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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The T-BCAs list comprises 32 genes disrupted by breakpoints of balanced chromosomal abnormalities observed in individuals with ASD, obtained from Talkowski et al.
“(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]
CHD8 is the gene most frequently affected by ASD-associated rare de novo variation.
“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]
CHD8 is one of the high-penetrance ASD risk genes recently identified by sequencing studies.
“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]
FOXP1 has also been implicated in several related cognitive phenotypes including language impairment and intellectual disability.
“FOXP1 has also been implicated in several related cognitive phenotypes including language impairment and intellectual disability [68–70].”
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“36 compiled a list of genes disrupted by de novo nonsense, frameshift, or splice-site point mutations in autism probands that were obtained from Iossifov et al. 5 (59 genes; referred to as “ I-exomes ”) and three other recent studies by Sanders et al. 8 , O’Roak et al. 7 , and Neale et al. 23 (65 genes combined from a…”
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- 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
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