Dental DNA Mutations Occurring after Death: A Novel Method for Post-Mortem Interval (PMI) Estimation
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
4.1. Data Loggers, Genetic Kits, and Chemical Reagents
- -
- IButton DS1923 Hygrochron Temperature/Humidity Data Logger, iButtonLink Technology, LLC, Whitewater, WI, USA
- -
- Express-Thermo, Eclo Solutions, 2014 version, Leiria, Portugal
- -
- SecurBiop® e FORMALeasy®, Techingreen Srl, Teramo, Italy; 4% buffered formaldehyde
- -
- MagCore genomic DNA FFPE onestep, Diatechlabline pharmacogenetics, Jesi, Italy
- -
- Myriapod NGS-L T 56G Oncopanel Kit
- -
- q-PCR, Rotor-gene, Qiagen, Hilden, Germany
- -
- Qubit dsDNA HS Assay kit, Invitrogen by Thermo Fisher Scientific, Midland, Canada
- -
- Ion One Touch 2 instrument, Life Technologies, Grand Island, The Netherlands
- -
- Dynabeats MyOne Streptavidin C1 Beads, Invitrogen by Thermo Fisher Scientific, Midland, ON, Canada
- -
- Ion S5 System, Ion Torrent platform, Invitrogen by Thermo Fisher Scientific, Midland, Canada
- -
- Myriapod NGS Data Analysis Software, Myriapod NGS Analysis software e Myriapod workstation NGS, Diatech Pharmacogenetics srl, Jesi, Italy
4.2. Sample Collection and Storage
- -
- Patients who underwent multiple tooth extractions for orthodontic reasons;
- -
- Unremarkable medical history of patients;
- -
- Permanent, completely mineralized, sound, and unrestored incisors, canines, premolars, and molars. All teeth were considered eligible to collect multiple elements, as possible, from the same subject.
- -
- Normal response to pulp vitality tests (i.e., thermal tests)
- -
- Decayed, fractured, or damaged teeth.
- -
- Teeth treated with conservative, endodontic, or prosthetic therapies.
- -
- Non-vital teeth or abnormal results of vital pulpal tests.
- -
- Medical history positive for relevant diseases (e.g., cancer, diabetes) or chronic drug treatments.
4.3. Dental Pulp Extraction
4.4. DNA Extraction and NGS Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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CASE | TOOTH * | PMI (Days) | ADD (°C) |
---|---|---|---|
8 | LLTM | 8 | 157.4 |
1 | URCI | 16 | 388.2 |
7 | LRFP | 16 | 369.2 |
10 | LRSP | 17 | 440.9 |
3 | ULFP | 23 | 551.2 |
9 | URFP | 28 | 678.3 |
2 | URSP | 30 | 738.1 |
4 | LLFP | 30 | 581.5 |
5 | LLSP | 35 | 753.8 |
6 | LRSP | 35 | 753.8 |
PMI (Days) | 16 | 23 | 28 | 30 | |
ADD (°C) | 369.2 | 551.2 | 678.3 | 581.5 | |
GENES | MUTATIONS | ||||
ABL1 | c.*1363G>A | ||||
APC | c.1162G>A | ||||
c.1749G>A | |||||
c.1840G>T | |||||
c.2176T>C | |||||
c.407C>T | |||||
c.5034G>A | |||||
c.5268T>G | |||||
c.5465T>A | |||||
c.5880G>A | |||||
BRAF | c.*1363G>A | ||||
