Development of a multiplex single base extension assay for mitochondrial DNA haplogroup typing

Croatian Medical Journal

Volumn 48, Issue 4, 2007, Pages 460-472

  Nelson, Tahnee M ^a   Just, Rebecca S ^b   Loreille, Odile ^b   Schanfield, Moses S ^a   Podini, Daniele ^a  

^a GEORGE WASHINGTON UNIVERSITY   (United States)

^b Armed Forces DNA Identification Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DNA DETERMINATION; DNA FINGERPRINTING; DNA POLYMORPHISM; DNA SEQUENCE; HUMAN; MITOCHONDRION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA PRIMERS; DNA, MITOCHONDRIAL; FORENSIC ANTHROPOLOGY; GENETICS, POPULATION; HAPLOTYPES; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 34548256391     PISSN: 03539504     EISSN: 13328166     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. Robin ED, Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol. 1988;136:507-13.
2. Paabo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci U S A. 1989;86:1939-43.
3. Ingman M, Kaessmann H, Paabo S, Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature. 2000;408:708-13.
4. Budowle B, Allard MW, Wilson MR, Chakraborty R. Forensics and mitochondrial DNA: applications, debates, and foundations. Annu Rev Genomics Hum Genet. 2003;4:119-41.
5. Hagelberg E, Clegg JB. Isolation and characterization of DNA from archaeological bone. Proc Biol Sci. 1991;244:45-50.
6. Foran DR. Relative degradation of nuclear and mitochondrial DNA: an experimental approach. J Forensic Sci. 2006;51:766-70.
7. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, et al. Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A. 2003;100:171-6.
8. Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science. 2004;303:223-6.
9. Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, et al. The role of selection in the evolution of human mitochondrial genomes. Genetics. 2006;172:373-87.
10. Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM. Major genomic mitochondrial lineages delineate early human expansions. BMC Genet. 2001;2:13.
11. Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, et al. Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet. 2000;67:1251-76.
12. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, et al. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science. 2005;308:1034-6.
13. Holland MM, Parsons TJ. Mitochondrial DNA sequence analysis - validation and use of forensic casework. Forensic Science Review. 1999;11:21-50.
14. Holland MM, Fisher DL, Michell LG, Rodriguez WC, Canik JJ, Merril CR, et al. Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War. J Forensic Sci. 1993;38:542-53.
15. Parsons TJ, Coble MD. Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J. 2001;42:304-9.
16. Just RS, Irwin JA, O'Callaghan JE, Saunier JL, Coble MD, Vallone PM, et al. Toward increased utility of mtDNA in forensic identifications. Forensic Sci Int. 2004;146 Suppl: S147-9.
17. Irwin JA, Edson SM, Loreille O, Just RS, Barritt SM, Lee DA, et al. DNA identification of "Earthquake McGoon" 50 years postmortem. J Forensic Sci. Forthcoming 2007.
18. Andelinovic S, Sutlovic D, Erceg Ivkosic I, Skaro V, Ivkosic A, Paic F, et al. Twelve-year experience in identification of skeletal remains from mass graves. Croat Med J. 2005;46:530-9.
19. Melton T, Nelson K. Forensic mitochondrial DNA analysis: two years of commercial casework experience in the United States. Croat Med J. 2001;42:298-303.
20. Kong QP, Bandelt HJ, Sun C, Yao YG, Salas A, Achilli A, et al. Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet. 2006;15:2076-86.
21. Roostalu U, Kutuev I, Loogvali EL, Metspalu E, Tambets K, Reidla M, et al. 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;24:436-48.
22. Palanichamy MG, Sun C, Agrawal S, Bandelt H, Kong QP, Khan F, et al. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet. 2004;75:966-78.
23. Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, Fuku N, et al. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 2004;14:1832-50.
24. Wallace DC. 1994 William Allan Award Address. Mitochondrial DNA variation in human evolution, degenerative disease, and aging. Am J Hum Genet. 1995;57:201-23.
25. Wallace DC, Brown MD, Lott MT. Mitochondrial DNA variation in human evolution and disease. Gene. 1999;238:211-30.
26. Finnila S, Lehtonen MS, Majamaa K. Phylogenetic network for European mtDNA. Am J Hum Genet. 2001;68:1475-84.
27. Smith DG, Malhi RS, Eshleman J, Lorenz JG, Kaestle FA. Distribution of mtDNA haplogroup X among Native North Americans. Am J Phys Anthropol. 1999;110:271-84.
