Recent developments in molecular diagnostic assays for genetic diseases

Journal of Clinical Ligand Assay

Volumn 19, Issue 1, 1996, Pages 27-42

  Mifflin, Theodore E ^a  

^a PRESBYTERIAN UNIVERSITY HOSPITAL   (United States)

Author keywords

Genetic disease; Microsatellite; Molecular genetics; Mutation; PCR; Polymorphism; RFLP; Screening

Indexed keywords

DENATURING GRADIENT GEL ELECTROPHORESIS; DNA DETERMINATION; EVOLUTION; GENE MUTATION; GENETIC ANALYSIS; HUMAN; HUMAN CELL; LABORATORY AUTOMATION; MOLECULAR GENETICS; POLYMERASE CHAIN REACTION; PROTEIN BINDING; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SINGLE STRAND CONFORMATION POLYMORPHISM;

EID: 0029877659     PISSN: 10811672     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (119)

1. Super M: Medical genetics. [Review]. Postgraduate Medical Journal 1991;67:613.
2. Reiss J, Cooper DN: Application of the polymerase chain reaction to the diagnosis of human genetic disease. [Review]. Human Genetics 1990;85:1.
3. Grompe M: The rapid detection of unknown mutations in nucleic acids. [Review]. Nature Genetics 1993;5:111.
4. Cotton RG: Current methods of mutation detection. [Review]. Mutation Research 1993;285:125.
5. Coutelle C: New DNA-analysis techniques (mini-review). [Review]. Biomedica Biochimica Acta 1991;50:3.
6. Trask BJ: DNA sequence localization in metaphase and interphase cells by fluorescence in situ hybridization. [Review]. Methods in Cell Biology 1991;35:3.
7. Trask BJ: Gene mapping by in situ hybridization. [Review]. Current Opinion in Genetics & Development 1991;1:82.
8. Sasaki K, Pinkel D, Tsukahara M, et al: Detection of a human chromosomal translocation t(8;9) in a baby with multiple malformations using two-color fluorescence in situ hybridization. Pathology International 1994;44:145.
9. Trask BJ: Fluorescence in situ hybridization: applications in cytogenetics and gene mapping. [Review]. Trends in Genetics 1991;7:149.
10. Kallioniemi A, Kallioniemi OP, Waldman FM, et al: Detection of retinoblastoma gene copy number in metaphase chromosomes and interphase nuclei by fluorescence in situ hybridization. Cytogenetics & Cell Genetics 1992;60:190.
11. Trask BJ, Allen S, Massa H, et al: Studies of metaphase and interphase chromosomes using fluorescence in situ hybridization. Cold Spring Harbor Symposia on Quantitative Biology 1993;58:767.
12. Kallioniemi OP, Kallioniemi A, Sudar D, et al: Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. [Review]. Seminars in Cancer Biology 1993;4:41.
13. Kallioniemi A, Kallioniemi OP, Sudar D, et al: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992;258:818.
14. Kallioniemi OP, Kallioniemi A, Piper J, et al: Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. [Review]. Genes, Chromosomes & Cancer 1994;10:231.
15. Levin NA, Brzoska PM, Warnock ML, et al: Identification of novel regions of altered DNA copy number in small cell lung tumors. Genes, Chromosomes & Cancer 1995;13:175.
16. Miller SA, Dykes DD, Polesky HF: A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 1988;16:1215.
17. Lopez-Fernandez C, Gosalvez J, Ferrucci L, et al: Restriction endonucleases in the study of eukaryotic chromosomes. [Review]. Genetica 1991;83:257.
18. Upcroft P, Upcroft JA: Comparison of properties of agarose for electrophoresis of DNA. [Review]. Journal of Chromatography 1993;618:79.
19. Kroczek RA: Southern and northern analysis. [Review]. Journal of Chromatography 1993;618:133.
20. Trnovsky J: Semi-dry electroblotting of DNA and RNA from agarose and polyacrylamide gels. Biotechniques 1992;13:800.
21. Hoheisel JD: Application of hybridization techniques to genome mapping and sequencing. [Review]. Trends in Genetics 1994;10:79.
22. Mansfield ES, Worley JM, McKenzie SE, et al: Nucleic acid detection of using non-radioactive labeling methods. Molecular & Cellular Probes 1995;9:145.
23. During K: Non-radioactive detection methods for nucleic acids separated by electrophoresis. [Review]. Journal of Chromatography 1993;618:105.
