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Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries
Open accessAbstract
Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We sequenced BCAs in patients with autism or related NDDs, revealing disruption of 33 loci in four general categories: (1) genes previously associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, and CDKL5), (2) single-gene contributors to microdeletion syndromes (MBD5, SATB2, EHMT1, and SNURF-SNRPN), (3) novel risk loci (e.g., CHD8, KIRREL3, and ZNF507), and (4) genes associated with later-onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3). We also discovered among neurodevelopmental cases a profoundly increased burden of copy-number variants from these 33 loci and a significant enrichment of polygenic risk alleles from genome-wide association studies of autism and schizophrenia. Our findings suggest a polygenic risk model of autism and reveal that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages.
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“(vii) A list of genes disrupted by breakpoints of balanced chromosomal abnormalities (BCAs) observed in individuals with ASD was obtained from Talkowski et al.56 (32 genes; referred to as ‘T-BCAs’).”
From Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism (2014) · cites this paper as [56]
In the citing paper
“chromodomain helicase DNA-binding protein 8 (CHD8)118, which is the gene most frequently affected by ASD-associated rare de novo variation72,119–121.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [119]
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“Chromodomain helicase DNA-binding protein 8 (CHD8), encoding a chromatin modifying gene on chromosome 14q11.2, is one of the high-penetrance ASD risk genes recently identified by sequencing studies [83, 165, 261, 347].”
From Autism spectrum disorder: neuropathology and animal models (2017) · cites this paper as [347]
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“FOXP1 has also been implicated in several related cognitive phenotypes including language impairment and intellectual disability [68–70].”
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Metadata
- Authors
- Talkowski, M. E., Rosenfeld, J. A., Blumenthal, I., Pillalamarri, V., Chiang, C., Heilbut, A., Ernst, C., Hanscom, C., Rossin, E., Lindgren, A. M., Pereira, S., Ruderfer, D., Kirby, A., Ripke, S., Harris, D. J., Lee, J.-H., Ha, K., Kim, H.-G., Solomon, B. D., Gropman, A. L., Lucente, D., Sims, K., Ohsumi, T. K., Borowsky, M. L., Loranger, S., Quade, B., Lage, K., Miles, J., Wu, B.-L., Shen, Y., Neale, B., Shaffer, L. G., Daly, M. J., Morton, C. C., & Gusella, J. F.
- Affiliations
- Broad Institute (US)
- Massachusetts General Hospital (US)
- Brigham and Women's Hospital (US)
- Boston Children's Hospital (US)
- National Human Genome Research Institute (US)
- Children's National (US)
- Autism Consortium (US)
- University of Missouri Hospital (US)
- Corresponding author
- Gusella, James F.
- ORCID
- Talkowski, Michael E.
- Rosenfeld, Jill A.
- Pillalamarri, Vamsee
- Chiang, Colby
- Heilbut, Adrian
- Ernst, Carl
- Rossin, Elizabeth
- Ruderfer, Douglas
- Ripke, Stephan
- Lee, Ji-Hyun
- Ha, Kyungsoo
- Kim, Hyung-Goo
- Solomon, Benjamin D.
- Gropman, Andrea L.
- Lucente, Diane
- Sims, Katherine
- Ohsumi, Toshiro K.
- Quade, Bradley
- Lage, Kasper
- Miles, Judith
- Shen, Yiping
- Neale, Benjamin
- Shaffer, Lisa G.
- Daly, Mark J.
- Morton, Cynthia C.
- Gusella, James F.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-04
- Volume
- 149
- Issue
- 3
- Pages
- 525-537
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3340505
- OpenAlex
- W2121484182
- Cited by
- 577
- References
- 127
- Citations by year
- 2026: 15 · 2025: 13 · 2024: 18 · 2023: 18 · 2022: 33 · 2021: 42 · 2020: 34 · 2019: 37 · 2018: 42 · 2017: 57 · 2016: 60 · 2015: 45 · 2014: 77 · 2013: 61 · 2012: 22
- FWCI
- 39.51
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- Funders
- Wellcome Trust
- National Institutes of Health
- National Institute of Mental Health (R00MH095867, F32MH087123, MH087123)
- National Institute of General Medical Sciences (T32GM007753, GM061354, P01GM061354)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD065286, R21HD065286)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Keywords
- neurodevelopmental disorders, autism spectrum disorder, copy number variation, polygenic risk, microdeletion syndromes, mental illness, mutational mechanisms, phenotypic variability, CHD8, TCF4, ZNF804A, NR2B subunit, ANK3, PDE10A, SATB2, EHMT1, AUTS2, FOXP1, CDKL5
- MeSH terms
- Autistic Disorder, Child, Child Development Disorders, Pervasive, Chromosome Aberrations, Chromosome Deletion, Humans, Nervous System, Schizophrenia, Signal Transduction, Sequence Analysis, DNA, Chromosome Breakage, Genetic Predisposition to Disease, Genome-Wide Association Study, DNA Copy Number Variations
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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