{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T15:37:08Z","timestamp":1770824228229,"version":"3.50.1"},"reference-count":35,"publisher":"Archives of Pathology and Laboratory Medicine","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Context.\u2014Renal epithelial neoplasms have characteristic chromosomal imbalances, and we have shown previously that virtual karyotypes derived from single-nucleotide polymorphism microarrays can be performed on formalin-fixed, paraffin-embedded tissue.<\/jats:p>\n                  <jats:p>Objective.\u2014To perform a direct comparison of virtual and conventional karyotypes to evaluate concordance of results.<\/jats:p>\n                  <jats:p>Design.\u2014Twenty 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.<\/jats:p>\n                  <jats:p>Results.\u2014Nineteen 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.<\/jats:p>\n                  <jats:p>Conclusions.\u2014Our 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.<\/jats:p>","DOI":"10.5858\/133.12.1917","type":"journal-article","created":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T09:05:13Z","timestamp":1613120713000},"page":"1917-1922","source":"Crossref","is-referenced-by-count":12,"title":["Detection of Chromosomal Aberrations in Renal Tumors: A Comparative Study of Conventional Cytogenetics and Virtual Karyotyping With Single-Nucleotide Polymorphism Microarrays"],"prefix":"10.5858","volume":"133","author":[{"given":"Federico A.","family":"Monzon","sequence":"first","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karla","family":"Alvarez","sequence":"additional","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zoran","family":"Gatalica","sequence":"additional","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia A.","family":"Bridge","sequence":"additional","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marilu","family":"Nelson","sequence":"additional","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyun-Jung","family":"Kim","sequence":"additional","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jill M.","family":"Hagenkord","sequence":"additional","affiliation":[{"name":"From the Department of Pathology (Drs Monzon and Kim and Ms Alvarez), The Methodist Hospital Research Institute, The Methodist Hospital, Houston, Texas; Weill Cornell Medical College, New York, New York (Dr Monzon); the Department of Pathology, Creighton University Medical Center, Omaha, Nebraska (Drs Gatalica and Hagenkord); the Department of Pathology, University of Nebraska Medical Center, Oma"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"3906","reference":[{"key":"2021021102104594500_i1543-2165-133-12-1917-b1","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1056\/NEJM199609193351207","article-title":"Renal-cell carcinoma.","volume":"335","author":"Motzer","year":"1996","journal-title":"N Engl J Med"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b2","article-title":"Kidney: renal cell carcinoma. Atlas Genet Cytogenet Oncol Haematol. June 2003.","author":"van den Berg"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1038\/modpathol.3800286","article-title":"Eosinophilic and classic chromophobe renal cell carcinomas have similar frequent losses of multiple chromosomes from among chromosomes 1, 2, 6, 10, and 17, and this pattern of genetic abnormality is not present in renal oncocytoma.","volume":"18","author":"Brunelli","year":"2005","journal-title":"Mod Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b4","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1002\/path.2239","article-title":"High-resolution analysis of DNA copy number alterations and gene expression in renal clear cell carcinoma.","volume":"213","author":"Yoshimoto","year":"2007","journal-title":"J Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/modpathol.2008.20","article-title":"Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors.","volume":"21","author":"Monzon","year":"2008","journal-title":"Mod Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b6","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1309\/KC2465ANDWVAXYDM","article-title":"Analysis of chromosome 1p abnormalities in renal oncocytomas by loss of heterozygosity studies: correlation with conventional cytogenetics and fluorescence in situ hybridization.","volume":"129","author":"Picken","year":"2008","journal-title":"Am J Clin Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b7","doi-asserted-by":"crossref","first-page":"528","DOI":"10.2353\/jmoldx.2006.060029","article-title":"Application of array-based comparative genomic hybridization to clinical diagnostics.","volume":"8","author":"Bejjani","year":"2006","journal-title":"J Mol Diagn"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b8","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1136\/jmg.2004.022855","article-title":"Molecular karyotyping using an SNP array for genomewide genotyping.","volume":"41","author":"Rauch","year":"2004","journal-title":"J Med Genet"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b9","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/humu.20424","article-title":"Deletion mapping in Xp21 for patients with complex glycerol kinase deficiency using SNP mapping arrays.","volume":"28","author":"Stanczak","year":"2007","journal-title":"Hum Mutat"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b10","doi-asserted-by":"crossref","first-page":"2063","DOI":"10.1002\/ajmg.a.31416","article-title":"Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation.","volume":"140","author":"Rauch","year":"2006","journal-title":"Am J Med Genet A"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/dnares\/dsm002","article-title":"Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.","volume":"14","author":"Hehir-Kwa","year":"2007","journal-title":"DNA Res"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b12","doi-asserted-by":"crossref","first-page":"e1225","DOI":"10.1371\/journal.pone.0001225","article-title":"SNP array karyotyping allows for the detection of uniparental disomy and cryptic chromosomal abnormalities in MDS\/MPD-U and MPD.","volume":"2","author":"Gondek","year":"2007","journal-title":"PLoS ONE"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b13","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1002\/gcc.20524","article-title":"Comprehensive analysis of loss of heterozygosity events in glioblastoma using the 100K SNP mapping arrays and comparison with copy number abnormalities defined by BAC array comparative genomic hybridization.","volume":"47","author":"Lo","year":"2008","journal-title":"Genes Chromosomes Cancer"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b14","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1182\/blood-2007-07-099432","article-title":"Genomic complexity identifies patients with aggressive chronic lymphocytic