Quantitative Single-letter Sequencing: A method for simultaneously monitoring numerous known allelic variants in single DNA samples

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Monsion, Baptiste ^a   Duborjal, Hervé ^b   Blanc, Stéphane ^a  

^a Campus International de Baillarguet   (France)

^b Genome Express   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PLASMID DNA; VIRUS DNA; DNA; PRIMER DNA;

ACCURACY; ARTICLE; CAULIFLOWER MOSAIC VIRUS; CONTROLLED STUDY; DNA DETERMINATION; DNA EXTRACTION; DNA FLANKING REGION; DNA SEQUENCE; ELECTROPHORESIS; FLUORESCENCE ANALYSIS; GENE AMPLIFICATION; GENETIC MARKER; GENETIC VARIABILITY; GENOTYPE; NONHUMAN; POLYMERASE CHAIN REACTION; POLYMORPHIC LOCUS; QUANTITATIVE ANALYSIS; RELIABILITY; VIRAL GENETICS; VIRAL PLANT DISEASE; VIRUS GENOME; ALLELE; GENETICS; GENOMICS; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLASMID;

CAULIFLOWER MOSAIC VIRUS; FUNGI;

ALLELES; BASE SEQUENCE; CAULIMOVIRUS; DNA; DNA PRIMERS; DNA, VIRAL; GENETIC MARKERS; GENOME, VIRAL; GENOMICS; MOLECULAR SEQUENCE DATA; PLASMIDS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 41549155482     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-85     Document Type: Article

References (46)

