eISSN: 2221-6197 DOI: 10.31301/2221-6197

Разнообразие методов детекции полиморфных нуклеотидов в известных снипах. III. Аллель-специфичная ПЦР

Год: 2022

Страницы: 32-51

Номер: Том 14, № 1

Тип: научная статья

Аннотация:

Замены одиночных нуклеотидов (SNP) составляют наибольшую долю полиморфизма ДНК практически любых организмов, включая человека, и оказывают заметное влияние на их жизненный статус. Детекция уже известных полиморфных нуклеотидов (SNP-типирование) приобретает важное значение, чем объясняется чрезвычайно большое разнообразие существующих методов анализа SNP. Одним из наиболее широко применяемых подходов является аллель-специфичная ПЦР (АС- ПЦР) с праймерами, характеризующимися различиями в строении и обусловленной этим способностью дискриминировать полиморфные нуклеотиды в ДНК. АС-ПЦР реализована во множестве вариантов (около полусотни), кратко рассмотренных в данном обзоре.

Ключевые слова:

НК, однонуклеотидный полиморфизм, ОНП, снип, ПЦР, аллель-специфичная ПЦР, АС-ПЦР, SNP-типирование

Библиографический список:

  1. Бреннер Е.В., Иванова Е.М., Пышный Д.В., Морозов И.В. Универсальный метод идентификации однонуклеотидных замен // Биоорг. Химия. Т.№ 2. С. 213-215.
  2. Галимова А.А., Гарафутдинов Р.Р., Сахабутдинова А.Р., Чемерис А.В. Аллель- специфическая полимеразная цепная реакция с использованием системы сближенных праймеров // Вестник Башкирского университета. 2014. Т.19(4). С. 1196-1199.
  3. Гарафутдинов Р.Р., Баймиев Ан.Х., Малеев Г.В., Алексеев Я.И., Зубов В.В., Чемерис Д.А., Кирьянова О.Ю., Губайдуллин И.М., Матниязов Р.Т., Сахабутдинова А.Р., Никоноров Ю.М., Кулуев Б.Р., Баймиев Ал.Х., Чемерис А.В. Разнообразие праймеров для ПЦР и принципы их подбора. Биомика. 2019. Т.11(1). С. 23 – 70. DOI: https://doi.org/31301/2221-6197.bmcs.2019-04
  4. Гарафутдинов Р.Р., Чемерис Д.А., Мавзютов А.Р., Ахметзянова Л.У., Давлеткулов Т.М., Губайдуллин И.М., Чемерис А.В. Петлевая LAMP амплификация нуклеиновых кислот. I. Два десятилетия развития и совершенствования // 2021.   Т.13(2).   С.   176-226. DOI: https://doi.org/10.31301/2221-6197.bmcs.2021-14
  5. Гарафутдинов Р.Р.,   Чемерис   Д.А., Сахабутдинова А.Р., Кулуев Б.Р., Чемерис А.В. Разнообразие методов детекции полиморфных нуклеотидов в известных снипах. I. Термины и краткий перечень подходов // Биомика. 2021. Т.13(4). С.434-443. DOI: https://doi.org/10.31301/2221-6197.bmcs.2021-30
  6. Сахабутдинова А.Р., Гарафутдинов Р.Р., Чемерис Д.А., Кулуев А.Р., Кулуев И.Р., 1Чемерис А.В. Разнообразие методов детекции полиморфных нуклеотидов в известных снипах. II. Аллель– специфичная гибридизация, ПЦР-ПДРФ, химический и ферментативный методы детекции мутаций в гетеродуплексах // Биомика. 2021. Т.13(4). С.444-456. DOI: https://doi.org/31301/2221-6197.bmcs.2021-31
  7. Asari M, Watanabe S, Matsubara K, Shiono H, Shimizu K. Single nucleotide polymorphism genotyping by mini-primer allele-specific amplification with universal reporter primers for identification of degraded DNA. Anal Biochem. 2009. V.386(1). P.85-90. doi: https://doi.org/1016/j.ab.2008.11.023
  8. Bi W., Stambrook P.J. Detection of known mutation by proof-reading PCR // Nucleic Acids Res. 1998.    26(12).   P.   3073-3075.   doi: https://doi.org/10.1093/nar/26.12.3073
  9. Bottema C.D., Sarkar G., Cassady J.D., Ii S., Dutton C.M., Sommer S.S. Polymerase chain reaction amplification of specific alleles: a general method of detection of mutations, polymorphisms, and haplotypes // Methods Enzymol. V. 218. P. 388-402. doi: https://doi.org/10.1016/0076-6879(93)18031-7
  10. Bottema C.D., Sommer S.S. PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms // Res. 1993. V. 288(1). P. 93 doi: https://doi.org/10.1016/0027-5107(93)90211-w .
