A new method for optimizing multiplex DNA microsatellite analysis in low quality archival specimens

Anticancer Research

Volumn 25, Issue 5, 2005, Pages 3251-3258

  Drobinskaya, Irina ^a   Gabbert, Helmut Erich ^a   Moeslein, Gabriela ^a   Mueller, Wolfram ^a,b  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b Gemeinschaftspraxis Pathologie Starnberg   (Germany)

Author keywords

DNA analysis; HNPCC; Microsatellite instability; Multiplex PCR

Indexed keywords

DNA;

ARTICLE; COLORECTAL CANCER; DNA DETERMINATION; FAMILIAL CANCER; FAMILY HISTORY; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MAJOR CLINICAL STUDY; MICROSATELLITE INSTABILITY; MULTIPLEX POLYMERASE CHAIN REACTION; NUCLEOTIDE SEQUENCE; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ALLELIC IMBALANCE; CARRIER PROTEINS; COLORECTAL NEOPLASMS, HEREDITARY NONPOLYPOSIS; DNA DAMAGE; DNA, NEOPLASM; DNA-BINDING PROTEINS; FORMALDEHYDE; HUMANS; IMMUNOHISTOCHEMISTRY; MICROSATELLITE REPEATS; MUTS HOMOLOG 2 PROTEIN; NEOPLASM PROTEINS; NUCLEAR PROTEINS; PARAFFIN EMBEDDING; POLYMERASE CHAIN REACTION; PROTO-ONCOGENE PROTEINS; TISSUE FIXATION;

