Abstract
This chapter provides a broad overview of the range of mutation detection techniques that are now available.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Vogel, F. and Motulsky, A. G. (1986) Human Genetics. Springer-Verlag, Berlin.
Taylor, G. R. (1997) Laboratory Methods for the Detection of Mutations and Polymorphisms in DNA, CRC Press, Boca Raton, FL.
Kan, Y. W. and Dozy, A. M. (1978) Antenatal diagnosis of sickle-cell anaemia by D.N.A. analysis of amniotic-fluid cells. Lancet 2, 910–912.
Kan, Y. W., et al. (1975) Deletion of alpha-globin genes in haemoglobin-H disease demonstrates multiple alpha-globin structural loci. Nature 255, 255–256.
Mullis, K, et al. (1975) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp. Quant. Biol. 51, 263–273.
Day, I. N. and Humphries, S. E. (1994) Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose. Anal. Biochem. 222, 389–395.
Weber, J. L. and May, P. E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44, 388–396.
Nickerson, D. A., et al. (1992) Identification of clusters of biallelic polymorphic sequence-tagged sites (Pstss) that generate highly informative and automatable markers for genetic-linkage mapping. Genomics 12, 377–387.
Sachidanandam, R., et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.
Reich, D. E., et al. (2001) Linkage disequilibrium in the human genome. Nature 411, 199–204.
Wang, D. G., et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082.
Newton, C. R., et al. (1989) Analysis of any point mutation in DNA—The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17, 2503–2516.
O’Dell, S. D., Gaunt, T. R., and Day, I. N. (2000) SNP genotyping by combination of 192-well MADGE, ARMS and computerized gel image analysis. Biotechniques 29, 500–506.
Krook, A., Stratton, I. M., and O’Rahilly, S. (1992) Rapid and simultaneous detection of multiple mutations by pooled and multiplex single nucleotide primer extension: application to the study of insulin-responsive glucose transporter and insulin receptor mutations in non-insulin-dependent diabetes. Hum. Mol. Genet. 1, 391–395.
Head, S. R., et al. (1997) Nested genetic bit analysis (N-GBA) for mutation detection in the p53 tumor suppressor gene. Nucleic Acids Res. 25, 5065–5071.
Sokolov, B. P. (1990) Primer extension technique for the detection of single nucleotide in genomic DNA. Nucleic Acids Res. 18, 3671.
Piggee, C. A., Muth, J., Carrilho, E., and Karger, B. L. (1997) Capillary electrophoresis for the detection of known point mutations by single-nucleotide primer extension and laser-induced fluorescence detection. J. Chromatogr. A 781, 367–375.
Parsons, B. L. and Heflich, R. H. (1998) Detection of basepair substitution mutation at a frequency of 1×10(−7) by combining two genotypic selection methods, MutEx enrichment and allele-specific competitive blocker PCR. Environ. Mol. Mutagen. 32, 200–211.
Ellis, L. A., Taylor, G. R., Banks, R., and Baumberg, S. (1994) MutS binding protects heteroduplex DNA from exonuclease digestion in-vitro—A simple method for detecting mutations. Nucleic Acids Res. 22, 2710–2711.
Pastinen, T., Partanen, J., and Syvanen, A. C. (1996) Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin. Chem. 42, 1391–1397.
Syvanen, A. C. and Landegren, U. (1994) Detection of point mutations by solid-phase methods. Hum. Mutat. 3, 172–179.
Kosaki, K., et al. (2001) Fluorescence-based DHPLC for allelic quantification by single-nucleotide primer extension. J. Biochem. Biophys. Methods 47, 111–119.
Metspalu, A., et al. (1997) Arrayed primer extension (APEX) for mutation detection using gene specific DNA chips. Am. J. Hum. Genet. 61, 1301.
Buetow, K. H., et al. (2001) High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. USA 98, 581–584.
Livak, K. J. (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genetic Analysis 14, 143–149.
Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49–53.
Thelwell, N., Millington, S., Solinas, A., Booth, J., and Brown, T. (2000) Mode of action and application of scorpion primers to mutation detection. Nucleic Acids Res. 28, 3752–3761.
Tong, J., Cao, W. G., and Barany, F. (1999) Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D. Nucleic Acids Res. 27, 788–794.
Pritchard, C. E. and Southern, E. M. (1997) Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases. Nucleic Acids Res. 25, 3403–3407.
Barany, F. (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88, 189–193.
Brinson, E. C., et al. (1997) Introduction to PCR/OLA/SCS, a multiplex DNA test, and its application to cystic fibrosis [published erratum appears in Genet. Test. 1998;2(4):385]. Genet. Test. 1, 61–68.
