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Recurrent 16p11.2 microdeletions in autism
Open accessAbstract
Autism is a childhood neurodevelopmental disorder with a strong genetic component, yet the identification of autism susceptibility loci remains elusive. We investigated 180 autism probands and 372 control subjects by array comparative genomic hybridization (aCGH) using a 19K whole-genome tiling path bacterial artificial chromosome microarray to identify submicroscopic chromosomal rearrangements specific to autism. We discovered a recurrent 16p11.2 microdeletion in two probands with autism and none in controls. The deletion spans approximately 500-kb and is flanked by approximately 147-kb segmental duplications (SDs) that are >99% identical, a common characteristic of genomic disorders. We assessed the frequency of this new autism genomic disorder by screening an additional 532 probands and 465 controls by quantitative PCR and identified two more patients but no controls with the microdeletion, indicating a combined frequency of 0.6% (4/712 autism versus 0/837 controls; Fisher exact test P = 0.044). We confirmed all 16p11.2 deletions using fluorescence in situ hybridization, microsatellite analyses and aCGH, and mapped the approximate deletion breakpoints to the edges of the flanking SDs using a custom-designed high-density oligonucleotide microarray. Bioinformatic analysis localized 12 of the 25 genes within the microdeletion to nodes in one interaction network. We performed phenotype analyses and found no striking features that distinguish patients with the 16p11.2 microdeletion as a distinct autism subtype. Our work reports the first frequency, breakpoint, bioinformatic and phenotypic analyses of a de novo 16p11.2 microdeletion that represents one of the most common recurrent genomic disorders associated with autism to date.
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In the citing paper
“Deletions and duplications of 16p11.2 have highly pleiotropic phenotypic effects, with strong links to ASD [8–19], ID [8, 10, 12, 14–16, 19–21], motor/developmental delay [8–10, 12, 13, 15–19, 22], dysmorphic features [8, 12, 16, 17, 22], and epilepsy/seizures [10, 12, 17].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [11]
In the citing paper
“Genetic screenings of ASD patients repeatedly identify 16p11.2 deletions & duplications, placing them among the strongest genetic risk factors for ASD [11, 13, 16, 38].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [11]
In the citing paper
“These include deletions and/or duplications at specific loci, including: 1q21.1, 15q11.2-13.1, 15q13.2-13.3, 16p11.2, 17q12, and 22q11.2”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Kumar et al., 2008
In the citing paper
“recurrent structural variations involving one or a small number of genes, including: Neurexin 1 (NRXN1), Contactin 4 (CNTN4), Neuroligin 1 (NLGN1), Astrotactin 2 (ASTN2), and the contiguous genes Patched Domain Containing 1 (PTCHD1) and DEAD box Protein 53 (DDX53)”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Kumar et al., 2008
In the citing paper
“identical mutations may be associated with highly divergent phenotype”
From Autism risk factors: genes, environment, and gene-environment interactions (2012) · cites this paper as [40]
In the citing paper
“identical CNVs have been associated with autism and schizophrenia, notably 16p11 rearrangements”
From Autism risk factors: genes, environment, and gene-environment interactions (2012) · cites this paper as [40]
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Metadata
- Authors
- Kumar, R. A., KaraMohamed, S., Sudi, J., Conrad, D. F., Brune, C., Badner, J. A., Gilliam, T. C., Nowak, N. J., Cook, E. H., Dobyns, W. B., & Christian, S. L.
- Affiliations
- University of Chicago (US)
- University of Illinois Chicago (US)
- Roswell Park Comprehensive Cancer Center (US)
- Corresponding author
- Christian, S. L.
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-11-07
- Volume
- 17
- Issue
- 4
- Pages
- 628-638
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- OpenAlex
- W2162066558
- Cited by
- 731
- References
- 42
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 16 · 2023: 17 · 2022: 16 · 2021: 37 · 2020: 33 · 2019: 25 · 2018: 30 · 2017: 32 · 2016: 21 · 2015: 41 · 2014: 42 · 2013: 46 · 2012: 57
- FWCI
- 35.84
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Human Molecular Genetics (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Autism Speaks
- National Institutes of Health
- National Institute of Mental Health (MH 64547, 1R01MH64547-01, R01MH064547)
- National Institute of Neurological Disorders and Stroke (R01NS051812, 1R01 NS51812)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- autism spectrum disorder, 16p11.2 microdeletion, genomic disorders, segmental duplication, de novo deletion, chromosomal rearrangements, gene interaction networks, autism subtypes
- MeSH terms
- Autistic Disorder, Base Sequence, Child, Chromosome Deletion, Chromosomes, Human, Pair 16, Female, Gene Frequency, Humans, Male, Pedigree, Phenotype, Case-Control Studies, Polymerase Chain Reaction, In Situ Hybridization, Fluorescence, DNA Primers, Microsatellite Repeats, Chromosome Breakage, Genetic Predisposition to Disease, Chromosomes, Artificial, Bacterial
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