Single nucleotide polymorphism array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas

Journal of Pathology

Volumn 212, Issue 3, 2007, Pages 269-277

  Lips, E H ^a   de Graaf, E J ^b   Tollenaar, R A E M ^a   van Eijk, R ^a   Oosting, J ^a   Szuhai, K ^a   Karsten, T ^c   Nanya, Y ^d   Ogawa, S ^d   van de Velde, C J ^a   Eilers, P H C ^a   van Wezel, Tom ^a   Morreau, H ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b IJSSELLAND HOSPITAL   (Netherlands)

^c Reinier deGraaf Gasthuis ^*  (Netherlands)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

Chromosomal aberrations; Chromosomal instability; Genomic profiling; Loss of heterozygosity; Rectal adenoma; Rectal cancer; SNP array; Total mesorectal excision; Transanal endoscopic microsurgery

Indexed keywords

ADULT; AGED; ARTICLE; CANCER SIZE; CANCER STAGING; CHROMOSOMAL INSTABILITY; CHROMOSOME 22Q; CHROMOSOME 8Q; CHROMOSOME ABERRATION; CHROMOSOME ADDITION; CHROMOSOME LOSS; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DIAGNOSTIC VALUE; DISEASE SEVERITY; DNA FINGERPRINTING; ENDOSCOPIC SURGERY; FEMALE; GENETIC HETEROGENEITY; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; HUMAN TISSUE; LOGISTIC REGRESSION ANALYSIS; MALE; PRIORITY JOURNAL; PROGNOSIS; RECTUM ADENOMA; RECTUM BIOPSY; RECTUM CARCINOMA; RECTUM SURGERY; SINGLE NUCLEOTIDE POLYMORPHISM; SURGICAL TECHNIQUE;

ADENOMA; ANALYSIS OF VARIANCE; CARCINOMA; CHROMOSOMAL INSTABILITY; DIAGNOSIS, DIFFERENTIAL; GENOME; HUMANS; LOGISTIC MODELS; LOSS OF HETEROZYGOSITY; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECTAL NEOPLASMS;

EID: 34347375399     PISSN: 00223417     EISSN: 10969896     Source Type: Journal    
DOI: 10.1002/path.2180     Document Type: Article

References (54)

