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Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
..., UTY (also known as KDM6AL or KDM6C), ZFY, and DDX3Y because the non-PAR X (NPX) homologs NLGN4X, KDM6A (also known as UTX), ZFX, and DDX3X, expressed from both X Chromosomes in KS males (Tukiainen et al. 2017), have been previously associated with autism spectrum disorder (ASD), intellectual deficits...
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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: Defining cell-type specificity at the transcriptional level in human disease
- Wenjun Ju,
- Casey S. Greene,
- Felix Eichinger,
- Viji Nair,
- Jeffrey B. Hodgin,
- Markus Bitzer,
- Young-suk Lee,
- Qian Zhu,
- Masami Kehata,
- Min Li,
- Song Jiang,
- Maria Pia Rastaldi,
- Clemens D. Cohen,
- Olga G. Troyanskaya,
- and Matthias Kretzler
Genome Res. November 2013 23: 1862-1873; Published in Advance August 15, 2013, doi:10.1101/gr.155697.113
...method significantly outperforms experimental strategies using fluorescenceactivated cell sorting (FACS) separated GFP-tagged murine cells for identification of cell-lineage–enriched transcripts. We further demonstrate that expression of the nanodissection predicted podocyte-specific genes significantly...
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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
...of the molecular basis for ASD and related NDDs.ResultsDepletion of ASD-linked transcriptional regulators affects gene expressionHere, we sought to define shared gene expression signatures among multiple ASD-linked transcriptional regulators, including ASH1L, CHD8, DNMT3A, KDM6B, KMT2C, MBD5, MED13L, SETD5...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...and the other daughter exhibited only milder phenotypes, such as pulmonary stenosis and atrial septal defects (ASDs) (Kodo et al. 2009). TA pathology is consistent with malfunction of normal neural crest cell migration during formation of the outflow tract (Neeb et al. 2013). When Gata6 deletion was tested...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
..., such as autism spectrum disorder (ASD) and congenital heart disorders (CHDs), in which de novo mutations were confirmed to play a pivotal causal role. However, the complexity and scale of data generated by sequencing large family collections surpass that of traditional genotyping studies. As a result...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...-cell transcriptional profiling in differentiating human neurons to rapidly assay the functions of multiple genes in a disease-relevant context, assess potentially convergent mechanisms, and prioritize genes for specific functional assays. For a set of 13 autism spectrum disorder (ASD)–associated genes, we show...
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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
...showed social impairment and reduced vocalizations, representing a valid ASD mouse model (Lee et al. 2015). As a regulator of multiple ASD-associated genes, the circARID1A-miR-204-3p axis may be useful circuitry/molecular mechanism for further developing potential therapeutic strategies to address ASD...
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Research: Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network
- Nicolas Chassaing,
- Erica E. Davis,
- Kelly L. McKnight,
- Adrienne R. Niederriter,
- Alexandre Causse,
- Véronique David,
- Annaïck Desmaison,
- Sophie Lamarre,
- Catherine Vincent-Delorme,
- Laurent Pasquier,
- Christine Coubes,
- Didier Lacombe,
- Massimiliano Rossi,
- Jean-Louis Dufier,
- Helene Dollfus,
- Josseline Kaplan,
- Nicholas Katsanis,
- Heather C. Etchevers,
- Stanislas Faguer,
- and Patrick Calvas
Genome Res. April 2016 26: 474-485; Published in Advance February 18, 2016, doi:10.1101/gr.196048.115
..., eithermonogenicorchromosomal, is identified in∼20%–40% of individuals who undergo genetic testing (Slavotinek 2011; Chassaing et al. 2014). ASD disorders encompass a wide variety of developmental conditions affecting the cornea, iris, and lens including corneal opacity, posterior embryotoxon, iris hypoplasia, corectopia...

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