  11. Bui M., Liu Z. Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping // Plant Methods. 2009. V. 5. P. 1. doi: https://doi.org/10.1186/1746-4811-5-1
  12. Cahill P., Bakis M., Hurley J., Kamath V., Nielsen W., Weymouth D., Dupuis J., Doucette-Stamm L., Smith R. Exo-proofreading, a versatile SNP scoring technology // Genome Res. 2003. V. 13(5). P. 925-931. doi: https://doi.org/10.1101/gr.939903
  13. Cha R.S., Zarbl H., Keohavong P., Thilly W.G. Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene // PCR Methods Appl. 1992. 2(1). P. 14-20. doi: https://doi.org/10.1101/gr.2.1.14
  14. Cheng J., Zhang Y., Li Q. Real-time PCR genotyping using displacing probes // Nucleic Acids Res. 2004. 32(7). e61. doi: https://doi.org/10.1093/nar/gnh055
  15. Chiapparino E., Lee D., Donini P. Genotyping single nucleotide polymorphisms in barley by tetra- primer ARMS-PCR // Genome. V. 47(2). P. 414-doi: https://doi.org/10.1139/g03-130
  16. Di Giusto DA, King GC. Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays. Nucleic Acids Res. 2004. V.32(3). e32. doi: https://doi.org/10.1093/nar/gnh036
  17. Dutton C., Sommer S.S. Simultaneous detection of multiple single-base alleles at a polymorphic site // Biotechniques. V. 11(6). P. 700-702.
  18. Ehlen T., Dubeau L. Detection of ras point mutations by polymerase chain reaction using mutation- specific, inosine-containing oligonucleotide primers // Biochem. Biophys. Res. Commun. 1989. V. 160(2). P. 441-447. doi: https://doi.org/1016/0006-291x(89)92452-2
  19. Eitan Y., Kashi Y. Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA) // Nucleic Acids Res. 2002. 30(12). e62. doi: https://doi.org/10.1093/nar/gnf062
  20. Fauser S., Wissinger B. Simultaneous detection of multiple point mutations using fluorescence-coupled competitive primer extension // 1997. V.22(5). P. 964-968. doi: https://doi.org/10.2144/97225rr05
  21. Ferrie R.M., Schwarz M.J., Robertson N.H., Vaudin S., Super M., Malone G., Little S. Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene // J. Hum. Genet. 1992.51(2). P. 251-262.
  22. Fortina P., Conant R., Parrella T., Rappaport E., Scanlin T., Schwartz E., Robertson J.M., Surrey S. Fluorescence-based, multiplex allele-specific PCR (MASPCR) detection of the delta F508 deletion in the cystic fibrosis transmembrane conductance regulator (CFTR) gene // Cell. Probes. 1992. V. 6(4). P. 353-doi: https://doi.org/10.1016/0890-8508(92)90013-n
  23. Fortina P., Dotti G., Conant R., Monokian G., Parrella T., Hitchcock W., Rappaport E., Schwartz E., Surrey S. Detection of the most common mutations causing beta-thalassemia in Mediterraneans using a multiplex amplification refractory mutation system (MARMS) // PCR Methods 1992a. V. 2(2). P. 163-doi: https://doi.org/10.1101/gr.2.2.163
  24. Gale JM, Tafoya GB. Evaluation of 15 polymerases and phosphorothioate primer modification for detection of UV-induced C:G to T:A mutations by allele-specific PCR. Photochem Photobiol. 2004. 79(5). P.461-469. doi: https://doi.org/10.1562/2003-11-12-ra.1
  25. Gibbs A., Nguyen P.N., Caskey C.T. Detection of single DNA base differences by competitive oligonucleotide priming // Nucleic Acids Res. 1989. V.17(7). P. 2437-2448. doi: https://doi.org/10.1093/nar/17.7.2437
  26. Gibson N.J., Newton C.R., Little S. A colorimetric assay for phosphate to measure amplicon accumulation in polymerase chain reaction // Anal. 1997. V. 254(1). P. 18-22. doi: https://doi.org/10.1006/abio.1997.2324
  27. Glaab W.E., Skopek T.R. A novel assay for allelic discrimination that combines the fluorogenic 5' nuclease polymerase  chain  reaction  (TaqMan)  and  mismatch amplification mutation assay // Mutat. Res. 1999.         V.           430(1).  P.            1-12.           doi:        https://doi.org/10.1016/s0027-5107(99)00147-5
