation (CNV)

MeSH Terms

Biology
Coat Protein Complex I
Cohort Studies
Comparative Genomic Hybridization
Mass Screening
Noise
Phosphatidylethanolamines
Coat Protein Complex I
Phosphatidylethanolamines