Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples

Forensic Science International: Genetics

Volumn 3, Issue 4, 2009, Pages 233-241

  Westen, Antoinette A ^a   Matai, Anuska S ^a   Laros, Jeroen F J ^b   Meiland, Hugo C ^b   Jasper, Mandy ^a   de Leeuw, Wiljo J F ^a   de Knijff, Peter ^c   Sijen, Titia ^a  

^a NETHERLANDS FORENSIC INSTITUTE   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Ancestry informative marker (AIM); Degraded DNA; Forensic science; Human identification; Mixtures; Tri allelic SNP

Indexed keywords

DNA;

ALGORITHM; AMPLICON; ARTICLE; BONE; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; DISASTER; DNA DEGRADATION; DNA DETERMINATION; FORENSIC IDENTIFICATION; GENE FREQUENCY; GENETIC DATABASE; GENOTYPE; HUMAN; HUMAN TISSUE; MOLAR TOOTH; NETHERLANDS; NETHERLANDS ANTILLES; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; VICTIM;

ALGORITHMS; ALLELES; DATABASES, GENETIC; DNA; DNA FINGERPRINTING; FORENSIC ANTHROPOLOGY; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPE; HUMANS; MALE; MICROSATELLITE REPEATS; NETHERLANDS; NETHERLANDS ANTILLES; POLYMORPHISM, SINGLE NUCLEOTIDE; REFERENCE STANDARDS;

EID: 67651250139     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2009.02.003     Document Type: Article

References (35)