  28. Haliassos A., Chomel J.C., Grandjouan S., Kruh J., Kaplan J.C., Kitzis A. Detection of minority point mutations by modified PCR technique: a new approach for a sensitive diagnosis of tumor-progression markers // Nucleic Acids Res. 1989. V. 17(20). P. 8093-8099. doi: https://doi.org/1093/nar/17.20.8093
  29. Haliassos , Chomel J.C., Tesson L., Baudis M., Kruh J., Kaplan J.C., Kitzis A. Modification of enzymatically amplified DNA for the detection of point mutations // Nucleic Acids Res. 1989a. P. 17(9). P. 3606. doi: https://doi.org/10.1093/nar/17.9.3606
  30. Hamajima N. PCR-CTPP: a new genotyping technique in the era of genetic epidemiology // Expert. Mol. Diagn. 2001. V. 1(1). P. 119-123. doi: https://doi.org/10.1586/14737159.1.1.119
  31. Hamajima N., Saito T., Matsuo K., Kozaki K., Takahashi T., Tajima K. Polymerase chain reaction with confronting two-pair primers for polymorphism genotyping // Jpn. J. Cancer Res. 2000. 91(9). P. 865- 868. doi: https://doi.org/10.1111/j.1349-7006.2000.tb01026.x
  32. Hayashi , Hagihara M., Kobori A., Nakatani K. Detection of L-DNA-tagged PCR products by surface plasmon resonance imaging // Chembiochem. 2007. V. 8(2). P. 169-171. doi: https://doi.org/10.1002/cbic.200600477
  33. Hayashi G., Hagihara M., Nakatani K. Genotyping by allele-specific L-DNA-tagged PCR // J. Biotechnol. V. 135(2). P. 157-160. doi: https://doi.org/10.1016/j.jbiotec.2008.03.011
  34. He C., Holme J., Anthony J. SNP Genotyping: The KASP Assay // Methods Mol. V.1145.2014. doi: https://doi.org/10.1007/978-1-4939-0446-4_7
  35. Hu Y.J., Li Z.F., Diamond A.M. Enhanced discrimination of single nucleotide polymorphism in genotyping by phosphorothioate proofreading allele- specific amplification // Biochem. 2007. V. 369(1).54-59. doi: https://doi.org/10.1016/j.ab.2007.04.042
  36. Huang M.M., Arnheim N., Goodman M.F. Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR // Nucleic Acids Res. 1992. V. 20(17). P. 4567-4573. doi: https://doi.org/10.1093/nar/20.17.4567
  37. Hwang I.T., Kim Y.J., Kim S.H., Kwak C.I., Gu Y.Y., Chun J.Y. Annealing control primer system for improving specificity of PCR amplification // Biotechniques. V. 35(6). P. 1180-1184. doi: https://doi.org/10.2144/03356st03
  38. Iliadi A, Petropoulou M, Ioannou PC, Christopoulos TK, Anagnostopoulos NI, Kanavakis E, Traeger-Synodinos J. Absolute quantification of the alleles in somatic point mutations by bioluminometric methods based on competitive polymerase chain reaction in the presence of a locked nucleic acid blockeror an allele-specific primer. Anal Chem. 2011. V.83(17). P.6545-6551. doi: https://doi.org/10.1021/ac200810h
  39. Imyanitov E.N., Buslov K.G., Suspitsin E.N., Kuligina E.Sh., Belogubova E.V., Grigoriev M.Y., Togo A.V., Hanson K.P. Improved reliability of allele-specific PCR // Biotechniques. V. 33(3). P. 484, 486, 488 passim. doi: https://doi.org/10.2144/02333bm04
  40. Ishiguro A., Kubota T., Soya Y., Sasaki H., Yagyu O., Takarada , Iga T. High-throughput detection of multiple genetic polymorphisms influencing drug metabolism with mismatch primers in allele-specific polymerase chain reaction // Anal. Biochem. 2005. V. 337(2).P.256-261.doi:   https://doi.org/10.1016/j.ab.2004.11.038
  41. Erratum in: Anal. Biochem. 2005. V. 343(2). P. 359. Jiang , Tong Y., Zhao R., Xiong G., Qiao B., Li An improved PCR-CTPP assay for the detection of ADH1B Arg48His polymorphism // J. Clin. Lab. Anal. 2018. V. 32(2). e22268. doi: https://doi.org/10.1002/jcla.22268
  42. Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Jatayev S, Hu YG, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET // Front Plant Sci. 2022. 12:747886. doi: https://doi.org/10.3389/fpls.2021.747886
  43. Kofiadi I.A., Rebrikov D.V. [Methods for detecting single nucleotide polymorphisms: allele- specific PCR and hybridization with oligonucleotide probe] // 2006. V. 42(1). P. 22-32. [in Russian].
