Rapid Screening of MtDNA Coding Region SNPs for the Identification of West European Caucasian Haplogroups

Overview

Journal Int J Legal Med

Specialty Forensic Sciences

Date 2003 Aug 26

PMID 12937995

Citations 35

Authors

Anita Brandstatter

Thomas J Parsons

Walther Parson

Affiliations

Soon will be listed here.

Abstract

This work presents a selection of 16 SNPs from the coding region of the human mitochondrial DNA. The selected markers are used for the assignment of individuals to one of the nine major European Caucasian mitochondrial haplogroups. The selected SNPs are targeted in two multiplex systems, via the application of the SNaPshot kit, a multiplex method based on the dideoxy single-base extension of unlabeled oligonucleotide primers. The method is conceived as a rapid screening technique prior to sequencing analysis, in order to eliminate multiple suspects from an inquiry or to discriminate between stains in a high volume casework example. Moreover, the ability to assign an unknown sample to an mtDNA type of known Caucasian origin could be of probative value in some investigations. A database of 277 Austrian Caucasians has been constructed, and the probability of a chance match between two unrelated individuals is calculated as 11.4%. This novel multiplex PCR amplification and typing system for mtDNA coding region SNPs promises to be a convenient and informative new DNA profiling system in the forensic field.

Citing Articles

Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era.

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Forensically relevant SNaPshot assays for human DNA SNP analysis: a review.

Mehta B, Daniel R, Phillips C, McNevin D Int J Legal Med. 2016; 131(1):21-37.

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STRs vs. SNPs: thoughts on the future of forensic DNA testing.

Butler J, Coble M, Vallone P Forensic Sci Med Pathol. 2015; 3(3):200-5.

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Multiplex minisequencing screening for PTC genotype associated with bitter taste perception.

Sagong B, Bae J, Rhyu M, Kim U, Ye M Mol Biol Rep. 2014; 41(3):1563-7.

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Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing.

Eduardoff M, Huber G, Bayer B, Schmid D, Anslinger K, Gobel T Forensic Sci Int Genet. 2013; 7(6):587-592.

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References

Stoneking M . Single nucleotide polymorphisms. From the evolutionary past. Nature. 2001; 409(6822):821-2. DOI: 10.1038/35057279. View

Malyarchuk B, Grzybowski T, Derenko M, Czarny J, Wozniak M, Miscicka-Sliwka D . Mitochondrial DNA variability in Poles and Russians. Ann Hum Genet. 2002; 66(Pt 4):261-83. DOI: 10.1017/S0003480002001161. View

Norton N, Williams N, Williams H, Spurlock G, Kirov G, Morris D . Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum Genet. 2002; 110(5):471-8. DOI: 10.1007/s00439-002-0706-6. View

Parsons T, Coble M . Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J. 2001; 42(3):304-9. View

Berger B, Holzl G, Oberacher H, Niederstatter H, Huber C, Parson W . Single nucleotide polymorphism genotyping by on-line liquid chromatography-mass spectrometry in forensic science of the Y-chromosomal locus M9. J Chromatogr B Analyt Technol Biomed Life Sci. 2002; 782(1-2):89-97. DOI: 10.1016/s1570-0232(02)00694-3. View

Lutz S, Weisser H, Heizmann J, Pollak S . Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany. Int J Legal Med. 1998; 111(2):67-77. DOI: 10.1007/s004140050117. View

Lee S, Lee Y, Lee J . Polymorphism in the mitochondrial cytochrome B gene in Koreans. An additional marker for individual identification. Int J Legal Med. 2002; 116(2):74-8. DOI: 10.1007/s004140100238. View

Ingman M, Kaessmann H, Paabo S, Gyllensten U . Mitochondrial genome variation and the origin of modern humans. Nature. 2000; 408(6813):708-13. DOI: 10.1038/35047064. View

Gill P . An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med. 2001; 114(4-5):204-10. DOI: 10.1007/s004149900117. View

10.

Torroni A, Richards M, Macaulay V, Forster P, Villems R, Norby S . mtDNA haplogroups and frequency patterns in Europe. Am J Hum Genet. 2000; 66(3):1173-7. PMC: 1288155. DOI: 10.1086/302789. View

11.

Tseng L, Chen P, Lin M, Singleton K, Martin E, Yen A . Simultaneous genotyping of single nucleotide polymorphisms in the IL-1 gene complex by multiplex polymerase chain reaction-restriction fragment length polymorphism. J Immunol Methods. 2002; 267(2):151-6. DOI: 10.1016/s0022-1759(02)00165-5. View

12.

van der Walt J, Nicodemus K, Martin E, Scott W, Nance M, Watts R . Mitochondrial polymorphisms significantly reduce the risk of Parkinson disease. Am J Hum Genet. 2003; 72(4):804-11. PMC: 1180345. DOI: 10.1086/373937. View

13.

Maca-Meyer N, Gonzalez A, Larruga J, Flores C, Cabrera V . Major genomic mitochondrial lineages delineate early human expansions. BMC Genet. 2001; 2:13. PMC: 55343. DOI: 10.1186/1471-2156-2-13. View

14.

Legros F, Chatzoglou E, Frachon P, Ogier de Baulny H, Laforet P, Jardel C . Functional characterization of novel mutations in the human cytochrome b gene. Eur J Hum Genet. 2001; 9(7):510-8. DOI: 10.1038/sj.ejhg.5200678. View

15.

Richards M, Forster P, Macaulay V, Demaine A, Papiha S, Hedges R . Paleolithic and neolithic lineages in the European mitochondrial gene pool. Am J Hum Genet. 1996; 59(1):185-203. PMC: 1915109. View

16.

Richards M, Macaulay V, Bandelt H, Sykes B . Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet. 1998; 62(Pt 3):241-60. DOI: 10.1046/j.1469-1809.1998.6230241.x. View

17.

Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V . Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet. 2000; 67(5):1251-76. PMC: 1288566. View

18.

Wallace D, Brown M, Lott M . Mitochondrial DNA variation in human evolution and disease. Gene. 1999; 238(1):211-30. DOI: 10.1016/s0378-1119(99)00295-4. View

19.

Gusmao L, Alves C, Costa S, Amorim A, Brion M, Sanchez-Diz P . Point mutations in the flanking regions of the Y-chromosome specific STRs DYS391, DYS437 and DYS438. Int J Legal Med. 2002; 116(6):322-6. DOI: 10.1007/s00414-002-0310-2. View

20.

Morley J, Bark J, Evans C, Perry J, Hewitt C, Tully G . Validation of mitochondrial DNA minisequencing for forensic casework. Int J Legal Med. 1999; 112(4):241-8. DOI: 10.1007/s004140050243. View