title: Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder.
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.
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA.|Graduate Program in Population Biology, Ecology and Evolution, Emory University, 1510 Clifton Road, Atlanta, 30322, GA, USA.|Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195, WA, USA.
authors.forename: Karyn Meltz
authors.initials: KM
authors.lastname: Steinberg
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA.
authors.forename: Dhanya
authors.initials: D
authors.lastname: Ramachandran
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA.
authors.forename: Viren C
authors.initials: VC
authors.lastname: Patel
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA.
authors.forename: Amol C
authors.initials: AC
authors.lastname: Shetty
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Cutler
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building, Suite 301, Atlanta, 30322, GA, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Zwick