No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (CNTNAP2), or in Other Contactin-Associated Proteins or Contactins

Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (CNTNAP2) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in CNTNAP2 and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the CNTN or CNTNAP genes, including CNTNAP2, placing marked limits on the scale of their plausible contribution to risk

Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism

SummaryWe have undertaken a genome-wide analysis of rare copy-number variation (CNV) in 1124 autism spectrum disorder (ASD) families, each comprised of a single proband, unaffected parents, and, in most kindreds, an unaffected sibling. We find significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome, characterized by a highly social personality. We identify rare recurrent de novo CNVs at five additional regions, including 16p13.2 (encompassing genes USP7 and C16orf72) and Cadherin 13, and implement a rigorous approach to evaluating the statistical significance of these observations. Overall, large de novo CNVs, particularly those encompassing multiple genes, confer substantial risks (OR = 5.6; CI = 2.6–12.0, p = 2.4 × 10-7). We estimate there are 130–234 ASD-related CNV regions in the human genome and present compelling evidence, based on cumulative data, for association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin 1

Rare Copy Number Variants in Tourette Syndrome Disrupt Genes in Histaminergic Pathways and Overlap with Autism

Background: Studies of copy number variation (CNV) have characterized loci and molecular pathways in a range of neuropsychiatric conditions. We analyzed rare CNVs in Tourette syndrome (TS) to identify novel risk regions and relevant pathways, to evaluate burden of structural variation in cases versus controls, and to assess overlap of identified variations with those in other neuropsychiatric syndromes. Methods: We conducted a case-control study of 460 individuals with TS, including 148 parent-child trios and 1131 controls. CNV analysis was undertaken using 370 K to 1 M probe arrays, and genotyping data were used to match cases and controls for ancestry. CNVs present in <1% of the population were evaluated. Results: While there was no significant increase in the number of de novo or transmitted rare CNVs in cases versus controls, pathway analysis using multiple algorithms showed enrichment of genes within histamine receptor (subtypes 1 and 2) signaling pathways (p = 5.8 x 10(-4) - 1.6 x 10(-2)), as well as axon guidance, cell adhesion, nervous system development, and synaptic structure and function processes. Genes mapping within rare CNVs in TS showed significant overlap with those previously identified in autism spectrum disorders but not intellectual disability or schizophrenia. Three large, likely pathogenic, de novo events were identified, including one disrupting multiple gamma-aminobutyric acid receptor genes. Conclusions: We identify further evidence supporting recent findings regarding the involvement of histaminergic and gamma-aminobutyric acidergic mechanisms in the etiology of TS and show an overlap of rare CNVs in TS and autism spectrum disorders

No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (<i>CNTNAP2</i>), or in Other Contactin-Associated Proteins or Contactins

<div><p>Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (<i>CNTNAP2</i>) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in <i>CNTNAP2</i> and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the <i>CNTN</i> or <i>CNTNAP</i> genes, including <i>CNTNAP2</i>, placing marked limits on the scale of their plausible contribution to risk.</p></div

Rates of mutation predicted deleterious^* by SIFT-or-PolyPhen2: all genes.

<p>*deleterious mutations were defined as “damaging” in SIFT and/or “possibly damaging” or “probably damaging” in PolyPhen2, as well as all nonsense and splice site mutations which were not evaluated by these programs but were regarded as deleterious intrinsically</p><p>Rates of mutation predicted deleterious^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t003fn001" target="_blank">*</a>} by SIFT-or-PolyPhen2: all genes.</p

Inheritance of mutations predicted deleterious^* by SIFT-or-PolyPhen2.

<p>*deleterious mutations were defined as “damaging” in SIFT and/or “possibly damaging” or “probably damaging” in PolyPhen2, as well as all nonsense and splice site mutations which were not evaluated by these programs but were regarded as deleterious intrinsically. Inheritance was a situation where recurrent mutations were counted more than once, because keeping only one instance of a variant and ignoring the rest would introduce arbitrary parent-of-origin bias</p><p>^†<i>CNTN6</i> and <i>CNTNAP4</i> each had one mutation that was confirmed to be de novo in whole blood</p><p>Inheritance of mutations predicted deleterious^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t004fn001" target="_blank">*</a>} by SIFT-or-PolyPhen2.</p

Overall rare^* variant mutation burden: all genes.

<p>*rare variants were defined as follows: seen only in either cases or controls exclusively, missense, nonsense, splice site, or start or stop codon disruptions with a frequency of less than 2% in this data, and less than 1% in all populations in the Exome Variant Server[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref038" target="_blank">38</a>] and SeattleSNP[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref039" target="_blank">39</a>] databases</p><p>Overall rare^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t001fn001" target="_blank">*</a>} variant mutation burden: all genes.</p

Rates of singleton^* mutations: all genes.

<p>*singleton mutations met the following criteria: seen only once in either cases or controls exclusively, missense, nonsense, splice site, or start or stop codon disruptions with a frequency of less than 2% in this data, and less than 1% in all populations in the Exome Variant Server[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref038" target="_blank">38</a>] and SeattleSNP[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref039" target="_blank">39</a>] databases</p><p>Rates of singleton^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t002fn001" target="_blank">*</a>} mutations: all genes.</p

Location of all mutations of interest, i.e. rare and exclusive to cases or controls.

<p>Mutations were counted if missense, nonsense, splice site, or frameshift in <i>CNTNAP2</i> (in point of fact, all were missense). Variants in red are exclusive to cases; those in green, controls. Those predicted to be deleterious in SIFT are underlined in orange; in PolyPhen2, purple. Domain names and approximate locations from Bakkaloglu et al.,</p