Reproducibility of methylated CpG typing with the Illumina MiSeq

Marie-Louise Kampmann; Olivia Strunge Meyer; Suzanne Greby Hougaard Schmidt; Claus Børsting; Niels Morling

doi:10.1016/j.fsigss.2017.09.150

Reproducibility of methylated CpG typing with the Illumina MiSeq

Marie-Louise Kampmann, Olivia Strunge Meyer, Suzanne Greby Hougaard Schmidt, Claus Børsting, Niels Morling

Section of Forensic Genetics

Abstract

DNA methylation patterns may be used for identification of body fluids and for age estimation of human individuals. We evaluated some of the challenges and pitfalls of studying methylated CpG sites. We compared the methylated CpG analysis of two different methods 1) massively parallel sequencing (MPS) using the Illumina MiSeq and 2) the iPLEX assay on the MassARRAY^® System. On the Illumina MiSeq, the standard deviation of the fraction of methylation was under 3% between replicates, whereas the reproducibility of the MassARRAY^® was very difficult to achieve. We tested the denaturation and conversion times of the Premium Bisulfite kit (Diagenode) in order to optimise the conversion rate and minimise DNA degradation. Finally, we tested the reproducibility of the methylation patterns using the Illumina MiSeq.

Original language	English
Journal	Forensic Science International: Genetics. Supplement Series
Volume	6
Pages (from-to)	e430-e432
Number of pages	2
ISSN	1875-1768
DOIs	https://doi.org/10.1016/j.fsigss.2017.09.150
Publication status	Published - Dec 2017

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title = "Reproducibility of methylated CpG typing with the Illumina MiSeq",

abstract = "DNA methylation patterns may be used for identification of body fluids and for age estimation of human individuals. We evaluated some of the challenges and pitfalls of studying methylated CpG sites. We compared the methylated CpG analysis of two different methods 1) massively parallel sequencing (MPS) using the Illumina MiSeq and 2) the iPLEX assay on the MassARRAY{\textregistered} System. On the Illumina MiSeq, the standard deviation of the fraction of methylation was under 3% between replicates, whereas the reproducibility of the MassARRAY{\textregistered} was very difficult to achieve. We tested the denaturation and conversion times of the Premium Bisulfite kit (Diagenode) in order to optimise the conversion rate and minimise DNA degradation. Finally, we tested the reproducibility of the methylation patterns using the Illumina MiSeq.",

author = "Marie-Louise Kampmann and Meyer, {Olivia Strunge} and Schmidt, {Suzanne Greby Hougaard} and Claus B{\o}rsting and Niels Morling",

year = "2017",

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doi = "10.1016/j.fsigss.2017.09.150",

language = "English",

volume = "6",

pages = "e430--e432",

journal = "Forensic Science International: Genetics. Supplement Series",

issn = "1875-1768",

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TY - GEN

T1 - Reproducibility of methylated CpG typing with the Illumina MiSeq

AU - Kampmann, Marie-Louise

AU - Meyer, Olivia Strunge

AU - Schmidt, Suzanne Greby Hougaard

AU - Børsting, Claus

AU - Morling, Niels

PY - 2017/12

Y1 - 2017/12

N2 - DNA methylation patterns may be used for identification of body fluids and for age estimation of human individuals. We evaluated some of the challenges and pitfalls of studying methylated CpG sites. We compared the methylated CpG analysis of two different methods 1) massively parallel sequencing (MPS) using the Illumina MiSeq and 2) the iPLEX assay on the MassARRAY® System. On the Illumina MiSeq, the standard deviation of the fraction of methylation was under 3% between replicates, whereas the reproducibility of the MassARRAY® was very difficult to achieve. We tested the denaturation and conversion times of the Premium Bisulfite kit (Diagenode) in order to optimise the conversion rate and minimise DNA degradation. Finally, we tested the reproducibility of the methylation patterns using the Illumina MiSeq.

AB - DNA methylation patterns may be used for identification of body fluids and for age estimation of human individuals. We evaluated some of the challenges and pitfalls of studying methylated CpG sites. We compared the methylated CpG analysis of two different methods 1) massively parallel sequencing (MPS) using the Illumina MiSeq and 2) the iPLEX assay on the MassARRAY® System. On the Illumina MiSeq, the standard deviation of the fraction of methylation was under 3% between replicates, whereas the reproducibility of the MassARRAY® was very difficult to achieve. We tested the denaturation and conversion times of the Premium Bisulfite kit (Diagenode) in order to optimise the conversion rate and minimise DNA degradation. Finally, we tested the reproducibility of the methylation patterns using the Illumina MiSeq.

U2 - 10.1016/j.fsigss.2017.09.150

DO - 10.1016/j.fsigss.2017.09.150

M3 - Conference article

SN - 1875-1768

VL - 6

SP - e430-e432

JO - Forensic Science International: Genetics. Supplement Series

JF - Forensic Science International: Genetics. Supplement Series

ER -

Reproducibility of methylated CpG typing with the Illumina MiSeq

Abstract

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