Using aCGH to Expand Your Cytogenetic Research
Using aCGH to Expand Your Cytogenetic Research
A review of High-resolution global profiling of genomic alterations with long oligonucleotide microarray.
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.
Research from Cameron Brennan and others at the Dana Farber Cancer Institute (2004) illustrates the power of oligo aCGH compared to more traditional cytogenetic techniques, such as spectral karyotyping (SKY) and quantitative PCR (qPCR). The group uses Agilent’s Oligo aCGH microarrays to perform detailed, high-resolution, genome-wide array comparative profiling of human and mouse tumors. The group was able to confirm their results that were obtained with oligo aCGH by independent SKY and qPCR analyses. The aCGH platform provides investigators with the immediate capacity to perform consistent DNA analysis of normal and diseased genomes in a global and extremely detailed and precise manner. The superior performance of this higher-resolution platform (over antecedent cDNA platforms) is clearly documented. The study finds that cancer genomes may harbor many focal chromosomal numerical aberrations that have escaped detection until now.
Figure 1. SKY verification of chromosomal numerical aberrations (CNAs) detected by aCGH.
To further validate the CGH data sets and robustness of assay conditions, the independent and highly reliable SKY method was used. The SKY ideogram is on top. The aCGH pseudo-karyotype, on the bottom, is based on segmented data in log2 ratio of the corresponding chromosomes. A. Copy numbers for various chromosomes in an HPAC sample. The green boxes highlight a 10q one-copy gain, where the third copy is translocated to the q arm of chromosome 12. The magenta boxes highlight a 12p amplification, where the fourth copy is translocated to chromosome 11p. B. Copy numbers for various chromosomes in an PANC1 sample. Orange boxes outline three 8q copies and yellow boxes. Yellow boxes highlight a two-copy translocation to chromosome 21.
Figure 2. Real-time qPCR verification of chromosomomal numerical aberrations (CNAs) detected by aCGH.
Real-time PCR was performed to assess the ability of aCGH to accurately and reproducibly report focal CNAs, especially those that may not be detected by SKY’s low-resolving power. Gene dosages detected by aCGH and qPCR in an ASPC1 sample were compared in two locations. Chromosome 7 from 80–110 MB (in A) and Chromosome 9 from 20–40 MB (in B). Raw log2 ratio values for each probe on the microarray are plotted in the left panel. Colored dots correspond to probes interrogating genomic regions assayed by qPCR on the right panel. The histogram bar height represents the relative gene copy numbers in log2 scale as measured by qPCR. The bar and dots of same color are measuring the gene dosage in the same genomic location. This data shows that the aCGH approach provides an accurate and reliable representation.
Title: High-resolution global profiling of genomic alterations with long oligonucleotide microarray.
Authors: Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ, Kim M, Protopopov A, Chin L.
Journal: Cancer Res. 2004 Jul 15;64(14):4744-8.
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