PCR-Based Detection of Minority Point Mutations

Human Mutation

Volumn 23, Issue 5, 2004, Pages 406-412

  Makrigiorgos, G Mike ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

ATM; Hairpin PCR; Ku80; Ligation mediated PCR; Minority mutations; Mutation detection; Mutation scanning; PCR; SNP; TP53; XRCC5

Indexed keywords

DNA POLYMERASE; GENOMIC DNA; PRIMER DNA;

ALLELE; AMINO ACID SUBSTITUTION; ANALYTICAL ERROR; CANCER CELL; CANCER SCREENING; DNA EXTRACTION; DNA SEQUENCE; EARLY DIAGNOSIS; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCATION; HUMAN; MINIMAL RESIDUAL DISEASE; MOLECULAR GENETICS; MUTAGENESIS; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNIQUE; WILD TYPE;

DNA MUTATIONAL ANALYSIS; DNA PRIMERS; HUMANS; POINT MUTATION; POLYMERASE CHAIN REACTION;

EID: 2342630688     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20024     Document Type: Review

References (46)

1. Babon JJ, McKenzie M, Cotton RG. 1999. Mutation detection using fluorescent enzyme mismatch cleavage with T4 endonuclease VII. Electrophoresis 20:1162-1170.
2. Barcellos LF, Klitz W, Field LL, Tobias R, Bowcock AM, Wilson R, Nelson MP, Nagatomi J, Thomson G. 1997. Association mapping of disease loci, by use of a pooled DNA genomic screen. Am J Hum Genet 61:734-747.
3. Bulychev NV, Varaprasad CV, Dorman G, Miller JH, Eisenberg M, Grollman AP, Johnson F. 1996. Substrate specificity of Escherichia coli MutY protein. Biochemistry 35:13147-13156.
4. Collins HE, Li H, Inda SE, Anderson J, Laiho K, Tuomilehto J, Seldin MF. 2000. A simple and accurate method for determination of microsatellite total allele content differences between DNA pools. Hum Genet 106:218-226.
5. Cotton RGH, Rodrigues NR, Campbell RD. 1988. Reactivity of cytosine and thymine in single base pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc Natl Acad Sci USA 85:4397-4401.
6. Daniels J, Holmons P, Williams N, Turic D, McGuffin P, Plomin R, Owen MJ. 1998. A simple method for analyzing microsatellite allele image patterns generated from DNA pools and its application to allelic association studies. Am J Hum Genet 62:1189-1197.
7. Dong SM, Traverso G, Johnson C, Geng L, Favis R, Boynton K, Hibi K, Goodman SN, D'Allessio M, Paty P, Hamilton SR, Sidransky D, Barany F, Levin B, Shuber A, Kinzler KW, Vogelstein B, Jen J. 2001. Detecting colorectal cancer in stool with the use of multiple genetic targets. J Natl Cancer Inst 93:858-865.
8. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. 1996. Laser capture microdissection. Science 274:998-1001.
9. Garrity PA, Wold BJ. 1992. Effects of different DNA polymerases in ligation-mediated PCR: enhanced genomic sequencing and in vivo footprinting. Proc Natl Acad Sci USA 89:1021-1025.
10. Haliassos A, Chomel JC, Grandjouan S, Kruh J, Kaplan JC, Kitzis A. 1989. Detection of minority point mutations by modified PCR technique: a new approach for a sensitive diagnosis of tumor-progression markers. Nucleic Acids Res 17:8093-8099.
11. Jackson BA, Alekseyev VY, Barton JK. 1999. A versatile mismatch recognition agent: specific cleavage of a plasmid DNA at a single base mispair. Biochemistry 38:4655-4662.
12. Kaur M, Makrigiorgos GM. 2003. Novel amplification of DNA in a hairpin structure: towards a radical elimination of PCR errors from amplified DNA. Nucl Acids Res 31:e26.
13. Kaur M, Zhang Y, Liu WH, Tetradis S, Price BD, Makrigiorgos GM. 2002. Ligation of a primer at a mutation: a method to detect low level mutations in DNA. Mutagenesis 17:365-374.
14. Keohavong P, Thilly WG. 1989. Fidelity of DNA polymerases in DNA amplification. Proc Natl Acad Sci USA 86:9253-9257.
15. Khrapko K, Andre P, Cha R, Hu G, Thilly WG. 1994. Mutational spectrometry: means and ends. Prog Nucleic Acid Res Mol Biol 49:285-312.
16. Li-Sucholeiki XC, Thilly WG. 2000. A sensitive scanning technology for low frequency nuclear point mutations in human genomic DNA. Nucleic Acids Res 28:E44.
17. Liu Q, Swiderski P, Sommer SS. 2002. Truncated amplification: a method for high-fidelity template-driven nucleic acid amplification. Biotechniques 33:129-138.
18. Liu W, Smith DI, Rechtzigel KJ, Thibodeau SN, James CD. 1998. Denaturing high performance liquid chromatography (DHPLC) used in the detection of germline and somatic mutations. Nucleic Acids Res 26:1396-1400.
19. Liu WH, Kaur M, Makrigiorgos GM. 2003. Detection of hotspot mutations and polymorphisms using an enhanced PCR-RFLP approach. Hum Mutat 21:535-541.
