HD-CGH Custom Arrays
HD-CGH Custom Arrays
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Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
Scientists studying genetics have long investigated global changes in chromosomal balance. Array-based comparative genomic hybridization (aCGH) has offered researchers an alternative to traditional microscopic-based cytogenetic techniques, enabling the detection of large or focal amplifications and deletions, elucidation of copy number boundaries within the genome, and characterization of chromosomal variations. The power of oligo aCGH stems from enhanced design flexibility and high-definition capabilities combined with full-genome representation by aCGH-specific, optimized probes. You now have the capability to scan genome-wide and then focus on regions of interest for high-definition analysis.
Agilent gives you the power to design custom HD-CGH arrays, offering the highest resolution tiling based on our database of 8 million CGH probes that cover exonic, intronic, and intergenic regions of the genome or using your uploaded probe designs. The custom design process is coupled with world-class technical support, offering insights into design options and processing.
Michael Barret’s group (2004) designed custom CGH arrays as a tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. The array consisted of 4,878 chromosome-X, 3,293 chromosome-18, 7,723 chromosome-17, and 5,464 chromosome-16 60-mer probes. The probes included both coding and noncoding sequences on the chromosomes. Using the custom CGH arrays, the group was able to identify single-copy losses and associated breakpoints, detect and map homozygous deletions, and map and characterize chromosomes with complex rearrangements in aneuploid tumor cells. This research demonstrates that custom oligo aCGH arrays can reproducibly detect genomic lesions including single-copy and homozygous deletions, as well as variable amplicons, even when using whole genomes as targets, poising the technology to serve as a standard tool for research and diagnosis of cancer and genetic disease.
Figure 1. Detection and mapping of single-copy intrachromosomal losses on chromosome 18q with CGH arrays.
(A) The log2 ratios of the 3,293 chromosome-18 probes are plotted as a function of chromosomal position (×10 Mb) for hybridization of the GM50122 18q-cell line to the CGH array using a 50-kb moving average. Regions of loss (green), gain (red), and no change (blue) were color-coded by using a noise model based on six independent hybridizations with samples containing normal chromosome 18 with the CGH array. (B) Localized view of breakpoint region on 18q21.3. Arrows indicate the nucleotide position (59,462,941) of the defined breakpoint in this cell line. The minimum error rate for detection of single-copy deletions of 18q21.3-qtel sequences in GM50122 versus XX hybridizations was 9% for the 637 18q probes that mapped distal to the breakpoint region on the CGH arrays.
Figure 2. Detection of homozygous deletions in HCT116 colon carcinoma cells with CGH arrays.
(A) The log2 ratios of the 5,464 chromosome-16 probes are plotted as a function of chromosomal position using a 50-kb weighted moving average. Regions of loss (green), gain (red), and no change (blue) were color-coded by using a noise model based on eight independent hybridizations with samples containing normal chromosome 16 with the CGH array. The known homozygous deletions at the (1) A2BP1 (16p) and (2) FRA16D (16q) loci are shown. (B and C) Localized view of 16p homozygous deletion (B) and 16q homozygous deletion (C). Also, loss of terminal 16p (3) and duplication of terminal 16q (4) were detected.
Figure 3. Detection of complex chromosome-17 rearrangements in MDA-MB-453 cells with CGH arrays.
The log2 ratios of the 7,723 chromosome-17 probes are plotted as a function of chromosomal position by using a 50-kb weighted moving average. (A) Regions of loss (green), gain (red), and no change (blue) in MDA-MB-453 cells were color-coded by using a noise model based on eight independent hybridizations of samples containing normal chromosome-17. Loss of 17p that spans the TP53 locus (p13.1) was observed. Also, distinct regions of amplification and loss were detected on the q arm. (B) Representative example of log2 ratios for chromosome-17 probes in a 46,XX self/self hybridization.
Original Research Paper:
Title: Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA.
Authors: Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z, Bruhn L, Laderman S.
Journal: Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765–70.
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