A common epigenetic clock from childhood to old age

2022
journal article
article
25
dc.abstract.enForensic age estimation is a DNA intelligence tool that forms an important part of Forensic DNA Phenotyping. Criminal cases with no suspects or with unsuccessful matches in searches on DNA databases; human identification analyses in mass disasters; anthropological studies or legal disputes; all benefit from age estimation to gain investigative leads. Several age prediction models have been developed to date based on DNA methylation. Although different DNA methylation technologies as well as diverse statistical methods have been proposed, most of them are based on blood samples and mainly restricted to adult age ranges. In the current study, we present an extended age prediction model based on 895 evenly distributed Spanish DNA blood samples from 2 to 104 years old. DNA methylation levels were detected using Agena Bioscience EpiTYPER® technology for a total of seven CpG sites located at seven genomic regions: ELOVL2, ASPA, PDE4C, FHL2, CCDC102B, MIR29B2CHG and chr16:85395429 (GRCh38). The accuracy of the age prediction system was tested by comparing three statistical methods: quantile regression (QR), quantile regression neural network (QRNN) and quantile regression support vector machine (QRSVM). The most accurate predictions were obtained when using QRNN or QRSVM (mean absolute prediction error, MAE of ± 3.36 and ± 3.41, respectively). Validation of the models with an independent Spanish testing set (N = 152) provided similar accuracies for both methods (MAE: ± 3.32 and ± 3.45, respectively). The main advantage of using quantile regression statistical tools lies in obtaining age-dependent prediction intervals, fitting the error to the estimated age. An additional analysis of dimensionality reduction shows a direct correlation of increased error and a reduction of correct classifications as the training sample size is reduced. Results indicated that a minimum sample size of six samples per year-of-age covered by the training set is recommended to efficiently capture the most inter-individual variability.pl
dc.affiliationWydział Biologii : Instytut Zoologii i Badań Biomedycznychpl
dc.affiliationPion Prorektora ds. badań naukowych : Małopolskie Centrum Biotechnologiipl
dc.contributor.authorFreire-Aradas, A.pl
dc.contributor.authorGirón-Santamaría, L.pl
dc.contributor.authorMosquera-Miguel, A.pl
dc.contributor.authorAmbroa-Conde, A.pl
dc.contributor.authorPhillips, C.pl
dc.contributor.authorCasares de Cal, M.pl
dc.contributor.authorGómez-Tato, A.pl
dc.contributor.authorÁlvarez-Dios, J.pl
dc.contributor.authorPośpiech, Ewelina - 108809 pl
dc.contributor.authorAliferi, A.pl
dc.contributor.authorSyndercombe Court, D.pl
dc.contributor.authorBranicki, Wojciech - 185426 pl
dc.contributor.authorLareu, M. V.pl
dc.date.accessioned2022-07-22T14:38:51Z
dc.date.available2022-07-22T14:38:51Z
dc.date.issued2022pl
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.versionostateczna wersja wydawcy
dc.description.volume60pl
dc.identifier.articleid102743pl
dc.identifier.doi10.1016/j.fsigen.2022.102743pl
dc.identifier.eissn1878-0326pl
dc.identifier.issn1872-4973pl
dc.identifier.urihttps://ruj.uj.edu.pl/xmlui/handle/item/297768
dc.languageengpl
dc.language.containerengpl
dc.rightsUdzielam licencji. Uznanie autorstwa - Użycie niekomercyjne - Bez utworów zależnych 4.0 Międzynarodowa*
dc.rights.licenceCC-BY-NC-ND
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/legalcode.pl*
dc.share.typeinne
dc.subject.enDNA methylationpl
dc.subject.enforensic age estimationpl
dc.subject.enquantile regressionpl
dc.subject.enmachine learningpl
dc.subject.enEpiTYPER®pl
dc.subtypeArticlepl
dc.titleA common epigenetic clock from childhood to old agepl
dc.title.journalForensic Science International. Geneticspl
dc.typeJournalArticlepl
dspace.entity.typePublication
dc.abstract.enpl
