Recurrent 16p11.2 microdeletions in autism

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.

doi:10.1093/hmg/ddm376

Cited by 731Genomic variations and chromosomal abnormalitiesAutism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Recurrent 16p11.2 microdeletions in autism

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Kumar, R. A., KaraMohamed, S., Sudi, J., Conrad, D. F., Brune, C., Badner, J. A., Gilliam, T. C., Nowak, N. J. +3 more·2007·Human Molecular Genetics

DOI 10.1093/hmg/ddm376

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Abstract

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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Deletions and duplications of 16p11.2 have highly pleiotropic phenotypic effects, with strong links to ASD, ID, motor/developmental delay, dysmorphic features, and epilepsy/seizures.
“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]
Genetic screenings of ASD patients repeatedly identify 16p11.2 deletions and duplications, placing them among the strongest genetic risk factors for ASD.
“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]
Deletions and/or duplications at specific loci including 1q21.1, 15q11.2-13.1, 15q13.2-13.3, 16p11.2, 17q12, and 22q11.2 show evidence for association with ASD.
“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
Recurrent structural variations involving NRXN1, CNTN4, NLGN1, ASTN2, PTCHD1, and DDX53 show evidence for association with ASD.
“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
Identical mutations may be associated with highly divergent phenotype.
“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]

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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.
ORCID: Conrad, D. F.
Cook, E. H.
Dobyns, W. B.
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
DOI: 10.1093/hmg/ddm376
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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Recurrent 16p11.2 microdeletions in autism

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