Samiotaki, M., Kwiatkowski, M., Parik, J., and Landegren, U. (1994) Dual-color detection of DNA sequence variants by ligase-mediated analysis. Genomics 20, 238–242.
Gasparini, P., et al. (1999) Analysis of 31 CFTR mutations by polymerase chain reaction/oligonucleotide ligation assay in a pilot screening of 4476 newborns for cystic fibrosis. J. Med. Screen. 6, 67–69.
Zirvi, M., et al. (1999) Ligase-based detection of mononucleotide repeat sequences. Nucleic Acids Res. 27, e40.
Baner, J., Nilsson, M., Mendel-Hartvig, M., and Landegren, U. (1998) Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 26, 5073–5078.
Lizardi, P. M., et al. (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19, 225–232.
Thomas, D. C., Nardone, G. A., and Randall, S. K. (1999) Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction. Arch. Pathol. Lab Med. 123, 1170–1176.
Ronaghi, M., Nygren, M., Lundeberg, J., and Nyren, P. (1999) Analyses of secondary structures in DNA by pyrosequencing. Anal. Biochem. 267, 65–71.
Nordstrom, T., et al. (2000) Direct analysis of single-nucleotide polymorphism on double-stranded DNA by pyrosequencing. Biotechnol. Appl. Biochem. 31, 107–112.
Garcia, C. A., et al. (2000) Mutation detection by pyrosequencing: sequencing of exons 5–8 of the p53 tumor suppressor gene. Gene 253, 249–257.
Mein, C. A., et al. (2000) Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res. 10, 330–343.
Ryan, D., Nuccie, B., and Arvan, D. (1999) Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay. Molecular Diagnosis 4, 135–144.
Conner, B. J., et al. (1983) Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 80, 278–282.
Heim, R. A., Sugarman, E. A., and Allitto, B. A. (2001) Improved detection of cystic fibrosis mutations in the heterogeneous U.S. population using an expanded, panethnic mutation panel. Genet. Med. 3, 168–176.
Blair, A., Bugawan, T. L., and Erlich, H. A. (1997) PCR-based DNA typing for the HLA-C locus using an immobilized oligonucleotide probe array in the line blot format. Hum. Immunol. 55, 144.
Howell, W. M., Jobs, M., Gyllensten, U., and Brookes, A. J. (1999) Dynamic allele-specific hybridization. a new method for scoring single nucleotide polymorphisms. Nat. Biotechnol. 17, 87–88.
Gotoh, M., et al. (1997) Rapid method for detection of point mutations using mismatch binding protein (MutS) and an optical biosensor. Genetic Analysis 14, 47–50.
Gotoh, M., Hasegawa, Y., Shinohara, Y., Shimizu, M., and Tosu, M. (1995) A new approach to determine the effect of mismatches on kinetic parameters in DNA hybridization using an optical biosensor. DNA Res. 2, 285–293.
Feriotto, G., et al. (2001) Biosensor technology for real-time detection of the cystic fibrosis W1282X mutation in CFTR. Hum. Mutat. 18, 70–81.
Feriotto, G., Lucci, M., Bianchi, N., Mischiati, C., and Gambari, R. (1999) Detection of the deltaF508 (F508del) tmutation of the cystic fibrosis gene by surface plasmon resonance and biosensor technology. Hum. Mutat. 13, 390–400.
Bugawan, T. L., Begovich, A. B., and Erlich, H. A. (1990) Rapid HLA-DPB typing using enzymatically amplified DNA and nonradioactive sequence-specific oligonucleotide probes. Immunogenetics 32, 231–241.
Brown, T. J. and Anthony, R. M. (2000) The addition of low numbers of 3′ thymine bases can be used to improve the hybridization signal of oligonucleotides for use within arrays on nylon supports. J. Microbiol. Methods 42, 203–207.
Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20–24.
Fodor, S. P. (1997) DNA sequencing—Massively parallel genomics. Science 277, 393.
Cronin, M. T., et al. (1996) Cystic-fibrosis mutation detection by hybridization to light-generated dna-probe arrays. Hum. Mutat. 7, 244–255.
Chee, M., et al. (1996) Accessing genetic information with high-density dna arrays. Science 274, 610–614.
Hacia, J. G., Brody, L. C., Chee, M. S., Fodor, S. P., and Collins, F. S. (1996) Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis [see comments]. Nat. Genet. 14, 441–447.
Ahrendt, S. A., et al. (1999) Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array. Proc. Natl. Acad. Sci. USA 96, 7382–7387.
