Clinical utilization of high-resolution single nucleotide polymorphism based oligonucleotide arrays in diagnostic studies of pediatric patients with solid tumors

High-resolution single nucleotide polymorphism (SNP) arrays have been effectively implemented as a first tier test in clinical cytogenetics laboratories for the detection of constitutional chromosomal abnormalities in patients with suspected genomic disorders. We recently published our experience utilizing SNP array analysis of bone marrow aspirates as a clinical test for patients with suspected leukemia or lymphoma in the Clinical Cancer Cytogenetics Laboratory at The Children’s Hospital of Philadelphia. In the present report we summarize our clinical experience using the Illumina HumanHap610 BeadChip array (Illumina, San Diego, CA) for whole genome analysis of pediatric solid tumors. A total of 168 DNA samples isolated from a variety of solid tumors, including brain tumors, sarcomas, neuroblastomas, and Wilms tumors, as well as benign neoplasms and reactive processes, were analyzed over a 2 1/2 year period. One hundred thirty-seven of 168 (82%) specimens had at least one copy number alteration or region of loss of heterozygosity detected by the SNP array. Thirty-three of 168 (20%) of cases had a normal karyotype or targeted fluorescence in situ hybridization (FISH) study, but had an abnormal finding by the array analysis. Sixty-three of 168 (37%) samples for which cytogenetic studies were unsuccessful or not performed demonstrated an abnormal array result. In 44 of 168 cases (26%) the array and karyotype or FISH were abnormal, but each demonstrated alterations not detected by the other methodology. Based on our experience in the last 2 1/2 years, we suggest that SNP array analysis can be used as a first tier clinical test for the majority of pediatric solid tumors.