COMPUTER IMAGE-ANALYSIS OF COMPARATIVE GENOMIC HYBRIDIZATION

被引:220
作者
PIPER, J
RUTOVITZ, D
SUDAR, D
KALLIONIEMI, A
KALLIONIEMI, OP
WALDMAN, FM
GRAY, JW
PINKEL, D
机构
[1] UNIV CALIF SAN FRANCISCO,DEPT LAB MED,DIV MOLEC CYTOMETRY,SAN FRANCISCO,CA 94143
[2] WESTERN GEN HOSP,MRC,HUMAN GENET UNIT,EDINBURGH EH4 2XU,MIDLOTHIAN,SCOTLAND
[3] UNIV TAMPERE,DEPT BIOMED SCI,SF-33101 TAMPERE,FINLAND
[4] TAMPERE UNIV HOSP,DEPT LAB MED,CANC GENET LAB,SF-33521 TAMPERE,FINLAND
[5] UNIV CALIF BERKELEY,LAWRENCE BERKELEY LAB,BERKELEY,CA 94720
来源
CYTOMETRY | 1995年 / 19卷 / 01期
关键词
AMPLIFICATION; BACKGROUND CORRECTION; DELETION; FLUORESCENCE IN SITU HYBRIDIZATION; GENOMIC DNA; IMAGE ANALYSIS; MOLECULAR CYTOGENETICS; INTENSITY PROFILE; RATIO PROFILE; SIMULATION; TUMOR CYTOGENETICS;
D O I
10.1002/cyto.990190104
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We describe and evaluate the image-processing and analysis techniques we have developed for the quantitative analysis of comparative genomic hybridization (CGH; Science 258:818, 1992), In a typical CGH application, two genomic DNA samples are simultaneously hybridized to metaphase chromosomes and detected with different fluorochromes. The primary data in CGH are contained in the intensity ratios of the fluorochromes as a function of position on the chromosomes, which reflect variation in DNA copy number ratio between the two DNA samples. Analysis involves chromosome segmentation, intensity normalization, background corrections, and calculation of the fluorescence intensity profiles and the ratio profile along the chromosome's length. Profiles from several copies of the same chromosome in different metaphases are averaged to reduce the noise, Confidence intervals are calculated and displayed for the mean profiles, The techniques were evaluated by examining the variability found in comparisons of two normal genomic DNAs, where the ratio was expected to be constant, and by measuring the ratios obtained for cell Lines with cytogenetically documented copy number changes involving several chromosomal segments. The Limits of sensitivity of CGH analysis were investigated by simulation. Guidelines for the interpretation of CGH data and indications of areas for future development of the analytical techniques are also presented. (C) 1995 Wiley-Liss, Inc.
引用
收藏
页码:10 / 26
页数:17
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