Karyotyping of comparative genomic hybridization human metaphases by using support vector machines.
BACKGROUND
Comparative genomic hybridization (CGH) is a relatively new molecular cytogenetic method for detecting chromosomal imbalance. Karyotyping of human metaphases is an important step to assign each chromosome to one of 23 or 24 classes (22 autosomes and two sex chromosomes). Automatic karyotyping in CGH analysis is needed. However, conventional karyotyping approaches based on DAPI images require complex image enhancement procedures.


METHODS
This paper proposes a simple feature extraction method, one that generates density profiles from original true color CGH images and uses normalized profiles as feature vectors without quantization. A classifier is developed by using support vector machine (SVM). It has good generalization ability and needs only limited training samples.


RESULTS
Experiment results show that the feature extraction method of using color information in CGH images can improve greatly the classification success rate. The SVM classifier is able to acquire knowledge about human chromosomes from relatively few samples and has good generalization ability. A success rate of moe than 90% has been achieved and the time for training and testing is very short.


CONCLUSIONS
The feature extraction method proposed here and the SVM-based classifier offer a promising computerized intelligent system for automatic karyotyping of CGH human chromosomes.
Kou
Zhenzhen
Z
Department of Automation, Tsinghua University, Beijing, Peoples Republic of China.
Ji
Liang
L
Zhang
Xuegong
X
D002877:Chromosomes, Human / Q000145:classification*; D006801:Humans; D019044:Image Cytometry / Q000379:methods*; D007091:Image Processing, Computer-Assisted; D007621:Karyotyping / Q000379:methods*; D009693:Nucleic Acid Hybridization