Haplotype block: a new type of forensic DNA markers

Abstract

Forensic DNA analysis is currently performed using highly discriminating short tandem repeat (STR) markers. SNPs are being investigated as adjunct tools for human identity testing because of their abundance in the human genome, utility for genotyping degraded DNA samples, and amenability to automation. While SNPs can provide an alternative approach, on a per locus basis they have a lower power of discrimination (PD) than STRs. With the discovery of block structures in the human genome, a novel set of SNP markers are available for further exploration of forensic utility. Several neighboring, tightly linked SNPs are inherited together and form a haplotype block, which as a haploblock has a higher discrimination power than the individual SNPs within the block. Candidate haplotype blocks were selected from three major populations (Caucasian, East Asian, and African) using the following parameters: maximum match probability reduction = 0.85, linkage disequilibrium (LD) r(2) ≥ 0.7, maximum F(st) = 0.06, minimum number of SNPs = 3, minimum heterozygosity = 0.2, and minimum number of haplotypes = 3. From the HapMap Phase II data, 253 haploblocks were identified on the 22 autosomal chromosomes. After removing haploblocks deviating from the Hardy-Weinberg equilibrium (HWE) or in LD with other haploblocks, 24 haploblocks remained as candidates for forensic consideration. The cumulative PD of these blocks can reach 10(-12) in the populations studied. The data support within and between haplotype independence even when they are syntenic. We propose guidelines for evidence interpretation that address the application of haplotype blocks for transfer evidence, mixture, and kinship analyses.