1. Mir KU Southern EM Sequence variation in genes and genomic DNA: Methods for large-scale analysis Annu Rev Genomics Hum Genet 2000, 1:329-360. 10.1146/annurev.genom.1.1.329 11701633
2. Gibson NJ The use of real-time PCR methods in DNA sequence variation analysis Clin Chim Acta 2006, 363(1-2):32-47. 10.1016/j.cccn.2005.06.022 16182268
3. Wittwer CT Herrmann MG Gundry CN Elenitoba-Johnson KS Real-time multiplex PCR assays Methods 2001, 25(4):430-442. 10.1006/meth.2001.1265 11846612
4. Rudi K Zimonja M Hannevik SE Dromtorp SM Multiplex real-time single nucleotide polymorphism detection and quantification by quencher extension Biotechniques 2006, 40(3):323-329. 16568821
5. Lindroos K Sigurdsson S Johansson K Ronnblom L Syvanen AC Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system Nucleic Acids Res 2002, 30(14):e70. 135771 12136118 10.1093/nar/gnf069
6. Archak S Lakshminarayanareddy V Nagaraju J High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa) Electrophoresis 2007, 28(14):2396-2405. 10.1002/elps.200600646 17577195
7. Norton N Williams NM O'Donovan MC Owen MJ DNA pooling as a tool for large-scale association studies in complex traits Ann Med 2004, 36(2):146-152. 10.1080/07853890310021724 15119834
8. Sham P Bader JS Craig I O'Donovan M Owen M DNA Pooling: A tool for large-scale association studies Nat Rev Genet 2002, 3(11):862-871. 10.1038/nrg930 12415316
9. Gilad Y Borevitz J Using DNA microarrays to study natural variation Curr Opin Genet Dev 2006, 16(6):553-558. 10.1016/j.gde.2006.09.005 17008090
10. Ng JK Liu WT Miniaturized platforms for the detection of single-nucleotide polymorphisms Anal Bioanal Chem 2006, 386(3):427-434. 10.1007/s00216-006-0552-9 16821029
11. Ragoussis J Elvidge GP Kaur K Colella S Matrix-assisted laser desorption/ ionisation, time-of-flight mass spectrometry in genomics research PLoS Genet 2006, 2(7):e100. 1523240 16895448 10.1371/journal.pgen.0020100
12. Edwards JR Ruparel H Ju J Mass-spectrometry DNA sequencing Mutat Res 2005, 573(1-2):3. 12 15829234
13. Corona G Toffoli G High throughput screening of genetic polymorphisms by matrix-assisted laser desorption ionization time-of-flight mass spectrometry Comb Chem High Throughput Screen 2004, 7(8):707-725. 10.2174/1386207043328283 15578933
14. Jurinke C Oeth P van den Boom D MALDI-TOF mass spectrometry: A versatile tool for high-performance DNA analysis Mol Biotechnol 2004, 26(2):147-164. 10.1385/MB:26:2:147 14764940
15. Wada K Kubota N Ito Y Yagasaki H Kato K Yoshikawa T Ono Y Ando H Fujimoto Y Kiuchi T Simultaneous quantification of Epstein-Barr virus, cytomegalovirus, and human herpesvirus 6 DNA in samples from transplant recipients by multiplex real-time PCR assay J Clin Microbiol 2007, 45(5):1426-1432. 1865882 17376882 10.1128/JCM.01515-06
16. Wu JH Liu WT Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction Nucleic Acids Res 2007, 35(11):e82. 1920266 17553831 10.1093/ nar/gkm413
17. Wilke CO Quasispecies theory in the context of population genetics BMC Evol Biol 2005, 5:44. 1208876 16107214 10.1186/1471-2148-5-44
18. Vignuzzi M Stone JK Arnold JJ Cameron CE Andino R Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Nature 2006, 439(7074):344-348. 1569948 16327776 10.1038/ nature04388
19. Watzinger F Ebner K Lion T Detection and monitoring of virus infections by real-time PCR Mol Aspects Med 2006, 27(2-3):254-298. 10.1016/ j.mam.2005.12.001 16481036
20. Saccheri I Hanski I Natural selection and population dynamics Trends Ecol Evol 2006, 21(6):341-347. 10.1016/j.tree.2006.03.018 16769435
21. Edwards CT Holmes EC Wilson DJ Viscidi RP Abrams EJ Phillips RE Drummond AJ Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1 BMC Evol Biol 2006, 6:28. 1444934 16556318 10.1186/1471-2148-6-28
22. de la Iglesia F Elena SF Fitness Declines in Tobacco Etch Virus upon Serial Bottleneck Transfers J Virol 2007, 81(10):4941-4947. Epub 2007 17344305 1900225 10.1128/JVI.02528-06
23. Langemeier JL Cook RF Issel CJ Montelaro RC Application of cycle dideoxy fingerprinting to screening heterogeneous populations of the equine infectious anemia virus Biotechniques 1994, 17(3):484-486. 488, 490. 7818901
24. Soucek P Skjelbred CF Svendsen M Kristensen T Kure EH Kristensen VN Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene BMC biotechnology 2004, 4:28. 544357 15563733 10.1186/1472-6750-4-28
25. Kim YJ Kim SO Chung HJ Jee MS Kim BG Kim KM Yoon JH Lee HS Kim CY Kim S Population genotyping of hepatitis C virus by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of short DNA fragments Clin Chem 2005, 51(7):1123-1131. 10.1373/ clinchem.2004.047506 15890891
26. Norton N Williams NM Williams HJ Spurlock G Kirov G Morris DW Hoogendoorn B Owen MJ O'Donovan MC Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools Hum Genet 2002, 110(5):471-478. 10.1007/s00439-002-0706-6 12073018
27. Li ZG Chen LY Huang J Qiao P Qiu JM Wang SQ Quantification of the relative levels of wild-type and lamivudine-resistant mutant virus in serum of HBV-infected patients using microarray J Viral Hepat 2005, 12(2):168-175. 10.1111/j.1365-2893.2005.00562.x 15720532
28. Wilkening S Hemminki K Thirumaran RK Bermejo JL Bonn S Forsti A Kumar R Determination of allele frequency in pooled DNA: Comparison of three PCR-based methods Biotechniques 2005, 39(6):853-858. 16382903
29. 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(6):429-434. 10.1006/mcpr.2002.0440 12490144
30. Trosvik P Skanseng B Jakobsen KS Stenseth NC Naes T Rudi K Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations Appl Environ Microbiol 2007, 73(15):4975-4983. 1951012 17575003 10.1128/AEM.00128-07
31. Franck A Guilley H Jonard J Richards K Hirth L Nucleotide sequence of cauliflower mosaic virus DNA Cell 1980, 21:285-294. 10.1016/ 0092-8674(80)90136-1 7407912
32. Froissart R Uzest M Ruiz-Ferrer V Drucker M Hebrard E T H Blanc S Splicing of the Cauliflower mosaic virus 35S RNA serves to downregulate a toxic gene product J Gen Virol 2004, 85(pt 9):2719-26. 15302965 10.1099/vir.0.80029-0
33. Melcher U Steffens DL Lyttle DJ Lebeurier G Lin H Choe IS Essenberg RC Infectious and non-infectious mutants of cauliflower mosaic virus DNA J Gen Virol 1986, 67(Pt 7):1491-1498. 3723112
34. Gardner RC Shepherd RJ A procedure for rapid isolation and analysis of cauliflower mosaic virus DNA Virology 1980, 106:159-161. 10.1016/ 0042-6822(80)90234-2
35. De Leeuw M Mouret J JP I WO03068987 (A3): Discriminative analysis of clone signature WO: Cogenics Genome Express SA, 11 Chemin des Prés, F-38944 Meylan, France 2003, 7.
36. Sanger F Nicklen S Coulson AR DNA sequencing with chain-terminating inhibitors Proc Natl Acad Sci USA 1977, 74(12):5463-5467. 431765 271968 10.1073/pnas.74.12.5463
37. STRand - Nucleic Acid Analysis Software http://www.vgl.ucdavis.edu/ informatics/download_strand.php
38. Zhou G Kamahori M Okano K Chuan G Harada K Kambara H Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER) Nucleic Acids Res 2001, 29(19):E93. 60253 11574695
39. Bang-Ce Y Peng Z Bincheng Y Songyang L Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA Anal Biochem 2004, 333(1):72-78. 10.1016/j.ab.2004.05.016 15351282
40. Meaburn E Butcher LM Schalkwyk LC Plomin R Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans Nucleic Acids Res 2006, 34(4):e27. 1368655 16478714 10.1093/nar/gnj027
41. Schnack HG Bakker SC van 't Slot R Groot BM Sinke RJ Kahn RS Pearson PL Accurate determination of microsatellite allele frequencies in pooled DNA samples Eur J Hum Genet 2004, 12(11):925-934. 10.1038/ sj.ejhg.5201234 15305176
42. 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(1-2):101-110. 10.1016/S0165-022X(00)00156-1 11179766
43. Gruber JD Colligan PB Wolford JK Estimation of single nucleotide polymorphism allele frequency in DNA pools by using Pyrosequencing Hum Genet 2002, 110(5):395-401. 10.1007/s00439-002-0722-6 12073008
44. Lavebratt C Sengul S Jansson M Schalling M Pyrosequencing-based SNP allele frequency estimation in DNA pools Hum Mutat 2004, 23(1):92-97. 10.1002/humu.10292 14695537
45. Germer S Holland MJ Higuchi R High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR Genome Res 2000, 10(2):258-266. 310828 10673283 10.1101/gr.10.2.258
46. Mattarucchi E Marsoni M Binelli G Passi A Lo Curto F Pasquali F Porta G Different real time PCR approaches for the fine quantification of SNP's alleles in DNA pools: Assays development, characterization and pre-validation J Biochem Mol Biol 2005, 38(5):555-562. 16202235