Wen, W. H., et al. (2000) Comparison of TP53 mutations identified by oligonucleotide microarray and conventional DNA sequence analysis. Cancer Res. 60, 2716–2722.
Favis, R., et al. (2000) Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2. Nat. Biotechnol. 18, 561–564.
Ben Dor, A., Karp, R., Schwikowski, B., and Yakhini, Z. (2000) Universal DNA tag systems: a combinatorial design scheme. J. Comput. Biol. 7, 503–519.
Hirschhorn, J. N., et al. (2000) SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. USA 97, 12,164–12,169.
Fan, J. B., et al. (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10, 853–860.
Ye, F., et al. (2001) Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification. Hum. Mutat. 17, 305–316.
Armstrong, B., Stewart, M., and Mazumder, A. (2000) Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping. Cytometry 40, 102–108.
Mathew, C. G., Rousseau, J., Rees, J. S., and Harley, E. H. (1983) The molecular basis of alpha thalassaemia in a South African population. Br. J. Haematol. 55, 103–111.
Borriello, F., Weinberg, D. S., and Mutter, G. L. (1994) Evaluation of gene deletions by quantitative polymerase chain-reaction—experience with the alpha-thalassemia model. Diagnostic Molecular Pathology 3, 246–254.
Kunkel, L. M. (1986) Analysis of deletions in DNA from patients with Becker and Duchenne muscular dystrophy. Nature 322, 73–77.
Puget, N., et al. (1999) Screening for germ-line rearrangements and regulatory mutations in BRCA1 led to the identification of four new deletions. Cancer Research 59, 455–461.
Mauillon, J. L., et al. (1996) Identification of novel germline hMLH1 mutations including a 22 kb Alu-mediated deletion in patients with familial colorectal cancer. Cancer Res. 56, 5728–5733.
Wijnen, J., et al. (1998) MSH2 genomic deletions are a frequent cause of HNPCC. Nat. Genet. 20, 326–328.
Krawczak, M. and Cooper, D. N. (1997) The Human Gene Mutation Database. Trends Genet. 13, 121–122.
CoulterMackie, M. B., Applegarth, D. A., Toone, J. R., and Gagnier, L. (1998) A protocol for detection of mitochondrial DNA deletions: Characterization of a novel deletion. Clin. Biochem. 31, 627–632.
Voskova-Goldman, A., Peier, A., Caskey, C. T., Richards, C. S., and Shaffer, L. G. (1997) DMD-specific FISH probes are diagnostically useful in the detection of female carriers of DMD gene deletions. Neurology 48, 1633–1638.
Worley, K. C., et al. (1995) Rapid molecular cytogenetic analysis of x-chromosomal microdeletions—fluorescence in-situ hybridization (Fish) For complex glycerol kinase-deficiency. Am. J. Med. Genet. 57, 615–619.
Armour, J. A. L., Sismani, C., Patsalis, P. C., and Cross, G. (2000) Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res. 28, 605–609.
Bentz, M., Plesch, A., Stilgenbauer, S., Dohner, H., and Lichter, P. (1998) Minimal sizes of deletions detected by comparative genomic hybridization. Genes Chromosomes Cancer 21, 172–175.
Kraus, J., et al. (1997) High-resolution comparative hybridization to combed DNA fibers. Hum. Genet. 99, 374–380.
Pinkel, D., et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20, 207–211.
Pollack, J. R., et al. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23, 41–46.
Parsons, D. W., et al. (1998) Diagnosis of spinal muscular atrophy in an SMN non-deletion patient using a quantitative PCR screen and mutation analysis. J. Med. Genet. 35, 674–676.
Celi, F. S., et al. (1994) Determination of gene dosage by a quantitative adaptation of the polymerase chain-reaction (Gd-pcr)—Rapid detection of deletions and duplications of gene-sequences. Genomics 21, 304–310.
Gelfi, C., Cossu, G., Carta, P., Serra, M., and Righetti, P. G. (1995) Gene dosage in capillary electrophoresis: Pre-natal diagnosis of Down’s syndrome. J Chromatogr. 718, 405–412.
Kallioniemi, O. P. (1996) Comparative genetic hybridization gaining in popularity. Trends Genet. 12, 237–238.
Ligon, A. H., Kashork, C. D., Richards, C. S., and Shaffer, L. G. (2000) Identification of female carriers for Duchenne and Becker muscular dystrophies using a FISH-based approach. Eur. J. Hum. Genet. 8, 293–298.
Wolf, S., et al. (1999) Direct visual resolution of gene copy number in the human photopigment gene array. Investig. Ophthalmol. Vis. Sci. 40, 1585–1589.