c.*1483A>G | |||||
c.*813T>C | |||||
c.*922G>C | |||||
c.3324A>G | |||||
c.5094C>T | |||||
c.6555C>T | |||||
c.75+60C>T | |||||
EGFR | c.1839C>T c.1880+55C>T | ||||
c.1881-1267C>A | |||||
c.1881-1585A>G | |||||
c.1881-2094A>G | |||||
c.1881-404T>G | |||||
c.1881-721G>A | |||||
c.1887T>A | |||||
c.2283+125T>C | |||||
c.2283+1296C>T | |||||
c.2283+1901G>A | |||||
c.2283+2225C>T | |||||
c.2283+269T>C | |||||
c.2283+2994A>G | |||||
c.274T>C | |||||
c.2868T>C | |||||
c.2983C>T | |||||
c.3014G>A | |||||
c.3127T>C | |||||
c.489C>T | |||||
c.563G>A | |||||
c.622-248G>A | |||||
c.686T>C | |||||
c.738C>T | |||||
ESR1 | c.1096+21499_1096+21500 | ||||
c.1236-18935G>A | |||||
ETV1 | c.182-3581A>G | ||||
c.182-3990C>T | |||||
c.182-4016G>C | |||||
c.182-4229 182-4228delinsGC | |||||
c.235+113A>G | |||||
c.235+11542C>T | |||||
GRM3 | c.879C>T | ||||
H3F3C | c.*2T>G | ||||
KRAS | c.*512T>C | ||||
c.-12+2376_-12+2391dup | |||||
c.2049A>G | |||||
c.2225G>C | |||||
c.2547= | |||||
c.2629A>T | |||||
c.2718A>G | |||||
c.387G>A | |||||
c.3906T>C | |||||
c.451-5617G>A | |||||
c.451-7404A>C | |||||
PDGFRA | c.1701 A>G | ||||
c.1787-269G>A | |||||
c.3222T>C | |||||
ROS1 | c.5231-1578A>G | ||||
c.5231-191C>T | |||||
c.5231-2516A>G | |||||
c.5231-2735T>C | |||||
c.5231-3291C>T | |||||
c.5231-3311T>C | |||||
c.5231-415C>T | |||||
c.5231-735T>C | |||||
c.5348+1319G>A | |||||
c.5348+361T>A | |||||
c.5624-1461G>T | |||||
c.5624-876A>G | |||||
c.5759+351 del | |||||
c.5759+468A>C | |||||
c.5759+603A>C | |||||
c.5760-137G>A | |||||
c.5760-281C>T | |||||
c.5760-53G>T | |||||
c.5922+434G>C |
PMI (Days) | 17 | 30 | |
ADD (°C) | 440.9 | 738.1 | |
GENES | MUTATIONS | ||
ABRAXAS1 | c.1117G>A | ||
ADGRA2 | c.3660C>T | ||
AKT2 | c.-84-5059-84-5052 | ||
AKT3 | c.*3694G>A | ||
c.*3731C>T | |||
APC | c.7504G>A | ||
BRCA1 | c.-19-216A>G | ||
c.2311T>C | |||
c.2612C>T | |||
c.3119G>A | |||
c.3548A>G | |||
c.4308T>C | |||
c.4837A>G | |||
c.5075-237C>A | |||
CCND1 | c.723+571 | ||
c.723G>A | |||
CCND2 | c.493C>T | ||
CCNE1 | c.1215C>T | ||
c.399T>C | |||
ETV6 | c.463+7490C>A | ||
c.463+7929G>A | |||
c.463+848G>C | |||
c.464-6175G>T | |||
c.464-6269C>T | |||
RPS6KB2 | c.1259C>T | ||
c.807C>T | |||
RPTOR | c.1269C>T | ||
TNFRSF14 | c.50A>G | ||
TP53 | c.1100+154C>G | ||
ZFHX3 | c.1212C>T | ||
c.1282A>C | |||
c.1602C>T |
PMI (Days) | 8 | 8 | 16 | 16 | 17 | 23 | 28 | 30 | 30 | 35 | 35 | |
ADD (°C) | 157.4 | 183.1 | 369.2 | 388.2 | 440.9 | 551.2 | 678.3 | 581.5 | 738.1 | 753.8 | 753.8 | |
GENES | MUTATIONS | |||||||||||
ABRAXAS1 | c.1117G>A | |||||||||||
AKT3 | c.*3909T>C | |||||||||||
ALK | c.3067+365C>T | |||||||||||
c.3068-415G C | ||||||||||||
c.3068-574C>A | ||||||||||||
