Methods for detection of point mutations: Performance and quality assessment

Clinical Chemistry

Volumn 43, Issue 7, 1997, Pages 1114-1128

  Nollau, Peter ^a   Wagener, Christoph ^a  

^a UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

Author keywords

Alleles; Electrophoresis; Gene deletions; Gene insertions; Polymerase chain reaction

Indexed keywords

ALLELE; ANALYTIC METHOD; GENE DELETION; GENE INSERTION; HUMAN; LABORATORY AUTOMATION; MUTANT; POINT MUTATION; POLYMERASE CHAIN REACTION; QUALITY CONTROL; REVIEW; STANDARDIZATION;

EID: 0030791025     PISSN: 00099147     EISSN: None     Source Type: Journal    
DOI: 10.1093/clinchem/43.7.1114     Document Type: Review

References (99)

1. Cotton RG. Current methods of mutation detection. Mutat Res 1993;285:125-44.
2. Grompe M. The rapid detection of unknown mutations in nucleic acids. Nature Genet 1993;5:111-7.
3. Reiss J, Krawczak M, Schloesser M, Wagner M, Cooper DN. The effect of replication errors on the mismatch analysis of PCR-amplified DNA. Nucleic Acids Res 1990;18:973-8.
4. Krawczak M, Reiss J, Schmidtke J, Rosler U. Polymerase chain reaction: replication errors and reliability of gene diagnosis. Nucleic Acids Res 1989;17:2197-201.
5. Lerman LS, Silverstein K. Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol 1987;155:482-501.
6. Myers RM, Sheffield VC, Cox DR. Detection of single base changes in DNA: ribonuclease cleavage and denaturing gradient gel electrophoresis. In: Davies KE, ed. Genome analysis. A practical approach. Oxford: IRL Press, 1988:95-139.
7. Myers RM, Fischer SG, Maniatis T, Lerman LS. Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acids Res 1985;13:3111-29.
8. Myers RM, Fischer SG, Lerman LS, Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 1985;13:3131-45.
9. Scholz RB, Milde Langosch K, Jung R, et al. Rapid screening for Tp53 mutations by temperature gradient gel electrophoresis: a comparison with SSCP analysis. Hum Mol Genet 1993;2:2155-8.
10. Myers RM, Lumelsky N, Lerman LS, Maniatis T. Detection of single base substitutions in total genomic DNA. Nature 1985; 313:495-8.
11. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A 1989;86:2766-70.
12. Danenberg PV, Horikoshi T, Volkenandt M, et al. Detection of point mutations in human DNA by analysis of RNA conformation polymorphism(s). Nucleic Acids Res 1992;20:573-9.
13. Sarkar G, Yoon HS, Sommer SS. Screening for mutations by RNA single-strand conformation polymorphism (rSSCP): comparison with DNA-SSCP. Nucleic Acids Res 1992;20:871-8.
14. Lee HH, Lo WJ, Choo KB. Mutational analysis by a combined application of the multiple restriction fragment-single strand conformation polymorphism and the direct linear amplification DNA sequencing protocols. Anal Biochem 1992;205:289-93.
15. Suzuki Y, Sekiya T, Hayashi K. Allele specific polymerase chain reaction: a method for amplification and sequence determination of a single component among a mixture of sequence variants. Anal Biochem 1991;192:82-4.
16. Lo YM, Patel P, Mehal WZ, Fleming KA, Bell JI, Wainscoat JS. Analysis of complex genetic systems by ARMS-SSCP: application to HLA genotyping. Nucleic Acids Res 1992;20:1005-9.
17. Virdi AS, Loughlin JA, Irven CM, Goodship J, Sykes BC. Mutation screening by a combination of biotin-SSCP and direct sequencing. Hum Genet 1994;93:287-90.
18. Kurvinen K, Hietanen S, Syrjanen K, Syrjanen S. Rapid and effective detection of mutations in the p53 gene using nonradioactive single-strand conformation polymorphism (SSCP) technique applied on PhastSystem. J Virol Methods 1995;51:43-53.
19. Iolascon A, Parrella T, Perrotta S, et al. Rapid detection of medium chain acyl-CoA dehydrogenase gene mutations by non-radioactive, single strand conformation polymorphism minigels. J Med Genet 1994;31:551-4.
20. Kuypers AW, Willems PM, van der Schans MJ, et al. Detection of point mutations in DNA using capillary electrophoresis in a polymer network. J Chromatogr 1993;621:149-56.
21. Sheffield VC, Beck JS, Kwitek AE, Sandstrom DW, Stone EM. The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics 1993; 16:325-32.