  44. Koizumi M., Morita K., Takagi M., Yasumo H., Kasuya A. Improvement of single nucleotide polymorphism genotyping by allele-specific PCR using primers modified with an ENA residue // Anal. 2005. V.   340(2).   P.   287-294.   doi: https://doi.org/10.1016/j.ab.2005.02.029
  45. Kwok , Kellogg D.E., McKinney N., Spasic D., Goda L., Levenson C., Sninsky J.J. Effects of primer- template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies // Nucleic Acids Res. 1990. V. 18(4). P. 999-1005. doi: https://doi.org/10.1093/nar/18.4.999
  46. Latorra D., Campbell K., Wolter A., Hurley J.M. Enhanced allele-specific PCR discrimination in SNP genotyping using 3' locked nucleic acid (LNA) primers // Hum. Mutat. 2003. V. 22(1). P. 79-85. doi: https://doi.org/1002/humu.10228
  47. Li X., Pan Q., Guo Y.G., Li Y., Gao H.F.,Zhang D., Hu H., Xing W.L., Mitchelson K., Xia K., Dai P., Cheng J. Construction of a multiplex allele-specific PCR-based universal array (ASPUA) and its application to hearing loss screening // Hum. Mutat. 2008. V. 29(2). 306-314. doi: https://doi.org/10.1002/humu.20622
  48. Li J, Makrigiorgos GM. Anti-primer quenching- based real-time PCR for simplex or multiplex DNA quantification and single-nucleotide polymorphism genotyping. Nat 2007. V.2(1). P.50-58. doi: https://doi.org/10.1038/nprot.2007.11
  49. Li K, Zhang J, Chen L, Sommer SS. Superb nucleotide discrimination by a novel on/off switch for DNA polymerization and its applications. Mol Biotechnol. 2005. 29(2). P.93-100. doi: https://doi.org/10.1385/MB:29:2:093
  50. Lin-Ling C., Zhang J., Sommer S.S., Li K. Single-base discrimination mediated by proofreading inert allele specific primers // J. Biochem. Biol. 2005. V.38(1). P.24-27. doi: https://doi.org/10.5483/bmbrep.2005.38.1.024
  51. Liu Q, Sommer SS. Detection of extremely rare alleles by bidirectional pyrophosphorolysis-activated polymerization allele-specific amplification (Bi-PAP-A): measurement of mutation load in mammalian tissues // Biotechniques. 2004. 36(1). P.156-166. doi: https://doi.org/10.2144/04361DD03
  52. Liu Q, Sommer SS. PAP: detection of ultra rare mutations depends on P* oligonucleotides: "sleeping beauties" awakened by the kiss of pyrophosphorolysis // Hum Mutat. 2004a. 23(5). P.426-436. doi: https://doi.org/10.1002/humu.20036
  53. Liu Q., Thorland E.C., Heit J.A., Sommer S.S. Overlapping PCR for bidirectional PCR amplification of specific alleles: a rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes // Genome Res. 1997. 7(4). P. 389-398. doi: https://doi.org/10.1101/gr.7.4.389
  54. Lo Y.M., Patel P., Newton C.R., Markham A.F., Fleming K.A., Wainscoat J.S. Direct haplotype determination by double ARMS: specificity, sensitivity and genetic applications // Nucleic Acids 1991. V.19(13). P. 3561-3567. doi: https://doi.org/10.1093/nar/19.13.3561
  55. McKinzie B., Parsons B.L. Detection of rare K- ras codon 12 mutations using allele-specific competitive blocker PCR // Mutat. Res. 2002. V. 517(1-2). P. 209 doi: https://doi.org/10.1016/s1383-5718(02)00077-3
