title: SNP-based arrays complement classic cytogenetics in the detection of chromosomal aberrations in Wilms' tumor.
abstract: Wilms' tumors have characteristic chromosomal abnormalities, such as the 11p13 deletion, in a subset of cases. This is one of the very few reports comparing single nucleotide polymorphism (SNP) array analysis with conventional karyotyping of Wilms' tumors. A total of 43 frozen tumor samples were analyzed using the Affymetrix Cytogenetics Whole-Genome 2.7M array. The findings from the SNP array analysis were then compared with those from conventional karyotyping. A comparison between SNP array and conventional karyotype findings was possible in 38 of 43 specimens (88.4%). The SNP array and classic cytogenetic results were concordant in 33 of 38 specimens (87%). SNP array analysis was able to support the findings of classic cytogenetics. The SNP array detected regions of loss of heterozygosity (LOH) in 41 of 43 (95%) specimens. However, it did not detect balanced translocations and inversions that were observed by conventional cytogenetics. Our results show that the data generated from these platforms are complementary. The SNP array also detected additional gains and losses as well as regions of LOH with associated disomy, which are likely to represent segmental uniparental disomy. The observed discrepancies can be explained by the inherent limitations of each technique.
authors.affiliation: School of Pathology and Laboratory Medicine, University of Western Australia, QEII Medical Centre, Nedlands, Western Australia. ayureena@gmail.com
authors.forename: Reena
authors.initials: R
authors.lastname: Zin
authors.forename: Kym
authors.initials: K
authors.lastname: Pham
authors.forename: Murch
authors.initials: M
authors.lastname: Ashleigh
authors.forename: David
authors.initials: D
authors.lastname: Ravine
authors.forename: Paul
authors.initials: P
authors.lastname: Waring
authors.forename: Adrian
authors.initials: A
authors.lastname: Charles
mesh_terms: D002869:Chromosome Aberrations; D002872:Chromosome Deletion; D002877:Chromosomes, Human; D002880:Chromosomes, Human, Pair 11; D020732:Cytogenetic Analysis; D005260:Female; D018628:Gene Dosage; D055106:Genome-Wide Association Study; D006801:Humans; D059785:Karyotype; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D024182:Uniparental Disomy; D009396:Wilms Tumor / Q000235:genetics*