24. Klein D, Grody WW, Tabor DE, et al: Pitfalls of restriction endonuclease digestion for direct detection of point mutations [letter]. Clinical Chemistry 1992;38:1392.
25. Saiki RK, Scharf S, Faloona F, et al: Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985;230:1350.
26. Saiki RK, Gelfand DH, Stoffel S, et al: Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988;239:487.
27. Saiki RK, Chang CA, Levenson CH, et al: Diagnosis of sickle cell anemia and beta-thalassemia with enzymatically amplified DNA and nonradioactive allele-specific oligonucleotide probes. New England Journal of Medicine 1988;319:537.
28. Saiki RK, Walsh PS, Levenson CH, et al: Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proceedings of the National Academy of Sciences of the United States of America 1989;86:6230.
29. Templeton NS: The polymerase chain reaction. History, methods, and applications. Diagnostic Molecular Pathology 1992;1:58.
30. Erlich HA, Gelfand D, Sninsky JJ: Recent advances in the polymerase chain reaction. [Review]. Science 1991;252:1643.
31. Belak S, Ballagi-Pordany A: Experiences on the application of the polymerase chain reaction in a diagnostic laboratory. [Review]. Molecular & Cellular Probes 1993;7:241.
32. Zeillinger R, Schneeberger C, Speiser P, et al: A simple method for isolation of DNA from blood clots suited for use in PCR. Biotechniques 1993;14:202.
33. Fujita M, Usui S, Kiyama M, et al: Chemical robot for enzymatic reactions and extraction processes of DNA in DNA sequence analysis. Biotechniques 1990;9:584.
34. Walsh PS, Metzger DA, Higuchi R: Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 1991;10:506.
35. Richards B, Skoletsky J, Shuber AP, et al: Multiplex PCR amplification from the CFTR gene using DNA prepared from buccal brushes/swabs. Human Molecular Genetics 1993;2:159.
36. Schneeberger C, Kury F, Larsen J, et al: A simple method for extraction of DNA from Guthrie cards. PCR Methods & Applicaions 1992;2:177.
37. Verlingue C, Mercier B, Lecoq I, et al: Retrospective study of the cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in Guthrie cards from a large cohort of neonatal screening for cystic fibrosis. Human Genetics 1994;93:429.
38. Seltzer WK, Accurso F, Fall MZ, et al: Screening for cystic fibrosis: feasibility of molecular genetic analysis of dried blood specimens. Biochemical Medicine & Metabolic Biology 1991;46:105.
39. DeMarchi JM, Richards CS, Fenwick RG, et al: A robotics-assisted procedure for large scale cystic fibrosis mutation analysis. Human Mutation 1994;4:281.
40. Balaguer P, Terouanne B, Allibert P, et al: Detection of single base substitutions in polynucleotides by capture with immobilized oligonucleotides. Molecular & Cellular Probes 1993;7:155.
41. Chevrier D, Rasmussen SR, Guesdon JL: PCR product quantification by non-radioactive hybridization procedures using an oligonucleotide covalently bound to microwells. Molecular & Cellular Probes 1993;7:187.
42. Rasmussen SR, Larsen MR, Rasmussen SE: Covalent immobilization of DNA onto polystyrene microwells: the molecules are only bound at the 5′ end. Analytical Biochemistry 1991;198:138.
43. Maskos U, Southern EM: Oligonucleotide hybridizations on glass supports: a novel linker for Oligonucleotide synthesis and hybridization properties of oligonucleotides synthesized in situ. Nucleic Acids Research 1992;20:1679.
44. Maskos U, Southern EM: A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesized on a glass support. Nucleic Acids Research 1993;21:4663.
45. Ziegle JS, Su Y, Corcoran KP, et al: Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics 1992;14:1026.
46. Mayrand PE, Corcoran KP, Ziegle JS, et al: The use of fluorescence detection and internal lane standards to size PCR products automatically. Applied & Theoretical Electrophoresis 1992;3:1.
47. Bronstein I, Voyta JC, Lazzari KG, et al: Rapid and sensitive detection of DNA in Southern blots with chemiluminescence. Biotechniques 1990;8:310.
