Platinum-Quality Mitogenome Haplotypes From United States Populations

• NCJ Number: 255684
• Journal: Genes Volume: 11 Dated: 2020 Pages: 1290-1313
• Author(s): Cassandra R. Taylor; Kevin M. Kiesler; Kimberly Sturk-Andreaggi; Joseph D. Ring; Walther Parson; Moses Schanfield; Peter M. Vallone; Charla Marshall
• Date Published: 2020
• Length: 24 pages
• Grant Number(s): DJO-NIJ-17-RO-0219
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Program/Project Description
• Award: Development of a Forensic Quality Mitogenome Haplotype Database from 5000 High Quality Samples Using Next-Generation Sequencing Methods

Annotation

A total of 1,327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC).

Abstract

The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 for low-frequency (5 percent) variant detection. Point heteroplasmies below 10 percent frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95 percent of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories. (publisher abstract modified)