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Series GSE65428 Query DataSets for GSE65428
Status Public on Jan 29, 2016
Title DNA methylation analyses in infants reveal signals correlated with fetal alcohol syndrome, maternal smoking, gender, and ethnicity
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Alcohol exposure is known to impact several components of the one-carbon metabolism pathway, which is vital for providing methyl groups for DNA and peptide synthesis and for methylation modification of nucleotides and proteins. Methylation patterning in DNA is known to be altered across generations in specific situations in humans, including nutrient deprivation and smoking during pregnancy. We were interested in seeing whether heavy alcohol exposure during pregnancy, which is associated with fetal alcohol syndrome, influences genome-wide infant methylation patterning.
From Guthrie card spots across over 100 infants of various genders, ethnicities, and maternal smoking and drinking status, we find two loci that are have significantly different methylation patterning associated with maternal drinking; cgXXX and cgYYY, the former near MCOLN3 and the latter in intergenic space. We also use available epidemiological information associated with our data set to replicate maternal smoking with infant methylation changes as well as replicate and expand upon methylation differences between genders and ethnicities.
Overall design Case Control design with 72 cases and 73 controls. Our study sample of Guthrie card DNA from NY state infants contains 150 unique samples. Four samples were removed due to poor performance in the PCA analysis and another was removed because there is a set of identical twins in the study. As we were interested in studying the role ethnicity plays in methylation differences, we removed eight of the Hispanic and other ethnicity samples, leaving a total of 137 samples. The populations of the FAS cases and controls are matched for gender and ethnicity
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Submission date Jan 29, 2015
Last update date Mar 22, 2019
Contact name David McGaughey
Organization name NIH
Department NHGRI
Lab Brody
Street address 50 South Drive Rm 5317
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (145)
GSM1595967 A05706
GSM1595968 A05761
GSM1595969 A07358
BioProject PRJNA273985

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE65428_RAW.tar 183.1 Mb (http)(custom) TAR
GSE65428_cg_used_mcgaughey_fas.geo.txt.gz 1.3 Mb (ftp)(http) TXT
GSE65428_matrix_signal_intensities.txt.gz 297.4 Mb (ftp)(http) TXT
GSE65428_p_and_q_significance_var_deltas_with_annotation_for_fas_smoking_ethnicity_gender_7.csv.gz 54.0 Mb (ftp)(http) CSV
Processed data included within Sample table

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