48. Iitia A, Hogdall E, Dahlen P, et al: Detection of mutation delta F508 in the cystic fibrosis gene using allele-specific PCR primers and time-resolved fluorometry. PCR Methods & Applications 1992;2:157.
49. DeMarchi JM, Beaudet AL, Caskey CT, et al: Experience of an academic reference laboratory using automation for analysis of cystic fibrosis mutations. Archives of Pathology & Laboratory Medicine 1994;118:26.
50. Southern EM: Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology 1975;98:503.
51. Highsmith WE, Jr., Chong GL, Orr HT, et al: Frequency of the delta Phe508 mutation and correlation with XV.2c/KM-19 haplotypes in an American population of cystic fibrosis patients: results of a collaborative study. Clinical Chemistry 1990;36:1741.
52. Cuppens H, Teng H, Raeymaekers P, et al: CFTR haplotype backgrounds on normal and mutant CFTR genes. Human Molecular Genetics 1994;3:607.
53. Beaudet AL, Feldman GL, Fernbach SD, et al: Linkage disequilibrium, cystic fibrosis, and genetic counseling. American Journal of Human Genetics 1989;44:319.
54. Suzuki H, Emi M, Komiya A, et al: Localization of a tumor suppressor gene associated with progression of human prostate cancer within a 1.2 Mb region of 8p22-p21.3. Genes, Chromosomes & Cancer 1995;13:168.
55. Mayrand PE, Hoff LB, McBride LJ, et al: Automation of specific human gene detection. Clinical Chemistry 1990;36:2063.
56. Mayrand PE, Robertson J, Ziegle J, et al: Automated genetic analysis. Annales de Biologie Clinique 1991;49:224.
57. Myers RM, Fischer SG, Maniatis T, et al: 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 Research 1985;13:3111.
58. Gray MR: Detection of DNA sequence polymorphisms in human genomic DNA by using denaturing gradient gel blots. American Journal of Human Genetics 1992;50:331.
59. Orita M, Iwahana H, Kanazawa H, et al: Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proceedings of the National Academy of Sciences of the United States of America 1989;86:2766.
60. Aly AM, Higuchi M, Kasper CK, et al: Hemophilia A due to mutations that create new N-glycosylation sites. Proceedings of the National Academy of Sciences of the United States of America 1992;89:4933.
61. Bourgeois F, Gu XF, Deybach JC, et al: Denaturing gradient gel electrophoresis for rapid detection of latent carriers of a subtype of acute intermittent porphyria with normal erythrocyte porphobilinogen deaminase activity. Clinical Chemistry 1992;38:93.
62. Gayther SA, Sud R, Wells D, et al: Rapid detection of rare variants and common polymorphisms in the APC gene by PCR-SSCP for presymptomatic diagnosis and showing allele loss. Journal of Medical Genetics 1995;32:568.
63. Rossetti S, Corra S, Biasi MO, et al: Comparison of heteroduplex and single-strand conformation analysis, followed by ethidium bromide visualization for the detection of mutations in four human genes. Molecular & Cellular Probes 1995;9:195.
64. Giannattasio G, Bisceglia L, Lattansio P, et al: Molecular screening of genetic defects with RNA-SSCP analysis: the PKU and custinuria model. Human Molecular Genetics 1995;9:201.
65. Chaubert P, Bautista D, Benhattar J: An improved method for rapid screening of DNA mutations by nonradioactive single-strand conformation polymorphism procedure. Biotechniques 1993;15:586.
66. Sugano K, Kyogoku A, Fukayama N, et al: Methods in laboratory investigation. Rapid and simple detection of c-Ki-ras2 gene codon 12 mutations by nonradioisotopic single-strand conformation polymorphism analysis. Laboratory Investigation 1993;68:361.
67. Smooker PM, Cotton RG: The use of chemical reagents in the detection of DNA mutations. [Review]. Mutation Research 1993;288:65.
68. Saleeba JA, Cotton RG: Chemical cleavage of mismatch to detect mutations. Methods in Enzymology 1993;217:286.
69. 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. Proceedings of the National Academy of Sciences of the United States of America 1988;85:4397.
