• Genomics & Informatics
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• v.6 no.3
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• pp.126-129
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• 2008

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.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.1
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• pp.225-229
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• 2012

Background: Males have a higher prevalence of hepatocellular carcinoma (HCC) than females in general, but the reasons for the sex disparity are still obscure. DNA copy number alteration (CNA) is a major feature of solid tumors including HCC, but whether CNA plays a role in sex-related differences in HCC development has never been evaluated. Methods: High-resolution array comparative genomic hybridization (CGH) was used to examine 17 female and 46 male HCC patients with chronic hepatitis B virus (HBV) infection in Shanghai, China. Two-tailed Fisher's exact or ${\chi}^2$ tests was used to compare CNAs between females and males. Results: The overall frequencies and patterns of CNAs in female and male cases were similar. However, female HCC tumors presented more copy number gains compared to those in males on 1q21.3-q22 (76.5% vs. 37.0%, P = 0.009), 11q11 (35.3% vs. 0.0%, P = 0.0002) and 19q13.31-q13.32 (23.5% vs. 0.0%, P = 0.004), and loss on 16p11.2 (35.3% vs. 6.5%, P = 0.009). Relative to females, male cases had greater copy number loss on 11q11 (63.0% vs. 17.6%, P = 0.002). Further analyses showed that 11q11 gain correlated with 19q13.31-q13.32 gain (P = 0.042), 11q11 loss (P = 0.011) and 16p11.2 loss (P = 0.033), while 1q21.3-q22 gain correlated with 19q13.31-q13.32 gain (P = 0.046). Conclusions: These findings suggest that CNAs may play a role in sex-related differences in HBVassociated HCC development.