28. Bonatto SL, Salzano FM. A single and early migration for the peopling of the Americas supported by mitochondrial DNA sequence data. Proc Natl Acad Sci U S A. 1997;94:1866-71.
29. Chen YS, Torroni A, Excoffier L, Santachiara-Benerecetti AS, Wallace DC. Analysis of mtDNA variation in African populations reveals the most ancient of all human continentspecific haplogroups. Am J Hum Genet. 1995;57:133-49.
30. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, et al. Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet. 2002;70:1152-71.
31. Schurr TG, Ballinger SW, Gan YY, Hodge JA, Merriwether DA, Lawrence DN, et al. Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they derived from four primary maternal lineages. Am J Hum Genet. 1990;46:613-23.
32. Bandelt HJ, Herrnstadt C, Yao YG, Kong QP, Kivisild T, Rengo C, et al. Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann Hum Genet. 2003;67:512-24.
33. Kivisild T, Tolk HV, Parik J, Wang Y, Papiha SS, Bandelt HJ, et al. The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol. 2002;19:1737-51.
34. Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP. Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences. Am J Hum Genet. 2003;73:671-6.
35. Vallone PM, Just RS, Coble MD, Butler JM, Parsons TJ. A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int J Legal Med. 2004;118:147-57.
36. Wiesbauer M, Meierhofer D, Mayr JA, Sperl W, Paulweber B, Kofler B. Multiplex primer extension analysis for rapid detection of major European mitochondrial haplogroups. Electrophoresis. 2006;27:3864-8.
37. Brandstatter A, Parsons TJ, Parson W. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int J Legal Med. 2003;117:291-8.
38. Alvarez-Iglesias V, Jaime JC, Carracedo A, Salas A. Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Science International: Genetics. 2007;1:44-55.
39. Quintans B, Alvarez-Iglesias V, Salas A, Phillips C, Lareu MV, Carracedo A. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci Int. 2004;140:251-7.
40. Grignani P, Peloso G, Achilli A, Turchi C, Tagliabracci A, Alu M, et al. Subtyping mtDNA haplogroup H by SNaPshot minisequencing and its application in forensic individual identification. Int J Legal Med. 2006;120:151-6.
41. Sigurdsson S, Hedman M, Sistonen P, Sajantila A, Syvänen AC. A microarray system for genotyping 150 single nucleotide polymorphisms in the coding region of human mitochondrial DNA. Genomics. 2006;87:534-42.
42. Salas A, Quintans B, Alvarez-Iglesias V. SNaPshot typing of mitochondrial DNA coding region variants. Methods Mol Biol. 2005;297:197-208.
43. Fiorentino F, Magli MC, Podini D, Ferraretti AP, Nuccitelli A, Vitale N, et al. The minisequencing method: an alternative strategy for preimplantation genetic diagnosis of single gene disorders. Mol Hum Reprod. 2003;9:399-410.
44. Szibor R, Plate I, Schmitter H, Wittig H, Krause D. Forensic mass screening using mtDNA. Int J Legal Med. 2006;120:372-6.
45. Bandelt HJ, Quintana-Murci L, Salas A, Macaulay V. The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet. 2002;71:1150-60.
46. Bandelt HJ, Salas A, Lutz-Bonengel S. Artificial recombination in forensic mtDNA population databases. Int J Legal Med. 2004;118:267-73.
47. Yao YG, Bravi CM, Bandelt HJ. A call for mtDNA data quality control in forensic science. Forensic Sci Int. 2004;141:1-6.
48. Salas A, Carracedo A, Macaulay V, Richards M, Bandelt HJ. A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun. 2005;335:891-9.
49. Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tanzer M, et al. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science. 2005;310:1016-8.
50. Yao YG, Kong QP, Man XY, Bandelt HJ, Zhang YP. Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA. Mol Biol Evol. 2003;20:214-9.
51. Malyarchuk BA, Grzybowski T, Derenko MV, Czarny J, Wozniak M, Miscicka-Sliwka D. Mitochondrial DNA variability in Poles and Russians. Ann Hum Genet. 2002;66:261-83.
52. Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA. Whole-mtDNA genome sequence analysis of ancient African lineages. Mol Biol Evol. 2007;24:757-68.
53. Ballinger SW, Schurr TG, Torroni A, Gan YY, Hodge JA, Hassan K, et al. Southeast Asian mitochondrial DNA analysis reveals genetic continuity of ancient mongoloid migrations. Genetics. 1992;130:139-52.
54. Torroni A, Sukernik RI, Schurr TG, Starikorskaya YB, Cabell MF, Crawford MH, et al. mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans. Am J Hum Genet. 1993;53:591-608.
55. Reidla M, Kivisild T, Metspalu E, Kaldma K, Tambets K, Tolk HV, et al. Origin and diffusion of mtDNA haplogroup X. Am J Hum Genet. 2003;73:1178-90.