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aCGH copy number data refers to array-based Comparative Genomic Hybridizationdata. Using microarray technology, the fluorescence intensities (of probes) of a target sample and a reference are measured. The copy number alterations can be calculated based on the changes in fluorescence intensities.

 

Data Overview

 

Array-based Comparative Genomic Hybridization (aCGH) is a powerful tool to study copy number alterations (CNA) in human diseases such as cancers. This high-throughput technique allows simultaneous measuring of copy number for thousands of genes throughout the genome. Copy number alterations are measured using log2 ratios of the fluorescence intensities from two channels (Cy3 and Cy5), one for the target sample and the other for the reference sample. For a given gene (or region), a negative log2 ratio is an indication of a loss, and a positive log2 ratio is an indication of a gain. If the log2 ratio equals zero, the target sample and the reference sample have the same copy number for that given gene (or region).

Notice that there are other techniques to generate copy number alteration data such as NextGen sequencing and array based SNP chip.

 

Available Platforms

 

Platform Code

Platform Alias

Platform Name

Available

Available

FTP Display

HG-CGH-415K_G4124A

HG-CGH-415K_G4124A

Agilent Human Genome CGH Custom Microarray 2x415K

YES

Yes

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-415k_g4124a/cna/

HG-CGH-244A  

HG-CGH-244A  

Agilent Human Genome CGH Microarray 244A

YES

Yes

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-244a/cna/

CGH-1x1M_G4447A      

CGH-1x1M_G4447A

Agilent SurePrint G3 Human CGH Microarray

YES

Yes

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
cgh-1x1m_g4447a/cna/

 

Examples of aCGH data files

 

Level 1 Data

Platform

File Extension

Example

FTP Display

HG-CGH-415K_G4124A

.txt

example icon

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hms.harvard.edu/hg-cgh-415k_g4124a/cna

HG-CGH-244A

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-244a/cna

CGH-1x1M_G4447A   

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
cgh-1x1m_g4447a/cna

Level 2 Data

Platform

File Extension

Example

FTP Display

HG-CGH-415K_G4124A

.tsv

example icon

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-415k_g4124a/cna

HG-CGH-244A

.mat

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-244a/cna

CGH-1x1M_G4447A   

.mat

example icon

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
cgh-1x1m_g4447a/cna

Level 3 Data

Platform

File Extension

Example

FTP address

HG-CGH-415K_G4124A

.tsv

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-415k_g4124a/cna

HG-CGH-244A

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-cgh-244a/cna

CGH-1x1M_G4447A   

.txt

example icon

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>
/cgh-1x1m_g4447a/cna

 

Specific Validation

Array CGH based copy number data do not have specific validation. It follows standard validation described below.

Standard Validations

 aCGH data undergo standard validation sets shown in the Standard Archive Validation chart.

MD5 Validation  

Archive Name Validation  

GCC Experiment Checking  

Manifest Validation  

GCC Experiment Validation  

Data Matrix File Validation  

SDRF Validation  

IDF Validation  

 

 

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