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Series GSE128827

Query DataSets for GSE128827

Status

Public on Oct 14, 2020

Title

Accurate ethnicity prediction from placental DNA methylation data

Organism

Homo sapiens

Experiment type

Methylation profiling by genome tiling array
Third-party reanalysis

Summary

The influence of genetics on DNA methylation (DNAme) variation is well documented, yet confounding from population stratification is often unaccounted for in DNAme association studies. Existing approaches have been developed to address confounding by population stratification by directly using DNAme data, but have not been validated in additional human populations or tissues, such as the placenta. Results: To aid future placental DNAme studies in assessing population stratification, we developed an ethnicity classifier, PLANET (placental elastic net DNAme ethnicity classifier), on combined Infinium Human Methylation 450k BeadChip array (HM450k) data from placental samples. We used data from five North American cohorts from private and public repositories (n = 509) and show that PLANET can not only accurately predict (accuracy = 0.9379, kappa = 0.8227) major classes of self-reported ethnicity/race (African: n = 58, Asian: n = 53, Caucasian: n = 389), but can also produce probabilities that are highly correlated with genetic ancestry inferred from genome-wide SNP (>2.5 million SNP) and ancestry informative markers (n=50) data. We found that PLANET’s ethnicity classification relies on 1860 DNAme microarray sites, and over half of these were also linked to nearby genetic polymorphisms (n=955). Lastly, we found our placental-optimized method outperforms existing approaches in assessing population stratification in our placental samples from individuals of Asian, African, and Caucasian ethnicities. Conclusion: PLANET outperforms existing methods and heavily relies on the genetic signal present in DNAme microarray data. PLANET can be used to address population stratification in future placental DNAme association studies, and will be especially useful when ethnicity information is missing and genotyping markers are unavailable.

Overall design

508 samples were used to develop and validate PLANET, our placental ethnicity classifier. These samples are mixed in phenotype (healthy, preeclamptic, IUGR, a range of gestational ages across the third trimester and birthweights), as they come from multiple studies. For ethnicity and sex, these samples mainly consist of Caucasian, Asian, and African samples and are matched for sex (259 males and 249 females). This repository contains processed DNAm data for all 508 samples in the form of a beta value matrix, with a corresponding detection p value matrix, and sample-specific metadata information (e.g. ethnicity, sex). The majority of the 508 samples were collected from other GEO repositories; therefore only raw idat files for never-published-before samples were included in this repository. This amounts to 6 samples (12 idat files). Please see the samples metadata .xls file for a list of these samples.

Contributor(s)

Yuan VW, Robinson WP

Citation(s)

31399127

Submission date

Mar 25, 2019

Last update date

Oct 24, 2020

Contact name

Wendy Robinson

E-mail(s)

wprobinsonlab@gmail.com

Organization name

University of British Columbia

Department

Medical Genetics

Lab

Robinosn

Street address

950 W 28th Ave

City

Vancouver

State/province

ZIP/Postal code

V5Z 4H4

Country

Canada

Platforms (1)

GPL13534

Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)

Samples (6)

More...

GSM3686800	genomic DNA from PM332_vc CONTROL chorionic villi
GSM3686801	genomic DNA from PM344_vc CONTROL chorionic villi
GSM3686802	genomic DNA from PM329 CONTROL chorionic villi

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE128827_Processed_Matrix.txt.gz	635.9 Mb	(ftp)(http)	TXT
GSE128827_RAW.tar	232.0 Mb	(http)(custom)	TAR (of IDAT)
GSE128827_Samples_metadata.xls.gz	51.3 Kb	(ftp)(http)	XLS
Processed data are available on Series record