22. Levesque P, Ramchurren N, Saini K, Joyce A, Libertino J, Summerhayes IC. Screening of human bladder tumors and urine sediments for the presence of H-ras mutations. Int J Cancer 1993;55:785-90.
23. Soto D, Sukumar S. Improved detection of mutations in the p53 gene in human tumors as single-stranded conformation polymorphs and double-stranded heteroduplex DNA. PCR Methods Appl 1992;2:96-8.
24. Nagamine CM, Chan K, Lau YF. A PCR artifact: generation of heteroduplexes. Am J Hum Genet 1989;45:337-9.
25. Tassabehji M, Read AP, Newton VE, et al. Waardenburg's syndrome patients have mutations in the human homologue of the Pax-3 paired box gene. Nature 1992;355:635-6.
26. Tassabehji M, Read AP, Newton VE, et al. Mutations in the PAX3 gene causing Waardenburg syndrome type 1 and type 2. Nature Genet 1993;3:26-30.
27. White MB, Carvalho M, Derse D, O'Brien SJ, Dean M. Detecting single base substitutions as heteroduplex polymorphisms. Genomics 1992;12:301-6.
28. Cheng J, Kasuga T, Mitchelson KR, et al. Polymerase chain reaction heteroduplex polymorphism analysis by entangled solution capillary electrophoresis. J Chromatogr A 1994;677:169-77.
29. Myers RM, Larin Z, Maniatis T. Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA:DNA duplexes. Science 1985;230:1242-6.
30. Cotton RG, Rodrigues NR, Campbell RD. 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 U S A 1988;85:4397-401.
31. Verpy E, Biasotto M, Meo T, Tosi M. Efficient detection of point mutations on color-coded strands of target DNA. Proc Natl Acad Sci U S A 1994;91:1873-7.
32. Saleeba JA, Cotton RG. 35S-labelled probes improve detection of mismatched base pairs by chemical cleavage. Nucleic Acids Res 1990;19:1712.
33. Saleeba JA, Ramus SJ, Cotton RG. Complete mutation detection using unlabeled chemical cleavage. Hum Mutat 1992;1:63-9.
34. Mashal RD, Koontz J, Sklar J. Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nature Genet 1995;9:177-83.
35. Youil R, Kemper BW, Cotton RGH. Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci U S A 1995;92:87-91.
36. Dean M. Resolving DNA mutations. Nature Genet 1995;9:103-4.
37. Lyamichev V, Brow MA, Dahlberg JE. Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases. Science 1993;260:778-83.
38. Lishanski A, Ostrander EA, Rine J. Mutation detection by mismatch binding protein, MutS, in amplified DNA: application to the cystic fibrosis gene. Proc Natl Acad Sci U S A 1994;91:2674-8.
39. Ellis LA, Taylor GR, Banks R, Baumberg S. MutS binding protects heteroduplex DNA from exonuclease digestion in vitro: a simple method for detecting mutations. Nucleic Acids Res 1994;22: 2710-1.
40. Jiricny J, Su SS, Wood SG, Modrich P. Mismatch-containing oligonucleotide duplexes bound by the E. coli mutS-encoded protein. Nucleic Acids Res 1988;16:7843-53.
41. Wagner R, Debbie P, Radman M. Mutation detection using immobilized mismatch binding protein (MutS). Nucleic Acids Res 1995; 23:3944-8.
42. Palombo F, Gallinari P, Iaccarino I, et al. GTBP, a 160-kilodalton protein essential for mismatch-binding activity in human cells. Science 1995;268:1912-4.
43. Roest PA, Roberts RG, Sugino S, van Ommen GJ, den Dunnen JT. Protein truncation test (PTT) for rapid detection of translation-terminating mutations. Hum Mol Genet 1993;2:1719-21.
44. Powell SM, Petersen GM, Krush AJ, et al. Molecular diagnosis of familial adenomatous polyposis. N Engl J Med 1993;329:1982-7.
45. van der Luijt R, Khan PM, Vasen H, et al. Rapid detection of translation-terminating mutations at the adenomatous polyposis coli (APC) gene by direct protein truncation test. Genomics 1994;20:1-4.
46. Varesco L, Groden J, Spirio L, et al. A rapid screening method to detect nonsense and frameshift mutations: identification of disease-causing APC alleles. Cancer Res 1993;53:5581-4.
47. Shattuck Eidens D, McClure M, Simard J, et al. A collaborative survey of 80 mutations in the BRCA1 breast and ovarian cancer susceptibility gene. Implications for presymptomatic testing and screening. JAMA 1995;273:535-41.