  56. Medintz , Wong W.W., Sensabaugh G., Mathies .A. High speed single nucleotide polymorphism typing of a hereditary haemochromatosis mutation with capillary array electrophoresis microplates // Electrophoresis. 2000. V. 21(12). P. 2352-2358. doi: https://doi.org/10.1002/1522-2683(20000701)21:12<2352::AID-ELPS2352>3.0.CO;2-G
  57. Medrano R.F., de Oliveira C.A. Guidelines for the tetra-primer ARMS-PCR technique development // Mol. Biotechnol. 2014. V. 56(7). P. 599-608. doi: https://doi.org/1007/s12033-014-9734-4
  58. Mesrian Tanha H., Mojtabavi Naeini M., Rahgozar S., Rasa S.M., Vallian S. Modified tetra-primer ARMS PCR as a single-nucleotide polymorphism genotyping tool // Test. Mol. Biomarkers. 2015.19(3). P. 156-161. doi: https://doi.org/10.1089/gtmb.2014.0289
  59. Myakishev M.V., Khripin , Hu S., Hamer D.H. High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers // Genome Res. 2001. V. 11(1). P. 163-169. doi: https://doi.org/10.1101/gr.157901
  60. Myers M.B., McKim K.L., Wang Y., Banda M., Parsons B.L. ACB-PCR Quantification of Low- Frequency Hotspot Cancer-Driver Mutations // Methods Mol. 2020. V. 2102. P. 395-417. doi: https://doi.org/10.1007/978- 1-0716-0223-2_23
  61. Nakitandwe J, Trognitz F, Trognitz B. Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping. Plant 2007. V.3. 2. doi: https://doi.org/10.1186/1746-4811-3-2
  62. Nazarenko IA, Bhatnagar SK, Hohman RJ. A closed tube format for amplification and detection of DNA based on energy transfer. Nucleic Acids Res. 1997. V.25(12). P.2516-2521. doi: https://doi.org/1093/nar/25.12.2516
  63. Newton C.R., Graham A., Heptinstall L.E., Powell S.J., Summers C., Kalsheker N., Smith J.C., Markham A.F. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS) // Nucleic Acids Res. 1989. V. 17(7). 2503-2516. doi: https://doi.org/10.1093/nar/17.7.2503
  64. Ochman H, Gerber AS, Hartl DL. Genetic applications of an inverse polymerase chain reaction // Genetics. 1988   120(3).   P.621-623.   doi:https://doi.org/10.1093/genetics/120.3.621
  65. Okayama H., Curiel D.T., Brantly M.L., Holmes M.D., Crystal R.G. Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification // J Lab Clin 1989. V.114(2). P.105 doi: https://doi.org/10.5555./uri:pii0022214389901078
  66. Okimoto R., Dodgson J.B. Improved PCR amplification of multiple specific alleles (PAMSA) using internally mismatched primers // 1996. V 21(1). P. 20-22, 24, 26. doi: 10.2144/96211bm03
  67. Orou A., Fechner B., Utermann G., Menzel H.J. Allele-specific competitive blocker PCR: a one-step method with applicability to pool screening // Hum. 1995. V. 6(2). P. 163-169. doi: https://doi.org/10.1002/humu.1380060209
  68. Parsons B.L., Heflich R.H. Detection of a mouse H-ras codon 61 mutation using a modified allele-specific competitive blocker PCR genotypic selection method // Mutagenesis. V. 13(6). P. 581-588. doi: https://doi.org/10.1093/mutage/13.6.581