20. Liu WH, Makrigiorgos GM. 2003. Sensitive and quantitative detection of mutations associated with clinical resistance to STI-571. Leuk Res 27:979-982.
21. McKinzie PB, Delongchamp RR, Heflich RH, Parsons BL. 2001. Prospects for applying genotypic selection of somatic oncomutation to chemical risk assessment. Mutat Res 489:47-78.
22. Myers RM, Lumelsky N, Lerman LS, Maniatis T. 1985. Detection of single base substitutions in total genomic DNA. Nature 313:495-498.
23. Neddermann P, Jiricny J. 1993. The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J Biol Chem 268:21218-21224.
24. Neoh SH, Brisco MJ, Firgaira FA, Trainor KJ, Turner DR, Morley AA. 1999. Rapid detection of the factor V Leiden (1691 G>A) and haemochromatosis (845 G>A) mutation by fluorescence resonance energy transfer (FRET) and real time PCR. J Clin Pathol 52:766-769.
25. Nghiem Y, Cabrera M, Cupples CG, Miller JH. 1988. The mutY gene: a mutator locus in Escherichia coli that generates G.C-T.A transversions. Proc Natl Acad Sci USA 85:2709-2713.
26. Nollau P, Wagener C. 1997. Methods for detection of point mutations: performance and quality assessment. IFCC Scientific Division, Committee on Molecular Biology Techniques. Clin Chem 43:1114-1128.
27. Nordfors L, Jansson M, Sandberg G, Lavebratt C, Sengul S, Schalling M, Amer P. 2002. Large-scale genotyping of single nucleotide polymorphisms by Pyrosequencing™ and validation against the 5′nuclease (Taqman®) assay. Hum Mutat 19:395-401.
28. Oleykowski CA, Bronson Mullins CR, Godwin AK, Yeung AT. 1998. Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26:4597-4602.
29. Parsons BL, Heflich RH. 1997. Genotypic selection methods for the direct analysis of point mutations. Mutat Res 387:97-121.
30. Perlin MW, Lancia G, Ng SK. 1995. Toward fully automated genotyping: genotyping microsatellite markers by deconvolution. Am J Hum Genet 57:1199-1210.
31. Pfeifer GP, Steigerwald SD, Mueller PR, Wold B, Riggs AD. 1989. Genomic sequencing and methylation analysis by ligation mediated PCR. Science 246:810-813.
32. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
33. Rodriguez H, Drouin R, Holmquist GP, O'Connor TR, Boiteux S, Laval J, Doroshow JH, Akman SA. 1995. Mapping of copper/ hydrogen peroxide-induced DNA damage at nucleotide resolution in human genomic DNA by ligation-mediated polymerase chain reaction. J Biol Chem 270:17633-17640.
34. Rubin MA. 2002. Understanding disease cell by cell. Science 296:1329-1330.
35. Sokurenko EV, Tchesnokova V, Yeung AT, Oleykowski CA, Trintchina E, Hughes KT, Rashid RA, Brint JM, Moseley SL, Lory S. 2001. Detection of simple mutations and polymorphisms in large genomic regions. Nucleic Acids Res 29:E111.
36. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293:489-493.
37. Sternberg D, Danan C, Lombes A, Laforet P, Girodon E, Goossens M, Amselem S. 1998. Exhaustive scanning approach to screen all the mitochondrial tRNA genes for mutations and its application to the investigation of 35 independent patients with mitochondrial disorders. Hum Mol Genet 7:33-42.
38. Taylor GR. 1999. Enzymatic and chemical cleavage methods. Electrophoresis 20:1125-1130.
39. Tessier DC, Brousseau R, Vernet T. 1986. Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase. Anal Biochem 158:171-178.
40. van Houten VM, Tabor MP, van den Brekel MW, Denkers F, Wishaupt RG, Kummer JA, Snow GB, Brakenhoff RH. 2000. Molecular assays for the diagnosis of minimal residual head-and-neck cancer:methods, reliability, pitfalls, and solutions. Clin Cancer Res 6:3803-3816.
41. Wasson J, Skolnick G, Love-Gregory L, Permutt MA. 2002. Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 32:1144-1146, 1148, 1150 passim.
42. Wilson VL, Wei Q, Wade KR, Chisa M, Bailey D, Kanstrup CM, Yin X, Jackson CM, Thompson B, Lee WR. 1999. Needle-in-a-haystack detection and identification of base substitution mutations in human tissues. Mutat Res 406:79-100.
43. Youil R, Kemper BW, Cotton RG. 1995. Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci USA 92:87-91.
44. Zhang Y, Kaur M, Price BD, Tetradis S, Makrigiorgos GM. 2002. An amplification and ligation-based method to scan for unknown mutations in DNA. Hum Mutat 20:139-147.
45. Zharkov DO, Grollman AP. 1998. MutY DNA glycosylase:base release and intermediate complex formation. Biochemistry 37:12384-12394.
46. Zhou G, Kamahori M, Okano K, Chuan G, Harada K, Kambara H. 2001. Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res 29:E93.