48. Heim RA, Kam Morgan LN, Binnie CG, et al. Distribution of 13 truncating mutations in the neurofibromatosis 1 gene. Hum Mol Genet 1995;4:975-81.
49. Lipshutz RJ, Morris D, Chee M, et al. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 1995;19: 442-7.
50. Southern EM. DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale. Trends Genet 1996;12:110-5.
51. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991;251:767-73.
52. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A 1994;91:5022-6.
53. Kozal MJ, Shah N, Shen N, et al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Med 1996;2:753-9.
54. Moyret C, Theillet C, Puig PL, Moles JP, Thomas G, Hamelin R. Relative efficiency of denaturing gradient gel electrophoresis and single strand conformation polymorphism in the detection of mutations in exons 5 to 8 of the p53 gene. Oncogene 1994;9: 1739-43.
55. Cohen JB, Levinson AD. A point mutation in the last intron responsible for increased expression and transforming activity of the c-Ha-ras oncogene. Nature 1988;334:119-24.
56. Friedman KJ, Highsmith WE Jr, Prior TW, Perry TR, Silverman LM. Cystic fibrosis deletion mutation detected by PCR-mediated site-directed mutagenesis [Tech Brief]. Clin Chem 1990;36:695-6.
57. Chen J, Viola MV. A method to detect ras point mutations in small subpopulations of cells. Anal Biochem 1991;195:51-6.
58. Kahn SM, Jiang W, Culbertson TA, et al. Rapid and sensitive nonradioactive detection of mutant K-ras genes via 'enriched' PCR amplification. Oncogene 1991;6:1079-83.
59. Day IN, Humphries SE. Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose. Anal Biochem 1994;222:389-95.
60. Bolla MK, Haddad L, Humphries SE, Winder AF, Day IN. High-throughput method for determination of apolipoprotein E genotypes with use of restriction digestion analysis by microplate array diagonal gel electrophoresis. Clin Chem 1995;41:1599-604.
61. Jacobson DR, Mills NE. A highly sensitive assay for mutant ras genes and its application to the study of presentation and relapse genotypes in acute leukemia. Oncogene 1994;9:553-63.
62. Nollau P, Moser C, Weinland G, Wagener C. Detection of K-ras mutations in stools of patients with colorectal cancer by mutant-enriched PCR. Int J Cancer 1996;66:332-6.
63. Wallace RB, Johnson MJ, Hirose T, Miyake T, Kawashima EH, Itakura K. The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA. Nucleic Acids Res 1981;9:879-94.
64. Conner BJ, Reyes AA, Morin C, Itakura K, Teplitz RL, Wallace RB. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci U S A 1983;80: 278-82.
65. Saiki RK, Walsh PS, Levenson CH, Erlich HA. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A 1989;86:6230-4.
66. Sidransky D, Tokino T, Hamilton SR, et al. Identification of ras oncogene mutations in the stool of patients with curable colorectal tumors. Science 1992;256:102-5.
67. Day IN, O'Dell SD, Cash ID, Humphries SE, Weavind GP. Electrophoresis for genotyping: temporal thermal gradient gel electrophoresis for profiling of oligonucleotide dissociation. Nucleic Acids Res 1995;23:2404-12.
68. 1-antitrypsin deficiency. Clin Chem 1993;39:1626-31.
69. Yershov G, Barsky V, Belgovskiy A, et al. DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A 1996;93:4913-8.
70. Farr CJ, Saiki RK, Erlich HA, McCormick F, Marshall CJ. Analysis of ras gene mutations in acute myeloid leukemia by polymerase chain reaction and oligonucleotide probes. Proc Natl Acad Sci U S A 1988;85:1629-33.
71. Newton CR, Graham A, Heptinstall LE, et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 1989;17:2503-16.
72. Wu DY, Ugozzoli L, Pal BK, Wallace RB. Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemia. Proc Natl Acad Sci U S A 1989;86:2757-60.
73. Sommer SS, Cassady JD, Sobell JL, Bottema CDK. A novel method for detecting point mutations or polymorphisms and its application to population screening for carriers of phenylketonuria. Mayo Clin Proc 1989;64:1361-72.