  69. Parsons BL, McKinzie PB, Heflich RH. Allele- specific competitive blocker-PCR detection of rare base substitution // Methods Biol. 2005. V. 291. P. 235 doi: https://doi.org/10.1385/1-59259-840-4:235
  70. Peruzzi B., Serra M., Pescucci C., Sica M., Lastraioli S., Rondelli T., Pedemonte S., Risitano A.M., De Angioletti M., Piccioli P., Notaro R. Easy genotyping of complement C3 'slow' and 'fast' allotypes by tetra- primer amplification refractory mutation system PCR // Mol. Probes. 2010. V. 24(6). P. 401-402. doi: 10.1016/j.mcp.2010.07.002
  71. Petruska J., Goodman M.F., Boosalis M.S., Sowers C., Cheong C., Tinoco I.Jr. Comparison between DNA melting thermodynamics and DNA polymerase fidelity // Proc. Natl. Acad. Sci. USA. 1988. 85(17). P. 6252-6256. doi: https://doi.org/10.1073/pnas.85.17.6252
  72. Piccioli P., Serra M., Pedemonte S., Balbi G., Loiacono F., Lastraioli S., Gargiulo L., Morabito A., Zuccaro D., Del Mastro L., Pistillo M.P., Venturini M., De Angioletti M., Notaro R. Hexaprimer amplification refractory mutation system PCR for simultaneous single- tube genotyping of 2 close polymorphisms // Clin. 2008. V.   54(1).   P.   227-229.   doi: https://doi.org/10.1373/clinchem.2007.095703
  73. Rasheed A, Wen W, Gao F, Zhai S, Jin H, Liu J, Guo Q, Zhang Y, Dreisigacker S, Xia X, He Z. Development and validation of KASP assays for genes underpinning key economic traits in bread wheat. Theor Appl Genet. 2016. V.129(10). P.1843-1860. doi: https://doi.org/1007/s00122-016-2743-x
  74. Roncallo PF, Beaufort V, Larsen AO, Dreisigacker S, Echenique V. Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. var durum) collection. PLoS One. 2019. V.14(6). e0218562. doi: https://doi.org/1371/journal.pone.0218562
  75. Ruano G., Kidd K.K. Direct haplotyping of chromosomal segments from multiple heterozygotes via allele-specific PCR amplification // Nucleic Acids Res. 1989. 17(20). P. 8392. doi: https://doi.org/10.1093/nar/17.20.8392
  76. Rupp J, Solbach W, Gieffers J. Single- nucleotide-polymorphism-specific PCR for quantification and discrimination of Chlamydia pneumoniae genotypes by use of a "locked" nucleic acid. Appl Environ Microbiol. 2006. V.72(5). P.3785-3787. doi: https://doi.org/1128/AEM.72.5.3785-3787.2006
  77. Rust S., Funke H., Assmann G. Mutagenically separated PCR (MS-PCR): a highly specific one step procedure for easy mutation detection // Nucleic Acids Res. 1993. 21(16). P. 3623-3629. doi: https://doi.org/10.1093/nar/21.16.3623
  78. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. Primer- directed enzymatic amplification of DNA with a thermostable DNA polymerase. 1988. V.239(4839). P.487-491.                        DOI: https://doi.org/10.1126/science.239.4839.487
  79. Sarkar , Cassady J., Bottema C.D., Sommer S.S. Characterization of polymerase chain reaction amplification of specific alleles // Anal. Biochem. 1990. 186(1). P. 64-68. doi: https://doi.org/10.1016/0003-2697(90)90573-r
  80. Sarkar G., Sommer S.S. Haplotyping by double PCR amplification of specific alleles // Biotechniques. V. 10(4). P. 436, 438, 440.
