Detection of chromosomal aberrations in renal tumors: A comparative study of conventional cytogenetics and virtual karyotyping with single-nucleotide polymorphism microarrays

Federico A. Monzon, Karla Alvarez, Zoran Gatalica, Julia A. Bridge, Marilu Nelson, Hyun Jung Kim, Jill M. Hagenkord

Research output: Contribution to journalArticle

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Abstract

Context. - Renal epithelial neoplasms have characteristic chromosomal imbalances, and we have shown previously that virtual karyotypes derived from single-nucleotide polymorphism microarrays can be performed on formalinfixed, paraffin-embedded tissue. Objective. - To perform a direct comparison of virtual and conventional karyotypes to evaluate concordance of results. Design. - Twenty archival formalin-fixed, paraffin-embedded tumor samples with preexisting, conventional cytogenetic results were analyzed with Affymetrix 10K 2.0 or 250K Nsp single-nucleotide polymorphism microarrays. Results. - Nineteen samples yielded adequate virtual karyotypes for interpretation. Eight samples showed complete agreement between the 2 techniques, and 8 samples showed partial agreement. The disease-defining lesions (eg, loss of 3p for clear cell carcinoma) were identified in all 19 cases by virtual karyotypes and in 15 cases by conventional karyotypes. Virtual and conventional karyotypic findings were concordant in the identification of these disease-defining lesions in 86% (13 of 15) of cases. In 3 cases, virtual karyotypes identified lesions consistent with the morphologic diagnosis, whereas the conventional karyotypes were unsuccessful because of insufficient tumor representation or stromal overgrowth. Two cases with acquired uniparental disomy were identified by single-nucleotide polymorphism arrays, and 5 cases with translocations were identified by conventional karyotype. Conclusions. - Our results show that both techniques are able to identify the characteristic chromosomal abnormality for renal tumor subtypes in most cases. Discrepancies can be explained by inherent limitations of each technique, inadequate tumor sampling, and tumor heterogeneity. We conclude that virtual karyotyping is a robust alternative to conventional cytogenetics for the evaluation of chromosomal anomalies in formalin-fixed, paraffin-embedded tissues from renal epithelial neoplasms.

Original languageEnglish (US)
Pages (from-to)1917-1922
Number of pages6
JournalArchives of Pathology and Laboratory Medicine
Volume133
Issue number12
StatePublished - Dec 1 2009

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Karyotyping
Karyotype
Cytogenetics
Chromosome Aberrations
Single Nucleotide Polymorphism
Kidney
Neoplasms
Paraffin
Glandular and Epithelial Neoplasms
Kidney Neoplasms
Formaldehyde
Uniparental Disomy
Carcinoma

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Medical Laboratory Technology

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Detection of chromosomal aberrations in renal tumors : A comparative study of conventional cytogenetics and virtual karyotyping with single-nucleotide polymorphism microarrays. / Monzon, Federico A.; Alvarez, Karla; Gatalica, Zoran; Bridge, Julia A.; Nelson, Marilu; Kim, Hyun Jung; Hagenkord, Jill M.

In: Archives of Pathology and Laboratory Medicine, Vol. 133, No. 12, 01.12.2009, p. 1917-1922.

Research output: Contribution to journalArticle

Monzon, Federico A. ; Alvarez, Karla ; Gatalica, Zoran ; Bridge, Julia A. ; Nelson, Marilu ; Kim, Hyun Jung ; Hagenkord, Jill M. / Detection of chromosomal aberrations in renal tumors : A comparative study of conventional cytogenetics and virtual karyotyping with single-nucleotide polymorphism microarrays. In: Archives of Pathology and Laboratory Medicine. 2009 ; Vol. 133, No. 12. pp. 1917-1922.
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abstract = "Context. - Renal epithelial neoplasms have characteristic chromosomal imbalances, and we have shown previously that virtual karyotypes derived from single-nucleotide polymorphism microarrays can be performed on formalinfixed, paraffin-embedded tissue. Objective. - To perform a direct comparison of virtual and conventional karyotypes to evaluate concordance of results. Design. - Twenty archival formalin-fixed, paraffin-embedded tumor samples with preexisting, conventional cytogenetic results were analyzed with Affymetrix 10K 2.0 or 250K Nsp single-nucleotide polymorphism microarrays. Results. - Nineteen samples yielded adequate virtual karyotypes for interpretation. Eight samples showed complete agreement between the 2 techniques, and 8 samples showed partial agreement. The disease-defining lesions (eg, loss of 3p for clear cell carcinoma) were identified in all 19 cases by virtual karyotypes and in 15 cases by conventional karyotypes. Virtual and conventional karyotypic findings were concordant in the identification of these disease-defining lesions in 86{\%} (13 of 15) of cases. In 3 cases, virtual karyotypes identified lesions consistent with the morphologic diagnosis, whereas the conventional karyotypes were unsuccessful because of insufficient tumor representation or stromal overgrowth. Two cases with acquired uniparental disomy were identified by single-nucleotide polymorphism arrays, and 5 cases with translocations were identified by conventional karyotype. Conclusions. - Our results show that both techniques are able to identify the characteristic chromosomal abnormality for renal tumor subtypes in most cases. Discrepancies can be explained by inherent limitations of each technique, inadequate tumor sampling, and tumor heterogeneity. We conclude that virtual karyotyping is a robust alternative to conventional cytogenetics for the evaluation of chromosomal anomalies in formalin-fixed, paraffin-embedded tissues from renal epithelial neoplasms.",
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