CGcgh: a tool for molecular karyotyping using DNA microarray-based comparative genomic hybridization (array-CGH).
Microarray-based comparative genomic hybridization (array-CGH) is a technique by which variations in copy numbers between two genomes can be analyzed using DNA microarrays. Array CGH has been used to survey chromosomal amplifications and deletions in fetal aneuploidies or cancer tissues. Herein we report a user-friendly, MATLAB-based, array CGH analyzing program, Chang Gung comparative genomic hybridization (CGcgh), as a standalone PC version. The analyzed chromosomal data are displayed in a graphic interface, and CGcgh allows users to launch a corresponding G-banding ideogram. The abnormal DNA copy numbers (gains and losses) can be identified automatically using a user defined window size (default value is 50 probes) and sequential student t-tests with sliding windows along with chromosomes. CGcgh has been tested in multiple karyotype-confirmed human samples, including five published cases and trisomies 13, 18, 21 and X from our laboratories, and 18 cases of which microarray data are available publicly. CGcgh can be used to detect the copy number changes in small genomic regions, which are commonly encountered by clinical geneticists. CGcgh works well for the data from cDNA microarray, spotted oligonucleotide microarrays, and Affymetrix Human Mapping Arrays (10K, 100K, 500K Array Sets). The program can be freely downloaded from http://www.mcu.edu.tw/department/biotec/en%5Fpage/CGcgh/ .
Lee
Yun-Shien
YS
Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan.
Chao
Angel
A
Chao
An-Shine
AS
Chang
Shuenn-Dyh
SD
Chen
Chun-Houh
CH
Wu
Wei-Ming
WM
Wang
Tzu-Hao
TH
Wang
Hsin-Shih
HS
D000465:Algorithms; D055028:Comparative Genomic Hybridization / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D007621:Karyotyping / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software