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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...effects on neuronal firing that may contribute to enhanced ASD risk.Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder (NDD) with numerous risk genes (De Rubeis et al. 2014; Iossifov et al. 2014; de la Torre-Ubieta et al. 2016; Sullivan and Geschwind 2019). Major functional...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...encodes a neuronal membrane protein that has roles in the plasticity and maintenance of neuronal networks. Duplications in CNTN4 have been observed in cohorts of individuals with autism spectrum disorder (Glessner et al. 2009; Zhang et al. 2020).Finally, we conducted gene set enrichment analysis (GSEA...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...studies of neurological disorders and provide new insights into the hidden regulatory mechanisms influenced by environmental factors in the brain.Understanding how gene regulatory variants function across different cellular and environmental contexts is essential for interpreting genetic associations...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...was associated with behavioral trait data collected from 46,000 dogs. Further, lineage-specific variation was associated with genes in neurodevelopmental coexpression networks, suggesting that the accumulation of many small effect variants drove behavioral diversification between breeds (Dutrow et al. 2022...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
..., Philadelphia, Pennsylvania 19104, USA Corresponding author: ekorb@pennmedicine.upenn.eduAbstractEpigenetic regulation plays a critical role in many neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). In particular, many such disorders are the result of mutations in genes that encode...
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Resource: Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders
- Guangsheng Pei,
- Yin-Ying Wang,
- Lukas M. Simon,
- Yulin Dai,
- Zhongming Zhao,
- and Peilin Jia
Genome Res. January 2021 31: 146-158; Published in Advance December 3, 2020, doi:10.1101/gr.265769.120
...brain regions or developmental stages were found to be involved in different diseases. For a few examples, autism spectrum disorder (ASD)–related and intellectual disability (ID)–related genes tended to be highly expressed during pre- and perinatal stages (Courchesne et al. 2007; D'Haene et al. 2016...
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Method: A general framework for identifying oligogenic combinations of rare variants in complex disorders
- Vijay Kumar Pounraja and
- Santhosh Girirajan
Genome Res. May 2022 32: 904-915; Published in Advance March 17, 2022, doi:10.1101/gr.276348.121
...related to nervous system development, such as NIN, HDC, NGF, and BRD8. Furthermore, 5/52 pairs and 59/230 triplets contained at least one gene associated with autism in the SFARI database—including FGFR1, associated with multiple disorders including Kallmann syndrome (Dodé et al. 2003) and Pfeiffer...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...these discoveries. (AD) Alzheimer disease, (ALS/FTD) amyotrophic lateral sclerosis/frontotemporal dementia, (ASD) autism spectrum disorder, (BAFME) benign adult familial myoclonic epilepsy, (BD) bipolar disorder, (BPES) blepharophimosis, ptosis, and epicanthus inversus syndrome, (CANVAS) cerebellar ataxia...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...motifs. (A) Quantile–quantile plot of gene-level eMotif discoveries across 20 human tissues from GTEx data sets. The expected P-values (x-axis) were drawn from Unif(0,1) and plotted against observed nominal association P-values. (B,C) Replication on the Geuvadis data set. (B) The quantile-quantile plot...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...(circRNAs), a class of long noncoding RNAs, are known to be enriched in mammalian neural tissues. Although a wide range of dysregulation of gene expression in autism spectrum disorder (ASD) have been reported, the role of circRNAs in ASD remains largely unknown. Here, we performed -wide circ...
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