Quantitative analysis of DNA methylation by pyrosequencing and MassARRAY technique for age estimation: a comparative study.
10.12122/j.issn.1673-4254.2020.12.21
- Author:
Ling WANG
1
;
Fuduan PENG
2
;
Hui ZHAO
1
;
Shanfei LI
1
;
Xiaomeng SUN
1
;
Tianzi LIU
2
;
Lei FENG
1
Author Information
1. Institute of Forensic Science, Ministry of Public Security//Ministry of Public Security Key Laboratory of Forensic Genetics, Beijing 100000, China.
2. Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100000, China.
- Publication Type:Journal Article
- Keywords:
DNA methylation;
MassARRAY detection;
Pyrosequencing;
Z-score;
age estimation;
stepwise multivariate linear regression model
- MeSH:
CpG Islands/genetics*;
DNA Methylation;
High-Throughput Nucleotide Sequencing;
Linear Models;
Sequence Analysis, DNA
- From:
Journal of Southern Medical University
2020;40(12):1831-1837
- CountryChina
- Language:Chinese
-
Abstract:
OBJECTIVE:To study the difference in age estimation based on quantitative analysis of DNA methylation by MassARRAY and pyrosequencing techniques.
METHODS:The methylation levels of 9 CpG sites from two independent whole blood sample sets (containing 65 and 62 samples) were detected using MassARRAY and pyrosequencing techniques. Z-score transformation was used to remove the batch effects of different techniques, and a linear regression model was used for age prediction.
RESULTS:For age prediction using the MassARRAY system, the 65 samples showed a mean absolute difference (MAD) of 2.49 years before Z-score transformation of the data and 2.44 years after the transformation, similar to the results in the 62 samples (MAD of 3.36 years before and 3.42 years after Z-score transformation). For data typed from pyrosequencing, the 65 samples showed a MAD of 4.20 years before and 2.76 years after data Z-score transformation, also similar to the results in the 62 samples (MAD of 3.92 years before and 3.63 years after data transformation).
CONCLUSIONS:Z-score transformation can effectively reduce the system batch effect between MassARRAY and pyrosequencing. Data from the MassARRAY system allows direct age estimation without further data processing, while the pyrosequencing data may increase the error in age estimation, which can be corrected by Z-score transformation of the data.
