title: Development of a multiplex single base extension assay for mitochondrial DNA haplogroup typing.
abstract: OBJECTIVE
  To provide a screening tool to reduce time and sample consumption when attempting mitochondrial DNA (mtDNA) haplogroup typing.
  
  
  METHODS
  A single base primer extension assay was developed to enable typing, in a single reaction, of twelve mtDNA haplogroup specific polymorphisms. For validation purposes a total of 147 samples were tested including 73 samples successfully haplogroup typed using mtDNA control region (CR) sequence data, 20 samples inconclusively haplogroup typed by CR sequence data, 21 samples previously haplogroup typed using RFLP analysis, and 31 samples of known ancestral origin without previous haplogroup typing. Additionally, two highly degraded human bones embalmed and buried in the early 1950s were analyzed using the SNP multiplex.
  
  
  RESULTS
  When the SNP multiplex was used to type the 96 previously CR sequenced specimens, an increase in haplogroup or macrohaplogroup assignment relative to conventional CR sequence analysis was observed. The single base extension assay was also successfully used to assign a haplogroup to decades-old, embalmed skeletal remains dating to World War II.
  
  
  CONCLUSIONS
  The SNP multiplex was successfully used to obtain haplogroup status of highly degraded human bones, and demonstrated the ability to eliminate possible contributors. The SNP multiplex provides a low-cost, high throughput method for typing of mtDNA haplogroups A, B, C, D, E, F, G, H, L1/L2, L3, M, and N that could be useful for screening purposes for human identification efforts and anthropological studies.
authors: The George Washington University Department of Forensic Sciences, Washington, DC, USA.
authors: Tahnee M
authors: TM
authors: Nelson
authors: Rebecca S
authors: RS
authors: Just
authors: Odile
authors: O
authors: Loreille
authors: Moses S
authors: MS
authors: Schanfield
authors: Daniele
authors: D
authors: Podini
mesh_terms: D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics*; D018732:Forensic Anthropology; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial
references: Mol Hum Reprod. 2003 Jul;9(7):399-410
references: 12802047
references: Int J Legal Med. 2004 Oct;118(5):267-73
references: 15257464
references: Ann Hum Genet. 2002 Jul;66(Pt 4):261-83
references: 12418968
references: Mol Biol Evol. 2002 Oct;19(10):1737-51
references: 12270900
references: Croat Med J. 2001 Jun;42(3):304-9
references: 11387644
references: Mol Biol Evol. 2007 Mar;24(3):757-68
references: 17194802
references: Genetics. 1992 Jan;130(1):139-52
references: 1346259
references: Science. 2004 Jan 9;303(5655):223-6
references: 14716012
references: Genome Res. 2004 Oct;14(10A):1832-50
references: 15466285
references: Int J Legal Med. 2003 Oct;117(5):291-8
references: 12937995
references: Int J Legal Med. 2006 May;120(3):151-6
references: 16333660
references: Am J Hum Genet. 2003 Sep;73(3):671-6
references: 12870132
references: Croat Med J. 2001 Jun;42(3):298-303
references: 11387643
references: Nature. 2000 Dec 7;408(6813):708-13
references: 11130070
references: J Forensic Sci. 1993 May;38(3):542-53
references: 8515208
references: Am J Hum Genet. 2004 Dec;75(6):966-78
references: 15467980
references: Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):171-6
references: 12509511
references: Annu Rev Genomics Hum Genet. 2003;4:119-41
references: 14527299
references: Forensic Sci Int. 2004 Dec 2;146 Suppl:S147-9
references: 15639563
references: Forensic Sci Int. 2004 Apr 20;141(1):1-6
references: 15066707
references: Am J Hum Genet. 1995 Jul;57(1):133-49
references: 7611282
references: Forensic Sci Rev. 1999 Jun;11(1):21-50
references: 26255820
references: Int J Legal Med. 2006 Nov;120(6):372-6
references: 16583247
references: BMC Genet. 2001;2:13
references: 11553319
references: Biochem Biophys Res Commun. 2005 Sep 30;335(3):891-9
references: 16102729
references: Am J Phys Anthropol. 1999 Nov;110(3):271-84
references: 10516561
references: Science. 2005 Nov 11;310(5750):1016-8
references: 16284177
references: Am J Hum Genet. 2000 Nov;67(5):1251-76
references: 11032788
references: Am J Hum Genet. 2003 Nov;73(5):1178-90
references: 14574647
references: Proc Natl Acad Sci U S A. 1989 Mar;86(6):1939-43
references: 2928314
references: J Forensic Sci. 2006 Jul;51(4):766-70
references: 16882217
references: Gene. 1999 Sep 30;238(1):211-30
references: 10570998
references: Am J Hum Genet. 2001 Jun;68(6):1475-84
references: 11349229
references: Am J Hum Genet. 1993 Sep;53(3):591-608
references: 7688933
references: Hum Mol Genet. 2006 Jul 1;15(13):2076-86
references: 16714301
references: Forensic Sci Int Genet. 2007 Mar;1(1):44-55
references: 19083727
references: Mol Biol Evol. 2007 Feb;24(2):436-48
references: 17099056
references: Ann Hum Genet. 2003 Nov;67(Pt 6):512-24
references: 14641239
references: Am J Hum Genet. 2002 May;70(5):1152-71
references: 11938495
references: Int J Legal Med. 2004 Jun;118(3):147-57
references: 14760491
references: Methods Mol Biol. 2005;297:197-208
references: 15570109
references: Am J Hum Genet. 1995 Aug;57(2):201-23
references: 7668244
references: Forensic Sci Int. 2004 Mar 10;140(2-3):251-7
references: 15036446
references: Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1866-71
references: 9050871
references: Am J Hum Genet. 2002 Nov;71(5):1150-60
references: 12384858
references: Electrophoresis. 2006 Oct;27(19):3864-8
references: 16960846
references: Genomics. 2006 Apr;87(4):534-42
references: 16406725
references: Science. 2005 May 13;308(5724):1034-6
references: 15890885
references: J Cell Physiol. 1988 Sep;136(3):507-13
references: 3170646
references: Mol Biol Evol. 2003 Feb;20(2):214-9
references: 12598688
references: J Forensic Sci. 2007 Sep;52(5):1115-8
references: 17645740
references: Croat Med J. 2005 Aug;46(4):530-9
references: 16100755
references: Proc Biol Sci. 1991 Apr 22;244(1309):45-50
references: 1677195
references: Am J Hum Genet. 1990 Mar;46(3):613-23
references: 1968708
references: Genetics. 2006 Jan;172(1):373-87
references: 16172508