EID: 23344445365     PISSN: 02507005     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. Aaltonen LA, Peltomaki P, Leach FS, Sistonen P, Pylkkanen I, Mecklin JP, Jarvinen H, Powell SM, Jen J, Hamilton SR, Peterson GM, Kinzler KW, Vogelstein B and de la Chapelle A: Clues to the pathogenesis of familial colorectal cancer. Science 260: 812-816, 1993.
2. Han HJ, Yanagisawa A, Kato Y, Park JG and Nakamura Y: Genetic instability in pancreatic cancer and poorly differentiated type of gastric cancer. Cancer Res 53: 5087-5089, 1993.
3. Rhyu M, Park WS and Meltzer SJ: Microsatellite instability occurs frequently in human gastric carcinoma. Oncogene 9: 29-32, 1994.
4. Aaltonen LA, Peltomaki P, Mecklin JP, Jarvinen H, Jass JR, Green JS, Lynch HT, Watson P, Tallqvist G, Juhola M, Sistonen P, Hamilton SR, Kinzler KW, Vogelstein B and de la Chapelle A: Replication errors in benign and malignant tumours from hereditary non-polyposis colorectal cancer patients. Cancer Res 54: 1645-1648, 1994.
5. Cawkwell L, Li D, Lewis FA, Martin I, Dixon MF and Quirke P: Microsatellite instability in colorectal cancer: improved assessment using fluorescent PCR. Gastroenterology 109: 465-471, 1995.
6. Fishel R, Lescoe MK, Rao MR, Copeland NG, Jenkins NA, Garber J, Kane M and Kolodner R: The human mutator gene homologue MSH2 and its association with the hereditary non-polyposis colon cancer. Cell 75: 1027-1038, 1993.
7. Bronner CE, Baker SM, Morrison PT, Warren G, Smith LG, Lescoe MK, Kane M, Earabino C, Lipford J, Linblom A, Tannergard P, Bollag RJ, Godwin AR, Ward DC, Nordenskjold M, Fishel R, Kolonder R and Liskay RM: Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. Nature 368: 258-261, 1994.
8. Liu B, Nicolaides N, Markowitz S, Willson JKV, Parsons RE, Jen J, Papadopoulos N, Peltomaki P, de la Chapelle A, Hamilton SR, Kinzler KW and Vogelstein B: Mismatch repair gene defects in sporadic colorectal cancers with microsatellite instability. Nature Genet 9: 48-55, 1995.
9. Kinzler KW and Vogelstein B: Lessons from hereditary non-polyposis colorectal cancer. Cell 87: 159-170, 1996.
10. Miyaki M, Konishi M, Tanaka K, Kikuchi-Yanoshita R, Muraoka M, Yasuno M, Igari T, Koike M, Chiba M and Mori T: Germline mutation of MSH6 as the cause of hereditary non-polyposis colorectal cancer. Nat Genet 17: 271-272, 1997.
11. Peltomaki P and Vasen HF: Mutations predisposing to hereditary non-polyposis colorectal cancer. Database and results of a collaborative study. The International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer. Gastroenterology 113: 1146-1158, 1997.
12. Wu Y, Berends MJW, Mensink RGJ, Kempinga C, Sijmons RH, van der Zee AGJ, Hollema H, Kleibeuker JH, Buys CHCM and Hofstra RM: Association of non-polyposis colorectal cancer-related tumours displaying low microsatellite instability with MSH6 germline mutations. Am J Hum Genet 65: 1291-1298, 1999.
13. Ionov Y, Peinado MA, Malkhosyan S, Shibata D and Perucho M: Ubiquitous somatic mutations in simple sequences reveal a new mechanism for colonic carcinogenesis. Nature 363: 558-561, 1993.
14. Parsons R, Li GM, Longley MJ, Fang WH, Papadopoulos N, Jen J, de la Capelle A, Kinzler KW, Vogelstein B and Modrich P: Hypermutability and mismatch repair deficiency in RER+ tumour cells. Cell 75: 1227-1236, 1993.
15. Hemminki A, Peltomaki P, Mecklin J-P, Jarvinen H, Salovaara R, Nystrom-Lahti M, de la Chapelle A and Aaltonen LA: Loss of wild type MLH1 gene is a feature of hereditary non-polyposis colorectal cancer. Nature Genet 8: 405-410, 1994.
16. Moslein G, Tester DJ, Lindor NM, Honchel R, Cunningham JM, French AJ, Hailing KC, Schwab M, Goretzki P and Thibodeau SN: Microsatellite instability and mutation analysis of hMSH2 and hMLH1 in patients with sporadic, familial, and hereditary colorectal cancer. Hum Mol Genet 5: 1245-1252, 1996.
17. Thibodeau SN, Bren G and Schaid D: Microsatellite instability in cancer of proximal colon. Science 260: 816-819, 1993.
18. Jass JR, Cottier DS, Jeevaratnam V, Pokos KM, Holdaway ML, Bowden NS, Van de Water PJ and Browett PJ: Diagnostic use of microsatellite instability in hereditary non-polyposis colorectal cancer. Lancet 346: 1200-1201, 1995.
19. Bocker T, Diermann J, Friedl W, Gebert J, Holinski-Feder E, Karner-Hanusch J, von Knebel-Doeberitz M, Koelble K, Moeslein G, Schackert HK, Wirtz HC, Fishel R and Ruschoff J: Microsatellite instability analysis: a multicenter study for reliability and quality control. Cancer Res 57: 4739-4743, 1997.
20. Dubeau L, Chandler LA, Gralow JR, Nichols PW and Jones PA: Southern blot analysis of DNA extracted from formalin-fixed pathology specimens. Cancer Res 46: 2964-2969, 1986.
21. Ben-Ezra J, Johnson DA, Rossi J, Cook N and Wu A: Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J Histochem Cytochem 39: 351-354, 1991.
22. Greer CE, Peterson SL, Kiviat NB and Manos MM: PCR amplification from paraffin-embedded tissue: effects of fixative and fixation time. Am J Clin Pathol 95: 117-124, 1991.
23. Frank TS, Svoboda-Newman SM and Hsi ED: Comparison of methods for extracting DNA from formalin-fixed paraffin sections for nonisotopic PCR. Diagn Mol Pathol 5: 220-224, 1996.
24. Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW, Meltzer SJ, Bigas-Rodriguez M, Fodde R, Ranzani GN and Srivastava S: A National Cancer Institute workshop on microsatellite instability for cancer detection and familiar predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res 58: 5248-5257, 1998.
25. Dietmaier W, Wallinger S, Bocker T, Kullmann F, Fishel R and Ruschoff J: Diagnostic microsatellite instability: definition and correlation with mismatch repair protein expression. Cancer Res 57: 4749-4756, 1997.
