Single nucleotide polymorphism genotyping: Biochemistry, protocol, cost and throughput

Pharmacogenomics Journal

Volumn 3, Issue 2, 2003, Pages 77-96

  Chen, X ^a   Sullivan, P F ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Allele discrimination; Cost; Genotyping; SNP; Throughput

Indexed keywords

DNA; DNA POLYMERASE; PHOSPHODIESTERASE I; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ALLELE; ANALYTIC METHOD; BIOCHEMISTRY; CLINICAL PROTOCOL; COST BENEFIT ANALYSIS; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SYNTHESIS; ELECTROPHORESIS; ENERGY TRANSFER; ENZYME ACTIVITY; ENZYME ASSAY; GENE AMPLIFICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENE TECHNOLOGY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE; HUMAN; INTERMETHOD COMPARISON; MASS SPECTROMETRY; MEDICAL INFORMATION; MEDICAL RESEARCH; NUCLEIC ACID DATABASE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ANIMALS; GENE AMPLIFICATION; GENETIC MARKERS; GENETICS; GENOTYPE; HUMANS; IN SITU HYBRIDIZATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 0037974735     PISSN: 1470269X     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.tpj.6500167     Document Type: Review

References (133)

1. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999; 22: 139-144.
2. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001; 409: 928-933.
3. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al. The sequence of the human genome. Science 2001; 291: 1304-1351.
4. Syvanen AC. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2001; 2: 930-942.
5. Kwok PY. Methods for genotyping single nucleotide polymorphisms. Annu Rev Genom Hum Genet 2001; 2: 235-258.
6. Shi MM. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin Chem 2001; 47: 164-172.
7. Kirk BW, Feinsod M, Favis R, Kliman RM, Barany F. Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Res 2002; 30: 3295-3311.
8. Qi X, Bakht S, Devos KM, Gale MD, Osbourn A. L-RCA (ligation-rolling circle amplification): a general method for genotypinq of sinqle nucleotide polymorphisms (SNPs). Nucleic Acids Res 2001; 29: E116.
9. Wu DY, Wallace RB. The ligation amplification reaction (LAR) - amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 1989; 4: 560-569.
10. Fors L, Lieder KW, Vavra SH, Kwiatkowski RW. Large-scale SNP scoring from unamplified genomic DNA. Pharmacogenomics 2000; 1: 219-229.
11. Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S et al. Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res 1994; 22: 4167-4175.
12. Sauer S, Lechner D, Berlin K, Plancon C, Heuermann A, Lehrach H et al. Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res 2000; 28: E100.
13. Tyagi S, Bratu DP, Kramer FR. Multicolor molecular beacons for allele discrimination. Nat Biotechnol 1998; 16: 49-53.
14. Livak KJ. Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet Anal 1999; 14: 143-149.
15. Chen X, Livak KJ, Kwok PY. A homogeneous, ligase-mediated DNA diagnostic test. Genome Res 1998; 8: 549-556.
16. Bray MS, Boerwinkle E, Doris PA. High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrometry: practice, problems and promise. Hum Mutat 2001; 17: 296-304.
17. Sun X, Ding H, Hung K, Guo B. A new MALDI-TOF based minisequencing assay for genotyping of SNPS. Nucleic Acids Res 2000; 28: E68.
18. Abdi F, Bradbury EM, Doggett N, Chen X. Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags. Nucleic Acids Res 2001; 29: E611-E61.
19. Chen X, Fei Z, Smith LM, Bradbury EM, Majidi V. Stable-isotopeassisted MALDI-TOF mass spectrometry for accurate determination of nucleotide compositions of PCR products. Anal Chem 1999; 71: 3118-3125.
20. Griffin TJ, Smith LM. Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry. Trends Biotechnol 2000; 18: 77-84.
21. Ross P, Hall L, Smirnov I, Haff L. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat Biotechnol 1998; 16: 1347-1351.
22. Ye F, Li MS, Taylor JD, Nguyen Q, Colton HM, Casey WM et al. Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification. Hum Mutat 2001; 17: 305-316.
23. Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T et al. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res 2000; 10: 853-860.
24. Ferguson JA, Steemers FJ, Walt DR. High-density fiber-optic DNA random microsphere array. Anal Chem 2000; 72: 5618-5624.
25. Walt DR. Techview: molecular biology. Bead-based fiber-optic arrays. Science 2000; 287: 451-452.
26. Hacia JG, Fan JB, Ryder O, Jin L, Edgemon K, Ghandour G et al. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat Genet 1999; 22: 164-167.
27. Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998; 280: 1077-1082.
28. Gilles PN, Wu DJ, Foster CB, Dillon PJ, Chanock SJ. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat Biotechnol 1999; 17: 365-370.
29. Liu Q, Sommer SS. Pyrophosphorolysis-activatable oligonucleotides may facilitate detection of rare alleles, mutation scanning and analysis of chromatin structures. Nucleic Acids Res 2002; 30: 598-604.
30. Liu Q, Sommer SS. Pyrophosphorolysis-activated polymerization (PAP): application to allele-specific amplification. Biotechniques 2000; 29: 1072-1080.
31. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74: 5463-5467.
32. Hsu TM, Chen X, Duan S, Miller RD, Kwok PY. Universal SNP genotyping assay with fluorescence polarization detection. Biotechniques 2001; 31: 560-568.
33. Syvanen AC. Solid-phase minisequencing as a tool to detect DNA polymorphism. Methods Mol Biol 1998; 98: 291-298.
34. Pastinen T, Partanen J, Syvanen AC. Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin Chem 1996; 42: 1391-1397.
35. Chen X, Levine L, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res 1999; 9: 492-498.
36. Lindroos K, Liljedahl U, Raitio M, Syvanen AC. Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries. Nucleic Acids Res 2001; 29: E69.
37. Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen AC. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res 2000; 10: 1031-1042.
38. Myakishev MV, Khripin Y, Hu S, Hamer DH. High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res 2001; 11: 163-169.
39. Germer S, Higuchi R. Single-tube genotyping without oligonucleotide probes. Genome Res 1999; 9: 72-78.
40. Ayyadevara S, Thaden JJ, Shmookler Reis RJ. Discrimination of primer 3′-nucleotide mismatch by taq DNA polymerase during polymerase chain reaction. Anal Biochem 2000; 284: 11-18.
41. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996; 242: 84-89.
42. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science 1998; 281: 363-365.
43. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001; 11: 3-11.
44. Dong F, Allawi HT, Anderson T, Neri BP, Lyamichev VI. Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA. Nucleic Acids Res 2001; 29: 3248-3257.
45. Kaiser MW, Lyamicheva N, Ma W, Miller C, Neri B, Fors L et al. A comparison of eubacterial and archaeal structure-specific 5′-exonucleases. J Biol Chem 1999; 274: 21387-21394.
46. Mein CA, Barratt BJ, Dunn MG, Siegmund T, Smith AN, Esposito L et al. Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res 2000; 10: 330-343.
47. Walburger DK, Afonina IA, Wydro R. An improved real time PCR method for simultaneous detection of C282Y and H63D mutations in the HFE gene associated with hereditary hemochromatosis. Mutat Res 2001; 432: 69-78.
48. de Kok JB, Wiegerinck ET, Giesendorf BA, Swinkels DW. Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes). Hum Mutat 2002; 19: 554-559.
49. Tong J, Barany F, Cao W. Ligation reaction specificities of an NAD(+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus. Nucleic Acids Res 2000; 28: 1447-1454.
50. Tong J, Cao W, Barany F. Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D. Nucleic Acids Res 1999; 27: 788-794.
51. Sriskanda V, Shuman S. Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res 1998; 26: 3536-3541.
52. Nilsson M, Antson DO, Barbany G, Landegren U. RNA-templated DNA ligation for transcript analysis. Nucleic Acids Res 2001; 29: 578-581.
53. Pickering J, Bamford A, Godbole V, Briggs J, Scozzafava G, Roe P et al. Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms. Nucleic Acids Res 2002; 30: E60.
54. Thomas DC, Nardone GA, Randall SK. Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction. Arch Pathol Lab Med 1999; 123: 1170-1176.
55. Nilsson M, Barbany G, Antson DO, Gertow K, Landegren U. Enhanced detection and distinction of RNA by enzymatic probe ligation. Nat Biotechnol 2000; 18: 791-793.
56. Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, Kashuk C et al. High-throughput variation detection and genotyping using microarrays. Genome Res 2001; 11: 1913-1925.
57. Jacobsen N, Bentzen J, Meldgaard M, Jakobsen MH, Fenger M, Kauppinen S et al. LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. Nucleic Acids Res 2002; 30: E100.
58. Simeonov A, Nikiforov TT. Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res 2002; 30: E91.
59. Prince JA, Feuk L, Howell WM, Jobs M, Emahazion T, Blennow K et al. Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res 2001; 11: 152-162.
60. Chen X, Kwok PY. Homogeneous genotyping assays for single nucleotide polymorphisms with fluorescence resonance energy transfer detection. Genet Anal 1999; 14: 157-163.
