A single multiplex PCR and SNaPshot minisequencing reaction of 42 SNPs to classify admixture populations into mitochondrial DNA haplogroups

Mitochondrion

Volumn 11, Issue 2, 2011, Pages 296-302

  Paneto, Greiciane G ^a   Köhnemann, Stephan ^a   Martins, Joyce A ^a   Cicarelli, Regina M B ^a   Pfeiffer, Heidi ^b  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

Admixture populations; Brazil; Haplogroup affiliation; Mitochondrial DNA; SNaPshot reaction

Indexed keywords

MITOCHONDRIAL DNA;

AMERICAN INDIAN; ARTICLE; ASIAN; BRAZIL; CAUCASIAN; CONTROLLED STUDY; DNA DETERMINATION; ETHNIC GROUP; GENOTYPE; HAPLOTYPE; HUMAN; MULTIPLEX POLYMERASE CHAIN REACTION; NEGRO; POPULATION GENETICS; PRIORITY JOURNAL; RELIABILITY; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SNAPSHOT MINISEQUENCING REACTION; VALIDATION STUDY;

BASE SEQUENCE; BRAZIL; DNA PRIMERS; DNA, MITOCHONDRIAL; FORENSIC GENETICS; HAPLOTYPES; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 79251593331     PISSN: 15677249     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mito.2010.12.010     Document Type: Article

References (35)