Pertl, B., et al. (1999) Rapid detection of chromosome aneuploidies by quantitative fluorescence PCR: first application on 247 chorionic villus samples. J. Med. Genet. 36, 300–303.
Yau, S. C., Bobrow, M., Mathew, C. G., and Abbs, S. J. (1996) Accurate diagnosis of carriers of deletions and duplications in Duchenne/Becker muscular dystrophy by fluorescent dosage analysis. J. Med. Genet. 33, 550–558.
Roetger, A., Brandt, B., and Barnekow, A. (1997) Competitive-differential polymerase chain reaction for gene dosage estimation of erbB-1 (egfr), erbB-2, and erbB-3 oncogenes. DNA Cell Biol. 16, 443–448.
Heid, C. A., Stevens, J., Livak, K. J., and Williams, P. M. (1996) Real time quantitative PCR. Genome Res. 6, 986–994.
Barnes, W. M. (1994) PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc. Natl. Acad. Sci. USA 91, 2216–2220.
Robertson, K. D. and Wolffe, A. P. (2000) DNA methylation in health and disease. Nat. Rev. Genet. 1, 11–19.
Clark, S. J., Harrison, J., Paul, C. L., and Frommer, M. (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997.
Oakeley, E. J. (1999) DNA methylation analysis: a review of current methodologies. Pharmacol. Ther. 84, 389–400.
Bird, A. P. and Southern, E. M. (1978) Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J. Mol. Biol. 118, 27–47.
Singer-Sam, J., LeBon, J. M., Tanguay, R. L., and Riggs, A. D. (1990) A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells. Nucleic Acids Res. 18, 687.
Chotai, K. A. and Payne, S. J. (1998) A rapid, PCR based test for differential molecular diagnosis of Prader—Willi and Angelman syndromes. J. Med. Genet. 35, 472–475.
Maxam, A. M. and Gilbert, W. (1977) A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 74, 560–564.
Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–1995.
Pfeifer, G. P., Steigerwald, S. D., Mueller, P. R., Wold, B., and Riggs, A. D. (1989) Genomic sequencing and methylation analysis by ligation mediated PCR. Science 246, 810–813.
Fritzsche, E., Hayatsu, H., Igloi, G. L., Iida, S., and Kossel, H. (1987) The use of permanganate as a sequencing reagent for identification of 5-methylcytosine residues in DNA. Nucleic Acids Res. 15, 5517–5528.
Frommer, M., et al. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89, 1827–1831.
Sadri, R. and Hornsby, P. J. (1996) Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification. Nucleic Acids Res. 24, 5058–5059.
Gonzalgo, M. L. and Jones, P. A. (1997) Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res. 25, 2529–2531.
Herman, J. G., Graff, J. R., Myohanen, S., Nelkin, B. D., and Baylin, S. B. (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821–9826.
Zeschnigk, M., Lich, C., Buiting, K., Doerfler, W., and Horsthemke, B. (1997) A single-tube PCR test for the diagnosis of Angelman and Prader-Willi syndrome based on allelic methylation differences at the SNRPN locus. Eur. J. Hum. Genet. 5, 94–98.
Muller-Tidow, C., et al. (2001) Analyses of the genomic methylation status of the human cyclin A1 promoter by a novel real-time PCR-based methodology. FEBS Lett. 490, 75–78.
Cotton, R. G. H. (1997) Slowly but surely towards better scanning for mutations. Trends Genet. 13, 43–46.
Jones, A. C., Sampson, J. R., Hoogendoorn, B., Cohen, D., and Cheadle, J. P. (2000) Application and evaluation of denaturing HPLC for molecular genetic analysis in tuberous sclerosis. Hum. Genet. 106, 663–668.
Nickerson, M. L., Warren, M. B., Zbar, B., and Schmidt, L. S. (2001) Random mutagenesis-PCR to introduce alterations into defined DNA sequences for validation of SNP and mutation detection methods. Hum. Mutat. 17, 210–219.
Arnold, N., et al. (1999) A highly sensitive, fast, and economical technique for mutation analysis in hereditary breast and ovarian cancers. Hum. Mutat. 14, 333–339.
Dobson-Stone, C., et al. (2000) Comparison of fluorescent single-strand conformation polymorphism analysis and denaturing high-performance liquid chromatography for detection of EXT1 and EXT2 mutations in hereditary multiple exostoses. Eur. J. Hum. Genet. 8, 24–32.
Klein, W., et al. (2000) The IL-10 gene is not involved in the predisposition to inflammatory bowel disease. Electrophoresis 21, 3578–3582.
