Automation in genotyping of single nucleotide polymorphisms

Human Mutation

Volumn 17, Issue 6, 2001, Pages 475-492

  Gut, Ivo G ^a  

^a CENTRE NATIONAL DE GÉNOTYPAGE   (France)

Author keywords

Arrays; Automation; DNA analysis; Genotyping; Mass spectrometry; Microarrays; Microspheres; Mutation detection; Robotics; SNP; Variation

Indexed keywords

ALLELE; AUTOMATION; GENE MUTATION; GENETIC ANALYSIS; GENOTYPE; HYBRIDIZATION; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNOLOGY;

GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

PANACEA;

EID: 0035010640     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.1131     Document Type: Review

References (82)

1. Anderson RC, Su X, Bogdan GJ, Fenton J. 2000. A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res (methods online) 28:e60.
2. Barany F. 1991. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci USA 88:189-193.
3. Baron H, Fung S, Aydin A, Bahring S, Luft FC, Schuster H. 1996. Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nat Biotechnol 14:1279-1282.
4. Brookes AJ, Kwok P-Y, White PS, Oefner PJ. 2001. SNiPpets from the Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis, September 8-11, 2000, Taos, New Mexico, USA. Hum Mutat 17:241-242.
5. Brown PO, Botstein D. 1999. Exploring the new world of the genome with DNA microarrays. Nat Genet 21 (suppl): 33-37.
6. Butler JM, Jiang-Baucom P, Huang M, Belgrader P, Girard J. 1996. Peptide nucleic acid characterization by MALDI-TOF mass spectrometry. Anal Chem 68:3283-3287.
7. Cai H, White PS, Torney D, Deshpande A, Wang Z, Marrone B, Nolan JP. 2000. Flow cytometry-base minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring. Genomics 66:135-143.
8. Chen J, Iannone MA, Li M-S, Taylor D, Rivers P, Nelsen AJ, Slentz-Kesler KA, Roses A, Weiner MP. 2000. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 10:549-557.
9. Chen X, Kwok P-Y. 1997. Template-directed dye-terminator incorporation (TDI) assay: a homogeneous DNA diagnostic method based on fluorescence resonance energy transfer. Nucleic Acids Res 25:347-353.
10. Chen X, Livak KJ, Kwok PY. 1998. A homogeneous ligase-mediated DNA diagnostic test. Genome Res 8:549-556.
11. Chen X, Zehnbauer B, Girnke A, Kwok P-Y. 1997. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc Natl Acad Sci USA 94:10756-10761.
12. Chen X, Levine L, Kwok PY. 1999. Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res 9:492-498.
13. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. 1999. Making and reading microarrays. Nat Genet 21(suppl):15-19.
14. Collins F. 2000. Keynote lecture at the Cold Spring Harbor meeting of genome sequencing and biology. Cold Spring Harbor, NY, USA, May 10-14.
15. Day DJ, Speiser PW, White PC, Barany F. 1995. Detection of steroid 21-hydroxylase alleles using gene-specific PCR and a multiplexed ligation detection reaction. Genomics 29:152-162.
16. Day INM, Humphries SE. 1994. Electrophoresis for genotyping: microtitre array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose. Anal Biochem 222:389-395.
17. Debouck C, Goodfellow PN. 1999. DNA microarrays in drug discovery and development. Nat Genet 21 (suppl):48-50.
18. DeFrancesco L. 1998. The next new wave in genome analysis: Invader™ assays developed by Third Wave Technologies Inc. The Scientist 12:16.
19. Edman CF, Raymond DE, Wu DJ, Tu E, Sosnowki RG, Butler WF, Nerenberg M, Heller MJ. 1997. Electric field directed nucleic acid hybridization on microchips. Nucleic Acids Res 25:4907-4914.
20. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE. 1993. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen bonding rules. Nature 365:566-568.
21. Fan J-B, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz RJ, Lockhart DJ, Chakravarti A. 2000. Parallel genotying of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res 10:853-860.
22. Genome International Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
23. Germer S, Holland MJ, Higuchi R. 2000. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res 10:258-266.
24. Griffin TJ, Tang W, Smith LM. 1997. Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry. Nat Biotech 15:1368-1372.