61. Hsu TM, Law SM, Duan S, Neri BP, Kwok PY. Genotyping single-nucleotide polymorphisms by the invader assay with dual-color fluorescence polarization detection. Clin Chem 2001; 47: 1373-1377.
62. De Angelis DA. Why FRET over genomics? Physiol Genom 1999; 1: 93-99.
63. Chen X, Zehnbauer B, Gnirke A, Kwok PY. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc Natl Acad Sci USA 1997; 94: 10756-10761.
64. Tapp I, Malmberg L, Rennel E, Wik M, Syvanen AC. Homogeneous scoring of single-nucleotide polymorphisms: comparison of the 5′-nuclease TaqMan assay and Molecular Beacon probes. Biotechniques 2000; 28: 732-738.
65. Dubertret B, Calame M, Libchaber AJ. Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat Biotechnol 2001; 19: 365-370.
66. Tong AK, Li Z, Jones GS, Russo JJ, Ju J. Combinatorial fluorescence energy transfer tags for multiplex biological assays. Nat Biotechnol 2001; 19: 756-759.
67. Ju J, Glazer AN, Mathies RA. Energy transfer primers: a new fluorescence labeling paradigm for DNA sequencing and analysis. Nat Med 1996; 2: 246-249.
68. Ju J, Ruan C, Fuller CW, Glazer AN, Mathies RA. Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. Proc Natl Acad Sci USA 1995; 92: 4347-4351.
69. Wilkins SP, Hall JG, Lyamichev V, Neri BP, Lu M, Wang L et al. Analysis of single nucleotide polymorphisms with solid phase invasive cleavage reactions. Nucleic Acids Res 2001; 29: E77.
70. Chen X, Kwok PY. Template-directed dye-terminator incorporation (TDI) assay: a homogeneous DNA diagnostic method based on fluorescence resonance energy transfer. Nucleic Acids Res 1997; 25: 347-353.
71. Whitcombe D, Theaker J, Guy SP, Brown T, Little S. Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 1999; 17: 804-807.
72. Solinas A, Brown LJ, McKeen C, Mellor JM,Nicol J, Thelwell N et al. Duplex Scorpion primers in SNP analysis and FRET applications. Nucleic Acids Res 2001; 29: E96.
73. Gibson NJ, Gillard HL, Whitcombe D, Ferrie RM, Newton CR, Little S. A homogeneous method for genotyping with fluorescence polarization. Clin Chem 1997; 43: 1336-1341.
74. Latif S, Bauer-Sardina I, Ranade K, Livak KJ, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis II: 5′-nuclease assay. Genome Res 2001; 11: 436-440.
75. Pusch W, Wurmbach JH, Thiele H, Kostrzewa M. MALDI-TOF mass spectrometry-based SNP genotyping. Pharmacogenomics 2002; 3: 537-548.
76. Fei Z, Ono T, Smith LM. MALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPs. Nucleic Acids Res 1998; 26: 2827-2828.
77. Pusch W, Kraeuter KO, Froehlich T, Stalgies Y, Kostrzewa M. Genotools SNP manager: a new software for automated high-throughput MALDI-TOF mass spectrometry SNP genotyping. Biotechniques 2001; 30: 210-215.
78. Werner M, Sych M, Herbon N, Illig T, Konig IR, Wjst M. Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum Mutat 2002; 20: 57-64.
79. Ross P, Hall L, Haff LA. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 2000; 29: 620-629.
80. Shifman S, Pisante-Shalom A, Yakir B, Darvasi A. Quantitative technologies for allele frequency estimation of SNPs in DNA pools. Mol Cell Probes 2002; 16: 429-434.
81. Buetow KH, Edmonson M, MacDonald R, Clifford R, Yip P, Kelley J et al. 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 2001; 98: 581-584.
82. Mohlke KL, Erdos MR, Scott LJ, Fingerlin TE, Jackson AU, Silander K et al. High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc Natl Acad Sci USA 2002; 99: 16928-16933.
83. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP et al. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat Genet 2000; 24: 381-386.
84. Iannone MA, Taylor JD, Chen J, Li MS, Rivers P, Slentz-Kesler KA et al. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 2000; 39: 131-140.
85. Medintz I, Wong WW, Berti L, Shiow L, Tom J, Scherer J et al. High-performance multiplex SNP analysis of three hemochromatosis-related mutations with capillary array electrophoresis microplates. Genome Res 2001; 11: 413-421.
