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== DNA Microarray Platforms ==

== DNA Microarray Platforms ==

Different types of DNA microarray platforms currently available for clinical testing include bacterial artificial chromosome–based array comparative genomic hybridization, oligonucleotide-based array comparative genomic hybridization, oligonucleotide plus single-nucleotide polymorphism (SNP)-based arrays that contain both copy-number (intensity-only) and SNP (allele-differentiating) probes, as well as SNP-only–based arrays.9,24,25,26

Different types of DNA microarray platforms currently available for clinical testing include bacterial artificial chromosome–based array comparative genomic hybridization, oligonucleotide-based array comparative genomic hybridization, oligonucleotide plus single-nucleotide polymorphism (SNP)-based arrays that contain both copy-number (intensity-only) and SNP (allele-differentiating) probes, as well as SNP-only–based arrays [9,24,25,26].

For comparative genomic hybridization–based microarrays, patient DNA and reference DNA are labeled with different fluorochromes and hybridized to probes on the microarray. SNP-based arrays use a single color dye compared with an in silico reference. A scanner measures differences in the intensities of the fluorochromes, and the data are expressed as having more or less signal as compared with the reference. For genomic regions with two copies of the DNA sequence, copy-number data are graphed as a log2 ratio with the expected normal copy number equaling “0.” Duplications will have signals of greater intensity (log2 > 0) and deletions less intensity (log2 < 0). Microarrays that incorporate SNP probes allow simultaneous detection of DNA copy-number changes and absence of heterozygosity (AOH) by providing information about the intensity of the signals at the loci. AOH may be due to LOH, hemizygosity, or homozygosity.

For comparative genomic hybridization–based microarrays, patient DNA and reference DNA are labeled with different fluorochromes and hybridized to probes on the microarray. SNP-based arrays use a single color dye compared with an in silico reference. A scanner measures differences in the intensities of the fluorochromes, and the data are expressed as having more or less signal as compared with the reference. For genomic regions with two copies of the DNA sequence, copy-number data are graphed as a log2 ratio with the expected normal copy number equaling “0.” Duplications will have signals of greater intensity (log2 > 0) and deletions less intensity (log2 < 0). Microarrays that incorporate SNP probes allow simultaneous detection of DNA copy-number changes and absence of heterozygosity (AOH) by providing information about the intensity of the signals at the loci. AOH may be due to LOH, hemizygosity, or homozygosity.