Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

Brian J O'Roak, Pelagia Deriziotis, Choli Lee, Laura Vives, Jerrod J Schwartz, Santhosh Girirajan, Emre Karakoc, Alexandra P Mackenzie, Sarah B Ng, Carl Baker, Mark J Rieder, Deborah A Nickerson, Raphael Bernier, Simon E Fisher, Jay Shendure, Evan E Eichler, Brian J O'Roak, Pelagia Deriziotis, Choli Lee, Laura Vives, Jerrod J Schwartz, Santhosh Girirajan, Emre Karakoc, Alexandra P Mackenzie, Sarah B Ng, Carl Baker, Mark J Rieder, Deborah A Nickerson, Raphael Bernier, Simon E Fisher, Jay Shendure, Evan E Eichler

Abstract

Evidence for the etiology of autism spectrum disorders (ASDs) has consistently pointed to a strong genetic component complicated by substantial locus heterogeneity. We sequenced the exomes of 20 individuals with sporadic ASD (cases) and their parents, reasoning that these families would be enriched for de novo mutations of major effect. We identified 21 de novo mutations, 11 of which were protein altering. Protein-altering mutations were significantly enriched for changes at highly conserved residues. We identified potentially causative de novo events in 4 out of 20 probands, particularly among more severely affected individuals, in FOXP1, GRIN2B, SCN1A and LAMC3. In the FOXP1 mutation carrier, we also observed a rare inherited CNTNAP2 missense variant, and we provide functional support for a multi-hit model for disease risk. Our results show that trio-based exome sequencing is a powerful approach for identifying new candidate genes for ASDs and suggest that de novo mutations may contribute substantially to the genetic etiology of ASDs.

Figures

Figure 1
Figure 1
Evaluation of de novo mutations by simulation, proband severity, and family 12817. a,b We compared the mean Grantham (black x-axis) and GERP scores (black y-axis) of the 10 proband de novo protein-changing substitutions to 20 HapMap control samples by building a distribution of the mean values of 10 randomly selected common or private variants over 1000 trials. Splice-site and nonsense events were given a maximum Grantham score (215) and indels were not included in the simulation. Histograms show the relative frequency (blue axes) of each distribution. Points show the proband variants, with variants from the same individual highlighted (blue=13708.p1, red=12499.p1). Proband mean values, GERP: 4.349 and Grantham: 104.3. *FOXP1 not included in proband mean values. a, Control common variants (GERP: p<0.001, Grantham: p=0.015). b, Control rare variants (GERP: p=0.026, Grantham: p=0.098). c,d We evaluated the disease severity of the mutation carriers 12817.p1-FOXP1 (brown), 12681.p1-GRIN2B (green), 12499-SCN1A (blue) and 11666.p1-LAMC3 (red). c, Box and whisker plot of Full Scale Intelligence Quotient (FSIQ) values. d, Box and whisker plot of Calibrated Severity Scores (CSS) based on the Autism Diagnostic Observation Schedule (ADOS). Data were available for 19/20 probands; CSS were estimated for two probands based on ADOS module 4 data. e, Pedigree for 12817 showing chromatogram traces surrounding FOXP1 (top) and CNTNAP2 (bottom) mutation events. Proband carries a de novo single-base (+A relative to mRNA) frameshifting mutation p.A339SfsX4 in FOXP1 and an inherited missense variant p.H275A in CNTNAP2.

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