86. Tabor S, Richardson CC. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy-and dideoxyribonucleotides. Proc Natl Acad Sci USA 1995; 92: 6339-6343.
87. Ward CP, Fensom AH, Green PM. Biallelic discrimination assays for the three common Ashkenazi Jewish mutations and a common non-Jewish mutation, in Tay-Sachs disease, using fluorogenic TaqMan probes. Genet Test 2000; 4: 351-358.
88. Restagno G, Gomez AM, Sbaiz L, De Gobbi M, Roetto A, Bertino E et al. A pilot C282Y hemochromatosis screening in Italian newborns by TaqMan technology. Genet Test 2000; 4: 177-181.
89. Matsubara Y, Fujii K, Rinaldo P, Narisawa K. A fluorogenic allele-specific amplification method for DNA-based screening for inherited metabolic disorders. Acta Paediatr Suppl 1999; 88: 65-68.
90. Giesendorf BA, Vet JA, Tyagi S, Mensink EJ, Trijbels FJ, Blom HJ. Molecular beacons: a new approach for semiautomated mutation analysis. Clin Chem 1998; 44: 482-486.
91. Ledford M, Friedman KD, Hessner MJ, Moehlenkamp C, Williams TM, Larson RS. A multi-site study for detection of the factor V (Leiden) mutation from genomic DNA using a homogeneous invader microtiter plate fluorescence resonance energy transfer (FRET) assay. J Mol Diagn 2000; 2: 97-104.
92. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001; 294: 1719-1723.
93. Kwok PY. GENOMICS: genetic association by whole-genome analysis? Science 2001; 294: 1669-1670.
94. Kwok PY. High-throughput genotyping assay approaches. Pharmacogenomics 2000; 1: 95-100.
95. Paracchini S, Arredi B, Chalk R, Tyler-Smith C. Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry. Nucleic Acids Res 2002; 30: E27.
96. Taylor JD, Briley D, Nguyen Q, Long K, Iannone MA, Li MS et al. Flow cytometric platform for high-throughput single nucleotide polymorphism analysis. Biotechniques 2001; 30: 661-669.
97. Cai H, White PS, Torney D, Deshpande A , Wang Z, Keller RA et al. Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring. Genomics 2000; 66: 135-143.
98. Chen J, Iannone MA, Li MS, Taylor JD, Rivers P, Nelsen AJ et al. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 2000; 10: 549-557.
99. Armstrong B, Stewart M, Mazumder A. Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping. Cytometry 2000; 40: 102-108.
100. Akula N, Chen YS, Hennessy K, Schulze TG, Singh G, McMahon FJ. Utility and accuracy of template-directed dye-terminator incorporation with fluorescence-polarization detection for genotyping single nucleotide polymorphisms. Biotechniques 2002; 32: 1072-1076, 1078.
101. Swan KA, Curtis DE, McKusick KB, Voinov AV, Mapa FA, Cancilla MR. High-throughput gene mapping in Caenorhabditis elegans. Genome Res 2002; 12: 1100-1105.
102. Straub RE, Jiang Y, MacLean CJ, Ma Y, Webb BT, Myakishev MV et al. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Am J Hum Genet 2002; 71: 337-348.
103. Nordfors L, Jansson M, Sandberg G, Lavebratt C, Sengul S, Schalling M et al. Large-scale genotyping of single nucleotide polymorphisms by Pyrosequencing trade mark and validation against the 5′nuclease (Taqman((R))) assay. Hum Mutat 2002; 19: 395-401.
104. Ringquist S, Alexander AM, Rudert WA, Styche A, Trucco M. Pyrosequence-based typing of alleles of the HLA-DQB1 gene. Biotechniques 2002; 33: 166-175.
105. Berg LM, Sanders R, Alderborn A. Pyrosequencing technology and the need for versatile solutions in molecular clinical research. Expert Rev Mol Diagn 2002; 2: 361-369.
106. Gharizadeh B, Kalantari M, Garcia CA, Johansson B, Nyren P. Typing of human papillomavirus by pyrosequencing. Lab Invest 2001; 81: 673-679.
107. Hessner MJ, Friedman KD, Voelkerding KV, Huber S, Ryan D, Nuccie B et al. Multisite study for genotyping of the factor II (prothrombin) G20210A mutation by the invader assay. Clin Chem 2001; 47: 2048-2050.
108. Agarwal P, Oldenburg MC, Czarneski JE, Morse RM, Hameed MR, Cohen S et al. Comparison study for identifying promoter allelic polymorphism in interleukin 10 and tumor necrosis factor alpha genes. Diagn Mol Pathol 2000; 9: 158-164.
