Comparative Genomic Hybridization to Dna Microarrays

1997 ◽  
Vol 3 (S2) ◽  
pp. 205-206
Author(s):  
D. Pinkel ◽  
R. Segraves ◽  
D. Sudar ◽  
L. van Vliet ◽  
S. Clark ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Dna Microarrays ◽  
Suppressor Gene ◽  
Comparative Genomic ◽  
Cancer Genes ◽  
Genomic Hybridization ◽  
Metaphase Chromosomes ◽  
Number Variation ◽  
Genetic Events

Comparative genomic hybridization (CGH), which involves the simultaneous hybridization of differentially labeled total genomic DNA from test cells and reference normal cells to metaphase chromosomes, has been used extensively to screen tumor genomes for regions of DNA sequence copy number variation. Analysis of these hybridizations requires quantitative analysis of the ratio of intensities of the fluorescent hybridization signals as a function of position along the chromosomes, which basically serve as a convenient genetic map. The ratios need to be measured very accurately since changes of about ± 20% from the average for the genome indicate important genetic events. Widespread use of CGH over the past several years has identified numerous regions of the genome that may contain currently unknown cancer genes. For example, regions of increased copy number may indicate sites of oncogenes, while regions of copy number decrease relative to average for the genome may signify the presence of a tumor suppressor gene.

Array-based comparative genomic hybridization and copy number variation in cancer research

2006 ◽  
Vol 115 (3-4) ◽  
pp. 262-272 ◽  
Author(s):  
E.K. Cho ◽  
J. Tchinda ◽  
J.L. Freeman ◽  
Y.-J. Chung ◽  
W.W. Cai ◽  
...  
Keyword(s):  
Cancer Research ◽  
Copy Number Variation ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation

scholarly journals Measurement of DNA sequence copy number variation using comparative genomic hybridization to microarrays

10.1038/14259 ◽  
1999 ◽  
Vol 23 (S3) ◽  
pp. 30-30
Author(s):  
D.G. Albertson ◽  
R. Segraves ◽  
B. Huey ◽  
X. Zhang ◽  
J. Palmer ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Dna Sequence ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation

scholarly journals Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization

2007 ◽  
Vol 8 (10) ◽  
pp. R228 ◽  
Author(s):  
John C Marioni ◽  
Natalie P Thorne ◽  
Armand Valsesia ◽  
Tomas Fitzgerald ◽  
Richard Redon ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation ◽  
The Waves

Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization

2014 ◽  
Vol 22 (1) ◽  
pp. 59-70 ◽  
Author(s):  
Benjamin M. Skinner ◽  
Abdullah Al Mutery ◽  
Deborah Smith ◽  
Martin Völker ◽  
Nilofour Hojjat ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation ◽  
Global Patterns

scholarly journals A tiling array-based comparative genomic hybridization approach to predict copy number variations between Plasmodium falciparum field isolates from the Indian Sub-continent

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1033
Author(s):  
Isha Pandey ◽  
Ramandeep Kaur ◽  
Amit Kumar Subudhi ◽  
P.A Boopathi ◽  
Raja C. Mugasimangalam ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Tiling Array ◽  
Copy Number Variations ◽  
Chromosome 8 ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Pseudouridine Synthase ◽  
Average Probe Spacing ◽  
Number Variation

Background: There are several techniques to analyse copy number variation in both research and clinical settings, such as whole genome amplification (sWGA), SNP arrays and one of the most commonly used techniques, array based comparative genomic hybridization (aCGH). In the latter, copy number comparison is obtained between differentially labelled target and reference DNAs by measuring ratio of fluorescence intensity of probes indicating loss or gain in the chromosomal region. Methods: Here we carry out a comparative analysis between two Plasmodium falciparum parasite isolates (Pf-isolate-2 and Pf-isolate-1) causing malaria using array CGH. The array contains approximately 418,577, 60mer custom-designed probes with an average probe spacing of 56 bp. The significant major variations (amplifications and deletions) copy number variations (CNV) in Pf-isolate-2 (Pf-2) in comparison with Pf-isolate-1 (Pf-1), are reported. Results: CNVs have been seen in all the chromosomes in Pf-2, most of the deletions have been seen mostly in sub-telomeric and telomeric regions of the chromosomes that comprises of variant surface antigen family genes. Apart from the subtelomeric regions other parts of the chromosomes have also shown CNVs. Novel variations ,  like continuous amplification of 28kb region (249817-278491) of chromosome-8, which covers for 3 genes two of which codes for conserved Plasmodium proteins with unknown function (MAL8P1.139, PF08_0122) and tRNA pseudouridine synthase, putative (PF08_0123). Amplifications in regions harboring genes like GTP cyclohydrolase I (GCH-1, PFL1155W) and ribosomal protein, L24, putative (PFL1150C) of chromosome 12 were seen. Conclusion: Other than known variations reported earlier, some novel variations have also been seen in the chromosomes of Pf-2. This is an experimental case study reporting major amplifications and deletions in Pf-isolate-2 in comparison with Pf-isolate-1 using a tiling array based comparative genomic hybridization approach.

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