Forensic age estimation is a DNA intelligence tool that forms an important part of Forensic DNA Phenotyping. Criminal cases with no suspects or with unsuccessful matches in searches on DNA databases; human identification analyses in mass disasters; anthropological studies or legal disputes; all benefit from age estimation to gain investigative leads. Several age prediction models have been developed to date based on DNA methylation. Although different DNA methylation technologies as well as diverse statistical methods have been proposed, most of them are based on blood samples and mainly restricted to adult age ranges. In the current study, we present an extended age prediction model based on 895 evenly distributed Spanish DNA blood samples from 2 to 104 years old. DNA methylation levels were detected using Agena Bioscience EpiTYPER® technology for a total of seven CpG sites located at seven genomic regions: ELOVL2, ASPA, PDE4C, FHL2, CCDC102B, MIR29B2CHG and chr16:85395429 (GRCh38). The accuracy of the age prediction system was tested by comparing three statistical methods: quantile regression (QR), quantile regression neural network (QRNN) and quantile regression support vector machine (QRSVM). The most accurate predictions were obtained when using QRNN or QRSVM (mean absolute prediction error, MAE of ± 3.36 and ± 3.41, respectively). Validation of the models with an independent Spanish testing set (N = 152) provided similar accuracies for both methods (MAE: ± 3.32 and ± 3.45, respectively). The main advantage of using quantile regression statistical tools lies in obtaining age-dependent prediction intervals, fitting the error to the estimated age. An additional analysis of dimensionality reduction shows a direct correlation of increased error and a reduction of correct classifications as the training sample size is reduced. Results indicated that a minimum sample size of six samples per year-of-age covered by the training set is recommended to efficiently capture the most inter-individual variability.
dc.affiliationpl
Wydział Biologii : Instytut Zoologii i Badań Biomedycznych
dc.affiliationpl
Pion Prorektora ds. badań naukowych : Małopolskie Centrum Biotechnologii
dc.contributor.authorpl
Freire-Aradas, A.
dc.contributor.authorpl
Girón-Santamaría, L.
dc.contributor.authorpl
Mosquera-Miguel, A.
dc.contributor.authorpl
Ambroa-Conde, A.
dc.contributor.authorpl
Phillips, C.
dc.contributor.authorpl
Casares de Cal, M.
dc.contributor.authorpl
Gómez-Tato, A.
dc.contributor.authorpl
Álvarez-Dios, J.
dc.contributor.authorpl
Pośpiech, Ewelina - 108809
dc.contributor.authorpl
Aliferi, A.
dc.contributor.authorpl
Syndercombe Court, D.
dc.contributor.authorpl
Branicki, Wojciech - 185426
dc.contributor.authorpl
Lareu, M. V.
dc.date.accessioned
2022-07-22T14:38:51Z
dc.date.available
2022-07-22T14:38:51Z
dc.date.issuedpl
2022
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.version
ostateczna wersja wydawcy
dc.description.volumepl
60
dc.identifier.articleidpl
102743
dc.identifier.doipl
10.1016/j.fsigen.2022.102743
dc.identifier.eissnpl
1878-0326
dc.identifier.issnpl
1872-4973
dc.identifier.uri
https://ruj.uj.edu.pl/xmlui/handle/item/297768
dc.languagepl
eng
dc.language.containerpl
eng
dc.rights*
Udzielam licencji. Uznanie autorstwa - Użycie niekomercyjne - Bez utworów zależnych 4.0 Międzynarodowa
dc.rights.licence
CC-BY-NC-ND
dc.rights.uri*
http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode.pl
dc.share.type
inne
dc.subject.enpl
DNA methylation
dc.subject.enpl
forensic age estimation
dc.subject.enpl
quantile regression
dc.subject.enpl
machine learning
dc.subject.enpl
EpiTYPER®
dc.subtypepl
Article
dc.titlepl
A common epigenetic clock from childhood to old age
dc.title.journalpl
Forensic Science International. Genetics
dc.typepl
JournalArticle
dspace.entity.type
Publication
Affiliations

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