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Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting
Article

Platinum-Quality Mitogenome Haplotypes from United States Populations

1
Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA
2
SNA International, LLC; Alexandria, VA 22314, USA
3
National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
4
Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
5
Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
6
Department of Forensic Sciences, The George Washington University, Washington, DC 20007, USA
*
Author to whom correspondence should be addressed.
Genes 2020, 11(11), 1290; https://doi.org/10.3390/genes11111290
Received: 2 October 2020 / Revised: 26 October 2020 / Accepted: 27 October 2020 / Published: 29 October 2020
(This article belongs to the Special Issue Forensic Mitochondrial Genomics)
A total of 1327 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). 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%) variant detection. Point heteroplasmies below 10% 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% 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. View Full-Text
Keywords: mtDNA; mitogenome; next-generation sequencing; haplotype; haplogroup; population statistics mtDNA; mitogenome; next-generation sequencing; haplotype; haplogroup; population statistics
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MDPI and ACS Style

Taylor, C.R.; Kiesler, K.M.; Sturk-Andreaggi, K.; Ring, J.D.; Parson, W.; Schanfield, M.; Vallone, P.M.; Marshall, C. Platinum-Quality Mitogenome Haplotypes from United States Populations. Genes 2020, 11, 1290. https://doi.org/10.3390/genes11111290

AMA Style

Taylor CR, Kiesler KM, Sturk-Andreaggi K, Ring JD, Parson W, Schanfield M, Vallone PM, Marshall C. Platinum-Quality Mitogenome Haplotypes from United States Populations. Genes. 2020; 11(11):1290. https://doi.org/10.3390/genes11111290

Chicago/Turabian Style

Taylor, Cassandra R., Kevin M. Kiesler, Kimberly Sturk-Andreaggi, Joseph D. Ring, Walther Parson, Moses Schanfield, Peter M. Vallone, and Charla Marshall. 2020. "Platinum-Quality Mitogenome Haplotypes from United States Populations" Genes 11, no. 11: 1290. https://doi.org/10.3390/genes11111290

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