No abstract

Three sampled populations of unrelated males--African American, Caucasian, and Hispanic, all from Texas-were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR Yfiler kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets. Haplotype diversities were 99.88%, 99.89%, and 99.87% for the African American, Caucasian, and Hispanic sample populations, respectively. F(ST) values were very small when a haplotype comprised 10-16 markers. This suggests that inclusion of substructure correction is not required. However, haplotypes consisting of fewer loci may require the inclusion of F(ST) corrections. The testing of independence of autosomal and Y STRs supports the proposition that the frequencies of autosomal and Y STR profiles can be combined using the product rule.

No 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.

Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR‐enriched libraries.