Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues

Diagnostic Molecular Pathology

Volumn 19, Issue 3, 2010, Pages 127-134

  Alvarez, Karla ^a   Kash, Shera F ^b   Lyons Weiler, Maureen A ^c   Kim, Hyun Jung ^a,d   Peterson, Leif E ^a   Mathai, Benita ^a   Hagenkord, Jill M ^b   Monzon, Federico A ^a,d,e  

^a HOUSTON METHODIST HOSPITAL   (United States)

^b CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF PITTSBURGH   (United States)

^d WEILL CORNELL MEDICAL COLLEGE   (United States)

^e Inje University College of Medicine   (South Korea)

Author keywords

chromosomal imbalance; FFPE; formalin fixed; SNP array; virtual karyotype

Indexed keywords

PARAFFIN;

ARTICLE; CHROMOSOME ABERRATION; GENE MAPPING; HETEROZYGOSITY LOSS; HUMAN; HUMAN TISSUE; IN SITU HYBRIDIZATION; KARYOTYPING; LABORATORY TEST; PRIORITY JOURNAL; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY;

ADOLESCENT; ANEUPLOIDY; CHILD; CHILD, PRESCHOOL; FIXATIVES; FORMALDEHYDE; HUMANS; INFANT; KARYOTYPING; MICROARRAY ANALYSIS; NEOPLASMS; PARAFFIN EMBEDDING; PATHOLOGY, MOLECULAR; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SPECIMEN HANDLING; TISSUE PRESERVATION;

EID: 77956255375     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/PDM.0b013e3181d527c5     Document Type: Article

References (30)

1. Mertens F, Johansson B, Hoglund M, et al. Chromosomal imbalance maps of malignant solid tumors: a cytogenetic survey of 3185 neoplasms. Cancer Res. 1997;57:2765-2780.
2. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7:85-97.
3. Greshock J, Feng B, Nogueira C, et al. A comparison of DNA copy number profiling platforms. Cancer Res. 2007;67:10173-10180.
4. Hehir-Kwa JY, Egmont-Petersen M, Janssen IM, et al. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleo-tide microarrays: a platform comparison based on statistical power analysis. DNA Res. 2007;14:1-11.
5. Bridge JA. Advantages and limitations of cytogenetic, molecular cytogenetic, and molecular diagnostic testing in mesenchymal neoplasms. J Orthop Sci. 2008;13:273-282.
6. Beaudet AL, Belmont JW. Array-based DNA diagnostics: let the revolution begin. Annu Rev Med. 2008;59:113-129.
7. Gibbs JR, Singleton A. Application of genome-wide single nucleo-tide polymorphism typing: simple association and beyond. PLoS Genet. 2006;2:e150.
8. Kamath BM, Thiel BD, Gai X, et al. SNP array mapping of chromosome 20p deletions: genotypes, phenotypes, and copy number variation. Hum Mutat. 2009;30:371-378.
9. Rauch A, Ruschendorf F, Huang J, et al. Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet. 2004;41:916-922.
10. Hagenkord JM, Chang CC. The rewards and challenges of array-based karyotyping for clinical oncology applications. Leukemia. 2009;23:829-833.
11. Hagenkord JM, Parwani AV, Lyons-Weiler MA, et al. Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors. Diagn Pathol. 2008;3:44.
12. Kim HJ, Shen SS, Ayala AG, et al. Virtual-karyotyping with SNP microarrays in morphologically challenging renal cell neoplasms: a practical and useful diagnostic modality. Am J Surg Pathol. 2009; 33:1276-1286.
13. Monzon FA, Hagenkord JM, Lyons-Weiler MA, et al. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Mod Pathol. 2008;21:599-608.
14. Lyons-Weiler M, Hagenkord J, Sciulli CM, et al. Optimization of the Affymetrix GeneChip mapping 10K 2.0 assay for routine clinical use on formalin fixed paraffin embedded tissues. Diagn Mol Pathol. 2008;17:3-13.
15. Jacobs S, Thompson ER, Nannya Y, et al. Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. Cancer Res. 2007;67:2544-2551.
16. Nannya Y, Sanada M, Nakazaki K, et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 2005;65:6071-6079.
17. Yamamoto G, Nannya Y, Kato M, et al. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays. Am J Hum Genet. 2007;81:114-126.
18. Monzon FA, Alvarez K, Gatalica Z, et al. Detection of chromosomal aberrations in renal tumors: a comparative study of conventional cytogenetics and virtual karyotyping with SNP microarrays. Arch Pathol Lab Med. 2009;133:1917-1922.
19. Barbashina V, Salazar P, Holland EC, et al. Allelic losses at 1p36 and 19q13 in gliomas: correlation with histologic classification, definition of a 150-kb minimal deleted region on 1p36, and evaluation of CAMTA1 as a candidate tumor suppressor gene. Clin Cancer Res. 2005;11:1119-1128.
20. Grundy PE BN, Li S, Perlman E, et al. Loss of heterozygosity for chromosomes 1p and 16q is an adverse prognostic factor in favorable-histology Wilms tumor: a report from the National Wilms Tumor Study Group. J Clin Oncol. 2005;23:7312-7321.
21. Janoueix-Lerosey I, Schleiermacher G, Michels E, et al. Overall genomic pattern is a predictor of outcome in neuroblastoma. J Clin Oncol. 2009;27:1026-1033.
22. Pfeifer D, Pantic M, Skatulla I, et al. Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood. 2007;109:1202-1210.
23. Ouillette P, Erba H, Kujawski L, et al. Integrated genomic profiling of chronic lymphocytic leukemia identifies subtypes of deletion 13q14. Cancer Res. 2008;68:1012-1021.
24. Avet-Loiseau H, Li C, Magrangeas F, et al. Prognostic significance of copy-number alterations in multiple myeloma. J Clin Oncol. 2009; 27:4585-4590.
25. Pfister S, Remke M, Benner A, et al. Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci. J Clin Oncol. 2009;27:1627-1636.
26. Prescher G, Bornfeld N, Hirche H, et al. Prognostic implications of monosomy 3 in uveal melanoma. Lancet. 1996;347:1222-1225.
27. Affymetrix. Copy Number and Genotype Analysis of FFPE-extracted DNA: Affymetrix, Inc; 2007.
28. Hagenkord JM, Monzon FA, Kash SF, et al. Array-based karyotyp-ing for prognostic assessment in chronic lymphocytic leukemia. Performance comparison of affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays. J Mol Diagn. 2010;12. [Epub ahead of print].
29. Gondek LP, Dunbar AJ, Szpurka H, et al. SNP array karyotyping allows for the detection of uniparental disomy and cryptic chromosomal abnormalities in MDS/MPD-U and MPD. PLoS One. 2007;2:e1225.
30. Gunn SR. The vanguard has arrived in the clinical laboratory. Array-based karyotyping for prognostic markers in chronic lymphocytic leukemia. J Mol Diagn. 2010;12. [Epub ahead of print].