Mitochondrial DNA Genome Sequencing and SNP Assay Development for Increased Power of Discrimination, Final Report

• NCJ Number: 213502
• Author(s): Thomas J. Parsons
• Date Published: March 2006
• Length: 118 pages
• Grant Number(s): 2000-IJ-CX-K010
• Agencies: NIJ-Sponsored
• Publication Type: Report (Study/Research)
• Award: National Institute of Justice Continuation Awards

Annotation

This report describes a 5-year project that developed a method for accessing the large reserve of genetic variation in the 15,000 bp mitochondrial DNA (mtDNA) coding region, in order to enhance the forensic identification provided by sequencing the hypervariable (HV) regions of the mtDNA control region.

Abstract

The project focused on the relatively small number of common types present in U.S. Caucasian, African-American, and Hispanic populations. The project's objective was to enable a forensic scientist who encounters a common HV type to turn to one or two multiplex assays that offer the best chance to detect additional variation of the HV type in question. For common Caucasian HV types, eight multiplex allele-specific primer extension (APE) assays were designed, optimized, and tested. These proved to be suitable regarding characteristics important for forensic mtDNA testing. Validation for sensitivity, mixture detection, and degraded samples was completed for seven of the eight panels (one is still in development). One multiplex has been applied in numerous case investigations. Population databases were established for the completed multiplexes. New control region databases were generated, including four regional Hispanic population samples that were significantly differentiated at the haplogroup and haplotype level. A collaborative project developed a multiplex APE single nucleotide polymorphism (SNP) assay for haplogroup assignment among mtDNAs of western European origin. The project involved the sequencing of 506 entire mtDNA genomes that corresponded to 56 common HV types present in 0.5 percent or more of the respective populations. Full genome sequencing resolved the 56 HV types into 423 haplotypes and permitted the identification of 123 SNP sites suitable for assay development. Extensive tables and figures and a list of 50 publications and presentations