Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder

• Type of Material: Article
• Authors: Karyn Meltz Steinberg, University of Washington; Dhanya Ramachandran, Emory University; Viren C. Patel, Emory University; Amol C. Shetty, Emory University; David J Cutler, Emory University; Michael Zwick, Emory University
• Language: English
• Date: 2012-09-28
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2012 Steinberg et al.; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.molecularautism.com/content/3/1/8
• Title of Journal or Parent Work: Molecular Autism
• ISSN: 2040-2392
• Volume: 3
• Issue: 8
• Start Page: 1
• End Page: 12
• Grant/Funding Information: This work was supported by the NIH/NIMH and Gift Fund (grant number: MH076439, MEZ); the Simons Foundation Autism Research Initiative (MEZ); and the Training Program in Human Disease Genetics (grant number: 1T32MH087977, DR). We gratefully acknowledge the resources provided by the AGRE Consortium and the participating AGRE families. We thank members of the Cutler and Zwick labs for comments on the manuscript, Jennifer Mulle for discussion, Cheryl T Strauss for editing, and the Emory-Georgia Research Alliance Genome Center (EGC), supported in part by PHS Grant UL1 RR025008 from the Clinical and Translational Science Award program, National Institutes of Health, National Center for Research Resources, for performing the Illumina sequencing runs. The ELLIPSE Emory High Performance Computing Cluster (EHPCC) was used for data analysis and the Emory Custom Cloning Core Facility (CCCF) generated constructs to our specifications for the expression analyses.
• Research Categories: Biology, Genetics; Biology, Ecology

Abstract

Background Autism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype. Methods We surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility. Results We found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3’ UTR variants did not show statistically significant effects on the expression of NLGN3 and NLGN4X. In addition, we identified two NLGN3 intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation. Conclusions These data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects.