Locked nucleic acid (LNA) probes in high-throughput genetic analysis: Application to an assay for type 1 diabetes-related HLA-DQB1 alleles

Clinical Biochemistry

Volumn 38, Issue 11, 2005, Pages 1015-1022

  Kiviniemi, Minna ^a   Nurmi, Jussi ^b   Lövgren, Timo ^b   Ilonen, Jorma ^a  

^a UNIVERSITY OF TURKU   (Finland)

^b UNIVERSITY OF TURKU   (Finland)

Author keywords

Homogeneous DNA assay; Locked nucleic acid; Time resolved fluorometry; Type 1 diabetes

Indexed keywords

DNA; HLA DQB1 ANTIGEN; LOCKED NUCLEIC ACID;

ALLELE; ARTICLE; BIOASSAY; BLOOD SAMPLING; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE PREDISPOSITION; DNA EXTRACTION; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SCREENING; GENETIC SUSCEPTIBILITY; GENOTYPE; HIGH THROUGHPUT SCREENING; HLA SYSTEM; HUMAN; HYBRIDIZATION; INSULIN DEPENDENT DIABETES MELLITUS; NUCLEIC ACID PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RISK FACTOR;

BASE SEQUENCE; BLOOD SPECIMEN COLLECTION; DESICCATION; DIABETES MELLITUS, TYPE 1; DNA PROBES; EUROPIUM; FLUOROMETRY; GENETIC SCREENING; HLA-DQ ANTIGENS; HUMANS; OLIGONUCLEOTIDES, ANTISENSE; POLYMERASE CHAIN REACTION;

EID: 27744458133     PISSN: 00099120     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2005.08.001     Document Type: Article

References (28)

1. J.C. Venter, M.D. Adams, and E.W. Myers The sequence of the human genome Science 291 2001 1304 1351
2. C.A. Foy, and H.C. Parkes Emerging homogeneous DNA-based technologies in the clinical laboratory Clin. Chem. 47 2001 990 1000
3. L.L. Field Genetic linkage and association studies of Type I diabetes: challenges and rewards Diabetologia 45 2002 21 35
4. S. Nejentsev, M. Sjöroos, and T. Soukka Population-based genetic screening for the estimation of Type 1 diabetes mellitus risk in Finland: selective genotyping of markers in the HLA-DQB1, HLA-DQA1 and HLA-DRB1 loci Diabet. Med. 16 1999 985 992
5. J. Ilonen, H. Reijonen, and E. Herva Rapid HLA-DQB1 genotyping for four alleles in the assessment of risk for IDDM in the Finnish population. The childhood diabetes in Finland (DiMe) study group Diabetes Care 19 1996 795 800
6. I.V. Kutyavin, I.A. Afonina, and A. Mills 3′-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures Nucleic Acids Res. 28 2000 655 661
7. I. Afonina, M. Zivarts, I. Kutyavin, E. Lukhtanov, H. Gamper, and R. Meyer Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder Nucleic Acids Res. 25 1997 2657 2660
8. J.B. de Kok, E.T. Wiegerinck, B.A. Giesendorf, and D.W. Swinkels Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes) Hum. Mutat. 19 2002 554 559
9. D.A. Braasch, and D.R. Corey Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA Chem. Biol. 8 2001 1 7
10. M. Petersen, and J. Wengel LNA: a versatile tool for therapeutics and genomics Trends Biotechnol. 21 2003 74 81
11. J-M. Costa, P. Ernault, M. Olivi, T. Gaillon, and K. Arar Chimeric LNA/DNA probes as a detection system for real-time PCR Clin. Biochem. 37 2004 930 932
12. M.P. Johnson, L.M. Haupt, and L.R. Griffiths Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR Nucleic Acids Res. 32 2004 e55
13. A. Simeonov, and T.T. Nikiforov Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection Nucleic Acids Res. 30 2002 e91
14. L.A. Ugozzoli, D. Latorra, R. Puckett, K. Arar, and K. Hamby Real-time genotyping with oligonucleotide probes containing locked nucleic acids Anal. Biochem. 324 2004 143 152
15. C. Letertre, S. Perelle, F. Dilasser, K. Arar, and P. Fach Evaluation of the performance of LNA and MGB probes in 5′-nuclease PCR assays Mol. Cell. Probes 17 2003 307 311
16. M. Kiviniemi, J. Nurmi, H. Turpeinen, T. Lövgren, and J. Ilonen A homogeneous high-throughput genotyping method based on competitive hybridization Clin. Biochem. 36 2003 633 640
17. J. Nurmi, T. Wikman, M. Karp, and T. Lövgren High-performance real-time quantitative RT-PCR using lanthanide probes and a dual-temperature hybridization assay Anal. Chem. 74 2002 3525 3532
18. O. Olerup, and H. Zetterquist HLA-DR typing by PCR amplification with sequence-specific primers (PCR-SSP) in 2 hours: an alternative to serological DR typing in clinical practice including donor-recipient matching in cadaveric transplantation Tissue Antigens 39 1992 225 235
19. M. Sjöroos, A. Iitiä, J. Ilonen, H. Reijonen, and T. Lövgren Triple-label hybridization assay for type-1 diabetes-related HLA alleles Biotechniques 18 1995 870 877
20. J.A. Sanchez, K.E. Pierce, J.E. Rice, and L.J. Wangh Linear-After-The- Exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis Proc. Natl. Acad. Sci. U. S. A. 101 2004 1933 1938
21. F. Arjomand-Nahad, K. Diefenbach, O. Landt, E. Gaikovitch, and I. Roots Genotyping of the triallelic variant G2677T/A in MDR1 using LightCycler with locked-nucleic-acid-modified hybridization probes Anal. Biochem. 334 2004 201 203
22. O. Goldenberg, O. Landt, R.R. Shumann, U.B. Göbel, and L. Hamann Use of locked nucleic acid oligonucleotides as hybridization/FRET probes for quantification of 16 s rDNA by real-time PCR Biotechniques 38 2005 29 32
23. N. Jacobsen, J. Bentzen, and M. Meldgaard LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E Nucleic Acids Res. 30 2002 e100
24. K.J. Livak Allelic discrimination using fluorogenic probes and the 5′ nuclease assay Genet. Anal. 14 1999 143 149
25. H. Sahlberg, P. Ollikka, A. Ylikoski, H-M. Raussi, H. Hakala, and I. Hemmila Integrated homogeneous genotyping assay using dried blood and saliva spots Clin. Chim. Acta 355 2005 S163 S164
26. J. Nurmi, M. Kiviniemi, M. Kujanpää, M. Sjöroos, J. Ilonen, and T. Lövgren High-throughput genetic analysis using time-resolved fluorometry and closed-tube detection Anal. Biochem. 299 2001 211 217
27. S. Tyagi, and F.R. Kramer Molecular beacons: probes that fluoresce upon hybridization Nat. Biotechnol. 14 1996 303 308
28. E. Soini, and T. Lövgren Time-resolved fluorescence of lanthanide probes and applications in biotechnology CRC Crit. Rev. Anal. Chem. 15 1987 105 154