Human CGH Arrays
Human CGH 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.
The Agilent platform offers global coverage of native DNA with CGH-specific probes to identify regions of interest. Agilent’s SurePrint inkjet technology ensures high-precision feature placement through base-by-base synthesis and a robust QC process, resulting in superior quality microarrays. Agilent's catalog of CGH formats features predesigned, high-resolution microarrays that enable genome-wide survey and chromosomal profiling. Oligo aCGH probes are selected based on proprietary CGH-optimized algorithms, delivering increased data quality and reproducible aberration detection.
Oligo aCGH technology has enabled scientists to study chromosomal variation with greater accuracy, coverage, and sensitivity than ever before offering a sensitive and flexible alternative to traditional cytogenetic techniques. Oligonucleotide microarrays can enable you to detect large or focal amplifications and deletions, elucidate copy number boundaries within the genome, and characterize chromosomal variations, offering new perspectives on genetically-linked diseases and mechanisms of tumorigenesis.
Michael Barret’s group (2004) examined the efficacy of comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA as an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. As an Agilent laboratory, the group assisted in the optimization of probes for currently available 60-mer human CGH arrays using custom designs containing a higher density of probes that represent unique genomic sequences for selected chromosomes. As with pre-designed human aCGH designs that are currently available, the content of the CGH array was biased toward gene regions, but it also included noncoding regions for chromosome-wide coverage. These arrays were used to explore performance improvements that could be made possible by developing oligonucleotide probe-selection methods specifically for CGH. This research demonstrates how optimization of CGH probes offers a vast improvement over adaptation of gene expression arrays for assessing chromosomal variations.
Figure 1. Detection of copy-number variations in sarcoma tissues with cDNA and oligonucleotide expression arrays.
Log2 ratios are plotted with no moving average as a function of chromosomal position (Mb) for the cDNA (A) and oligonucleotide (B) arrays, showing detection of amplified regions in ST112, ST130, and ST240. The custom cDNA arrays contained PCR products representing 511 clones mapped to chromosome 12. The oligonucleotide-array data plots include ratios from 399 oligonucleotide probes from chromosome 12 that represent unique genomic sequences and had mean signals in the reference channel greater than three standard deviations above the mean of the negative-control feature signals.
Figure 2. Performance of expression and CGH arrays for detecting varying copy numbers of the X chromosome.
Distributions and medians (dashed lines) of logLog2 ratios from X-chromosome oligonucleotide probes in XY/XX (blue), XX/XX (green), XXX/XX (red), XXXX/XX (teal), and XXXXX/XX (purple) hybridizations on expression (A) and CGH (C) arrays. Measured mean (open circles) and median (filled circles) fluorescence ratios of X-chromosome probes are plotted versus theoretical ratios for the expression (B) and CGH (D) arrays. Median fluorescence ratios were as follows: 0.7 (XY/XX), 1.0 (XX/XX), 1.1 (XXX/XX), 1.3 (XXXX/XX), and 1.7 (XXXXX/XX) for the expression array; and 0.5 (XY/XX), 1.0 (XX/XX), 1.4 (XXX/XX), 2.1 (XXXX/XX), and 2.6 (XXXXXXX) for the CGH arrays. The expression arrays contain 644 X-chromosome probes designed for transcriptional analysis. A total of 269 of these X-chromosome probes failed the homology filter, and another two X-chromosome probes failed the low-signal filter. CGH array plots include all of the 4,878 chromosome-X probes on these arrays. The minimum error rate for detection of single copy deletions of X-chromosome sequences in XY versus XX hybridizations was 21% for the 373 filtered X-chromosome probes on the expression arrays and 5% for the 4,878 X-chromosome probes on the CGH arrays.
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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Human Genome CGH 244A a high-resolution tool for genome-wide DNA variation profiling without amplification or complexity reduction that features comprehensive probe coverage spanning both coding and noncoding regions on a 244K array
For detailed specifications and ordering information visit agilent.com
Human Genome CGH 105A a similar tool to the 244A array with the flexibility to run two samples on a single 105K chip, significantly reducing costs
For detailed specifications and ordering information visit agilent.com