  81. Sasvari-Szekely M., Gerstner , Ronai Z., Staub M., Guttman A. Rapid genotyping of factor V Leiden mutation using single-tube bidirectional allele-specific amplification and automated ultrathin-layer agarose gelelectrophoresis // Electrophoresis. 2000. V. 21(4). P. 816-821. doi:https://doi.org/10.1002/(SICI)15222683(20000301)21:4<816AID-ELPS816>3.0.CO;2-Y 
  82. Semagn K., Babu R., Hearne S.Olsen M. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement // Mol. Breeding.2014. V. 33. P. 1-14. doi: https://doi.org/10.1007/s11032-013-9917-x
  83. Seyama T., Ito T., Hayashi T., Mizuno T., Nakamura , Akiyama M. A novel blocker-PCR method for detection of rare mutant alleles in the presence of an excess amount of normal DNA // Nucleic Acids Res. 1992. V.   20(10).   P.   2493-2496.   doi: https://doi.org/10.1093/nar/20.10.2493
  84. Sinha P, Banerjee T, Srivastava GN, Anupurba Rapid detection of drug-resistant Mycobacterium tuberculosis directly from clinical specimens using allele- specific polymerase chain reaction assay // Indian J Med Res. 2019. V.150(1). P.33-42. doi: https://doi.org/10.4103/ijmr.IJMR_374_18
  85. Smith S.M., Maughan P.J. SNP genotyping using KASPar assays // Methods Mol. 2015. V. 1245. P. 243-256. doi: https://doi.org/10.1007/978-1-4939-1966-6_18
  86. Sommer S., Cassady J.D., Sobell J.L., Bottema C.D. A novel method for detecting point mutations or polymorphisms and its application to population screening for carriers of phenylketonuria // Mayo Clin. Proc. 1989. V. 64(11). P. 1361-1372. doi: https://doi.org/10.1016/s0025-6196(12)65378-6  
  87. Sommer S.S., Groszbach A.R., Bottema C.D. PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single-base changes // Biotechniques. 1992. V. 12(1). P. 82-87.
  88. Takeda S., Ichii S., Nakamura Detection of K- ras mutation in sputum by mutant-allele-specific amplification (MASA) // Hum. Mutat. 1993. V. 2(2). P. 112-117. doi: https://doi.org/10.1002/humu.1380020209
  89. Takei F, Igarashi M, Oka Y, Koga Y, Nakatani Competitive allele-specific hairpin primer PCR for extremely high allele discrimination in typing of single nucleotide polymorphisms. Chembiochem. 2012. V.13(10). P.1409-1412. doi: https://doi.org/10.1002/cbic.201200266
  90. Triglia T, Peterson MG, Kemp DJ. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences // Nucleic Acids Res. 1988. 16(16). P.8186. doi: https://doi.org/10.1093/nar/16.16.8186
  91. Wang H., Jiang J., Mostert B., Sieuwerts A., Martens J.W., Sleijfer S., Foekens J.A., Wang Y. Allele- specific, non-extendable primer blocker PCR (AS-NEPB- PCR) for DNA mutation detection in cancer // J. Mol. 2013. V. 15(1). P. 62-69. doi: https://doi.org/10.1016/j.jmoldx.2012.08.007
  92. Watanabe G., Umetsu K., Yuasa I., Sato M., Sakabe M., Naito E., Yamanouchi H., Suzuki T. A novel technique for detecting single nucleotide polymorphisms by              analyzing             consumed         allele-specific                  primers              // Electrophoresis. 2001. V. 22(3). P. 418-420. doi: https://doi.org/10.1002/1522-2683(200102)22:3<418::AID-ELPS418>3.0.CO;2-8
  93. Waterfall C.M., Cobb B.D. Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis // Nucleic Acids 2001. V. 29(23). e119. doi: https://doi.org/10.1093/nar/29.23.e119
  94. Wegmüller B, Lüthy J, Candrian U. 3'-5' proofreading-induced detection of point mutations by PCR using Tli DNA polymerase. Nucleic Acids Res. 1995. V.23(2). P.311-312. doi: https://doi.org/1093/nar/23.2.311
  95. Wu D.Y., Ugozzoli L., Pal B.K., Wallace R.B. Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemia // Proc. Natl. Acad. Sci. USA. 1989. V. 86(8). P. 2757-2760. doi: https://doi.org/1073/pnas.86.8.2757
