Quality control measures for placental sample purity in DNA methylation array analyses

Qianhui Wan; Shalem Yiner-Lee Leemaqz; Stephen Martin Pederson; Dylan McCullough; Dale Christopher McAninch; Tanja Jankovic-Karasoulos; Melanie Denise Smith; Konstantinos Justinian Bogias; Ning Liu; James Breen; Claire Trelford Roberts; Tina Bianco-Miotto

doi:10.1016/j.placenta.2019.09.006

Quality control measures for placental sample purity in DNA methylation array analyses

Qianhui Wan, Shalem Yiner-Lee Leemaqz, Stephen Martin Pederson, Dylan McCullough, Dale Christopher McAninch, Tanja Jankovic-Karasoulos, Melanie Denise Smith, Konstantinos Justinian Bogias, Ning Liu, James Breen, Claire Trelford Roberts, Tina Bianco-Miotto

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is globally hypomethylated compared to other tissues. Placental villous tissue from early pregnancy terminations can be difficult to separate from non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placenta samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.

Original language	English
Pages (from-to)	8-11
Number of pages	4
Journal	PLACENTA
Volume	88
DOIs	https://doi.org/10.1016/j.placenta.2019.09.006
Publication status	Published - Dec 2019
Externally published	Yes

Keywords

DNA methylation
Human placenta
Methylation Bead Chip
Quality control

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.placenta.2019.09.006Licence: In Copyright

Cite this

@article{f0170b9090d34964adf22cb74b0ba209,

title = "Quality control measures for placental sample purity in DNA methylation array analyses",

abstract = "The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is globally hypomethylated compared to other tissues. Placental villous tissue from early pregnancy terminations can be difficult to separate from non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placenta samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.",

keywords = "DNA methylation, Human placenta, Methylation Bead Chip, Quality control",

author = "Qianhui Wan and {Yiner-Lee Leemaqz}, Shalem and Pederson, {Stephen Martin} and Dylan McCullough and McAninch, {Dale Christopher} and Tanja Jankovic-Karasoulos and Smith, {Melanie Denise} and Bogias, {Konstantinos Justinian} and Ning Liu and James Breen and Roberts, {Claire Trelford} and Tina Bianco-Miotto",

year = "2019",

month = dec,

doi = "10.1016/j.placenta.2019.09.006",

language = "English",

volume = "88",

pages = "8--11",

journal = "PLACENTA",

issn = "0143-4004",

publisher = "Elsevier",

}

TY - JOUR

T1 - Quality control measures for placental sample purity in DNA methylation array analyses

AU - Wan, Qianhui

AU - Yiner-Lee Leemaqz, Shalem

AU - Pederson, Stephen Martin

AU - McCullough, Dylan

AU - McAninch, Dale Christopher

AU - Jankovic-Karasoulos, Tanja

AU - Smith, Melanie Denise

AU - Bogias, Konstantinos Justinian

AU - Liu, Ning

AU - Breen, James

AU - Roberts, Claire Trelford

AU - Bianco-Miotto, Tina

PY - 2019/12

Y1 - 2019/12

N2 - The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is globally hypomethylated compared to other tissues. Placental villous tissue from early pregnancy terminations can be difficult to separate from non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placenta samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.

AB - The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is globally hypomethylated compared to other tissues. Placental villous tissue from early pregnancy terminations can be difficult to separate from non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placenta samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.

KW - DNA methylation

KW - Human placenta

KW - Methylation Bead Chip

KW - Quality control

UR - http://www.scopus.com/inward/record.url?scp=85072648411&partnerID=8YFLogxK

U2 - 10.1016/j.placenta.2019.09.006

DO - 10.1016/j.placenta.2019.09.006

M3 - Article

C2 - 31569011

AN - SCOPUS:85072648411

SN - 0143-4004

VL - 88

SP - 8

EP - 11

JO - PLACENTA

JF - PLACENTA

ER -

Quality control measures for placental sample purity in DNA methylation array analyses

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this