109. Ryan D, Nuccie B, Arvan D. Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay. Mol Diagn 1999; 4: 135-144.
110. Baron H, Fung S, Aydin A, Bahring S, Jeschke E, Luft FC et al. Oligonucleotide ligation assay for detection of apolipoprotein E polymorphisms. Clin Chem 1997; 43: 1984-1986.
111. Edelstein RE, Nickerson DA, Tobe VO, Manns-Arcuino LA, Frenkel LM. Oligonucleotide ligation assay for detecting mutations in the human immunodeficiency virus type 1 pol gene that are associated with resistance to zidovudine, didanosine, and lamivudine. J Clin Microbiol 1998; 36: 569-572.
112. Shahgholi M, Garcia BA, Chiu NH, Heaney PJ, Tang K. Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved. Nucleic Acids Res 2001; 29: E91.
113. Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 2001; 70: 437-473.
114. Bell PA, Chaturvedi S, Gelfand CA, Huang CY, Kochersperger M, Kopla R et al. SNPstream UHT: ultra-high throughput SNP genotyping for pharmacogenomics and drug discovery. Biotechniques 2002; 3: 70-77.
115. Nyren P, Karamohamed S, Ronaghi M. Detection of single-base changes using a bioluminometric primer extension assay. Anal Biochem 1997; 244: 367-373.
116. Gruber JD, Colligan PB, Wolford JK. Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Hum Genet 2002; 110: 395-401.
117. Wasson J, Skolnick G, Love-Gregory L, Permutt MA. Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 2002; 32: 1144-1150.
118. Lyamichev V, Brow MA, Varvel VE, Dahlberg JE. Comparison of the 5′ nuclease activities of taq DNA polymerase and its isolated nuclease domain. Proc Natl Acad Sci USA 1999; 96: 6143-6148.
119. Griffin TJ, Smith LM. Genetic identification by mass spectrometric analysis of single- nucleotide polymorphisms: ternary encoding of genotypes. Anal Chem 2000; 72: 3298-3302.
120. Griffin TJ, Hall JG, Prudent JR, Smith LM. Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry. Proc Natl Acad Sci USA 1999; 96: 6301-6306.
121. Ohnishi Y, Tanaka T, Ozaki K, Yamada R, Suzuki H, Nakamura Y. A high-throughput SNP typing system for genome-wide association studies. J Hum Genet 2001; 46: 471-477.
122. Giordano M, Mellai M, Hoogendoorn B, Momigliano-Richiardi P. Determination of SNP allele frequencies in pooled DNAs by primer extension genotyping and denaturing high-performance liquid chromatography. J Biochem Biophys Methods 2001; 47: 101-110.
123. Germer S, Holland MJ, Higuchi R. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res 2000; 10: 258-266.
124. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW et al. SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 2002; 30: E74.
125. Xiao M, Latif SM, Kwok PY. Kinetic FP-TDI assay for SNP allele frequency determination. Biotechniques 2003; 34: 190-197.
126. Pfeiffer RM, Rutter JL, Gail MH, Struewing J, Gastwirth JL. Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium. Genet Epidemiol 2002; 22: 94-102.
127. Barratt BJ, Payne F, Rance HE, Nutland S, Todd JA, Clayton DG. Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann Hum Genet 2002; 66: 393-405.
128. Bansal A, van den BD, Kammerer S, Honisch C, Adam G, Cantor CR et al. Association testing by DNA pooling: an effective initial screen. Proc Natl Acad Sci USA 2002; 99: 16871-16874.
129. Fei Z, Smith LM. Analysis of single nucleotide polymorphisms by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2000; 14: 950-959.
130. Stoerker J, Mayo JD, Tetzlaff CN, Sarracino DA, Schwope I, Richert C. Rapid genotyping by MALDI-monitored nuclease selection from probe libraries. Nat Biotechnol 2000; 18: 1213-1216.
131. Nordstrom T, Alderborn A, Nyren P. Method for one-step preparation of double-stranded DNA template applicable for use with pyrosequencing technology. J Biochem Biophys Methods 2002; 52: 71-82.
132. Nordstrom T, Nourizad K, Ronaghi M, Nyren P. Method enabling pyrosequencing on double-stranded DNA. Anal Biochem 2000; 282: 186-193.
133. Kwiatkowski RW, Lyamichev V, de Arruda M, Neri B. Clinical, genetic, and pharmacogenetic applications of the Invader assay. Mol Diagn 1999; 4: 353-364.