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Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
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DNA methylation-based age estimation from semen: Genome-wide marker identification and model development.
Ya Li1, Xiaozhao Liu2, Maomin Chen1
1Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
Forensic Science International. Genetics
|January 3, 2025
Summary
This study identifies novel semen-specific age-related CpG sites using advanced sequencing, improving DNA methylation-based forensic age estimation. A robust random forest model was developed for accurate age prediction in semen samples.
Area of Science:
- Forensic Science
- Epigenetics
- Genomics
Background:
- DNA methylation at age-related CpG (AR-CpG) sites is promising for forensic age estimation.
- Somatic models perform poorly in semen due to unique methylation dynamics during spermatogenesis.
- Current studies are limited by the low coverage of methylation microarrays.
Purpose of the Study:
- Identify novel semen-specific AR-CpG sites using double-enzyme reduced representation bisulfite sequencing (dRRBS).
- Validate these markers and previously reported sites using bisulfite amplicon sequencing (BSAS).
- Develop robust age estimation models for semen samples.
Main Methods:
- Conducted a methylome-wide association study on semen samples from 21 healthy Chinese men using dRRBS.
- Analyzed over 4 million CpG sites per sample, focusing on 721,840 shared sites.
- Validated age-related CpGs using multiplex PCR-based BSAS in 129 and 247 semen samples across different age groups.
Main Results:
- Identified 139 AR-CpG sites, with over 95% not covered by conventional methylation microarrays.
- Validated 71 AR-CpG sites with high age correlation (|rho| > 0.50), including chr2:129071885 (cg19998819) as the strongest marker (rho = 0.81).
- Developed optimized random forest (RF) age estimation models, with a 9-CpG RF model achieving a root mean square error of 4.73 years and mean absolute error of 3.30 years.
Conclusions:
- dRRBS is effective for large-scale AR-CpG discovery in semen.
- A robust age estimation model using semen-specific AR-CpGs was developed.
- This study provides a comprehensive database of semen-specific AR-CpGs for forensic applications.