Mir, K. U. and Southern, E. M. (1999) Determining the influence of structure on hybridization using oligonucleotide arrays. Nat. Biotechnol. 17, 788–792.
Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., and Sekiya, T. (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86, 2766–2770.
Ravnik-Glavac, M., Glavac, D., and Dean, M. (1994) Sensitivity of single-strand conformation polymorphism and heteroduplex method for mutation detection in the cystic fibrosis gene. Hum. Mol. Genet. 3, 801–807.
Vidal-Puig, A. and Moller, D. E. (1994) Comparative sensitivity of alternative single-strand conformation polymorphism (SSCP) methods. Biotechniques 17, 490–492, 494, 496.
Sheffield, V. C., et al. (1993) The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics 16, 325–332.
Hayashi, K. and Yandell, D. W. (1993) How sensitive is PCR-SSCP? Hum. Mutat. 2, 338–346.
Ellison, J. S. (1996) Fluorescence-based mutation detection. Single-strand conformation polymorphism analysis (F-SSCP). Mol. Biotechnol. 5, 17–31.
Larsen, L., Christiansen, M., Vuust, J., and Andersen, P. S. (1999) High-throughput single-tranded conformation polymorphism analysis by automated capillary electrophoresis: Robust multiplex analysis and pattern based identification of allelic variants. Hum. Mutat. 13, 318–327.
Ellis, L. A., Taylor, C. F., and Taylor, G. R. (2000) A Comparison of Fluorescent SSCP and Denaturing HPLC for High Throughput Mutation Scanning. Hum. Mutat. 15, 556–564.
Liu, Q., Feng, J., and Sommer, S. S. (1996) Bi-directional dideoxy fingerprinting (Bi-ddF): a rapid method for quantitative detection of mutations in genomic regions of 300–600 bp. Hum. Mol. Genet. 5, 107–114.
Larsen, L. A., et al. (2001) Automated mutation screening using dideoxy fingerprinting and capillary array electrophoresis. Hum. Mutat. 18, 451–457.
Nagamine, C. M., Chan, K., and Lau, Y. F. (1989) A PCR artifact: generation of heteroduplexes. Am. J. Hum. Genet. 45, 337–339.
White, M. B., Carvalho, M., Derse, D., O’Brien, S. J., and Dean, M. (1992) Detecting single base substitutions as heteroduplex polymorphisms. Genomics 12, 301–306.
Boyd, M., Lanyon, W. G., and Connor, J. M. (1993) Screening for molecular pathologies in Lesch-Nyhan syndrome. Hum. Mutat. 2, 127–130.
Spritz, R. A. and Holmes, S. A. (1993) Polymerase chain reaction detection of a novel human KIT (mast/stem cell growth factor receptor) gene polymorphism by single-strand conformation polymorphism analysis or by SmaI or BstNI cleavage. Hum. Genet. 92, 208–209.
Ganguly, A., Rock, M. J., and Prockop, D. J. (1993) Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexes. Proc. Natl. Acad. Sci. USA 90, 10,325–10,329.
Korkko, J., Annunen, S., Pihlajamaa, T., Prockop, D. J., and Ala-Kokko, L. (1998) Conformation sensitive gel electrophoresis for simple and accurate detection of mutations: Comparison with denaturing gradient gel electrophoresis and nucleotide sequencing. Proc. Natl. Acad. Sci. USA 95, 1681–1685.
Ganguly, T., Dhulipala, R., Godmilow, L., and Ganguly, A. (1998) High throughput fluorescence-based conformation-sensitive gel electrophoresis (F-CSGE) identifies six unique BRCA2 mutations and an overall low incidence of BRCA2 mutations in high-risk BRCA1-negative breast cancer families. Hum. Genet. 102, 549–556.
Edwards, S. M., Kote-Jarai, Z., Hamoudi, R., and Eeles, R. A. (2001) An improved high throughput heteroduplex mutation detection system for screening BRCA2 mutations-fluorescent mutation detection (F-MD). Hum. Mutat. 17, 220–232.
Rozycka, M., Collins, N., Stratton, M. R., and Wooster, R. (2000) Rapid detection of DNA sequence variants by conformation-sensitive capillary electrophoresis. Genomics 70, 34–40.
Fischer, S. G. and Lerman, L. S. (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. USA 80, 1579–1583.
Myers, R. M., Fischer, S. G., Maniatis, T., and Lerman, L. S. (1985) 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. 13, 3111–3129.
