Investigation of Rare Single-Nucleotide <i>PCDH15</i> Variants in Schizophrenia and Autism Spectrum Disorders

<div><p>Both schizophrenia (SCZ) and autism spectrum disorders (ASD) are neuropsychiatric disorders with overlapping genetic etiology. <i>Protocadherin 15</i> (<i>PCDH15</i>), which encodes a member of the cadherin super family that contributes to neural development and function, has been cited as a risk gene for neuropsychiatric disorders. Recently, rare variants of large effect have been paid attention to understand the etiopathology of these complex disorders. Thus, we evaluated the impacts of rare, single-nucleotide variants (SNVs) in <i>PCDH15</i> on SCZ or ASD. First, we conducted coding exon-targeted resequencing of <i>PCDH15</i> with next-generation sequencing technology in 562 Japanese patients (370 SCZ and 192 ASD) and detected 16 heterozygous SNVs. We then performed association analyses on 2,096 cases (1,714 SCZ and 382 ASD) and 1,917 controls with six novel variants of these 16 SNVs. Of these six variants, four (p.R219K, p.T281A, p.D642N, c.3010-1G>C) were ultra-rare variants (minor allele frequency < 0.0005) that may increase disease susceptibility. Finally, no statistically significant association between any of these rare, heterozygous <i>PCDH15</i> point variants and SCZ or ASD was found. Our results suggest that a larger sample size of resequencing subjects is necessary to detect associations between rare <i>PCDH15</i> variants and neuropsychiatric disorders.</p></div

Rare <i>PCDH15</i> SNVs identified in this study.

<p>Rare <i>PCDH15</i> SNVs identified in this study.</p

Multiple alignments of amino acid sequences for PCDH15 eight vertebrate homologs.

<p>Multiple alignments of amino acid sequences for PCDH15 eight vertebrate homologs.</p

Location for each variant of interest.

<p>PCDH15 protein structure is based on NCBI Reference Sequence NP_149045. Each variant was located in the extracellular domain. EC: extracellular cadherin repeat, TM: Transmembrane.</p

Association analysis of novel rare SNVs.

<p>Association analysis of novel rare SNVs.</p

Resequencing and Association Analysis of <i>PTPRA</i>, a Possible Susceptibility Gene for Schizophrenia and Autism Spectrum Disorders

<div><p>Background</p><p>The <i>PTPRA</i> gene, which encodes the protein RPTP-α, is critical to neurodevelopment. Previous linkage studies, genome-wide association studies, controlled expression analyses and animal models support an association with both schizophrenia and autism spectrum disorders, both of which share a substantial portion of genetic risks.</p><p>Methods</p><p>We sequenced the protein-encoding areas of the <i>PTPRA</i> gene for single nucleotide polymorphisms or small insertions/deletions (InDel) in 382 schizophrenia patients. To validate their association with the disorders, rare (minor allele frequency <1%), missense mutations as well as one InDel in the 3′UTR region were then genotyped in another independent sample set comprising 944 schizophrenia patients, 336 autism spectrum disorders patients, and 912 healthy controls.</p><p>Results</p><p>Eight rare mutations, including 3 novel variants, were identified during the mutation-screening phase. In the following association analysis, L59P, one of the two missense mutations, was only observed among patients of schizophrenia. Additionally, a novel duplication in the 3′UTR region, 174620_174623dupTGAT, was predicted to be located within a Musashi Binding Element.</p><p>Major Conclusions</p><p>No evidence was seen for the association of rare, missense mutations in the <i>PTPRA</i> gene with schizophrenia or autism spectrum disorders; however, we did find some rare variants with possibly damaging effects that may increase the susceptibility of carriers to the disorders.</p></div

Novel Rare Missense Variations and Risk of Autism Spectrum Disorder: Whole-Exome Sequencing in Two Families with Affected Siblings and a Two-Stage Follow-Up Study in a Japanese Population

<div><p>Rare inherited variations in multiplex families with autism spectrum disorder (ASD) are suggested to play a major role in the genetic etiology of ASD. To further investigate the role of rare inherited variations, we performed whole-exome sequencing (WES) in two families, each with three affected siblings. We also performed a two-stage follow-up case-control study in a Japanese population. WES of the six affected siblings identified six novel rare missense variations. Among these variations, <i>CLN8</i> R24H was inherited in one family by three affected siblings from an affected father and thus co-segregated with ASD. In the first stage of the follow-up study, we genotyped the six novel rare missense variations identified by WES in 241 patients and 667 controls (the Niigata sample). Only <i>CLN8</i> R24H had higher mutant allele frequencies in patients (1/482) compared with controls (1/1334). In the second stage, this variation was further genotyped, yet was not detected in a sample of 309 patients and 350 controls (the Nagoya sample). In the combined Niigata and Nagoya samples, there was no significant association (odds ratio = 1.8, 95% confidence interval = 0.1–29.6). These results suggest that <i>CLN8</i> R24H plays a role in the genetic etiology of ASD, at least in a subset of ASD patients.</p></div

In silico functional effect prediction for rs61742029 and L59P.

<p>In silico functional effect prediction for rs61742029 and L59P.</p

Targeted sequencing areas of the <i>PTPRA</i> Gene.

<p>Targeted sequencing areas of the <i>PTPRA</i> Gene.</p

Clinical phenotypes of the six individuals heterozygous for <i>CLN8</i> R24H.

<p>IQ, intelligence quotient; PDD-NOS, pervasive developmental disorder not otherwise specified.</p><p>Clinical phenotypes of the six individuals heterozygous for <i>CLN8</i> R24H.</p