26. Berg KD, Glaser CL, Thompson RE, Hamilton SR, Griffin CA and Eshleman JR: Detection of microsatellite instability by fluorescence multiplex polymerase chain reaction. J Mol Diagn 2: 20-28, 2000.
27. Breslauer KJ, Frank R, Blocker H and Marky LA: Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83: 3746-3750, 1986.
28. Dietmaier W, Riedlinger W, Köhler A, Wegele P, Beyser K, Sagner G, Wartbichler R and Rüschoff J: Detection of microsatellite instability (MSI) and loss of heterozygosity (LOH) in colorectal tumours by fluorescence-based multiplex microsatellite PCR. BIOCHEMICA (Roche Molecular Biochemicals) No 2: 42-45, 1999.
29. Henegariu O, Heerema NA, Dlouhy SR, Vance GH and Vogt PH: Multiplex PCR: critical parameters and step by step protocol. Bio Techniques 23: 504-511, 1997.
30. Zangenberg G, Saiki RK and Reynolds R: Multiplex PCR optimisation guidelines. PCR applications: In: Protocols for Functional Genomics. Innis MA, Gelfand DH, Sninsky JJ (eds.). San Diego, Academic Press, pp. 73-94, 1999.
31. Chan TL, Yuen ST, Chung LP, Ho JWC, Kwan KYM, Chan ASY, Ho JCY, Leung SY and Wyllie AH: Frequent microsatellite instability and mismatch repair gene mutations in young Chinese patients with colorectal cancer. J Natl Cancer Inst 91: 1221-1226, 1999.
32. Frazier ML, Sinicrope FA, Amos CI, Clcary KR, Lynch PM. Levin B and Luthra R: Loci for efficient detection of microsatellite instability in hereditary non-polyposis colon cancer. Oncol Rep 6: 497-505, 1999.
33. Dietmaier W and Hofstädter F: Detection of microsatellite instability by real time PCR and hybridisation probe melting point analysis. Lab Invest 81: 1453-1456, 2001.
34. Loukola A, Eklin K, Laiho P, Salovaara R, Kristo P, Jarvinen H, Mecklin JP, Launonen V and Aaltonen LA: Microsatellite marker analysis in screening for hereditary non-polyposis colorectal cancer (HNPCC). Cancer Res 61: 4545-4549, 2001.
35. Potocnik U, Glavac D, Golouh R and Ravnik-Glavac M: Causes of microsatellite instability in colorectal tumours: implications for hereditary non-polyposis colorectal cancer screening. Cancer Genet Cytogenet 126: 85-96, 2001.
36. Stone JG, Tomlinson IP and Houlston RS: Optimising methods for determining RER status in colorectal cancers. Cancer Lett 149: 15-20, 2000.
37. Wirtz HC, Muller W, Noguchi T, Scheven M, Ruschoff J. Hommel G and Gabbert HE: Prognostic value and clinicopathological profile of microsatellite instability in gastric cancer. Clin Cancer Res 4: 1749-1754, 1998.
38. Liu T, Tannergard P, Hackman P, Rubio C, Kressner U, Lindmark G, Hellgren D. Lambert B and Lindblom A: Missense mutations in hMLH1 associated with colorectal cancer. Hum Genet 105: 437-441, 1999.
39. Liu T, Wahlberg S, Burek E, Lindblom P. Rubio C and Lindblom A: Microsatellite instability as a predictor of a mutation in a DNA mismatch repair gene in familial colorectal cancer. Genes Chromosomes Cancer 27: 17-25, 2000.
40. Umetani N, Sasaki S, Watanabe T, Ishigami H, Ueda E and Nagawa H: Diagnostic primer sets for microsatellite instability optimised for a minimal amount of damaged DNA from colorectal tissue samples. Ann Surg Oncol 7: 276-280, 2000.
41. Toh Y, Oki E, Oda S, Tomoda M, Tomisaki S, Ichiyoshi Y, Ohno S and Sugimachi K: An integrated microsatellite length analysis using an automated fluorescent DNA sequencer. Cancer Res 56: 2688-2691, 1996.
42. Debniak T, Kurzawski G, Gorski B, Kladny J, Domagala W and Lubinski J: Value of pedigree/clinical data, immunohistochemistry and microsatellite instability analysis in reducing the cost of determining hMLH1 and hMSH2 gene mutations in patients with colorectal cancer. Eur J Cancer 36: 49-54, 2000.
43. Fleisher AS, Esteller M, Tamura G, Rashid A, Stine OC, Yin J, Zou T-T, Abraham JM, Kong D, Nishizuka S, James SP, Wilson KT, Hermann JG and Meltzer SJ: Hypermethylation of the hMLH1 gene promoter is associated with microsatellite instability in early human gastric neoplasma. Oncogene 20: 329-335, 2001.
44. Hoang J-M, Cottu PH, Thuille B, Salmon RJ, Thomas G and Hamelin R: BAT-26, an indicator of the replication error phenotype in colorectal cancers and cell lines. Cancer Res 57: 300-303, 1997.
45. Planck M, Rambech E, Moslein G, Muller W, Olsson H and Nilbert M: High frequency of microsatellite instability and loss of mismatch-repair protein expression in double primary cancers of the endometrium and colorectum. Cancer 94: 2502-2510, 2002.
46. Masuda N, Ohnishi T, Kawamoto S, Monden M and Okubo K: Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 27: 4436-4443, 1999.
47. Schramm M, Vajna R, Pereverzev A, Klockner U, Pietrobon D, Hescheler J and Schneider T: Isoforms of alpha1E voltage-gated calcium channels in rat cerebellar granule cells - detection of major calcium channel alphal-transcripts by reverse transcription polymerase chain reaction. Neuroscience 92: 565-575, 1999.
48. Ailenberg M and Silverman M: Controlled hot start and improved specificity in carrying out PCR utilising touch-up and loop incorporated primers (TULIPS). Bio Techniques 29: 1018-1023, 2000.
49. Thibodeau SN, French AJ, Cunningham JM, Burgart LJ, Roche PC, McDonnell SK, Schaid DJ, Vockley CW, Michels VV, Farr GH Jr and O'Connell MJ: Microsatellite instability in colorectal cancer: different mutator phenotypes and the principal involvement of hMLH1. Cancer Res 58: 1713-1717, 1998.
50. Cawkwell L, Sutherland F, Murgatroyd H, Jarvis P, Gray S, Cross D, Shepherd N, Day D and Quirke P: Defective hMSH2/hMLH1 protein expression is seen infrequently in ulcerative colitis associated colorectal cancers. Gut 46: 367-369, 2000.
51. Kievit W, de Bruin JHFM, Adang EMM, Severens JL, Kleibeuker JH, Sijmons RH, Ruers TJ, Nagengast FM, Vasen HFA, van Krieken JHJM, Ligtenberg MJL and Hoogerbrugge N: Cost effectiveness of a new strategy to identify HNPCC patients. Gut 54: 97-102, 2005.