25. Griffin TJ, Hall JG, Prudent JR, Smith LM. 1999. Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry. Proc Natl Acad Sci USA 96:6301.
26. Grossman PD, Bloch W, Brinson E, Chang CC, Eggerding FA, Fung S, Iovannisci DA, Woo S, Winn-Deen ES. 1994. High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res 22:4527-4534.
27. Haff L, Smirnov IP. 1997. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res 7:378-388.
28. Harrington JJ, Lieber MR. 1994. Functional domains within FEN-1 and RAD2 define a family of structure specific endonucleases: implications for nucleotide excision repair. Genes Dev 8:1344-1355.
29. Healey BG, Matson RS, Walt DR. 1997. Fiberoptic DNA sensor array capable of detecting point mutations. Anal Chem 251:270-279.
30. Holland PM, Abramson RD, Watson R, Gelfand DH. 1991. Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA 88:7276-7280.
31. Iannone MA, Taylor JD, Chen J, Li M-S, Rivers P, Slentz KA, Weiner MP. 2000. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39:131-140.
32. Kalinina O, Lebedeva I, Brown J, Silver J. 1997. Nanoliter scale PCR with TaqMan detection. Nucleic Acids Res 25:1999-2004.
33. Khanna M, Park P, Zirvi M, Cao W, Picon A, Day J, Paty P, Barany F. 1999. Multiplex PCR/LDR for detection of K-ras mutations in primary colon tumors. Oncogene 18:27-38.
34. Kruglyak L. 1997. The use of a genetic map of biallelic markers in linkage studies. Nat Genet 17:21-24.
35. Kruglyak L. 1999. Prospect for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139-144.
36. Kwok P-Y. 1998. Genotyping by mass spectrometry takes flight. Nat Biotechnol 16:1314-1315.
37. Landegren U, Samiotaki M, Nilsson M, Malmgren H, Kwiatkowski M. 1996. Detecting genes with ligases. Methods (a companion to Methods Enzymol) 9:84-90.
38. Landegren U, Nilson M, Kwok P-Y. 1998. Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res 8:769-776.
39. Li J, Butler JM, Tan Y, Lin H, Royer S, Ohler L, Shaler TA, Hunter JM, Pollart DJ, Montforte JA, Becker CA. 1999. Single nucleotide polymorphism determination using primer extension and time-of-flight mass spectrometry. Electrophoresis 20:1258-1265.
40. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ. 1999. High density synthetic oligonucleotide arrays. Nat Genet 21(suppl):20-24.
41. Little DP, Braun A, Darnhofer-Demar B, Frilling A, Li Y, McIver RT, Köster H. 1997 Detection of RET protooncogene codon 634 mutations using mass spectrometry. J Mol Med 75:745-750.
42. Livak K, Marmaro J, Todd JA. 1995. Towards fully automated genome-wide polymorphism screening. Nat Genet 9:341-342.
43. Maier E, Lehrach H. 1997. Neue Techniken zur Automatisierung in der DNA-Sequenzierung. Chemie in unserer Zeit 31:66-75.
44. McCarthy JJ, Hilfiker R. 2000. The use of single nucleotide polymorphism maps in pharmacogenomics. Nat Biotechnol 18:505-508.
45. Mei R, Galipeau PC, Prass C, Berno A, Ghandour G, Patil N, Wolff RK, Chee MS, Reid BJ, Lockhart DJ. 2000. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res 10: 1126-1137.
46. Mein CA, Barrat BJ, Dunn MG, Siegmund T, Smith AN, Esposito L, Nutland S, Stevens HE, Wilson AJ, Phillips MS, Jarvis LS, deArruda M, Todd JA. 2000. Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res 10:330-343.
47. Meldrum D. 2000a. Automation for genomics, part one: preparation for sequencing. Genome Res 10:1081-1092.
48. Meldrum D. 2000b. Automation for genomics, part two: sequencers, microarrays, and future trends. Genome Res 10:1288-1303.
49. Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17:2503-2516.
50. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U. 1994. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265:2085-2088.
51. Nilsson M, Krejci K, Koch J, Kwiatkowski M, Gustavsson P, Landegren U. 1997. Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nat Genet 16:252-255.
52. Pang H-M, Yeung ES. 2000. Automated one-step DNA sequencing based on nanoliter reaction volumes and capillary electrophoresis. Nucleic Acids Res (methods online) 28:e73.
53. Parsons BL, Heflich RH. 1997. Genotypic selection methods for the direct analysis of point mutations. Mutat Res 387:97-121.
54. Pastinen T, Partanen J, Syvänen A-C. 1996. Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin Chem 42:1391-1397.