Gejman, P. V., Cao, Q., Guedj, F., and Sommer, S. (1998) The sensitivity of denaturing gradient gel electrophoresis: a blinded analysis. Mutat. Res. 382, 109–114.
Henco, K., Harders, J., Wiese, U., and Riesner, D. (1994) Temperature gradient gel electrophoresis (TGGE) for the detection of polymorphic DNA and RNA. Methods Mol. Biol. 31, 211–228.
Hovig, E., Smith-Sorensen, B., Brogger, A., and Borrensen, A. L. (1991) Constant denaturant gel electrophoresis, a modification of denaturing gradient gel electrophoresis, in mutation detection. Mutat. Res. 263, 61.
Khrapko, K., et al. (1994) Constant denaturant capillary electrophoresis (CDCE): a high resolution approach to mutational analysis. Nucleic Acids Res. 22, 364–369.
Gao, Q. F. and Yeung, E. S. (2000) High-throughput detection of unknown mutations by using multiplexed capillary electrophoresis with poly(vinylpyrrolidone) solution. Analyt. Chem. 72, 2499–2506.
Underhill, P. A., Jin, L., Zemans, R., Oefner, P. J., and Cavalli-Sforza, L. L. (1996) A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc. Natl. Acad. Sci. USA 93, 196–200.
Jones, A. C., et al. (1999) Optimal temperature selection for mutation detection by denaturing HPLC and comparison to single-stranded conformation polymorphism and heteroduplex analysis. Clin. Chem. 45, 1133–1140.
O’Donovan, M. C., et al. (1998) Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 52, 44–49.
Liu, W. G., Smith, D. I., Rechtzigel, K. J., Thibodeau, S. N., and James, C. D. (1998) Denaturing high performance liquid chromatography (DHPLC) used in the detection of germline and somatic mutations. Nucleic Acids Res. 26, 1396–1400.
Hecker, K. H., Taylor, P. D., and Gjerde, D. T. (1999) Mutation detection by denaturing DNA chromatography using fluorescently labeled polymerase chain reaction products. Anal. Biochem. 272, 156–164.
Novack, D. F., Casna, N. J., Fischer, S. G., and Ford, J. P. (1986) Detection of single base-pair mismatches in dna by chemical modification followed by electrophoresis in 15-percent polyacrylamide-gel. Proc. Natl. Acad. Sci. USA 83, 586–590.
Ganguly, A. and Prockop, D. J. (1990) Detection of single-base mutations by reaction of DNA heteroduplexes with a water-soluble carbodiimide followed by primer extension: application to products from the polymerase chain reaction. Nucleic Acids Res. 18, 3933–3939.
Cotton, R. G. H., Rodrigues, N. R., and Campbell, R. D. (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.
Condie, A., et al. (1993) Detection of point mutations in the P53 gene—comparison of single-strand conformation polymorphism, constant denaturant gel-electrophoresis, and hydroxylamine and osmium-tetroxide techniques. Hum. Mutat. 2, 58–66.
Forrest, S. M., Dahl, H. H., Howells, D. W., Dianzani, I., and Cotton, R. G (1991) Mutation detection in phenylketonuria by using chemical cleavage of mismatch: importance of using probes from both normal and patient samples. Am. J. Hum. Genet. 49, 175–183.
Hull, J., Shackleton, S., and Harris, A. (1994) Analysis of mutations and alternative splicing patterns in the CFTR gene using mRNA derived from nasal epithelial cells. Hum. Mol. Genet. 3, 1141–1146.
Verpy, E., Biasotto, M., Meo, T., and Tosi, M. (1994) Efficient detection of point mutations on color-coded strands of target DNA. Proc. Natl. Acad. Sci. USA 91, 1873–1877.
Rowley, G., Saad, S., Gianelli, F., and Green, P. M. (1995) Ultrarapid mutation detection by multiplex, solid-phase chemical cleavage. Genomics 30, 574–582.
Hansen, L. L., Justesen, J., and Kruse, T. A. (1996) Sensitive and fast mutation detection by solid phase chemical cleavage. Hum. Mutat. 7, 256–263.
Roberts, E., Deeble, V. J., Woods, C. G., and Taylor, G. R. (1997) Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch. Nucleic Acids Res. 25, 3377–3378.
Solaro, P. C., Birkenkamp, K., Pfeiffer, P., and Kemper, B. (1993) Endo-nuclease VII of phage T4 triggers mismatch correction in vitro. J. Mol. Biol. 230, 868–877.
Youil, R., Kemper, B. W., and Cotton, R. G. H. (1995) Screening for mutations by enzyme mismatch cleavage with T4 endonuclease-7. Proc. Natl. Acad. Sci. USA 92, 87–91.