leukemia.","volume":"112","author":"Kujawski","year":"2008","journal-title":"Blood"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b15","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1002\/cncr.23270","article-title":"Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia.","volume":"112","author":"Lehmann","year":"2008","journal-title":"Cancer"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b16","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1158\/0008-5472.CAN-07-3105","article-title":"Integrated genomic profiling of chronic lymphocytic leukemia identifies subtypes of deletion 13q14.","volume":"68","author":"Ouillette","year":"2008","journal-title":"Cancer Res"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b17","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1097\/PDM.0b013e31815aca30","article-title":"Optimization of the Affymetrix GeneChip mapping 10K 2.0 assay for routine clinical use on formalin fixed paraffin embedded tissues.","volume":"17","author":"Lyons-Weiler","year":"2008","journal-title":"Diagn Mol Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b18","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1746-1596-3-44","article-title":"Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors.","volume":"3","author":"Hagenkord","year":"2008","journal-title":"Diagn Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b19","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b20","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1038\/modpathol.3800090","article-title":"Cytogenetic and molecular cytogenetic findings in 43 aneurysmal bone cysts: aberrations of 17p mapped to 17p13.2 by fluorescence in situ hybridization.","volume":"17","author":"Althof","year":"2004","journal-title":"Mod Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b21","article-title":"ISCN 2005: An International System for Human Cytogenetic Nomenclature (2005): Recommendations of the International Standing Committee on Human Cytogenetic Nomenclature.","author":"Shaffer"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b22","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1002\/humu.20220","article-title":"Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue.","volume":"26","author":"Thompson","year":"2005","journal-title":"Hum Mutat"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b23","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1158\/0008-5472.CAN-06-3597","article-title":"Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays.","volume":"67","author":"Jacobs","year":"2007","journal-title":"Cancer Res"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b24","doi-asserted-by":"crossref","first-page":"6071","DOI":"10.1158\/0008-5472.CAN-05-0465","article-title":"A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays.","volume":"65","author":"Nannya","year":"2005","journal-title":"Cancer Res"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/modpathol.3800967","article-title":"Loss of chromosome 9p is an independent prognostic factor in patients with clear cell renal cell carcinoma.","volume":"21","author":"Brunelli","year":"2008","journal-title":"Mod Pathology"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b26","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1002\/path.1165","article-title":"Chromosome 14q LOH in localized clear cell renal cell carcinoma.","volume":"198","author":"Mitsumori","year":"2002","journal-title":"J Pathol"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b27","article-title":"Molecular Genetic Testing in Surgical Pathology.","author":"Pfeifer"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b28","doi-asserted-by":"crossref","article-title":"Cytogenetics of solid tumors.","author":"Fletcher","DOI":"10.1385\/1-59259-833-1:421"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b29","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/S0165-4608(00)00417-9","article-title":"Cytogenetic characterization of Ewing tumors using fine needle aspiration samples: a 10-year experience and review of the literature.","volume":"127","author":"Udayakumar","year":"2001","journal-title":"Cancer Genet Cytogenet"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b30","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1002\/1097-0142(19870201)59:3<387::AID-CNCR2820590306>3.0.CO;2-X","article-title":"The cytogenetics of solid tumors: relation to diagnosis, classification and pathology.","volume":"59","author":"Sandberg","year":"1987","journal-title":"Cancer"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b31","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/s00776-007-1215-1","article-title":"Advantages and limitations of cytogenetic, molecular cytogenetic, and molecular diagnostic testing in mesenchymal neoplasms.","volume":"13","author":"Bridge","year":"2008","journal-title":"J Orthop Sci"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b32","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/BF00210747","article-title":"Significance of the clonal and sporadic chromosome abnormalities in non-neoplastic renal tissue.","volume":"90","author":"Casalone","year":"1992","journal-title":"Hum Genet"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b33","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/BF00209393","article-title":"Trisomy 7 in non-neoplastic tubular epithelial cells of the kidney.","volume":"95","author":"Knuutila","year":"1995","journal-title":"Hum Genet"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b34","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/0165-4608(95)00035-6","article-title":"Chromosomal abnormalities in non-neoplastic renal tissue.","volume":"85","author":"van den Berg","year":"1995","journal-title":"Cancer Genet Cytogenet"},{"key":"2021021102104594500_i1543-2165-133-12-1917-b35","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1080\/01913120801897141","article-title":"Contribution of cytogenetics to the management of poorly differentiated sarcomas.","volume":"32","author":"Bridge","year":"2008","journal-title":"Ultrastruct Pathol"}],"container-title":["Archives of Pathology &amp; Laboratory Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/meridian.allenpress.com\/aplm\/article-pdf\/133\/12\/1917\/2766711\/1543-2165-133_12_1917.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/meridian.allenpress.com\/aplm\/article-pdf\/133\/12\/1917\/2766711\/1543-2165-133_12_1917.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T19:34:27Z","timestamp":1764790467000},"score":1,"resource":{"primary":{"URL":"https:\/\/aplm.kglmeridian.com\/view\/journals\/arpa\/133\/12\/article-p1917.xml"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12,1]]},"references-count":35,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2009,12,1]]}},"URL":"https:\/\/doi.org\/10.5858\/133.12.1917","relation":{},"ISSN":["1543-2165","0003-9985"],"issn-type":[{"value":"1543-2165","type":"electronic"},{"value":"0003-9985","type":"print"}],"subject":[],"published":{"date-parts":[[2009,12,1]]}}}