Placenta Methylation and Autism Risk in the Early Autism Risk Longitudinal Investigation (EARLI)
Objectives: We measured DNAm across the genome in placenta tissue to identify genomic regions at which DNAm differed according to autism risk as quantified by the Autism Observational Scale for Infants (AOSI) administered at 12 months.
Methods: We isolated genomic DNA from the fetal side of 133 placenta samples from the Early Autism Risk Longitudinal Investigation (EARLI), an ongoing autism-enriched pregnancy cohort which enrolls families with a previously diagnosed ASD child during a new pregnancy. Families are followed throughout the gestational period and infants are followed from birth through 36 months. Recruitment was carried out at 4 sites: Drexel University School of Public Health & Children’s Hospital of Philadelphia, University of California Davis & MIND Institute, Johns Hopkins Bloomberg School of Public Health & Kennedy Krieger Institute, and Northern California Kaiser Permanente. Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina by New England BioLabs Inc. Whole-genome bisulfite sequencing at 13x coverage used 125 base pair, paired-end reads with the Illumina HiSeq 2500. We are currently performing alignment using Bowtie2, calculating methylation at single-nucleotide resolution, and searching for differentially methylated regions (DMRs) according to AOSI score, adjusting for ancestry and sex using the BSmooth algorithm as implemented in the R package ‘bsseq’.
Results: AOSI score was available on 115 of the 133 children with available placental samples (range 0-19, mean [sd] = 5.25 [3.86]). We will report at the meeting the top-ranked DMRs and explore their implicated regions for their potential functional relevance to ASD and towards placenta functionality more generally.
Conclusions: This study comprises the largest and most comprehensive survey of the placenta methylome in the context of ASD to date. Discovered regions may help define the role of placenta methylation in ASD etiology and may support the development of a placenta-based DNAm biomarker for autism risk.