1. Coble M.D., and Butler J.M. Characterization of new miniSTR loci to aid analysis of degraded DNA. J. Forensic Sci. 50 (2005) 43-53
2. Dixon L.A., Murray C.M., Archer E.J., Dobbins A.E., Koumi P., and Gill P. Validation of a 21-locus autosomal SNP multiplex for forensic identification purposes. Forensic Sci. Int. 154 (2005) 62-77
3. Grubwieser P., Muhlmann R., Berger B., Niederstatter H., Pavlic M., and Parson W. A new "miniSTR-multiplex" displaying reduced amplicon lengths for the analysis of degraded DNA. Int. J. Legal Med. 120 (2006) 115-120
4. Westen A.A., Gerretsen R.R.R., and Maat G.J.R. Femur, rib, and tooth sample collection for DNA analysis in disaster victim identification. Forensic Sci. Med. Pathol. 4 (2008) 15-21
5. Butler J.M., Coble M.D., and Vallone P.M. STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci. Med. Pathol. 3 (2007) 200-205
6. Dixon L.A., Dobbins A.E., Pulker H.K., Butler J.M., Vallone P.M., Coble M.D., Parson W., Berger B., Grubwieser P., Mogensen H.S., Morling N., Nielsen K., Sanchez J.J., Petkovski E., Carracedo A., Sanchez-Diz P., Ramos-Luis E., Brion M., Irwin J.A., Just R.S., Loreille O., Parsons T.J., Syndercombe-Court D., Schmitter H., Stradmann-Bellinghausen B., Bender K., and Gill P. Analysis of artificially degraded DNA using STRs and SNPs - results of a collaborative European (EDNAP) exercise. Forensic Sci. Int. 164 (2006) 33-44
7. Gill P., Fereday L., Morling N., and Schneider P.M. The evolution of DNA databases - recommendations for new European STR loci. Forensic Sci. Int. 156 (2006) 242-244
8. Butler J.M., Shen Y., and McCord B.R. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 48 (2003) 1054-1064
9. Hill C.R., Kline M.C., Coble M.D., and Butler J.M. Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. J. Forensic Sci. 53 (2008) 73-80
10. Parsons T.J., Huel R., Davoren J., Katzmarzyk C., Milos A., Selmanovic A., Smajlovic L., Coble M.D., and Rizvic A. Application of novel "mini-amplicon" STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci. Int. Genet. 1 (2007) 175-179
11. Budowle B. SNP typing strategies. Forensic Sci. Int. 146 (2004) S139-S142
12. Sanchez J.J., Phillips C., Borsting C., Balogh K., Bogus M., Fondevila M., Harrison C.D., Musgrave-Brown E., Salas A., Syndercombe-Court D., Schneider P.M., Carracedo A., and Morling N. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27 (2006) 1713-1724
13. Budowle B., and van Daal A. Forensically relevant SNP classes. Biotechniques 44 (2008) 603-610
14. Fondevila M., Phillips C., Naveran N., Cerezo M., Rodriguez A., Calvo R., Fernandez L.M., Carracedo A., and Lareu M.V. Challenging DNA: assessment of a range of genotyping approaches for highly degraded forensic samples. Forensic Sci. Int. Genet. Supplement Series 1 (2008) 26-28
15. Borsting C., Sanchez J.J., Hansen H.E., Hansen A.J., Bruun H.Q., and Morling N. Performance of the SNPforID 52 SNP-plex assay in paternity testing. Forensic Sci. Int. Genet. 2 (2008) 292-300
16. Phillips C., Fondevila M., Garcia-Magarinos M., Rodriguez A., Salas A., Carracedo A., and Lareu M.V. Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers. Forensic Sci. Int. Genet. 2 (2008) 198-204
17. Kidd K.K., Pakstis A.J., Speed W.C., Grigorenko E.L., Kajuna S.L., Karoma N.J., Kungulilo S., Kim J.J., Lu R.B., Odunsi A., Okonofua F., Parnas J., Schulz L.O., Zhukova O.V., and Kidd J.R. Developing a SNP panel for forensic identification of individuals. Forensic Sci. Int. 164 (2006) 20-32
18. Musgrave-Brown E., Ballard D., Balogh K., Bender K., Berger B., Bogus M., Borsting C., Brion M., Fondevila M., Harrison C., Oguzturun C., Parson W., Phillips C., Proff C., Ramos-Luis E., Sanchez J.J., Sanchez Diz P., Sobrino Rey B., Stradmann-Bellinghausen B., Thacker C., Carracedo A., Morling N., Scheithauer R., Schneider P.M., and Syndercombe-Court D. Forensic validation of the SNPforID 52-plex assay. Forensic Sci. Int. Genet. 1 (2007) 186-190
19. Sanchez J.J., Borsting C., Balogh K., Berger B., Bogus M., Butler J.M., Carracedo A., Syndercombe-Court D., Dixon L.A., Filipovic B., Fondevila M., Gill P., Harrison C., Hohoff C., Huel R., Ludes B., Parson W., Parsons T.J., Petkovski E., Phillips C., Schmitter H., Schneider P.M., Vallone P.M., and Morling N. Forensic typing of autosomal SNPs with a 29 SNP-multiplex - Results of a collaborative EDNAP exercise. Forensic Sci. Int. Genet. 2 (2008) 176-183
20. Phillips C., Lareu V., Salas A., and Carracedo A. Nonbinary single-nucleotide polymorphism markers. Int. Congress Ser. 1261 (2004) 27-29
21. Chakraborty R., Stivers D.N., Su B., Zhong Y., and Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 20 (1999) 1682-1696
22. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med. 114 (2001) 204-210
23. Amorim A., and Pereira L. Pros and cons in the use of SNPs in forensic kinship investigation: a comparative analysis with STRs. Forensic Sci. Int. 150 (2005) 17-21
24. The Y Chromosome Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12 (2002) 339-348
25. Rozen S., and Skaletsky H.J. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S., and Misener S. (Eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology (2000), Humana Press, Totowa, NJ 365-386
26. Vallone P.M., and Butler J.M. AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37 (2004) 226-231
27. Sobrino B., Brion M., and Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 154 (2005) 181-194
28. Park S.D.E. Trypanotolerance in West African Cattle and the Population Genetic Effects of Selection (2001), University of Dublin
29. Rousset F. GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol. Ecol. Resour. 8 (2008) 103-106
30. Promega, http://www.promega.com/geneticidtools/powerstats/, 2000.
31. Phillips C., Fang R., Ballard D., Fondevila M., Harrison C., Hyland F., Musgrave-Brown E., Proff C., Ramos-Luis E., Sobrino B., Carracedo A., Furtado M.R., Syndercombe-Court D., and Schneider P.M. Evaluation of the Genplex SNP typing system and a 49plex forensic marker panel. Forensic Sci. Int. Genet. 1 (2007) 180-185
32. Phillips C., Salas A., Sanchez J.J., Fondevila M., Gomez-Tato A., Alvarez-Dios J., Calaza M., Casares de Cal M., Ballard D., Lareu M.V., and Carracedo A. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci. Int. Genet. 1 (2007) 273-280
33. Harrison C., Musgrave-Brown E., Bender K., Carracedo A., Morling N., Schneider P., and Syndercombe-Court D. A sensitive issue: pyrosequencing as a valuable forensic SNP typing platform. Int. Congress Ser. 1288 (2006) 52-54
34. P. Oeth, M. Beaulieu, C. Park, D. Kosman, G. del Mistro, D. van den Boom, C. Jurinke, iPLEX Assay: increased plexing efficiency and flexibility for MassARRAY system through single base primer extension with mass-modified terminators, Sequenom Application Note (2006).
35. Paabo S., Poinar H., Serre D., Jaenicke-Despres V., Hebler J., Rohland N., Kuch M., Krause J., Vigilant L., and Hofreiter M. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38 (2004) 645-679