A Novel Multiplex Tetra-Primer ARMS-PCR for the Simultaneous Genotyping of Six Single Nucleotide Polymorphisms Associated with Female Cancers

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Zhang, Chen ^a   Liu, Ying ^a,b   Ring, Brian Z ^c   Nie, Kai ^a   Yang, Mengjie ^a   Wang, Miao ^a   Shen, Hongwei ^a   Wu, Xiyang ^b   Ma, Xuejun ^a  

^a BEIJING HOSPITAL   (China)

^b JINAN UNIVERSITY   (China)

^c HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMPLICON; ARTICLE; BREAST CANCER; CANCER RISK; CAPILLARY ELECTROPHORESIS; CONTROLLED STUDY; FEMALE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENOTYPING TECHNIQUE; HUMAN; MULTIPLEX TETRA PRIMER AMPLIFICATION REFRACTORY MUTATION SYSTEM POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; RISK ASSESSMENT; SINGLE NUCLEOTIDE POLYMORPHISM; UTERINE CERVIX CANCER;

BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; DNA PRIMERS; ELECTROPHORESIS, AGAR GEL; FEMALE; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; GENOTYPING TECHNIQUES; HUMANS; MOLECULAR SEQUENCE DATA; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATION; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

TETRA;

EID: 84876214253     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062126     Document Type: Article

References (35)