c.3359+24G>C | ||||||||||||
c.3375C>A | ||||||||||||
c.4338C>T | ||||||||||||
c.4472A>G | ||||||||||||
AMER1 | c.135C>T | |||||||||||
ANKRD26 | c.4204C>T | |||||||||||
ATR | c.7274G>A | |||||||||||
AXIN1 | c.1284G>A | |||||||||||
c.1549G>A | ||||||||||||
c.1827T>C | ||||||||||||
BAP1 | c.501G>A | |||||||||||
BCL2L11 | c.394+3056G>C | |||||||||||
c.394+3849C>T | ||||||||||||
BCL2L2 | c.128A>G | |||||||||||
BCL6 | c.492G>T | |||||||||||
BLM | c.1046G>A | |||||||||||
c.3102G>A | ||||||||||||
c.3531C>A | ||||||||||||
c.3945C T | ||||||||||||
BMPR1A | c.1140C>T | |||||||||||
BRAF | c.1140+757A>G | |||||||||||
c.1141-1305T>C | ||||||||||||
BRCA1 | c.134+1967T>C | |||||||||||
c.134+2983_134+3004delinsAAACCCCTACTGATGAA | ||||||||||||
c.-19-115T>C | ||||||||||||
c.-19-216A>G | ||||||||||||
c.3113A>G | ||||||||||||
c.3119G>A | ||||||||||||
c.3548A>G | ||||||||||||
c.4308T>C | ||||||||||||
c.4837A>G | ||||||||||||
c.5075-237C>A | ||||||||||||
CCND1 | c.723+571 | |||||||||||
c.723G>A | ||||||||||||
EGFR | c.1881-721G>A | |||||||||||
c.1881-781C>T | ||||||||||||
c.747+548C>T | ||||||||||||
c.748-235C>T | ||||||||||||
c.89-25201A>G | ||||||||||||
EML4 | c.*1941A>G | |||||||||||
ERBB2 | c.2086-29G>A | |||||||||||
c.2273delA | ||||||||||||
FAT1 | c.8523C>T | |||||||||||
FGFR3 | c.2393delC | |||||||||||
c.840C>T | ||||||||||||
c.843A>C | ||||||||||||
FLI1 | c.203G>T | |||||||||||
c.942C>G | ||||||||||||
HNF1A | c.1375C>T | |||||||||||
c.1460G>A | ||||||||||||
KAT6A | c.401T>C | |||||||||||
c.4455C>T | ||||||||||||
KDM5A | c.2594T>C | |||||||||||
c.4149C>T | ||||||||||||
PDGFRA | c.2003-11delT | |||||||||||
PTEN | c.802-18delC | |||||||||||
c.802-19dupT | ||||||||||||
c.802-23C>T | ||||||||||||
c.802-29C>T | ||||||||||||
c.80-3023C>T | ||||||||||||
ROS1 | c.5624-1340T>C | |||||||||||
TNFRSF14 | c.50A>G |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Bianchi, I.; Grassi, S.; Nardi, E.; Castiglione, F.; Focardi, M. Dental DNA Mutations Occurring after Death: A Novel Method for Post-Mortem Interval (PMI) Estimation. Int. J. Mol. Sci. 2024, 25, 8832. https://doi.org/10.3390/ijms25168832
Bianchi I, Grassi S, Nardi E, Castiglione F, Focardi M. Dental DNA Mutations Occurring after Death: A Novel Method for Post-Mortem Interval (PMI) Estimation. International Journal of Molecular Sciences. 2024; 25(16):8832. https://doi.org/10.3390/ijms25168832
Chicago/Turabian StyleBianchi, Ilenia, Simone Grassi, Eleonora Nardi, Francesca Castiglione, and Martina Focardi. 2024. "Dental DNA Mutations Occurring after Death: A Novel Method for Post-Mortem Interval (PMI) Estimation" International Journal of Molecular Sciences 25, no. 16: 8832. https://doi.org/10.3390/ijms25168832