Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns
Abstract
:1. Introduction
2. Materials and Methods
2.1. Skeletal Samples
2.2. DNA Extraction
2.3. Library Preparation
2.3.1. In House MPI Method
2.3.2. SRSLY Kit
2.3.3. KAPA Hyper Prep Kit
2.3.4. Quantification
2.4. MtDNA Hybridization Capture
2.5. Sequencing and Data Processing
3. Results
3.1. Evaluation of Extraction Methods
3.2. Characteristics of Recovered DNA
3.3. Evaluation of Library Preparartion Protocols
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Disclaimer
References
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Sample ID | Skeletal Element | Context | Cemetery of Disinterment | Formalin Treatment | Powder Application | Casework Results |
---|---|---|---|---|---|---|
2224 | Tibia | WWII-Tarawa | NMCP 1 | Unknown | Not visible | High Coverage |
0858 | Temporal | WWII-USS Oklahoma | NMCP 1 | No, Oil Soaked | Likely | High Coverage |
0994 | Femur | WWII-Buna | MAC 2 | Unknown | Not visible | High Coverage |
2255 | Humerus | WWII-Cabanatuan | MAC 2 | Unknown | Not visible | High Coverage |
0899 | Humerus | WWII-Tarawa | NMCP 1 | Unknown | Yes | Low Coverage |
0100 | Femur | Korea | NMCP 1 | Likely | Yes | Low Coverage |
1001 | Os coxa | WWII-Yugoslavia | SRAC 3 | Unknown | Not visible | Low Coverage |
3140 | Radius | WWII-Burma | NMCP 1 | Unknown | Yes | Low Coverage |
0378 | Femur | WWII-Tarawa | NMCP 1 | Unknown | Yes | Failed |
1837 | Tibia | WWII-Tarawa | NMCP 1 | Unknown | Yes | Failed |
1198 | Tibia | Korea | NMCP 1 | Likely | Yes | Failed |
1964 | Humerus | Korea | NMCP 1 | Likely | Yes | Failed |
0917 | Tibia | Korea | NMCP 1 | Likely | Yes | Failed |
3825 | Radius | Korea | NMCP 1 | Likely | Yes | Failed |
1487 | Femur | WWII-Italy | SRAC 3 | Unknown | Yes | Failed |
Method | Bone Powder (g) | Digestion Buffer | Digestion Buffer Volume (mL) | Proteinase K (20 mg/mL) (µL) | Incubation Temperature (°C) | DNA Purification | Repair Protocol |
---|---|---|---|---|---|---|---|
AFDIL (PM) | 1.0 | Demin buffer 1 | 7.5 | 200 | 56 | PCIA with buffer exchange | NA (MinElute purification) |
AFDIL-USER (PUM) | 1.0 | Demin buffer 1 | 7.5 | 200 | 56 | PCIA with buffer exchange | USER (NEB, Ipswich, MA, USA) |
AFDIL-FFPE (PFM) | 1.0 | Demin buffer 1 | 7.5 | 200 | 56 | PCIA with buffer exchange | NEBNext FFPE DNA Repair Mix (NEB) |
Dabney—37 (aDNA37) | 0.2 | Dabney buffer 2 | 1.0 | 25 | 37 | Silica column and PB Buffer | NA |
Dabney—56 (aDNA56) | Dabney 37 remaining pellet | Dabney buffer 2 | 1.0 | 25 | 56 | Silica column and PB Buffer | NA |
AFDIL-Dabney (A_D) | 0.2 | Demin buffer 1 | 4.0 | 200 | 56 | Silica column and PB Buffer | NA |
Sample ID | Casework | MPI | SRSLY (Pig Out) | |||||
---|---|---|---|---|---|---|---|---|
Reported Bases | Predicted Haplogroup | Reported Bases | Predicted Haplogroup | Discordant Sites (Compared to Casework) | Reported Bases | Predicted Haplogroup | Discordant Sites (Compared to Casework) | |
High Coverage | ||||||||
2224 | 16507 | H18 | 16569 | H18 | 0 | 16568 | H18 | 0 |
0858 | 16507 | V3c | 16568 | V3c | 0 | 16569 | V3c | 0 |
0994 | 16507 | J1c4b | 16569 | J1c4b | 0 | 16569 | J1c4b | 0 |
2255 | 16507 | J1c3 | 16268 | J1c3/J1c3h/J1c3k | 1 | 16144 | J1c3 | 1 |
Low Coverage | ||||||||
0899 | 16507 | H4a1a4b | 16565 | H4a1a4b | 0 | 16563 | H4a1a4b | 0 |
0100 | 16183 | H24a | 16181 | H24a | 0 | 13585 | H24/H24a | 0 |
1001 | 15765 | H1c6 | 16566 | H1c6 | 0 | 16567 | H1c6 | 0 |
3140 | 16505 | U5b1b1-16192 | 16555 | U5b1b1- 16192 | 0 | 16515 | U5b1b1-16192 | 0 |
Failed in Casework | ||||||||
0378 | NA | NA | 15951 | U5a1a1+16362/U5a1a1d/U5a1a1d1 | NA | 15681 | U5a1a1+16362/U5a1a1d/U5a1a1d1 | NA |
1837 | NA | NA | 13504 | K1c2 | NA | 11526 | K1c2 | NA |
1198 | NA | NA | 16091 | H1c3b | NA | 15821 | H1c3b | NA |
1964 | NA | NA | 16010 | L2a1c+16086/L2a1c3b | NA | 14871 | L2a1c+16086 | NA |
0917 | NA | NA | 16386 | K1a1b2b | NA | 16004 | K1a1b2b | NA |
3825 | NA | NA | 16550 | H11a | NA | 16319 | H11a | NA |
1487 | NA | NA | 10715 | K1a (and subhaplogroups of K1a) | NA | 12009 | K1a9 | NA |
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Zavala, E.I.; Thomas, J.T.; Sturk-Andreaggi, K.; Daniels-Higginbotham, J.; Meyers, K.K.; Barrit-Ross, S.; Aximu-Petri, A.; Richter, J.; Nickel, B.; Berg, G.E.; et al. Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns. Genes 2022, 13, 129. https://doi.org/10.3390/genes13010129
Zavala EI, Thomas JT, Sturk-Andreaggi K, Daniels-Higginbotham J, Meyers KK, Barrit-Ross S, Aximu-Petri A, Richter J, Nickel B, Berg GE, et al. Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns. Genes. 2022; 13(1):129. https://doi.org/10.3390/genes13010129
Chicago/Turabian StyleZavala, Elena I., Jacqueline Tyler Thomas, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Kerriann K. Meyers, Suzanne Barrit-Ross, Ayinuer Aximu-Petri, Julia Richter, Birgit Nickel, Gregory E. Berg, and et al. 2022. "Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns" Genes 13, no. 1: 129. https://doi.org/10.3390/genes13010129
APA StyleZavala, E. I., Thomas, J. T., Sturk-Andreaggi, K., Daniels-Higginbotham, J., Meyers, K. K., Barrit-Ross, S., Aximu-Petri, A., Richter, J., Nickel, B., Berg, G. E., McMahon, T. P., Meyer, M., & Marshall, C. (2022). Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns. Genes, 13(1), 129. https://doi.org/10.3390/genes13010129