Giunta, C., et al. (1996) Rapid diagnosis of germline p53 mutation using the enzyme mismatch cleavage method. Diagnostic Molecular Pathology 5, 265–270.
Mashal, R. D., Koontz, J., and Sklar, J. (1995) Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat. Genet. 9, 177–183.
DelTito, B. J., et al. (1998) Automated fluorescent analysis procedure for enzymatic mutation detection. Clin. Chem. 44, 731–739.
Otway, R., Tetlow, N., Hornby, J., and Kohonen-Corish, M. (2000) Evaluation of enzymatic mutation detectiontrade mark in hereditary nonpolyposis colorectal cancer. Hum. Mutat. 16, 61–67.
Oleykowski, C. A., Bronson, M. C., Godwin, A. K., and Yeung, A. T. (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 26, 4597–4602.
Kulinski, J., Besack, D., Oleykowski, C. A., Godwin, A. K., and Yeung, A. T. (2000) CEL I enzymatic mutation detection assay. Biotechniques 29, 44–46, 48.
Colbert, T., et al. High-throughput screening for induced point mutations. Plant Physiol. 126, 480–484.
Huang, J., Lu, J., Barany, F., and Cao, W. (2001) Multiple cleavage activities of endonuclease V from Thermotoga maritima: recognition and strand nicking mechanism. Biochemistry 40, 8738–8748.
Myers, R. M., Larin, Z., and Maniatis, T. (1985) Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA-DNA duplexes. Science 230, 1242–1246.
Winter, E., Yamamoto, F., Almoguera, C., and Perucho, M. (1985) A method to detect and characterize point mutations in transcribed genes—amplification and overexpression of the mutant c-ki-ras allele in human tumor cells. Proc. Natl. Acad. Sci. USA 82, 7575–7579.
Lopez-Galindez, C., et al. (1988) Analysis of genetic variability and mapping of point mutations in influenza virus by the RNase A mismatch cleavage method. Proc. Natl. Acad. Sci. USA 85, 3522–3526.
Miki, Y., et al. (1992) Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52, 643–645.
Goldrick, M. M., et al. (1996) NIRCA™—A rapid robust method for screening for unknown point mutations. Biotechniques 21, 106–112.
Prescott, J., (1999) Cleavage of double-stranded copy RNA by RNase 1 and RNase T1 provides a robust means to detect p53 gene mutations in clinical specimens. 20, 1149–1161.
Faudoa, R., Xue, Z., Lee, F., Baser, M. E., and Hung, G. (2000) Detection of novel NF2 mutations by an RNA mismatch cleavage method. Hum. Mutat. 15, 474–478.
Hawkins, G. A. and Hoffman, L. M. (1997) Mutation detection and DNA fingerprinting at single nucleotide resolution using base excision sequence scanning (BESS). Clin. Chem. 43, 23.
Hawkins, G. A. and Hoffman, L. M. (1999) Rapid DNA mutation identification and fingerprinting using base excision sequence scanning. Electrophoresis 20, 1171–1176.
Brow, M. A., et al. (1996) Differentiation of bacterial 16S rRNA genes and intergenic regions and Mycobacterium tuberculosis katG genes by structure-specific endonuclease cleavage. J. Clin. Microbiol. 34, 3129–3137.
Marshall, D. J., et al. (1997) Determination of hepatitis C virus genotypes in the United States by Cleavase Fragment Length Polymorphism analysis. J. Clin. Microbiol. 35, 3156–3162.
Rossetti, S., Englisch, S., Bresin, E., Pignatti, P. F., and Turco, A. E. (1997) Detection of mutations in human genes by a new rapid method: cleavage fragment length polymorphism analysis (CFLPA). Molecular and Cellular Probes 11, 155–160.
Jiricny, J., Su, S. S., Wood, S. G., and Modrich, P. (1988) Mismatch-containing oligonucleotide duplexes bound by the escherichia-coli muts-encoded protein. Nucleic Acids Res. 16, 7843–7853.
Lishanski, A., Ostrander, E. A., and Rine, J. (1994) Mutation detection by mismatch binding-protein, MUTS, in amplified DNA—application to the cystic-fibrosis gene. Proc. Natl. Acad. Sci. USA 91, 2674–2678.
Wagner, R., Debbie, P., and Radman, M. (1995) Mutation detection using immobilized mismatch binding-protein (MUTS). Nucleic Acids Res. 23, 3944–3948.
Sanger, F., Nicklen, S., and Coulson, A. R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463–5467.
