Development of SNP-based human identification system

Single nucleotide polymorphisms (SNPs) appeal to the forensic DNA community because of their abundance in the human genome, low mutation rate, small amplicon size, and feasibility of high-throughput genotyping technologies. In an initial screening, we identified six SNP markers of sex determination by resequencing the amelogenin genes and the zinc finger protein genes located on the sex chromosomes. Furthermore, for use in human identification, we selected 30 highly polymorphic autosomal SNP markers from among a human population and examined the potential utility of these SNP markers for human identification. The combined mean match probability of 30 SNP markers was 4.83 × 10−13. Using genotyping data from 8,842 unrelated Korean individuals, we also found that discrimination power increased 10-fold for the addition of every five SNP markers in human identification. In this study, we demonstrated that SNP markers are very useful for sex determination and human identification, even in a very homogeneous population.

[1]  T. Egeland,et al.  Y‐chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci , 2004, Human mutation.

[2]  Jorge Amigo,et al.  The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project , 2008, International Journal of Legal Medicine.

[3]  Rong-yu Li,et al.  SNP genotyping by multiplex amplification and microarrays assay for forensic application. , 2006, Forensic science international.

[4]  D. Nickerson,et al.  PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. , 1997, Nucleic acids research.

[5]  Myung Jin Park,et al.  Selection of twenty-four highly informative SNP markers for human identification and paternity analysis in Koreans. , 2005, Forensic science international.

[6]  K. Kidd,et al.  Candidate SNPs for a universal individual identification panel , 2007, Human Genetics.

[7]  K. Gunderson,et al.  Illumina universal bead arrays. , 2006, Methods in enzymology.

[8]  P. Gill,et al.  Validation of a 21-locus autosomal SNP multiplex for forensic identification purposes. , 2005, Forensic science international.

[9]  Levi Garraway,et al.  SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines , 2008, Nucleic acids research.

[10]  K. Kidd,et al.  Developing a SNP panel for forensic identification of individuals. , 2006, Forensic science international.

[11]  U. Frey,et al.  Amelogenin sex determination by pyrosequencing of short PCR products , 2008, International Journal of Legal Medicine.

[12]  Hui Shen,et al.  Mutation patterns at dinucleotide microsatellite loci in humans. , 2002, American journal of human genetics.

[13]  Á. Carracedo,et al.  A multiplex assay with 52 single nucleotide polymorphisms for human identification , 2006, Electrophoresis.

[14]  Eric S. Lander,et al.  Human genome sequence variation and the influence of gene history, mutation and recombination , 2002, Nature Genetics.

[15]  B. Olaisen,et al.  Y‐chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci , 2004 .

[16]  H. Pfeiffer,et al.  A rapid mtDNA assay of 22 SNPs in one multiplex reaction increases the power of forensic testing in European Caucasians , 2008, International Journal of Legal Medicine.

[17]  M. Commane,et al.  A rare mutation in the primer binding region of the amelogenin gene can interfere with gender identification. , 2004, The Journal of molecular diagnostics : JMD.

[18]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[19]  Angel Carracedo,et al.  SNPs in forensic genetics: a review on SNP typing methodologies. , 2005, Forensic science international.

[20]  Niels Morling,et al.  Performance of the SNPforID 52 SNP-plex assay in paternity testing. , 2008, Forensic science international. Genetics.

[21]  Taesung Park,et al.  A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits , 2009, Nature Genetics.

[22]  Á. Carracedo,et al.  Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. , 2007, Forensic science international. Genetics.

[23]  K. Kristjánsson,et al.  Preimplantation prevention of X-linked disease: reliable and rapid sex determination of single human cells by restriction analysis of simultaneously amplified ZFX and ZFY sequences. , 1993, Human molecular genetics.

[24]  B. Ludes,et al.  Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis , 2009, International Journal of Legal Medicine.

[25]  Gregory Sykes,et al.  Utility of gender determination in cell line identity , 2000, In Vitro Cellular & Developmental Biology - Animal.

[26]  Takaki Ishikawa,et al.  A new 39-plex analysis method for SNPs including 15 blood group loci. , 2004, Forensic science international.

[27]  A. Urquhart,et al.  Variation in Short Tandem Repeat sequences —a survey of twelve microsatellite loci for use as forensic identification markers , 2005, International Journal of Legal Medicine.