Platinum-Quality Mitogenome Haplotypes from United States Populations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Description
2.2. Two-Amplicon Mitogenome Enrichment, Library Preparation, and Sequencing
2.3. Data Analysis
2.4. Sample Reprocessing
2.5. Quality Control
2.6. Population-Level Analyses
3. Results
3.1. Sample Quality Metrics
3.2. NUMT Interference in Four-Amplicon Data
3.3. STR and Kinship Analyses of Samples with Shared Haplotypes
3.4. CR Sanger Concordance
3.5. Heteroplasmy
3.6. Population-Level Analyses
3.7. Haplogroup Distribution
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample Set | Source | U.S. Geographic Origin | Metapopulation | Sample Type | Count |
---|---|---|---|---|---|
COAF | Analytical Genetic Testing Center (Denver, CO) | Colorado * | African American | Whole blood, buccal swabs | 123 |
COCN | Analytical Genetic Testing Center (Denver, CO) | Colorado * | Caucasian | Whole blood, buccal swabs | 118 |
COHS | Analytical Genetic Testing Center (Denver, CO) | Colorado * | Hispanic | Whole blood, buccal swabs | 113 |
NTAF | National Institute of Standards and Technology (Gaithersburg, MD) | Multiple States | African American | Whole blood | 258 |
NTCN | National Institute of Standards and Technology (Gaithersburg, MD) | Multiple States | Caucasian | Whole blood | 262 |
NTHS | National Institute of Standards and Technology (Gaithersburg, MD) | Multiple States | Hispanic | Whole blood | 139 |
DSAS | Department of Defense Serum Repository (Silver Spring, CO) | Multiple States/Territories | Asian American | Serum | 175 |
DSNA | Department of Defense Serum Repository (Silver Spring, CO) | Multiple States | Native American | Serum | 175 |
Sample Source | Processing Laboratory | Amplification Input (µL) | Amplicon Purification | Library Preparation | Sequencing | ||||
---|---|---|---|---|---|---|---|---|---|
Input (ng) | Reaction | Method | Input (pM) | Reagent Kit | Read Type | ||||
AGTC-CO | AFMES-AFDIL | 3 | Yes | 150 | Half-reaction | Manual | 12 | 150 cycle v3 | Single end |
NIST | NIST | 2 | No | 350 | Full-reaction | Manual | 20 | 600 cycle v3 | Paired end |
DoDSR | AFMES-AFDIL | 5 | Yes | 50 | Half-reaction | Automated | 12 | 600 cycle v3 | Paired end |
Dataset | Samples Attempted | Finalized Samples | Passing | Excluded | ||||
---|---|---|---|---|---|---|---|---|
Two Amplicon | Four Amplicon | Failed | Mixed | Duplicate | Related | |||
COAF | 123 | 112 | 112 | 0 | 6 | 3 | 2 | 0 |
COCN | 118 | 112 | 112 | 0 | 5 | 1 | 0 | 0 |
COHS | 113 | 109 | 109 | 0 | 1 | 3 | 0 | 0 |
NTAF | 258 | 256 | 251 | 5 | 1 | 1 | 0 | 0 |
NTCN | 262 | 260 | 258 | 2 | 1 | 0 | 0 | 1 |
NTHS | 139 | 138 | 138 | 0 | 0 | 0 | 0 | 1 |
DSAS | 175 | 169 | 165 | 4 | 3 | 3 | 0 | 0 |
DSNA | 175 | 171 | 158 | 13 | 1 | 3 | 0 | 0 |
Total | 1363 | 1327 | 1303 | 24 | 18 | 14 | 2 | 2 |
Data Source | Total Reads | Reads After Trim | Reads Mapped | Trimmed Reads Mapped (%) | Average Read Depth | Average Major Base Frequency (%) | Average Major Base Frequency Excluding Heteroplasmy (%) | Average Variant Position Read Depth |
---|---|---|---|---|---|---|---|---|
AGTC-CO | 352,136 | 313,022 | 293,667 | 94 | 1658.8 | 98.6 | 99.5 | 1499.6 |
NIST | 383,834 | 272,090 | 256,309 | 95 | 1558.4 | 98.0 | 99.1 | 1466.0 |
DoDSR | 688,530 | 566,775 | 504,600 | 90 | 2385.4 | 97.5 | 99.2 | 2198.7 |
Dataset | Total Individuals | Total PHPs | Individuals with PHPs | Individuals with 1 PHP | Individuals with 2 PHPs | Individuals with 3 PHPs |
---|---|---|---|---|---|---|
COAF | 112 | 37 | 31 (28%) | 26 | 4 | 1 |
COCN | 112 | 41 | 30 (27%) | 20 | 9 | 1 |
COHS | 109 | 36 | 27 (25%) | 20 | 5 | 2 |
NTAF | 256 | 77 | 60 (23%) | 43 | 17 | 0 |
NTCN | 260 | 92 | 77 (30%) | 65 | 10 | 2 |
NTHS | 138 | 53 | 43 (31%) | 34 | 8 | 1 |
DSAS | 169 | 62 | 54 (32%) | 49 | 2 | 3 |
DSNA | 171 | 48 | 43 (25%) | 38 | 5 | 0 |
All | 1327 | 446 | 365 (28%) | 295 | 60 | 10 |
Dataset | Sample Size | Including PHP | Excluding PHP | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Total Haplotypes | Unique Haplotypes | Observed RMP (%) | Empirical RMP (%) | Haplotype Diversity | Total Haplotypes | Unique Haplotypes | Observed RMP (%) | Empirical RMP (%) | Haplotype Diversity | ||
COAF | 112 | 112 | 112 | 0.89 | 0.00 | 1 | 110 | 108 | 0.92 | 0.03 | 0.9997 |
COCN | 112 | 112 | 112 | 0.89 | 0.00 | 1 | 112 | 112 | 0.89 | 0.00 | 1 |
COHS | 109 | 102 | 97 | 1.09 | 0.17 | 0.9983 | 94 | 83 | 1.34 | 0.42 | 0.9958 |
NTAF | 256 | 251 | 247 | 0.41 | 0.02 | 0.9998 | 246 | 237 | 0.42 | 0.03 | 0.9997 |
NTCN | 260 | 254 | 250 | 0.41 | 0.02 | 0.9998 | 250 | 244 | 0.43 | 0.05 | 0.9995 |
NTHS | 138 | 131 | 127 | 0.86 | 0.14 | 0.9986 | 125 | 116 | 0.97 | 0.24 | 0.9976 |
DSAS | 169 | 167 | 165 | 0.61 | 0.01 | 0.9999 | 165 | 161 | 0.62 | 0.03 | 0.9997 |
DSNA | 171 | 167 | 163 | 0.61 | 0.03 | 0.9997 | 164 | 159 | 0.65 | 0.07 | 0.9993 |
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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
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 StyleTaylor, 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
APA StyleTaylor, C. R., Kiesler, K. M., Sturk-Andreaggi, K., Ring, J. D., Parson, W., Schanfield, M., Vallone, P. M., & Marshall, C. (2020). Platinum-Quality Mitogenome Haplotypes from United States Populations. Genes, 11(11), 1290. https://doi.org/10.3390/genes11111290