70. Dianzani I, Camaschella C, Saglio G, et al: Simultaneous screening for beta-thalassemia mutations by chemical cleavage of mismatch. Genomics 1991;11:48.
71. Dianzani I, Forrest SM, Camaschella C, et al: Screening for mutations in the phenylalanine hydroxylase gene from Italian patients with phenylketonuria by using the chemical cleavage method: a new splice mutation. American Journal of Human Genetics 1991;48:631.
72. Dianzani I, Forrest SM, Camaschella C, et al: Heterozygotes and homozygotes: discrimination by chemical cleavage of mismatch [letter]. American Journal of Human Genetics 1991;48:423.
73. Kilimann MW, Pizzuti A, Grompe M, et al: Point mutations and polymorphisms in the human dystrophin gene identified in genomic DNA sequences amplified by multiplex PCR. Human Genetics 1992;89:253.
74. Myers RM, Larin Z, Maniatis T: Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA:DNA duplexes. Science 1985;230:1242.
75. Meyer CG, Tannich E, Harders J, et al: Direct sequencing of variable HLA gene segments after in vitro amplification and allele separation by temperature-gradient gel electrophoresis. Journal of Immunological Methods 1991;142:251.
76. Gayther SA, Harrington P, Russell P, et al: Rapid Detection of Regionally Clustered Germ-Line BRCA1 Mutations by Multiplex Heteroduplex Analysis. American Journal of Human Genetics 1996;58:451.
77. White MB, Carvalho M, Derse D, et al: Detecting single base substitutions as heteroduplex polymorphisms. Genomics 1992;12:301.
78. Tsongalis GJ, Kaufmann WK, Wilson SJ, et al: Rapid screening for p53 mutations with a sensitive heteroduplex detection technique. Clinical Chemistry 1994;40:485.
79. Chamberlain JS, Gibbs RA, Ranier JE, et al: Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Research 1988;16:11141.
80. Hentemann M, Reiss J, Wagner M, et al:. Rapid detection of deletions in the Duchenne muscular dystrophy gene by PCR amplification of deletion-prone exon sequences. Human Genetics 1990;84:228.
81. Chakraborty R, Zhong Y, de Andrade M, et al: Linkage disequilibria among (CA)n polymorphisms in the human dystrophin gene and their implications in carrier detection and prenatal diagnosis in Duchenne and Becker muscular dystrophies. Genomics 1994;21:567.
82. King SC, Stapleton PM, Walker AP, et al: Two dinucleotide repeat polymorphisms at the DMD locus. Human Molecular Genetics 1994;3:523.
83. Weber JL, May PE: Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. American Journal of Human Genetics 1989;44:388.
84. Weber JL: Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 1990;7:524.
85. King SC, Roche AL, Passos-Bueno MR, et al: Molecular characterization of further dystrophin gene microsatellites. Molecular & Cellular Probes 1995;9:361.
86. Gyapay G, Morissette J, Vignal A, et al:. The 1993-94 Genethon human genetic linkage map [see comments]. Nature Genetics 1994;7:246.
87. Rommens J, Kerem BS, Greer W, et al: Rapid nonradioactive detection of the major cystic fibrosis mutation [letter]. American Journal of Human Genetics 1990;46:395.
88. Dianzani I, Camaschella C, Ponzone A, et al: Dilemmas and progress in mutation detection. Trends in Genetics 1993;9:403.
89. Ferrie RM, Schwarz MJ, Robertson NH, et al: Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene. American Journal of Human Genetics 1992;51:251.
90. Friedman KJ, Highsmith WE, Jr., Silverman LM: Detecting multiple cystic fibrosis mutations by polymerase chain reaction-mediated site-directed mutagenesis. Clinical Chemistry 1991;37:753.
91. Reiss J, Krawczak M, Schloesser M, et al: The effect of replication errors on the mismatch analysis of PCR-amplified DNA. Nucleic Acids Research 1990;18:973.
92. Cros P, Allibert P, Mandrand B, et al: Oligonucleotide genotyping of HLA polymorphism on microtitre plates. Lancet 1992;340:870.
93. Barranger JA, Rice E, Sakallah SA et al: Enzymatic and molecular diagnosis of Gaucher disease, in McPherson RA (ed): Clinics In Laboratory Medicine. Philadelphia, W.B. Saunders, 1995, p 899.