55. Pastinen T, Kurg A, Metspalu A, Peltonen L, Syvänen A-C. 1997. Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res 7:606-614.
56. Pastinen T, Raito M, Lindroos K, Tainola P, Peltonen L, Syvänen A-C. 2000. A system for specific, high-through-put genotyping by allele-specific primer extension on microarrays. Genome Res 10:1031-1042.
57. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes C, Fodor SPA. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 91:5022-5026.
58. Pusch W, Kraeuter K-O, Froehlich T, Staalgies Y, Kostrzewa M. 2001. The GenoTool SNP manager: a new software for automated high-throughput MALDI-TOF MS SNP genotyping. Biotechniques 30:210-215.
59. Ramsay G. 1998. DNA chips: state-of-the-art. Nat Biotech 16:40-44.
60. Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C, Fizames C, Winckler P, Brottier P, Quetier F, Saurin W, Weissenbach J. 2000. Estimate of human gene number provided by genome-wide analysis using Tetraodon negroviridis DNA sequence. Nat Genet 25: 235-238.
61. Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyren P. 1996. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242:84-89.
62. Ronaghi M, Nygren M, Lundeberg J, Nyren P. 1999. Analyses of secondary structures in DNA by pyrosequencing. Anal Biochem 267:65-71.
63. Ross P, Hall L, Smirnov I, Haff L. 1998. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat Biotechnol 16:1347-1351.
64. Ross P, Hall L, Haff LA. 2000. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. BioTechniques 29:620-629.
65. Ryan D, Nuccie B, Arvan D. 1999. Non-PCR dependent detection of factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay. Mol Diag 4:135-144.
66. Samiotaki M, Kwiatkowski M, Parik J, Landegren U. 1994. Dual-color detection of DNA sequence variants by ligase-mediated analysis. Genomics 20:238-242.
67. Sauer S, Lechner D, Berlin K, Lehrach H, Escary J-L, Fox N, Gut IG. 2000a. A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res (methods online) 28:e13.
68. Sauer S, Lechner D, Berlin K, Plançon C, Heuermann A, Lehrach H, Gut IG. 2000b. Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res (methods online) 28:e100.
69. Schmalzing D, Belenky A, Novotny MA, Koutny L, Salas-Solano O, El-Difrawy S, Adourian P, Ehrlich D. 2000. Microchip electrophoresis: a method for high-speed SNP detection. Nucleic Acids Res (methods online) 28:e43.
70. Shalon D, Smith SJ, Brown PO. 1996. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6:639-645.
71. Shchepinov MS, Chalk R, Southern EM. 1999. Trityl mass-tags for encoding in combinatorial oligonucleotide synthesis. Nucleic Acids Symp Ser 42:107-108.
72. Shi MM, Bleavins MR, de la Iglesia FA. 1999. Technologies for detecting genetic polymorphisms in pharmacogenomics. Mol Diagn 4:343-351.
73. Shuber AP, Michalowsky LA, Nass GS, Skoletsky J, Hire LM, Kotsopoulos SK, Phipps MF, Barberio DM, Klinger KW. 1997. High throughput parallel analysis of hundreds of patient samples for more than 100 mutations in multiple disease genes. Hum Mol Genet 6:337-347.
74. Shumaker JM, Metspalu A, Caskey CT. 1996. Mutation detection by solid phase primer extension. Hum Mutat 7:346-354.
75. Sosnowski RG, Tu E, Butler WF, O'Connell JP, Heller MJ. 1997. Rapid determination of single base mismatch mutations in DNA hybrids by electric field control. Proc Natl Acad Sci USA 94:1119-1123.
76. Syvänen A-C, Sajantila A, Lukka M. 1993. Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am J Hum Genet 52:46-59.
77. Syvänen A-C. 1994. Detection of point mutations in human genes by the solid-phase minisequencing method. Clin Chim Acta 226:225-236.
78. Syvänen A-C. 1999. From gels to chips: "minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 13:1-10.
79. Tyagi S, Kramer FR. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14:303-308.
80. Tyagi S, Bratu DP, Kramer FR. 1998. Multicolor molecular beacons for allele discrimination. Nat Biotechnol 16:49-53.
81. Venter JC, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
82. Wang DG, Fan J-B, Siao C-J, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lipshutz R, Chee M, Lander ES. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077-1082.