title: Approaches for identifying multiple-SNP haplotype blocks for use in human identification.
abstract: Single nucleotide polymorphism (SNP) discrimination effectiveness is low due to the bi-allelic nature of SNPs, and large numbers of loci must be analyzed for human identification in forensic casework. To resolve these issues, the authors support the use of multiple SNP haplotypes that will generate many haplotypes based on the combination of SNP alleles. First, 27 regions were selected from the JSNP database (http://snp.ims.u-tokyo.ac.jp) according to the following criteria: (1) 3 or more SNP loci within 100bp; (2) on-intron or out-of-gene location; and (3) frequency of more than 40% for each SNP allele. PCR amplification and high-resolution melting curve (HRM) analysis were then carried out for all selected regions to determine variation in the haplotypes of each. HRM analysis indicated that 7 regions (1q25, 1q42.2, 3p24, 10p13, 11p15.1, 14q12-q13, and 20q12) containing 3 SNP loci had more than 2 haplotypes. The frequencies of the haplotypes for each region were observed via direct sequencing of more than 100 individuals. Not only haplotyping increases the effectiveness of individual identification but also the analysis region is shorter than in common short tandem repeat analysis, representing a further advantage for fragmented DNA samples in SNP typing.
authors.affiliation: National Research Institute of Police Science, Chiba 277-0882, Japan; Juntendo University School of Medicine, Tokyo 113-8421, Japan. Electronic address: senju@nrips.go.jp.
authors.forename: Nakahara
authors.initials: N
authors.lastname: Hiroaki
authors.affiliation: National Research Institute of Police Science, Chiba 277-0882, Japan.
authors.forename: Fujii
authors.initials: F
authors.lastname: Koji
authors.affiliation: National Research Institute of Police Science, Chiba 277-0882, Japan.
authors.forename: Kitayama
authors.initials: K
authors.lastname: Tetsushi
authors.affiliation: National Research Institute of Police Science, Chiba 277-0882, Japan.
authors.forename: Sekiguchi
authors.initials: S
authors.lastname: Kazumasa
authors.affiliation: Juntendo University School of Medicine, Tokyo 113-8421, Japan.
authors.forename: Nakanishi
authors.initials: N
authors.lastname: Hiroaki
authors.affiliation: Juntendo University School of Medicine, Tokyo 113-8421, Japan.
authors.forename: Saito
authors.initials: S
authors.lastname: Kazuyuki
mesh_terms: D053803:Forensic Genetics / Q000379:methods; D056426:Genetic Loci; D006239:Haplotypes; D006801:Humans; D020641:Polymorphism, Single Nucleotide
keywords: DNA typing; Forensic; Haplotype; Individual identification; SNP