1. Erichsen HC, Chanock SJ, (2004) SNPs in cancer research and treatment. Br J Cancer 90: 747-751.
2. Cully M, You H, Levine AJ, Mak TW, (2006) Beyond PTEN mutations: the PI3K pathway as an integrator of multiple inputs during tumorigenesis. Nat Rev Cancer 6: 184-192.
3. Hollstein M, Sidransky D, Vogelstein B, Harris CC, (1991) p53 mutations in human cancers. Science 253: 49-53.
4. Hanahan D, Weinberg RA, (2000) The hallmarks of cancer. Cell 100: 57-70.
5. Sjoqvist F, (1999) The past, present and future of clinical pharmacology. Eur J Clin Pharmacol 55: 553-557.
6. Wiechec E, Hansen LL, (2009) The effect of genetic variability on drug response in conventional breast cancer treatment. Eur J Pharmacol 625: 122-130.
7. Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, et al. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17: 2503-2516.
8. Ye S, Humphries S, Green F, (1992) Allele specific amplification by tetra-primer PCR. Nucleic Acids Res 20: 1152.
9. Piccioli P, Serra M, Gismondi V, Pedemonte S, Loiacono F, et al. (2006) Multiplex tetra-primer amplification refractory mutation system PCR to detect 6 common germline mutations of the MUTYH gene associated with polyposis and colorectal cancer. Clin Chem 52: 739-743.
10. Balbi G, Ferrera F, Rizzi M, Piccioli P, Morabito A, et al. (2007) Association of-318 C/T and +49 A/G cytotoxic T lymphocyte antigen-4 (CTLA-4) gene polymorphisms with a clinical subset of Italian patients with systemic sclerosis. Clin Exp Immunol 149: 40-47.
11. Peruzzi B, Serra M, Pescucci C, Sica M, Lastraioli S, et al. (2010) Easy genotyping of complement C3 'slow' and 'fast' allotypes by tetra-primer amplification refractory mutation system PCR. Mol Cell Probes 24: 401-402.
12. Shuber AP, Grondin VJ, Klinger KW, (1995) A simplified procedure for developing multiplex PCRs. Genome Res 5: 488-493.
13. Wang QX, Li K, Zhou YX, Xiao JH, (2009) [Development, optimization and application of the expression analysis platform based on multiplex quantitative RT-PCR using fluorescent universal primers]. Yi Chuan 31: 552-561.
14. Beck O, Seidl C, Lehrnbecher T, Kreyenberg H, Schwabe D, et al. (2006) Quantification of chimerism within peripheral blood, bone marrow and purified leukocyte subsets: comparison of singleplex and multiplex PCR amplification of short tandem repeat (STR) loci. Eur J Haematol 76: 237-244.
15. Dupont M, Goldsborough A, Levayer T, Savare J, Rey JM, et al. (2002) Multiplex fluorescent RT-PCR to quantify leukemic fusion transcripts. Biotechniques 33: 158-160, 162, 164.
16. Hu X, Zhang Y, Zhou X, Xu B, Yang M, et al. (2012) Simultaneously typing nine serotypes of enteroviruses associated with hand, foot, and mouth disease by a GeXP analyzer-based multiplex reverse transcription-PCR assay. J Clin Microbiol 50: 288-293.
17. Hofmann MA, (2003) Construction of an infectious chimeric classical swine fever virus containing the 5'UTR of bovine viral diarrhea virus, and its application as a universal internal positive control in real-time RT-PCR. J Virol Methods 114: 77-90.
18. Jemal A, Bray F, Center MM, Ferlay J, Ward E, et al. (2011) Global cancer statistics. CA Cancer J Clin 61: 69-90.
19. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
20. Garcia-Closas M, Chanock S, (2008) Genetic susceptibility loci for breast cancer by estrogen receptor status. Clin Cancer Res 14: 8000-8009.
21. Yu KJ, Rader JS, Borecki I, Zhang Z, Hildesheim A, (2009) CD83 polymorphisms and cervical cancer risk. Gynecol Oncol 114: 319-322.
22. Setiawan VW, Doherty JA, Shu XO, Akbari MR, Chen C, et al. (2009) Two estrogen-related variants in CYP19A1 and endometrial cancer risk: a pooled analysis in the Epidemiology of Endometrial Cancer Consortium. Cancer Epidemiol Biomarkers Prev 18: 242-247.
23. Goodman MT, Lurie G, Thompson PJ, McDuffie KE, Carney ME, (2008) Association of two common single-nucleotide polymorphisms in the CYP19A1 locus and ovarian cancer risk. Endocr Relat Cancer 15: 1055-1060.
24. Long J, Cai Q, Shu XO, Qu S, Li C, et al. (2010) Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium. PLoS Genet 6: e1001002.
25. Reeves GK, Travis RC, Green J, Bull D, Tipper S, et al. (2010) Incidence of breast cancer and its subtypes in relation to individual and multiple low-penetrance genetic susceptibility loci. JAMA 304: 426-434.
26. Jia C, Cai Y, Ma Y, Fu D, (2010) Quantitative assessment of the effect of FGFR2 gene polymorphism on the risk of breast cancer. Breast Cancer Res Treat 124: 521-528.
27. Lu PH, Yang J, Li C, Wei MX, Shen W, et al. (2011) Association between mitogen-activated protein kinase kinase kinase 1 rs889312 polymorphism and breast cancer risk: evidence from 59,977 subjects. Breast Cancer Res Treat 126: 663-670.
28. Qin M, Wang DY, Huang F, Nie K, Qu M, et al. (2010) Detection of pandemic influenza A H1N1 virus by multiplex reverse transcription-PCR with a GeXP analyzer. J Virol Methods 168: 255-258.
29. Harlid S, Ivarsson MI, Butt S, Grzybowska E, Eyfjord JE, et al. (2012) Combined effect of low-penetrant SNPs on breast cancer risk. Br J Cancer 106: 389-396.
30. Millis MP, (2011) Medium-throughput SNP genotyping using mass spectrometry: multiplex SNP genotyping using the iPLEX(R) Gold assay. Methods Mol Biol 700: 61-76.
31. Xiu-Cheng Fan A, Garritsen HS, Tarhouny SE, Morris M, Hahn S, et al. (2008) A rapid and accurate approach to identify single nucleotide polymorphisms of mitochondrial DNA using MALDI-TOF mass spectrometry. Clin Chem Lab Med 46: 299-305.
32. Shi X, Tang C, Zhou D, Sun J, Lu Z, (2009) PCR-product microarray based on polyacrylic acid-modified surface for SNP genotyping. Electrophoresis 30: 1286-1296.
33. Yanagawa T, Koga H, (2009) Modified multiple primer extension method. Methods Mol Biol 578: 425-435.
34. Tebbutt SJ, Ruan J, (2008) Combining multiple PCR primer pairs for each amplicon can improve SNP genotyping accuracy by reducing allelic drop-out. Biotechniques 45: 637-638, 640, 642 passim.
35. Toubanaki DK, Christopoulos TK, Ioannou PC, Flordellis CS, (2009) Identification of single-nucleotide polymorphisms by the oligonucleotide ligation reaction: a DNA biosensor for simultaneous visual detection of both alleles. Anal Chem 81: 218-224.