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Series GSE140730 Query DataSets for GSE140730
Status Public on Mar 24, 2020
Title Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. Since the neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development, we performed whole-genome bisulfite sequencing of 152 umbilical cord blood samples from the MARBLES and EARLI high-familial risk prospective cohorts to identify an epigenomic signature of ASD at birth. We identified differentially-methylated regions (DMRs) stratified by sex that discriminated ASD from control cord blood samples in discovery and replication sets. At a region level, 7 DMRs in males and 31 DMRs in females replicated across two independent groups of subjects, while 537 DMR genes in males and 1762 DMR genes in females replicated by gene association. These DMR genes were significantly enriched for brain and embryonic expression, X chromosome location, and identification in prior epigenetic studies of ASD in post-mortem brain. In males and females, autosomal ASD DMRs were significantly enriched for promoter and bivalent chromatin states across most cell types, while sex differences were observed for X-linked ASD DMRs. Lastly, these DMRs identified in cord blood were significantly enriched for binding sites of methyl-sensitive transcription factors relevant to fetal brain development. At birth, prior to the diagnosis of ASD, a distinct DNA methylation signature was detected in cord blood over regulatory regions and genes relevant to early fetal neurodevelopment. Differential cord methylation in ASD supports the developmental and sex-biased etiology of ASD, and provides novel insights for early diagnosis and therapy.
 
Overall design Investigation of DNA methylation with whole-genome bisulfite sequencing in umbilical cord blood from two high-risk cohorts of newborns diagnosed with autism spectrum disorder (ASD) or typical development (TD) at 36 months (TD n = 76, ASD n = 76).
Web link https://www.biorxiv.org/content/10.1101/850529v1
 
Contributor(s) Mordaunt CE, LaSalle JM
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NIH grant(s)
Grant ID Grant title Affiliation Name
K12 HD051958 Building Interdisciplinary Careers in Women's Health at UC Davis UNIVERSITY OF CALIFORNIA DAVIS Claire Pomeroy
P01 ES011269 Project 1: Epidemiology and the Environment in Autism (Hertz-Picciotto) UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
P01 ES011269 Project 2: Perinatal Epigenetic Signature of Environmental Exposure UNIVERSITY OF CALIFORNIA DAVIS Janine M LaSalle
P30 ES023513 UC Davis Environmental Health Sciences Core Center UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
R01 ES016443 Early Autism Risk Longitudinal Investigation (EARLI) Network DREXEL UNIVERSITY CRAIG J NEWSCHAFFER
R01 ES017646 Environment, The Perinatal Epigenome, and Risk for Autism and Related Disorders JOHNS HOPKINS UNIVERSITY M Daniele Fallin
R01 ES020392 Autism Risk, Prenatal Environmental Exposures, and Pathophysiologic Markers UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
R01 ES020392 Autism Risk, Prenatal Environmental Exposures, and Pathophysiologic Markers UNIVERSITY OF CALIFORNIA DAVIS Sally Ozonoff
R01 ES025531 Prenatal exposure to metals and risk for Autism Spectrum Disorder in MARBLES and EARLI JOHNS HOPKINS UNIVERSITY M Daniele Fallin
R01 ES025574 Folic Acid Prevention Pathways for ASD in High Risk Families UNIVERSITY OF CALIFORNIA DAVIS Rebecca Jean Schmidt
R01 ES028089 Environmental Influence on Infant Microbiome Development and ASD Symptoms UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
R24 ES028533 BUILDS MARBLES: Biorepository Upkeep and Infrastructure for Longitudinal Data Sharing for MARBLES UNIVERSITY OF CALIFORNIA DAVIS Rebecca Jean Schmidt
U54 HD079125 Biostatistics, Bioinformatics and Research Design Core UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
U54 HD079125 Clinical Translational Core UNIVERSITY OF CALIFORNIA DAVIS Sally Ozonoff
UG3 OD023365 Pre-adolescent and Late-adolescent Follow-up of the CHARGE Study Children UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
UH3 OD023365 Pre-adolescent and Late-adolescent Follow-up of the CHARGE Study Children UNIVERSITY OF CALIFORNIA DAVIS Irva Hertz-Picciotto
Submission date Nov 20, 2019
Last update date Mar 24, 2020
Contact name Charles E Mordaunt
E-mail(s) cemordaunt@ucdavis.edu
Organization name University of California, Davis
Department Medical Microbiology and Immunology
Lab LaSalle Lab
Street address 3318 Tupper Hall, One Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (130)
GSM4182609 Discovery_TD_M_01
GSM4182610 Discovery_TD_M_02
GSM4182611 Discovery_TD_M_03
Relations
BioProject PRJNA590702
SRA SRP230793

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Supplementary file Size Download File type/resource
GSE140730_RAW.tar 32.8 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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