Novel quantitative real-time LCR for the sensitive detection of SNP frequencies in pooled DNA: Method development, evaluation and application

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Psifidi, Androniki ^a   Dovas, Chrysostomos ^a   Banos, Georgios ^a  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

EXONUCLEASE; FLUORESCENT DYE; OLIGONUCLEOTIDE; PHOSPHATASE; DIAGNOSTIC AGENT; DNA;

ACCURACY; ALLELE; ARTICLE; BRAIN DISEASE; CODON; CONTROLLED STUDY; DEVELOPMENTAL GENE; DNA BINDING; DNA DETERMINATION; DNA EXTRACTION; EVALUATION; GENE FREQUENCY; GENE MUTATION; GENE POOL; GENETIC SUSCEPTIBILITY; GENOTYPE; LIGASE CHAIN REACTION; LIMIT OF DETECTION; LIMIT OF QUANTITATION; MILK; NONHUMAN; ONCOGENE; PLASMID; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SENSITIVITY ANALYSIS; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; SENSITIVITY AND SPECIFICITY; STANDARD; TECHNIQUE;

OVIS; OVIS ARIES;

ANIMALS; DNA; DNA MUTATIONAL ANALYSIS; FLUORESCENT DYES; GENE FREQUENCY; LIGASE CHAIN REACTION; LIMIT OF DETECTION; METHODS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SHEEP;

EID: 79251625179     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014560     Document Type: Article

References (36)

1. Wang DG, Fan JB, Siao CJ, Berno A, Young P, et al. (1998) Large scale identification, mapping, genotyping of single nucleotide polymorphisms in the human genome. Science 280: 1077-1082.
2. Mhlanga MM, Malmberg L (2001) Using molecular beacons to detect single nucleotide polymorphisms with real-time PCR. Methods 25: 463-471.
3. Yu A, Geng H, Zhou X (2006) Quantify single nucleotide polymorphism (SNP) ratio in pooled DNA based on normalized fluorescence real-time PCR. BMC genomics 7: 143.
4. Abravaya K, Carrino JJ, Muldoon S, Lee HH (1995) Detection of point mutations with modified ligase chain reaction (Gap-LCR). Nucleic Acids Res 23: 675-682.
5. Norton N, Williams N, O'Donovan M, Owen M (2004) DNA pooling as a tool for large scale association studies in complex traits. Ann Med 36(2): 146-152.
6. Bagnato A, Schiavini F, Rossoni A, Maltecca C, Dolezal M, et al. (2008) Quantitative trait loci affecting milk yield and protein percentage in a threecountry Brown Swiss population. J of Dairy Sci 91: 767-783.
7. Buitkamp J, Gotz K (2004) Use of milk samples from a milk evaluation programme for the genotyping of cows. Arch Tierz Dummerstorf 47: 15-26.
8. Know PY (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genom Hum G 2: 235-258.
9. Gut LG (2001) Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 17: 475-492.
10. Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere ML, et al. (2000) Cheap, Accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extention and DHPLC in DNA pools. Hum Genet 107: 488-493.
11. Zhou G, Kamahori M, Okano K, Chuan G, Harada K, et al. (2001) Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extention reactions (BAMPER). Nucleic Acids Res 29: e93.
12. Macgregor S, Visscher PM, Montgomery G (2006) Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates. Nucleid Acids Res 34: e55.
13. Gruber JD, Colligan PB, Wolford JK (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Hum Genet 110: 395-401.
14. Tapp I, Malmberg L, Rennel E, Wik M, Syvanen AC (2000) Homogeneous scoring of single-nucleotide polymoephisms: comparison of the 59-nuclease TaqMan assay and Molecular Beacons probes. Biotechniques 28: 732-738.
15. Mattarucchi E, Marsoni M, Binelli G, Passi, A, Lo Curto F, et al. (2005) Different real-time PCR approaches for fine quantification of SNP's alleles in DNA pools: assays development, characterization and pre-validation. Biochem Mol Biol 38: 555-562.
16. Sidransky D (2002) Emerging molecular markers for cancer. Nat Rev Cancer 2: 210-219.
17. Diehl F, Li M, Dressman D, He Y, Shen D (2005) Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA 102: 16386-16373.
18. Wiedmann M, Wilson WJ, Czajka J, Luo J, Barrany F, et al. (1994) Ligase chain reaction (LCR)-overview and applications. PCR methods Appl 3S: 51-64.
19. Harden S, Thomas D, Benoit N, Minhas K, Westra W, et al. (2004) Real-time Gap Ligase Chain Reaction: A rapid semiquantitative assay for detection p53 mutation at low levels in surgical margins and lymph nodes from resected lung and head and neck tumors. Clin Cancer Res 10: 2379-2385.
20. Birkenmeyer L, Armstrong A (1992) Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae. J Clin Microbiol 30: 3089-3094.
21. Cao W (2004) Recent developments in ligase-mediated amplification and detection. Trends Biotechnol 22.
22. Tooley PW, Hatziloukas E, Scott DL, Carras MM (2002) Use of ligase chain reaction for enhanced detection of Phytophora infestans. Can J Plant Pathol 24: 294-301.
23. Marshall RL, Laffler TG, Cerney MB, Sustachek JC, Kratochvi JD, et al. (1994) Detection of HCV RNA by the asymmetric gap-ligase chain reaction. PCR Meth Appl 4: 80-84.
24. Tian F, Wu Y, Zhou Y, Liu X, Visvikis-Siest S, et al. (2008) A new single nucleotide polymorphism genotyping method based on gap ligase chain reaction and a microsphere detection assay. Clin Chem Lab Med 46(4): 486-489.
25. Psifidi A, Basdagianni Z, Dovas CI, Arsenos G, Sinapis E, et al. (2010) Characterisation of the PRNP gene locus in Chios dairy sheep and its association with milk production and reproduction traits. Animal Genetics (in press).
26. Psifidi A, Dovas CI, Banos G (2010) A comparison of six methods for genomic DNA extraction suitable for PCR-based genotyping amplifications using ovine milk samples. Mol Cell Probes 24: 93-98.
27. 171 is associated with high susceptibility to scrapie in purebred and crossbred German Merinoland sheep. Arch Virol 149: 1571-1580.
28. Wang W, Chen K, Xu C (2006) DNA quantification using EvaGreen and a realtime PCR instrument. Anal Biochem 356: 303-305.
29. Ihrig J, Lill R, Muhlenhoff U (2006) Application of the DNA-specific dye EvaGreen for the routine quantification of DNA in microplates. Anal Biochem 359: 265-267.
30. Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33: W577-W581.
31. Schwarz G, Baumler S, Block A, Felsenstein F, Wenzel G (2004) Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using real-time PCR. Nucleic Acids Res 32: e 24.
32. Inczedy J, Lengyel T, Ure AM (1998) Compedium on analytical Nomenclature. Definite Rules 1997. Third Edition. New York: Blackwell Science.
33. Borodina T, Lehrach H, Soldatov A (2004) Ligation detection reaction-Taq- Man procedure for single nucleotide polymorphism detection on genomic DNA. Anal Biochem 333: 309-319.
34. De Noronha CMC, Mullins JI (1992) Amplimers with 39-terminal phosphorothioate linkages resist degradation by Vent polymerase and reduce Taq polymerase mispriming. PCR Meth Appl 2: 131-136.
35. Di Giusto DA, King GC (2004) Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implication for genotyping assays. Nucleic Acids Res 32(3): e32.
36. Dovas CI, Papanastassopoulou M, Georgiadis MP, Chatzinasiou E, Maliogka VI, et al. (2010) Detection and quantification of infectious avian influenza A (H5N1) virus in environmental water by using real-time reverse transcription-PCR. Appl Environ Microbiol 76: 2165-74.