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

Functional Analysis of Porcine Circovirus 2 VP3 Localization Through Truncation Mutagenesis

The Porcine Circovirus 2 (PCV2) VP3 protein induces apoptosis in transformed cells. This apoptotic activity, like that of other VP3 homologs, may be related to subcellular localization. Previous studies of other VP3 homologs indicate that nuclear localization is important apoptosis induction, however, PCV VP3 localizes to the cytosol. In this study, we isolate the nuclear localization sequence and nuclear export sequence through the use of truncation mutants tagged with green fluorescent protein (GFP). Experiments were also performed to assess the pathway used to export the protein from the nucleus. These results provide further evidence that nuclear localization may not be necessary for induction of apoptosis for PCV2 VP3

Investigation of Carbon Reduction from Overnight Lighting in Non-Domestic Building Stock

The use of electricity, specifically through overnight lighting in non-domestic buildings, is a cause for increasing carbon dioxide emissions. Through our project, we developed and implemented a new methodology for nighttime observations of overnight lighting in non-domestic buildings. Analysis of our data has led to a more robust image of overnight lighting which Carbon Reduction in Buildings can combine with existing data to develop a socio-technical model for estimating carbon dioxide emissions in the United Kingdom

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

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

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

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

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