Platinum-Quality Mitogenome Haplotypes from United States Populations
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-amplifica...
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doaj-e0efa3f75aa84c68997782233559c84e2020-11-25T02:20:42ZengMDPI AGGenes2073-44252020-10-01111290129010.3390/genes11111290Platinum-Quality Mitogenome Haplotypes from United States PopulationsCassandra R. Taylor0Kevin M. Kiesler1Kimberly Sturk-Andreaggi2Joseph D. Ring3Walther Parson4Moses Schanfield5Peter M. Vallone6Charla Marshall7Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USANational Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USAArmed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USAArmed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USAInstitute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, AustriaDepartment of Forensic Sciences, The George Washington University, Washington, DC 20007, USANational Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USAArmed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USAA 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.https://www.mdpi.com/2073-4425/11/11/1290mtDNAmitogenomenext-generation sequencinghaplotypehaplogrouppopulation statistics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cassandra R. Taylor Kevin M. Kiesler Kimberly Sturk-Andreaggi Joseph D. Ring Walther Parson Moses Schanfield Peter M. Vallone Charla Marshall |
spellingShingle |
Cassandra R. Taylor Kevin M. Kiesler Kimberly Sturk-Andreaggi Joseph D. Ring Walther Parson Moses Schanfield Peter M. Vallone Charla Marshall Platinum-Quality Mitogenome Haplotypes from United States Populations Genes mtDNA mitogenome next-generation sequencing haplotype haplogroup population statistics |
author_facet |
Cassandra R. Taylor Kevin M. Kiesler Kimberly Sturk-Andreaggi Joseph D. Ring Walther Parson Moses Schanfield Peter M. Vallone Charla Marshall |
author_sort |
Cassandra R. Taylor |
title |
Platinum-Quality Mitogenome Haplotypes from United States Populations |
title_short |
Platinum-Quality Mitogenome Haplotypes from United States Populations |
title_full |
Platinum-Quality Mitogenome Haplotypes from United States Populations |
title_fullStr |
Platinum-Quality Mitogenome Haplotypes from United States Populations |
title_full_unstemmed |
Platinum-Quality Mitogenome Haplotypes from United States Populations |
title_sort |
platinum-quality mitogenome haplotypes from united states populations |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2020-10-01 |
description |
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. |
topic |
mtDNA mitogenome next-generation sequencing haplotype haplogroup population statistics |
url |
https://www.mdpi.com/2073-4425/11/11/1290 |
work_keys_str_mv |
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