94. Kant JA, Mifflin TE, McGlennen R et al: Molecular diagnosis of cystic fibrosis, in McPherson RA (ed): Clinics In Laboratory Medicine. Philadelphia, W.B. Saunders, 1995, p 877.
95. Chehab FF, Wall J: Detection of multiple cystic fibrosis mutations by reverse dot blot hybridization: a technology for carrier screening. Human Genetics 1992;89:163.
96. Wall J, Cai S, Chehab FF: A 31-mutation assay for cystic fibrosis testing in the clinical molecular diagnostics laboratory. Human Mutation 1995;5:333.
97. Rady M, D'Almaco E, Seia M, et al: Simultaneous detection of fourteen Italian cystic fibrosis mutations in seven exons by reverse dot-blot analysis. Molecular & Cellular Probes 1995;9:357.
98. Shuber AP, Michalowsky L, Nass S, et al: Multiple allele specific diagnostic assay (MASDA): A high throughput, low cost procedure for DNA diagnostics [Abstract]. American Journal of Human Genetics 1995;57:A228.
99. Smith V, Craxton M, Bankier AT, et al: Preparation and fluorescent sequencing of M13 clones: microtiter methods. Methods in Enzymology 1993;218:173.
100. Ruano G, Kidd KK: Coupled amplification and sequencing of genomic DNA. Proceedings of the National Academy of Sciences of the United States of America 1991;88:2815.
101. McBride LJ, Koepf SM, Gibbs RA, et al: Automated DNA sequencing methods involving polymerase chain reaction. Clinical Chemistry 1989;35:2196.
102. Lee LG, Connell CR, Bloch W: Allelic discrimination by nick-translation PCR with fluorogenic probes. Nucleic Acids Research 1993;21:3761.
103. Maskos U, Southern EM: A novel method for the analysis of multiple sequence variants by hybridization to oligonucleotides. Nucleic Acids Research 1993;21:2267.
104. Drmanac R, Drmanac S, Strezoska Z, et al: DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing [published erratum appears in Science 1994 Feb 4;163(5147):596]. Science 1993;260:1649-52.
105. Strezoska Z, Paunesku T, Radosavljevic D, et al: DNA sequencing by hybridization: 100 bases read by a non-gel-based method. Proceedings of the National Academy of Sciences of the United States of America 1991;88:10089.
106. Pease AC, Solas D, Sullivan EJ, et al: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proceedings of the National Academy of Sciences of the United States of America 1994;91:5022.
107. Fodor SP, Read JL, Pirrung MC, et al: Light-directed, spatially addressable parallel chemical synthesis. Science 1991;251:767.
108. Roest PA, Roberts RG, Sugino S, et al: Protein truncation test (PTT) for rapid detection of translation-terminating mutations. Human Molecular Genetics 1993;2:1719.
109. Plummer SJ, Culver-Anton H, Webster L, et al: Detection of BRCA1 mutations by the protein truncation test Human Molecular Genetics 1995;4:1989.
110. Hogervorst FB, Cornelis RS, Bout M, et al: Rapid detection of BRCA1 mutations by the protein truncation test. Nature Genetics 1995;10:208.
111. 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.
112. Dean M: Resolving DNA mutations. Nature Genetics 1995;9:103.
113. Mashal RD, Koontz J, Sklar J: Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nature Genetics 1995;9:177.
114. Youil R, Kemper BW, Cotton RG: Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proceedings of the National Academy of Sciences of the United 1995;92:87.
115. Mifflin TE: Use and applications of nucleic acid probes in the clinical laboratory. [Review]. Clinical Chemistry 1989;35:1819.
116. Glowniak JV: Bushway MK. Computer networks as a medical resource. Accessing and using the Internet. JAMA 1994;271:1934.
117. Billings P, Beckwith J: Genetic testing in the workplace: a view from the USA. [Review]. Trends in Genetics 1992;8:198.
118. Swynghedauw B, Barrieux A: An introduction to the jargon of molecular biology. Part I. [Review]. Cardiovascular Research 1993;27:1414.
119. Swynghedauw B, Moalic JM, Bourgeois F, et al: An introduction to the jargon of molecular biology. Part II. [Review]. Cardiovascular Research 1993;27:1566.