  96. Xiong H, Li Y, Guo H, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Genetic Mapping by Integration of 55K SNP Array and KASP Markers Reveals Candidate Genes for Important Agronomic Traits in Hexaploid Wheat. Front Plant Sci. 2021. V.12. 628478. doi: https://doi.org/3389/fpls.2021.628478
  97. Yang HL, Jiang HJ, Fang WY, Xu YY, Liao DF, He High fidelity PCR with an off/on switch mediated by proofreading polymerases combining with phosphorothioate-modified primer. Biochem Biophys Res Commun. 2005. V.328(1). P.265-272. doi: https://doi.org/10.1016/j.bbrc.2004.12.159
  98. Yang L, Zhao D, Meng Z, Xu K, Yan J, Xia X, Cao S, Tian Y, He Z, Zhang Y. QTL mapping for grain yield-related traits in bread wheat via SNP-based selective genotyping. Theor Appl Genet. 2020. V.133(3). P.857-872. doi: https://doi.org/1007/s00122-019-03511-0
  99. Yang S., Shi H., Zhang Z., Chen Z., Yang W., Zhu W. Detection of Tri-allelic Single Nucleotide Polymorphisms of ABCB1 and CRP Genes by Penta- Primer Amplification Refractory Mutation System- Polymerase Chain Reaction // Genet. Test. Mol. Biomarkers. 2022. V. 26(1). P. 43-48. doi: https://doi.org/1089/gtmb.2021.0145
  100. Ye S., Dhillon S., Ke X., Collins A.R., Day I.N. An efficient procedure for genotyping single nucleotide polymorphisms // Nucleic Acids Res. 2001. 29(17). E88-8. doi: https://doi.org/10.1093/nar/29.17.e88
  101. Ye S., Humphries S., Green F. Allele specific amplification by tetra-primer PCR // Nucleic Acids Res. 1992. 20(5). P. 1152. doi: https://doi.org/10.1093/nar/20.5.1152
  102. Yin G., Mitsuda Y., Ezaki T., Hamajima N. A new PCR method: one primer amplification of PCR- CTPP products // Mol. 2012. V. 52(2). P. 180-183. doi: https://doi.org/10.1007/s12033-011-9485-4
  103. Zetterquist H, Olerup O. Identification of the HLA-DRB1*04, -DRB1*07, and -DRB1*09 alleles by PCR amplification with sequence-specific primers (PCR- SSP) in 2 hours. Hum Immunol. 1992. V.34(1). P.64-74. doi: https://doi.org/10.1016/0198-8859(92)90086-3
  104. Zhang J., Li K. Single-base discrimination mediated by proofreading 3' phosphorothioate-modified primers // Mol. 2003. V. 25(3). P. 223-228. doi: https://doi.org/10.1385/MB:25:3:223
  105. Zhang J., Li K. The 3’ terminal labeled primer extension: A new method of high throughput screening for SNP Current Drug Discov. 2001. V.9. P.21-
  106. (cited upon Zhang J., Li K., Pardinas J.R., Sommer S.S., Yao K.T. Proofreading genotyping assays mediated by high fidelity exo+ DNA polymerases. Trends Biotechnol. 2005. V. 23(2). P. 92-96. doi: https://doi.org/10.1016/j.tibtech.2004.12.009
  107. Zhang J., Li K., Liao D., Pardinas J.R., Chen L., Zhang X. Different applications of polymerases with and without proofreading activity in single-nucleotide polymorphism analysis // Lab. 2003. V. 83(8). P. 1147-1154. doi: https://doi.org/10.1097/01.lab.0000081589.91390.df
  108. Zhang J, Li K, Pardinas JR, Liao DF, Li HJ, Zhang X. SNP discrimination through proofreading and OFF-switch of exo+ polymerase. Mol Biotechnol. 2004. V.27(1). P.75-80. doi: https://doi.org/1385/MB:27:1:75
  109. Zhang , Li K., Pardinas J.R., Sommer S.S., Yao K.T. Proofreading genotyping assays mediated by high fidelity exo+ DNA polymerases // Trends Biotechnol. 2005.    V.    23(2).    P.    92-96. doi:https://doi.org/10.1016/j.tibtech.2004.12.009
  110. Zhu K.Y., Clark J.M. Addition of a competitive primer can dramatically improve the specificity of PCR amplification of specific alleles // 1996.21(4). P. 586, 590. doi: 10.2144/96214bm04
  111. Zhu S., Fushimi H., Cai S., Komatsu K. Species identification from Ginseng drugs by multiplex amplification refractory mutation system (MARMS) // Planta Med. 2004. V. 70(2). P. 189-192. doi: https://doi.org/10.1055/s-2004-815502
Скачать pdf
наверх
eISSN: 2221-6197 DOI: 10.31301/2221-6197