74. Okayama H, Curiel DT, Brantly ML, Holmes MD, Crystal RG. Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. J Lab Clin Med 1989;114:105-13.
75. Gibbs RA, Nguyen PN, Caskey CT. Detection of single DNA base differences by competitive oligonucleotide priming. Nucleic Acids Res 1989;17:2437-48.
76. Chehab FF, Kan YW. Detection of specific DNA sequences by fluorescence amplification: a color complementation assay. Proc Natl Acad Sci U S A 1989;86:9178-82.
77. Ferrie RM, Schwarz MJ, Robertson NH, et al. Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene. Am J Hum Genet 1992;51:251-62.
78. Kropp GL, Fucharoen S, Embury SH. Asymmetrically primed selective amplification/temperature shift fluorescence polymerase chain reaction to detect the hemoglobin constant spring mutation. Blood 1991;78:26-9.
79. Ye S, Humphries S, Green F. Allele specific amplification by tetra-primer PCR. Nucleic Acids Res 1992;20:1152.
80. Li H, Cui X, Arnheim N. Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reaction. Proc Natl Acad Sci U S A 1990;87: 4580-4.
81. Dutton C, Sommer SS. Simultaneous detection of multiple single-base alleles at a polymorphic site. Biotechniques 1991;11: 700-2.
82. Lo YM, Patel P, Newton CR, Markham AF, Fleming KA, Wainscoat JS. Direct haplotype determination by double ARMS: specificity, sensitivity and genetic applications. Nucleic Acids Res 1991;19: 3561-7.
83. Kwok S, Kellogg DE, McKinney N, et al. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res 1990; 18:999-1005.
84. Sommer SS, Groszbach AR, Bottema CD. PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single-base changes. Biotechniques 1992;12:82-7.
85. Bottema CD, Sommer SS. PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms. Mutat Res 1993;288:93-102.
86. Tada M, Omata M, Kawai S, et al. Detection of ras gene mutations in pancreatic juice and peripheral blood of patients with pancreatic adenocarcinoma. Cancer Res 1993;53:2472-4.
87. Stork P, Loda M, Bosari S, Wiley B, Poppenhusen K, Wolfe H. Detection of K-ras mutations in pancreatic and hepatic neoplasms by non-isotopic mismatched polymerase chain reaction. Oncogene 1991;6:857-62.
88. Smith Ravin J, England J, Talbot IC, Bodmer W. Detection of c-Ki-ras mutations in faecal samples from sporadic colorectal cancer patients. Gut 1995;36:81-6.
89. Kornher JS, Livak KJ. Mutation detection using nucleotide analogs that alter electrophoretic mobility. Nucleic Acids Res 1989;17: 7779-84.
90. Sokolov BP. Primer extension technique for the detection of single nucleotide in genomic DNA. Nucleic Acids Res 1989;18:3671.
91. Syvanen AC, Aalto Setala K, Harju L, Kontula K, Soderlund H. A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 1990;8:684-92.
92. Kuppuswamy MN, Hoffmann JW, Kasper CK, Spitzer SG, Groce SL, Bajaj SP. Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc Natl Acad Sci U S A 1991;88:1143-7.
93. Torigoe S, Shuin T, Kubota Y, Horikoshi T, Danenberg K, Danenberg PV. p53 gene mutation in primary human renal cell carcinoma. Oncol Res 1992;4:467-72.
94. Lee JS, Anvret M. Identification of the most common mutation within the porphobilinogen deaminase gene in Swedish patients with acute intermittent porphyria. Proc Natl Acad Sci U S A 1991;88:10912-5.
95. Syvanen AC, Ikonen E, Manninen T, et al. Convenient and quantitative determination of the frequency of a mutant allele using solid-phase minisequencing: application to aspartylglucosaminuria in Finland. Genomics 1992;12:590-5.
96. Alves AM, Carr FJ. Dot blot detection of point mutations with adjacently hybridising synthetic oligonucleotide probes. Nucleic Acids Res 1988;16:8723.
97. Landegren U, Kaiser R, Sanders J, Hood L. A ligase-mediated gene detection technique. Science 1988;241:1077-80.
98. Nickerson DA, Kaiser R, Lappin S, Stewart J, Hood L. Landegren U. Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc Natl Acad Sci U S A 1990;87:8923-7.
99. Mills NE, Fishman CL, Scholes J, Anderson SE, Rom WN, Jacobson DR. Detection of K-ras oncogene mutations in bronchoalveolar lavage fluid for lung cancer diagnosis. J Natl Cancer Inst 1995;87:1056-60.