Assessment of the frequency of allelic imbalance in human tissue using a multiplex polymerase chain reaction system

Journal of Molecular Diagnostics

Volumn 9, Issue 2, 2007, Pages 266-271

  Heaphy, Christopher M ^a   Hines, William C ^a   Butler, Kimberly S ^a   Haaland, Christina M ^a   Heywood, Glenroy ^a,b   Fischer, Edgar G ^a   Bisoffi, Marco ^a,b   Griffith, Jeffrey K ^a,b  

^a UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALLELIC IMBALANCE; ARTICLE; BREAST RECONSTRUCTION; CANCER GENETICS; CHROMOSOME BREAKAGE; DIAGNOSTIC VALUE; ENDOMETRIUM ABLATION; FINANCIAL MANAGEMENT; FROZEN SECTION; GENE DISRUPTION; GENE LOCUS; GENOMIC INSTABILITY; HETEROZYGOSITY; HIGH THROUGHPUT SCREENING; HOMOZYGOSITY; HUMAN; INTERMETHOD COMPARISON; KARYOTYPE; MULTIPLEX POLYMERASE CHAIN REACTION; NEPHRECTOMY; PANCREAS RESECTION; PHENOTYPE; PROGNOSIS; PROSTATECTOMY; QUANTITATIVE ANALYSIS; TISSUE SECTION; AGAR GEL ELECTROPHORESIS; ALLELE; GENETIC SCREENING; GENETICS; KIDNEY CARCINOMA; KIDNEY TUMOR; METHODOLOGY; NEOPLASM; POLYMERASE CHAIN REACTION; REPRODUCIBILITY;

ALLELES; ALLELIC IMBALANCE; CARCINOMA, RENAL CELL; DNA, NEOPLASM; ELECTROPHORESIS, AGAR GEL; GENETIC SCREENING; HUMANS; KIDNEY NEOPLASMS; NEOPLASMS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS;

EID: 34247851055     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2007.060115     Document Type: Article

References (25)

1. Lengauer C, Kinzler KW, Vogelstein B: Genetic instabilities in human cancers. Nature 1998, 396:643-649
2. Payne SR, Kemp CJ: Tumor suppressor genetics. Carcinogenesis 2005, 26:2031-2045
3. Hanahan D, Weinberg RA: The hallmarks of cancer. Cell 2000, 100:57-70
4. Mundle SD, Sokolova I: Clinical implications of advanced molecular cytogenetics in cancer. Expert Rev Mol Diagn 2004, 4:71-81
5. Gray JW, Collins C: Genome changes and gene expression in human solid tumors. Carcinogenesis 2000, 21:443-452
6. Kallioniemi A, Kallionemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D: Comparative genomic hybridization for molecular cytogenic analysis of solid tumors. Science 1992, 258:818-821
7. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosom Cancer 1997, 20:399-407
8. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: Quantitative high resolution analysis of DNA copy number variation in breast cancer using comparative genomic hybridization to DNA microarrays. Nat Genet 1998, 20:207-211
9. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999, 23:41-46
10. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001, 29:263-264
11. Albertson DG: Profiling breast cancer by array CGH. Breast Cancer Res Treat 2003, 78:289-298
12. Rauch A, Ruschendorf F, Huang J, Trautmann U, Becker C, Thiel C, Jones KW, Reis A, Nurnberg P: Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 2004, 41:916-922
13. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M: An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004, 64:3060-3071
14. Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS: Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 2003, 68:69-78
15. Ellsworth RE, Ellsworth DL, Lubert SM, Hooke J, Somiari RI, Shriver CD: High-throughput loss of heterozygosity mapping in 26 commonly deleted regions in breast cancer. Cancer Epidemiol Biomarkers Prev 2003, 129:915-919
16. Ellsworth DL, Ellsworth RE, Love B, Deyarmin B, Lubert SM, Mittal V, Hooke JA, Shriver CD: Outer breast quadrants demonstrate increased levels of genomic instability. Ann Surg Oncol 2004, 11:861-868
17. Ellsworth RE, Ellsworth DL, Deyarmin B, Hoffman LR, Love B, Hooke JA, Shriver CD: Timing of critical genetic changes in human breast disease. Ann Surg Oncol 2005, 12:1054-1060
18. Zhou X, Mok SC, Chen Z, Li Y, Wong DT: Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet 2004, 115:327-330
19. Meaburn E, Butcher LM, Schalkwyk LC, Plomin R: Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans. Nucleic Acids Res 2006, 34:e27
20. Murray SS, Oliphant A, Shen R, McBride C, Steeke RJ, Shannon SG, Rubano T, Kermani BG, Fan JB, Chee MS, Hansen MS: A highly informative SNP linkage panel for human genetic studies. Nat Methods 2004, 1:113-117
21. Lips EH, Dierssen JW, van Eijk R, Costing J, Eilers PH, Tollenaar RA, de Graaf EJ, van't Slot R, Wijmenga C, Morreau H, van Wezel T: Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. Cancer Res 2005, 65:10188-10191
22. Davies JJ, Wilson IM, Lam WL: Array CGH technologies and their applications to cancer genomes. Chromosome Res 2005, 13:237-248
23. Paulson TG, Galipeau PC, Reid BJ: Loss of heterozygosity analysis using whole genome amplification, cell sorting, and fluorescence-based PCR. Genome Res 1999, 9:482-491
24. Medintz IL, Lee CC, Wong WW, Pirkola K, Sidransky D, Mathies RA: Loss of heterozygosity assay for molecular detection of cancer using energy-transfer primers and capillary array electrophoresis. Genome Res 2000, 10:1211-1218
25. Skotheim RI, Diep CB, Kraggerud SM, Jakobsen KS, Lothe RA: Evaluation of loss of heterozygosity/allelic imbalance scoring in tumor DNA. Cancer Genet Cytogenet 2001, 127:64-70