1. Kapiteijn E, Marijnen CA, Nagtegaal ID, Putter H, Steup WH, Wiggers T, et al. Preoperative radiotherapy combined with total mesorectal excision for resectable rectal cancer. N Engl J Med 2001; 345:638-646.
2. Peeters KC, van de Velde CJ, Leer JW, Martijn H, Junggeburt JM, Kranenbarg EK, et al. Late side effects of short-course preoperative radiotherapy combined with total mesorectal excision for rectal cancer: increased bowel dysfunction in irradiated patients - a Dutch colorectal cancer group study. J Clin Oncol 2005; 23:6199-6206.
3. Buess G, Mentges B, Manncke K, Starlinger M, Becker HD. Technique and results of transanal endoscopic microsurgery in early rectal cancer. Am J Surg 1992;163:63-69.
4. de Graaf EJ, Doornebosch PG, Stassen LP, Debets JM, Tetteroo GW, Hop WC. Transanal endoscopic microsurgery for rectal cancer. Eur J Cancer 2002;38:904-910.
5. Rokke O, Iversen KB, Ovrebo K, Maartmann-Moe H, Skarstein A, Halvorsen JF. Local resection of rectal tumors by transanal endoscopic microsurgery: experience with the first 70 cases. Dig Surg 2005; 22:182-189.
6. Casadesus D. Transanal endoscopic microsurgery: a review. Endoscopy 2006;38:418-423.
7. Ganai S, Kanumuri P, Rao RS, Alexander AI. Local recurrence after transanal endoscopic microsurgery for rectal polyps and early cancers. Ann Surg Oncol 2006;13:547-556.
8. Maslekar S, Beral DL, White TJ, Pillinger SH, Monson JR. Transanal endoscopic microsurgery: where are we now? Dig Surg 2006; 23:12-22.
9. Sakamoto GD, MacKeigan JM, Senagore AJ. Transanal excision of large, rectal villous adenomas. Dis Colon Rectum 1991;34:880-885.
10. Sengupta S, Tjandra JJ. Local excision of rectal cancer: what is the evidence? Dis Colon Rectum 2001;44:1345-1361.
11. Floyd ND, Saclarides TJ. Transanal endoscopic microsurgical resection of pT1 rectal tumors. Dis Colon Rectum 2006;49:164-168.
12. Guerrieri M, Baldarelli M, Morino M, Trompetto M, Da Rold A, Selmi I, et al. Transanal endoscopic microsurgery in rectal ladenomas: experience of six Italian centres. Dig Liver Dis 2006; 38:202-207.
13. Nastro P, Beral D, Hartley J, Monson JR. Local excision of rectal cancer: review of literature. Dig Surg 2005;22:6-15.
14. Stipa F, Burza A, Lucandri G, Ferri M, Pigazzi A, Ziparo V, et al. Outcomes for early rectal cancer managed with transanal endoscopic microsurgery: a 5-year follow-up study. Surg Endosc 2006; 20:541-545.
15. Hermanek P, Gall FP. Early (microinvasive) colorectal carcinoma. Pathology, diagnosis, surgical treatment. Int J Colorectal Dis 1986;1:79-84.
16. Balmain A, Gray J, Ponder B. The genetics and genomics of cancer. Nat Genet 2003;33:(Suppl): 238-244.
17. Lanza G Jr, Maestri I, Dubini A, Gafa R, Santini A, Ferretti S, et al. p53 expression in colorectal cancer: relation to tumor type, DNA ploidy pattern and short-term survival. Am J Clin Pathol 1996; 105:604-612.
18. Diep CB, FJeivi K, Ribeiro FR, Teixeira MR, Lindgjaerde OC, Lothe RA. The order of genetic events associated with colorectal cancer progression inferred from meta-analysis of copy number changes. Genes Chromosomes Cancer 2006;45:31-41.
19. Grade M, Ghadimi BM, Varma S, Simon R, Wangsa D, Barenboim-Stapleton L, etal. Aneuploidy-dependent massive deregulation of the cellular transcriptome and apparent divergence of the Wnt/beta-catenin signaling pathway in human rectal carcinomas. Cancer Res 2006; 66:267-282.
20. Hermsen M, Postma C, Baak J, Weiss M, Rapallo A, Sciutto A, et al. Colorectal adenoma to carcinoma progression follows multiple pathways of chromosomal instability. Gastroenterology 2002; 123:1109-1119.
21. Hoglund M, Gisselsson D, Hansen GB, Sall T, Mitelman F, Nilbert M. Dissecting karyotypic patterns in colorectal tumors: two distinct but overlapping pathways in the adenoma-carcinoma transition. Cancer Res 2002;62:5939-5946.
22. Ried T, Knutzen R, Steinbeck R, Blegen H, Schrock E, Heselmeyer K, et al. Comparative genomic hybridization reveals a specific pattern of chromosomal gains and losses during the genesis of colorectal tumors. Genes Chromosomes Cancer 1996;15:234-245.
23. Sugai T, Takahashi H, Habano W, Nakamura S, Sato K, Orii S, et al. Analysis of genetic alterations, classified according to their DNA ploidy pattern, in the progression of colorectal adenomas and early colorectal carcinomas. J Pathol 2003;200:168-176.
24. Thiagalingam S, Laken S, Willson JK, Markowitz SD, Kinzler KW, Vogelstein B, et al. Mechanisms underlying losses of heterozygosity in human colorectal cancers. Proc Natl Acad Sci USA 2001;98:2698-2702.
25. Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, et al. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 2004;1:287-299.
26. Lieberfarb ME, Lin M, Lechpammer M, Li C, Tanenbaum DM, Febbo PG, et al. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res 2003;63:4781-4785.
27. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004;64:3060-3071.
28. Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004;14:287-295.
29. Calhoun ES, Gallmeier E, Cunningham SC, Eshleman JR, Hruban RH, Kern SE. Copy-number methods dramatically underestimate loss of heterozygosity in cancer. Genes Chromosomes Cancer 2006;45:1070-1071.
30. Bardi G, Fenger C, Johansson B, Mitelman F, Heim S. Tumor karyotype predicts clinical outcome in colorectal cancer patients. J Clin Oncol 2004;22:2623-2634.
31. Leslie A, Stewart A, Baty DU, Mechan D, McGreavey L, Smith G, et al. Chromosomal changes in colorectal adenomas: relationship to gene mutations and potential for clinical utility. Genes Chromosomes Cancer 2006;45:126-135.
32. Ghadimi BM, Grade M, Liersch T, Langer C, Siemer A, Fuzesi L, et al. Gain of chromosome 8q23-24 is a predictive marker for lymph node positivity in colorectal cancer. Clin Cancer Res 2003; 9:1808-1814.
33. Anwar S, Frayling IM, Scott NA, Carlson GL. Systematic review of genetic influences on the prognosis of colorectal cancer. Br J Surg 2004;91:1275-1291.
34. Kapiteijn E, Liefers GJ, Los LC, Kranenbarg EK, Hermans J, Tollenaar RA, et al. Mechanisms of oncogenesis in colon versus rectal cancer. J Pathol 2001;195:171-178.
35. Frattini M, Balestra D, Suardi S, Oggionni M, Alberici P, Radice P, et al. Different genetic features associated with colon and rectal carcinogenesis. Clin Cancer Res 2004;10(Pt 1):4015-4021.
36. Beart RW, Melton LJ III, Maruta M, Dockerty MB, Frydenberg HB, O'Fallon WM. Trends in right and left-sided colon cancer. Dis Colon Rectum 1983;26:393-398.
37. Scott N, Sagar P, Stewart J, Blair GE, Dixon MF, Quirke P. p53 in colorectal cancer: clinicopathological correlation and prognostic significance. Br J Cancer 1991;63:317-319.
38. Thibodeau SN, Bren G, Schaid D. Microsatellite instability in cancer of the proximal colon. Science 1993;260:816-819.
39. Rex DK, Ulbright TM, Cummings OW. Coming to terms with pathologists over colon polyps with cancer or high-grade dysplasia. J Clin Gastroenterol 2005;39:1-3.
40. West AB, Mitsuhashi T. Cancer or high-grade dysplasia? The present status of the application of the terms in colonic polyps. J Clin Gastroenterol 2005;39:4-6.
41. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988;16:1215.
42. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, et al. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 2004; 14:414-425.
43. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004; 20:1233-1240.
44. Eilers PH, de Menezes RX. Quantile smoothing of array CGH data. Bioinformatics 2005;21:1146-1153.
45. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005;65:6071-6079.
46. Lips EH, Dierssen JW, van Eijk R, Oosting J, Eilers PH, Tollenaar RA, et al. 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.
47. Knijnenburg J, Szuhai K, Giltay J, Molenaar L, Sloos W, Poot M, et al. Insights from genomic microarrays into structural chromosome rearrangements. Am J Med Genet A 2005;132:36-40.
48. Oosting J, Lips EH, van Eijk R, Eilers PH, Szuhai K, Wijmenga C, et al. High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Genome Res 2007.
49. Rajagopalan H, Nowak MA, Vogelstein B, Lengauer C. The significance of unstable chromosomes in colorectal cancer. Nat Rev Cancer 2003; 3:695-701.
50. Knosel T, Schluns K, Stein U, Schwabe H, Schlag PM, Dietel M, et al. Chromosomal alterations during lymphatic and liver metastasis formation of colorectal cancer. Neoplasia 2004;6:23-28.
51. Bartos JD, Stoler DL, Matsui S, Swede H, Willmott LJ, Sait SN, et al. Genomic heterogeneity and instability in colorectal cancer: spectral karyotyping, glutathione transferase-MI and ras. Mutat Res 2004; 568:283-292.
52. Di Vinci A, Infusini E, Peveri C, Sciutto A, Orecchia R, Geido E, et al. Intratumor heterogeneity of chromosome 1, 7, 17, and 18 aneusomies obtained by FISH and association with flow cytometric DNA index in human colorectal adenocarcinomas. Cytometry 1999; 35:369-375.
53. Saraga E, Bautista D, Dorta G, Chaubert P, Martin P, Sordat B, et al. Genetic heterogeneity in sporadic colorectal adenomas. J Pathol 1997;181:281-286.
54. Tollenaar RA, Bonsing BA, Kuipers-Dijkshoorn NJ, Hermans J, van de Velde CJ, Cornelisse CJ, et al. Evidence of clonal divergence in colorectal carcinoma. Cancer 1997;79:1304-1314.