1. Alvarez-Iglesias V., Jaime J.C., Carracedo A., Salas A. Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Sci. Int. Genet. 2007, 1:44-55.
2. Alves-Silva J., da Silva Santos M., Guimarães P.E., Ferreira A.C., Bandelt H.J., Pena S.D., Prado V.F. The ancestry of Brazilian mtDNA lineages. Am. J. Hum. Genet. 2000, 67:444-461.
3. Ban M., Elson J., Walton A., Turnbull D., Compston A., Chinnery P., Sawcer S. Investigation of the role of mitochondrial DNA in multiple sclerosis susceptibility. PLoS ONE 2008, 3:e2891.
4. Bandelt H.-J., Macaulay V., Richards M. Human Mitochondrial DNA and the Evolution of Homo sapiens 2006, Springer-Verlag, Berlin.
5. Bethell L. Nota sobre as populações americanas às vésperas das invasões européias. América Latina Colonial 1997, 129-131. Editora da Universidade de São Paulo, São Paulo. L. Bethell (Ed.).
6. Brandstätter A., Salas A., Niederstätter H., Gassner C., Carracedo A., Parson W. Dissection of mitochondrial superhaplogroup H using coding region SNPs. Electrophoresis 2006, 27:2541-2550.
7. Brown W.M. Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proc. Natl Acad. Sci. USA 1980, 77:3605-3609.
8. Cann R.L., Stoneking M., Wilson A.C. Mitochondrial DNA and human evolution. Nature 1987, 325:31-36.
9. Chen Y.S., Torroni A., Excoffier L., Santachiara-Benerecetti A.S., Wallace D.C. Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am. J. Hum. Genet. 1995, 57:133-149.
10. Gilbert M.T., Sanchez J.J., Haselkorn T., Jewell L.D., Lucas S.B., Van Marck E., Børsting C., et al. Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue. Electrophoresis 2007, 28:2361-2367.
11. Gonçalves V.F., Carvalho C.M., Bortolini M.C., Bydlowski S.P., Pena S.D. The phylogeography of African Brazilians. Hum. Hered. 2008, 65:23-32.
12. González A.M., Larruga J.M., Abu-Amero K.K., Shi Y., Pestano J., Cabrera V.M. Mitochondrial lineage M1 traces an early human backflow to Africa. B.M.C. Genomics 2007, 8:223.
13. Grignani P., Turchi C., Achilli A., Peloso G., Alù M., Ricci U., Robino C., et al. Multiplex mtDNA coding region SNP assays for molecular dissection of haplogroups U/K and J/T. Forensic Sci. Int. Genet. 2009, 4:21-25.
14. Hünemeier T., Carvalho C., Marrero A.R., Salzano F.M., Junho Pena S.D., Bortolini M.C. Niger-Congo speaking populations and the formation of the Brazilian gene pool: mtDNA and Y-chromosome data. Am. J. Phys. Anthropol. 2007, 133:854-867.
15. Ji Y., Zhang A.M., Jia X., Zhang Y.P., Xiao X., Li S., Guo X., et al. Mitochondrial DNA haplogroups M7b1?2 and M8a affect clinical expression of leber hereditary optic neuropathy in Chinese families with the m.11778 G>A mutation. Am. J. Hum. Genet. 2008, 83:760-768.
16. Köhnemann S., Sibbing U., Pfeiffer H., Hohoff C. A rapid mtDNA assay of 22 SNPs in one multiplex reaction increases the power of forensic testing in European Caucasians. Int. J. Legal Med. 2008, 122:517-523.
17. Köhnemann S., Hohoff C., Pfeiffer H. An economical mtDNA SNP assay detecting different mitochondrial haplogroups in identical HVR 1 samples of Caucasian ancestry. Mitochondrion 2009, 9:370-375.
18. Marshall O.J. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 2004, 20:2471-2472.
19. Mosquera-Miguel A., Alvarez-Iglesias V., Cerezo M., Lareu M.V., Carracedo A., Salas A. Testing the performance of mtSNP minisequencing in forensic samples. Forensic Sci. Int. Genet. 2009, 3:261-264.
20. Nei M. Molecular Evolutionary Genetics 1987, Columbia University Press, New York.
21. Nohira C., Maruyama S., Minaguchi K. Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences. Int. J. Legal Med. 2010, 124:7-12.
22. Olivieri A., Achilli A., Pala M., Battaglia V., Fornarino S., Al-Zahery N., Scozzari R., et al. The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 2006, 314:1767-1770.
23. Parson W., Bandelt H.J. Extended guidelines for mtDNA typing of population data in forensic science. Forensic Sci. Int. Genet. 2007, 1:13-19.
24. Pereira L., Prata M.J., Amorim A. Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation. Ann. Hum. Genet. 2000, 64:491-506.
25. Reis J.J. Brasil: 500 Anos de Povoamento. IBGE 2000, 80-99. IBGE, Rio de Janeiro.
26. Roostalu U., Kutuev I., Loogväli E.L., Metspalu E., Tambets K., Reidla M., Khusnutdinova E.K. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol. Biol. Evol. 2007, 24:436-448.
27. Salas A., Fachal L., Marcos-Alonso S., Veja A., Martinón-Torres F. Investigating the role of mitochondrial haplogroups in genetic predisposition to meningococcal disease. PLoS ONE 2009, 4:e8347.
28. Salzano F.M., Freire-Maia N. Populações Brasileiras, Aspectos Demográficos, Genéticos e Antropológicos 1967, Companhia Editora Nacional, São Paulo.
29. Sanchez J.J., Phillips C., Børsting C., Balogh K., Bogus M., Fondevila M., Harrison C.D., et al. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 2006, 27:1713-1724.
30. Singer-Sam J., Tanguay R., Riggs A.D. Use of chelex to improve the PCR signal from a small number of cells. Amplifications: A Forum for PCR Users 3 1989, 11.
31. Schlebusch C.M., Naidoo T., Soodyall H. SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa. Electrophoresis 2009, 30:3657-3664.
32. Torroni A., Schurr T.G., Cabell M.F., Brown M.D., Neel J.V., Larsen M., Smith D.G., et al. Asian affinities and continental radiation of the four founding Native American mtDNAs. Am. J. Hum. Genet. 1993, 53:563-590.
33. Turchi C., Buscemi L., Previderè C., Grignani P., Brandstätter A., Achilli A., Parson W., et al. Italian mitochondrial DNA database: results of a collaborative exercise and proficiency testing. Int. J. Legal Med. 2008, 122:199-204.
34. Vallone P.M., Butler J.M. AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 2004, 37:226-231.
35. van Oven M., Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 2009, 30:e386-e394.