scholarly journals Analysis of age-dependent DNA methylation changes in plucked hair samples using massive parallel sequencing

Rechtsmedizin ◽  
2021 ◽  
Author(s):  
Jana Naue ◽  
Julia Winkelmann ◽  
Ulrike Schmidt ◽  
Sabine Lutz-Bonengel
Keyword(s):  
Dna Methylation ◽  
Forensic Genetics ◽  
Methylation Pattern ◽  
Massive Parallel Sequencing ◽  
Degraded Dna ◽  
Tissue Cell ◽  
Sample Type ◽  
Parallel Sequencing ◽  
Hair Samples ◽  
Age Dependent

AbstractThe analysis of age-dependent DNA methylation changes is a valuable tool in epigenetic research and forensic genetics. With some exceptions, most studies in the past concentrated on the analysis of blood, buccal, and saliva samples. Another important sample type in forensic investigations is hair, where age-dependent DNA methylation has not been investigated so far. In this pilot study a deeper look was taken at the possibilities and challenges of DNA methylation analysis in hair. The DNA methylation of selected age-dependent 5’-C-phosphate-G‑3’ (CpG) sites were characterized for their potential use as a biomarker for age prediction using plucked hair samples and massive parallel sequencing. Plucked hair roots of 49 individuals were included in the study. The DNA methylation of 31 hairs was successfully analyzed. The DNA methylation pattern of 10 loci, including ELOVL2, F5, KLF14, and TRIM59, was determined by amplicon-based massive parallel sequencing. Age-dependent changes were found for several markers. The results demonstrate the possible use of already established age-dependent markers but at the same time they have tissue/cell type-specific characteristics. Special challenges such as low amounts of DNA and degraded DNA as well as the possible heterogeneous cellular composition of plucked hair samples, have to be considered.

Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing

2018 ◽  
Vol 36 ◽  
pp. 152-159 ◽  
Author(s):  
Jana Naue ◽  
Timo Sänger ◽  
Huub C.J. Hoefsloot ◽  
Sabine Lutz-Bonengel ◽  
Ate D. Kloosterman ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Massive Parallel Sequencing ◽  
Proof Of Concept ◽  
Parallel Sequencing ◽  
Concept Study ◽  
Age Dependent ◽  
Different Tissues

scholarly journals Chronological age prediction based on DNA methylation: Massive parallel sequencing and random forest regression

2017 ◽  
Vol 31 ◽  
pp. 19-28 ◽  
Author(s):  
Jana Naue ◽  
Huub C.J. Hoefsloot ◽  
Olaf R.F. Mook ◽  
Laura Rijlaarsdam-Hoekstra ◽  
Marloes C.H. van der Zwalm ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Random Forest ◽  
Massive Parallel Sequencing ◽  
Chronological Age ◽  
Random Forest Regression ◽  
Parallel Sequencing ◽  
Age Prediction

Performance of a massive parallel sequencing microhaplotypes assay on degraded DNA

2019 ◽  
Vol 7 (1) ◽  
pp. 782-783
Author(s):  
Chiara Turchi ◽  
Filomena Melchionda ◽  
Mauro Pesaresi ◽  
Paolo Fattorini ◽  
Adriano Tagliabracci
Keyword(s):  
Massive Parallel Sequencing ◽  
Degraded Dna ◽  
Parallel Sequencing

Exploring the usefulness of microhaplotypes in forensic identification using massive parallel sequencing technology

2020 ◽  
Vol 140 (1) ◽  
Author(s):  
Chiara Turchi ◽  
Filomena Melchionda ◽  
Mauro Pesaresi ◽  
Eleonora Ciarimboli ◽  
Carla Bini ◽  
...  
Keyword(s):  
Forensic Identification ◽  
Massive Parallel Sequencing ◽  
Sequencing Technology ◽  
Parallel Sequencing

Examination of the dynamics of global DNA methylation pattern establishment during spermatogenesiss

2007 ◽  
Vol 30 (4) ◽  
pp. 90
Author(s):  
Kirsten Niles ◽  
Sophie La Salle ◽  
Christopher Oakes ◽  
Jacquetta Trasler
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Germ Cells ◽  
Epigenetic Modification ◽  
Methylation Pattern ◽  
Chromosome 9 ◽  
Specific Gene ◽  
Global Methylation ◽  
Dna Methylation Pattern ◽  
Methylation Patterns

Background: DNA methylation is an epigenetic modification involved in gene expression, genome stability, and genomic imprinting. In the male, methylation patterns are initially erased in primordial germ cells (PGCs) as they enter the gonadal ridge; methylation patterns are then acquired on CpG dinucleotides during gametogenesis. Correct pattern establishment is essential for normal spermatogenesis. To date, the characterization and timing of methylation pattern acquisition in PGCs has been described using a limited number of specific gene loci. This study aimed to describe DNA methylation pattern establishment dynamics during male gametogenesis through global methylation profiling techniques in a mouse model. Methods: Using a chromosome based approach, primers were designed for 24 regions spanning chromosome 9; intergenic, non-repeat, non-CpG island sequences were chosen for study based on previous evidence that these types of sequences are targets for testis-specific methylation events. The percent methylation was determined in each region by quantitative analysis of DNA methylation using real-time PCR (qAMP). The germ cell-specific pattern was determined by comparing methylation between spermatozoa and liver. To examine methylation in developing germ cells, spermatogonia from 2 day- and 6 day-old Oct4-GFP (green fluorescent protein) mice were isolated using fluorescence activated cell sorting. Results: As compared to liver, four loci were hypomethylated and five loci were hypermethylated in spermatozoa, supporting previous results indicating a unique methylation pattern in male germ cells. Only one region was hypomethylated and no regions were hypermethylated in day 6 spermatogonia as compared to mature spermatozoa, signifying that the bulk of DNA methylation is established prior to type A spermatogonia. The methylation in day 2 spermatogonia, germ cells that are just commencing mitosis, revealed differences of 15-20% compared to day 6 spermatogonia at five regions indicating that the most crucial phase of DNA methylation acquisition occurs prenatally. Conclusion: Together, these studies provide further evidence that germ cell methylation patterns differ from those in somatic tissues and suggest that much of methylation at intergenic sites is acquired during prenatal germ cell development. (Supported by CIHR)

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