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November 01, 2010 (Vol. 30, No. 19)

Improving LOH Detection on CGH Microarrays

Technology Strives to Bypass a Number of Limitations of Current Products

  • Due to its higher resolution, oligo array CGH has recently made strong inroads in the cytogenetic lab. It’s not surprising. With an increased sensitivity of more than 1,000-fold, microarrays can detect much smaller genetic aberrations—microduplications and microdeletions—that may be linked to abnormal phenotypes and diseases than can karyotype analysis.

    As basic research studies revealing the role of varied chromosomal aberrations in susceptibility to diseases like autism, mental retardation, and developmental delays continue to amass, cytogenetic researchers are beginning to understand the need to detect more and smaller changes.

    One problem, however, with array CGH microarrays is that they only detect copy-number changes, since they measure total copies of alleles present in a sample. Copy-neutral changes such as loss of heterozygosity (LOH), uniparental disomy (UPD), and consanguinity, as well as balanced translocations, go undetected. 

    During cell division, recombination between chromosomes might occur, resulting in material exchange with maintenance of the copy number. One of the resulting possibilities is UPD, where a person inherits two copies of a chromosome pair from one parent and no copy from the other parent. If the chromosomes involved are imprinted such that the genes on these chromosomes are monoallelically active (i.e., only the maternal or paternal allele of the pair is expressed), the resulting phenotype may be abnormal. UPD in tumor cells is often referred to as acquired UPD or copy-neutral LOH (cnLOH). Copy-neutral LOH is common in both hematologic and solid tumors.

    Being able to detect copy-neutral and copy-number changes simultaneously would go a long way toward improving upon current efforts to create detailed genomic profiles of disease susceptibility and disease states.

    Agilent Technologies’  new SurePrint G3 CGH+SNP microarray was designed to overcome the limitations of current array CGH microarrays. It allows cytogenetic researchers to detect both copy-number and copy-neutral chromosomal changes using one microarray. The same labeling and hybridization assay can be used, and an algorithm has been incorporated into Agilent Genomic Workbench 6.5 software to report both copy-number and copy-neutral changes.

    The basis of Agilent’s new array is the inclusion of both CGH and SNP probes. Like with Agilent’s SurePrint CGH microarrays, the CGH probes measure the total number of alleles in a chromosomal region. The SNP probes, however, make it possible to measure copy-neutral, allele-specific changes.

    Using a restriction fragment enzymatic digestion assay, SNPs located in the enzymes’ recognition site can be genotyped. Regions of copy-neutral LOH or UPD are then located by identifying genomic regions with a scarcity of heterozygous SNP calls.

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