Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology
Abstract
:1. Introduction
2. Results
2.1. CpG Sites Identified and Individual Correlations with Age
2.2. Construction of Prediction Models for Age Estimation
3. Discussion
4. Material and Methods
4.1. Sample Collection and Teeth Processing
4.2. DNA Extraction
4.3. DNA Quantification
4.4. Bisulfite Conversion and PCR
4.5. Pyrosequencing
4.6. Methylation Results Analyses and Statistics
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Site | r | p-Value |
---|---|---|---|
ELOVL2 | CpG1 | 0.353 | 0.024 |
CpG2 | 0.308 | 0.043 | |
CpG3 | 0.341 | 0.028 | |
CpG4 | 0.318 | 0.038 | |
CpG5 | 0.240 | 0.093 | |
CpG6 | 0.342 | 0.028 | |
CpG7 | 0.365 | 0.020 | |
KLF14 | CpG1 | 0.168 | 0.480 |
CpG2 | 0.316 | 0.174 | |
CpG3 | 0.154 | 0.518 | |
CpG4 | 0.278 | 0.236 | |
CpG5 | 0.267 | 0.256 | |
CpG6 | 0.220 | 0.350 | |
CpG7 | 0.468 | 0.037 | |
SCGN | CpG1 | 0.313 | 0.180 |
CpG2 | 0.344 | 0.138 | |
CpG3 | 0.529 | 0.017 | |
CpG4 | 0.340 | 0.142 | |
CpG5 | −0.103 | 0.665 | |
CpG6 | 0.268 | 0.254 | |
CpG7 | 0.258 | 0.272 | |
CpG8 | 0.508 | 0.022 | |
CpG9 | 0.156 | 0.512 | |
CpG10 | 0.291 | 0.213 | |
NPTX2 | CpG1 | 0.280 | 0.076 |
CpG2 | −0.105 | 0.514 | |
CpG3 | −0.084 | 0.601 | |
CpG4 | 0.327 | 0.037 | |
CpG5 | 0.214 | 0.179 | |
CpG6 | 0.022 | 0.890 | |
CpG7 | 0.121 | 0.449 | |
CpG8 | 0.151 | 0.346 | |
CpG9 | 0.076 | 0.637 | |
CpG10 | 0.136 | 0.396 | |
CpG11 | 0.172 | 0.282 | |
CpG12 | 0.127 | 0.428 | |
CpG13 | 0.166 | 0.300 | |
CpG14 | 0.136 | 0.556 | |
FHL2 | CpG1 | −0.367 | 0.111 |
CpG2 | −0.376 | 0.094 | |
CpG3 | −0.251 | 0.285 | |
CpG4 | −0.288 | 0.217 | |
CpG5 | −0.262 | 0.264 | |
CpG6 | −0.241 | 0.305 | |
CpG7 | −0.088 | 0.713 | |
CpG8 | −0.086 | 0.720 |
Model | R | R2 | SE | p-Value | MAE | MAE (LOOCV) |
---|---|---|---|---|---|---|
Age (years) = 12.763 + 4.034(ELOVL2CpG3) + 3.535(ELOVL2CpG4) − 3.040(ELOVL2CpG7) + 7.815(NPTX2CpG4) + 3.791(SCGNCpG3) + 9.122(SCGNCpG8) − 5.013(ELOVL2CpG2) − 1.643(ELOVL2CpG5) − 4.341(FHL2CpG1) + 3.571(FHL2CpG3) − 1.093(FHL2CpG4) + 3.882(FHL2CpG5) − 1.229(FHL2CpG6) − 1.662(KLF14CpG7) | 0.987 | 0.975 | 3.671 | 0.004 | 1.5474 | 2.128 |
Age (years) = 14.710 + 3.675(ELOVL2CpG3) + 3.972(ELOVL2CpG4) − 2.978(ELOVL2CpG7) + 5.278(NPTX2CpG4) + 4.044(SCGNCpG3) + 8.378(SCGNCpG8) − 4.853(ELOVL2CpG2) − 1.875(ELOVL2CpG5) − 4.273(FHL2CpG1) + 3.547(FHL2CpG3) − 1.145(FHL2CpG4) + 3.640(FHL2CpG5) − 0.937(FHL2CpG6) | 0.986 | 0.972 | 3.505 | 0.001 | 1.711 | 1.706 |
Age (years) = 14.349 + 4.635(ELOVL2CpG3) + 3.049(ELOVL2CpG4) − 3.681(ELOVL2CpG7) + 5.254(NPTX2CpG4) + 3.810(SCGNCpG3) + 9.503(SCGNCpG8) − 4.835(ELOVL2CpG2) − 0.982(ELOVL2CpG5) − 4.191(FHL2CpG1) + 3.778(FHL2CpG3) − 1.447(FHL2CpG4) + 2.638(FHL2CpG5) | 0.980 | 0.961 | 3.874 | 0.001 | 2.047 | 2.083 |
Age (years) = 14.854 + 5.139(ELOVL2CpG3) + 2.249(ELOVL2CpG4) − 4.086(ELOVL2CpG7) + 6.927(NPTX2CpG4) + 3.505(SCGNCpG3) + 10.363(SCGNCpG8) − 4.983(ELOVL2CpG2) − 4.223(FHL2CpG1) + 4.075(FHL2CpG3) − 1.562(FHL2CpG4) + 2.506(FHL2CpG5) | 0.977 | 0.955 | 3.866 | 0.0001 | 2.1313 | 1.942 |
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C. Zapico, S.; Gauthier, Q.; Antevska, A.; McCord, B.R. Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology. Int. J. Mol. Sci. 2021, 22, 3717. https://doi.org/10.3390/ijms22073717
C. Zapico S, Gauthier Q, Antevska A, McCord BR. Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology. International Journal of Molecular Sciences. 2021; 22(7):3717. https://doi.org/10.3390/ijms22073717
Chicago/Turabian StyleC. Zapico, Sara, Quentin Gauthier, Aleksandra Antevska, and Bruce R. McCord. 2021. "Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology" International Journal of Molecular Sciences 22, no. 7: 3717. https://doi.org/10.3390/ijms22073717
APA StyleC. Zapico, S., Gauthier, Q., Antevska, A., & McCord, B. R. (2021). Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology. International Journal of Molecular Sciences, 22(7), 3717. https://doi.org/10.3390/ijms22073717