Developing multiplexed SNP assays with special reference to degraded DNA templates

Nature Protocols

Volumn 1, Issue 3, 2006, Pages 1370-1378

  Sanchez, Juan J ^a   Endicott, Phillip ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CAPILLARY ELECTROPHORESIS; GENETIC SCREENING; GENETICS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA; ELECTROPHORESIS, CAPILLARY; GENETIC SCREENING; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34347208718     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.247     Document Type: Article

References (34)

1. Lindblad-Toh, K. et al. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat. Genet. 24 381-386 (2000).
2. Hardenbol, P. et al. Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 15, 269-275 (2005).
3. Anderson, E.C. et al. The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics 172, 2567-2582 (2006).
4. Bandelt, H.J. Mosaics of ancient mitochondrial DNA: Positive indicators of nonauthenticity. Eur J. Hum. Genet. 13, 1106-1112 (2005).
5. Römpler, H. et al. Multiplex amplification of ancient DNA. Nat. Protocols 1, 720-728 (2006).
6. Syvänen, A.C. From gels to chips: "minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum. Mutat. 13, 1-10 (1999).
7. Noonan, J.P. et al. Genomic sequencing of Pleistocene cave bears. Science 309, 597-599 (2005).
8. Smith, C.I. et al. The thermal history of human fossils and the likelihood of successful DNA amplification. J. Hum. Evol. 45 203-217 (2003).
9. Quintans, B. et al. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci. Int. 140, 251-257 (2004).
10. Brandstätter, A. et al. Dissection of mitochondrial superhaplogroup H using coding region SNPs. Electrophoresis 27 2541-2550 (2006).
11. Rachlin, J. et al. Computational tradeoffs in multiplex PCR assay design for SNP genotyping. B.M.C. Genomics 6, 102 (2005).
12. Umetsu, K. et al. Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations. Electrophoresis 26, 91-98 (2005).
13. Pastinen, T. et al. Minisequencing: A specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7, 606-614 (1997).
14. Sanchez, J.J. et al. Multiplex PCR and minisequencing of SNPs - a model with 35 Y chromosome SNPs. Forensic Sci. Int. 137, 74-84 (2003).
15. Brion, M. et al. Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages. Electrophoresis 26, 4411-4420 (2005).
16. Sanchez, J.J. et al. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27, 1713-1724 (2006).
17. McKay, S.J. et al. AcePrimer: Automation of PCR primer design based on gene structure. Bioinformatics 18, 1538-1539 (2002).
18. Kaplinski, L. et al. MultiPLX: Automatic grouping and evaluation of PCR primers. Bioinformatics 21, 1701-1702 (2005).
19. Rachlin, J. et al. MuPLex: Multi-objective multiplex PCR assay design. Nucleic Acids Res. 33, 544-547 (2005).
20. Yamada, T. et al. PrimerStation: A highly specific multiplex genomic PCR primer design server for the human genome. Nucleic Acids Res. 34, 665-669 (2006).
21. Weckx, S. et al. SNPbox: Web-based high-throughput primer design from gene to genome. Nucleic Acids Res. 32, 170-172 (2004).
22. Rozen, S. et al. Primer3 on the WWW for general users and for biologist programmers. Meth. Mol. Biol. 132, 365-386 (2003).
23. Cooper, A. et al. Ancient DNA: Do it right or not at all. Science 289, 1139 (2000).
24. Pääbo, S. et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38, 645-679 (2004).
25. Vallone, P.M. et al. AutoDimer a screening tool for primer-dimer and hairpin structures. Biotechniques 37, 226-231 (2004).
26. Yuryev, A. et al. Predicting the success of primer extension genotyping assays using statistical modeling. Nucleic Acids Res. 30, 131 (2002).
27. Kaderali, L. et al. Primer-design for multiplexed genotyping. Nucleic Acids Res. 31, 1796-1802 (2003).
28. Henegariu, O. et al. Multiplex PCR: Critical parameters and step-by-step protocol. Biotechniques 23, 504-511 (1997)
29. Doi, Y. et al. A new method for ABO genotyping using a multiplex single-base primer extension reaction and its application to forensic casework samples. Leg. Med. 6, 213-223 (2004).
30. Palanichamy, M.G. et al. The dazzling array of basal branches in the mtDNA macrohaplogroup N from India as inferred from complete genomes. Mol. Biol Evol. 23, 683-690 (2006).
31. Behar, D. et al. The matrilineal ancestry of Ashkenazi Jews: portrait of a recent founder event. Am. J. Hum. Genet. 78, 487-497 (2006).
32. Kivisild, T. et al. The role of selection in the evolution of human mitochondrial genomes. Genetics 172, 373-387 (2006).
33. Bandelt, H.J. et al. More evidence for non-maternal inheritance of mitochondrial DNA? J. Med. Genet. 42, 957-960 (2005).
34. Salas, A. et al. A practical guide to mitochondrial DNA error prevention in clinical, forensic and population genetics. Biochem. Biophys. Res. Commun. 335, 891-899 (2005).