Parinov, S., et al. (1996) DNA sequencing by hybridization to microchip octa-and decanucleotides extended by stacked pentanucleotides. Nucleic Acids Res. 24, 2998–3004.
Lander, E. S., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
Nickerson, D. A., Tobe, V. O., and Taylor, S. L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745–2751.
Duddy, P. M., Hanby, A. M., Barnes, D. M., and Camplejohn, R. S. (2000) Improving the detection of p53 mutations in breast cancer by use of the FASAY, a functional assay. J. Mol. Diagn. 2, 139–144.
Bonfield, J. K., Rada, C., and Staden, R. (1998) Automated detection of point mutations using fluorescent sequence trace subtraction. Nucleic Acids Res. 26, 3404–3409.
Mattocks, C., Tarpey, P., Bobrow, M., and Whittaker, J. (2000) Comparative sequence analysis (CSA): a new sequence-based method for the identification and characterization of mutations in DNA. Hum. Mutat. 16, 437–443.
Hattori, M., Shibata, A., Yoshioka, K., and Sakaki, Y (1993) Orphan peak analysis: a novel method for detection of point mutations using an automated fluorescence DNA sequencer. Genomics 15, 415–417.
Fu, D. J., et al. (1998) Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16, 381–384.
Ginot, F. (1997) Oligonucleotide micro-arrays for identification of unknown mutations: how far from reality? Hum. Mutat. 10, 1–10.
Kozal, M. J., et al. (1996) Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2, 753–759.
Wikman, F. P., et al. (2000) Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples. Clin. Chem. 46, 1555–1561.
Roest, P. A., Roberts, R. G., Sugino, S., van Ommen, G. J., and Den Dunnen, J. T. (1993) Protein truncation test (PTT) for rapid detection of translation-terminating mutations. Hum. Mol. Genet. 2, 1719–1721.
Powell, S. M., et al. (1993) Molecular diagnosis of familial adenomatous polyposis. N. Engl. J. Med. 329, 1982–1987.
Den Dunnen, J. T. and van Ommen, G. J. (1999) The protein truncation test: A review. Hum. Mutat. 14, 95–102.
Ishioka, C., et al. (1997) Detection of heterozygous truncating mutations in the BRCA1 and APC genes by using a rapid screening assay in yeast. Proc. Natl. Acad. Sci. USA 94, 2449–2453.
Flaman, J. M., et al. (1995) A simple p53 functional assay for screening cell lines, blood, and tumors. Proc. Natl. Acad. Sci. USA 92, 3963–3967.
Kruger, W. D. and Cox, D. R. (1995) A yeast assay for functional detection of mutations in the human cystathionine beta-synthase gene. Hum. Mol. Genet. 4, 1155–1161.
Schwartz, H., Alvares, C. P., White, M. B., and Fields, S. (1998) Mutation detection by a two-hybrid assay. Hum. Mol. Genet. 7, 1029–1032.
Bougeard, G., et al. (2001) Detection of 11 germline inactivating TP53 mutations and absence of TP63 and HCHK2 mutations in 17 French families with Li-Fraumeni or Li-Fraumeni-like syndrome. J. Med. Genet. 38, 253–257.
Davies, R. C., Bratt, E., and Hastie, N. D. (2000) Did nucleotides or amino acids drive evolutionary conservation of the WT1 +/−KTS alternative splice? Hum. Mol. Genet. 9, 1177–1183.
Xue, G., Pang, H. M., and Yeung, E. S. (2001) On-line nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing. J. Chromatogr. A 914, 245–256.
Dunnen, J. T. and Antonarakis, S. E. (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat. 15, 7–12.
Beutler, E., McKusick, V. A., Motulsky, A. G., Scriver, C. R., and Hutchinson, F. (1996) Mutation nomenclature: nicknames, systematic names, and unique identifiers. Hum. Mutat. 8, 203–206.
Auerbach, A. D. (2000) 8th International HUGO-Mutation Database Initiative Meeting, April 9, 2000, Vancouver, Canada. Hum. Mutat. 16, 265–268.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Humana Press Inc.
About this protocol
Cite this protocol
Taylor, C.F., Taylor, G.R. (2004). Current and Emerging Techniques for Diagnostic Mutation Detection. In: Elles, R., Mountford, R. (eds) Molecular Diagnosis of Genetic Diseases. Methods in Molecular Medicine™, vol 92. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-432-8:9
Download citation
DOI: https://doi.org/10.1385/1-59259-432-8:9
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-932-2
Online ISBN: 978-1-59259-432-0
eBook Packages: Springer Protocols