SNP-based arrays complement classic cytogenetics in the detection of chromosomal aberrations in Wilms' tumor

Reena Rahayu Md Zain, Kym Pham, Murch Ashleigh, David Ravine, Paul Waring, Adrian Charles

Research output: Contribution to journalArticle

8 Citations (Scopus)

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 2.7. M 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.

Original languageEnglish
Pages (from-to)80-93
Number of pages14
JournalCancer genetics
Volume205
Issue number3
DOIs
Publication statusPublished - Mar 2012
Externally publishedYes

Fingerprint

Wilms Tumor
Cytogenetics
Chromosome Aberrations
Single Nucleotide Polymorphism
Karyotyping
Loss of Heterozygosity
Uniparental Disomy
Karyotype
Genome
Neoplasms

Keywords

  • Cytogenetics
  • SNP array
  • Wilms' tumors

ASJC Scopus subject areas

  • Cancer Research
  • Genetics
  • Molecular Biology

Cite this

SNP-based arrays complement classic cytogenetics in the detection of chromosomal aberrations in Wilms' tumor. / Md Zain, Reena Rahayu; Pham, Kym; Ashleigh, Murch; Ravine, David; Waring, Paul; Charles, Adrian.

In: Cancer genetics, Vol. 205, No. 3, 03.2012, p. 80-93.

Research output: Contribution to journalArticle

Md Zain, Reena Rahayu ; Pham, Kym ; Ashleigh, Murch ; Ravine, David ; Waring, Paul ; Charles, Adrian. / SNP-based arrays complement classic cytogenetics in the detection of chromosomal aberrations in Wilms' tumor. In: Cancer genetics. 2012 ; Vol. 205, No. 3. pp. 80-93.
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