This study constructs a high-resolution placental mQTL resource and investigates how placental DNA methylation relates to early- and later-life traits and their shared vulnerability.

medRxiv · Jul 9, 2026 · PreprintGenetic & Genomic Medicine

Placenta DNA methylation at ZNF300 is associated with fetal sex and placental morphology

Christine Ladd‐Acosta, Shan V. Andrews, Kelly M. Bakulski, Jason I. Feinberg, Rakel Tryggvadóttir, Ruofan Yao, Lisa Croen, Irva Hertz‐Picciotto, Craig J. Newschaffer, Carolyn M. Salafia, Andrew P. Feinberg, Kasper D. Hansen, M. Daniele Fallin

The paper identifies DNA methylation at ZNF300 associated with fetal sex and placental morphology using whole genome bisulfite sequencing and multiple datasets.

bioRxiv · Mar 5, 2021 · PreprintGenomics

Expression changes in immune and epigenetic gene pathways associated with nutritional metabolites in maternal blood from pregnancies resulting in autism and atypical neurodevelopment

Yihui Zhu, Charles E. Mordaunt, Blythe P Durbin-Johnson, Marie A. Caudill, Olga Malysheva, Joshua W. Miller, Ralph Green, S. Jill James, Stepan B. Melnyk, M. Daniele Fallin, Irva Hertz‐Picciotto, Rebecca J. Schmidt, Janine M. LaSalle

The paper examines gene expression and metabolite associations in maternal blood during pregnancy to link prenatal nutrition with neurodevelopmental outcomes in children.

Autism Research · Nov 7, 2020Peer-reviewedBioinformatics

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes

Charles E. Mordaunt, Julia M. Jianu, Benjamin I. Laufer, Yihui Zhu, Hyeyeon Hwang, Keith W. Dunaway, Kelly M. Bakulski, Jason I. Feinberg, Heather E. Volk, Kristen Lyall, Lisa Croen, Craig J. Newschaffer, Sally J. Ozonoff, Irva Hertz‐Picciotto, M. Daniele Fallin, , Janine M. LaSalle

The paper identifies DNA methylation differences in cord blood samples from newborns later diagnosed with ASD, revealing sex-specific epigenomic signatures linked to neurodevelopmental and X-linked genes.

Genome Medicine · Oct 14, 2020Peer-reviewedGenomics

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood

Charles E. Mordaunt, Bo Young Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J. Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca J. Schmidt, M. Daniele Fallin

This study identifies ASD-specific transcriptional changes in umbilical cord blood through a meta-analysis of two high-risk cohorts, highlighting environmental, immune, and epigenetic factors.

Molecular Autism · Oct 24, 2019Peer-reviewedGenomics

Peripheral blood DNA methylation and autism spectrum disorder

Shan V. Andrews, Brooke K. Sheppard, Gayle C. Windham, Laura A. Schieve, Diana Schendel, Lisa Croen, Pankaj Chopra, Reid S. Alisch, Craig J. Newschaffer, Stephen T. Warren, Andrew P. Feinberg, M. Daniele Fallin, Christine Ladd‐Acosta

This paper presents the largest case-control epigenome-wide association study (EWAS) for autism spectrum disorder (ASD) using blood DNA methylation data, finding no significant CpG sites but suggestive associations and concordance with brain samples.

Molecular Autism · Jun 28, 2018Peer-reviewedGenomics

Elevated polygenic burden for autism is associated with differential DNA methylation at birth.

Eilis J. Hannon, Diana Schendel, Christine Ladd‐Acosta, Jakob Grove, iPSYCH-Broad ASD Group, Christine Søholm Hansen, Shan V. Andrews, DAVID MICHAEL HOUGAARD, Michaeline A. Bresnahan, Ole N Mors, Mads V. Hollegaard, Marie Bækvad‐Hansen, Mady Hornig, Preben Bo Mortensen, Anders Dupont Børglum, , Jonathan S. Mill

The paper associates elevated polygenic autism risk with differential DNA methylation at birth, using a large cohort of infants and integrating genetic and epigenetic data.

Genome Medicine · Mar 28, 2018Peer-reviewedGenetics

Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder

Shan V. Andrews, Shannon Ellis, Kelly M. Bakulski, Brooke K. Sheppard, Lisa Croen, Irva Hertz‐Picciotto, Craig J. Newschaffer, Andrew P. Feinberg, Dan E. Arking, Christine Ladd‐Acosta, M. Daniele Fallin

The paper integrates genetic and epigenetic data to identify ASD-associated SNPs enriched in tissue-specific meQTLs and reveals immune-related pathways and psychiatric condition links.

Nature Communications · Oct 12, 2017Peer-reviewedGenomics

“Gap hunting” to characterize clustered probe signals in Illumina methylation array data

Shan V. Andrews, Christine Ladd‐Acosta, Andrew P. Feinberg, Kasper D. Hansen, M. Daniele Fallin

The paper identifies gap probes in Illumina methylation array data that show clustered methylation distributions, showing they can reflect genetic variation and aid in population stratification adjustment.

Epigenetics & Chromatin · Dec 1, 2016Peer-reviewedGenomics