Detecting copy-neutral LOH in cancer using Agilent SurePrint G3 Cancer CGH+SNP Microarrays Authors

The Agilent SurePrint G3 CGH+SNP microarray platform enables high-resolution CGH analysis, making it a powerful tool for detecting genome-wide copy number and copy-neutral genetic aberrations. Now, the platform has been extended to support hematologic cancer research. Algorithms developed for the concurrent analysis of CGH and SNP probes now support the analysis of samples with the genomic complexity often observed in cancers as a consequence of copy number changes, tumor heterogeneity, and admixtures of tumor and normal cells. In parallel with the algorithm improvements, a cancer-specifi c 4x180K CGH+SNP microarray was designed by the Cancer Cytogenomics Microarray Consortium (CCMC). Here, we used the cancer microarrays to study copy number (CN) and copy-neutral loss of heterozygosity (cnLOH) in aneuploid chronic lymphocytic leukemia (CLL) and constructed a mosaic model to calculate clonal fractions in aberrant samples. We conclude that the new computational methods developed for cancer sample analysis accurately determined the genotypes, total copy numbers, and clonal fractions in aneuploid samples highly mixed with normal cell populations. Detecting copy-neutral LOH in cancer using Agilent SurePrint G3 Cancer CGH+SNP Microarrays