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Sporadic Autism Exomes Reveal a Highly Interconnected Protein Network of De Novo Mutations

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Sporadic Autism Exomes Reveal a Highly Interconnected Protein Network of De Novo Mutations LETTER doi:10.1038/nature10989 Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations Brian J. O’Roak1,LauraVives1, Santhosh Girirajan1,EmreKarakoc1, Niklas Krumm1,BradleyP.Coe1,RoieLevy1,ArthurKo1,CholiLee1, Joshua D. Smith1, Emily H. Turner1, Ian B. Stanaway1, Benjamin Vernot1, Maika Malig1, Carl Baker1, Beau Reilly2,JoshuaM.Akey1, Elhanan Borenstein1,3,4,MarkJ.Rieder1, Deborah A. Nickerson1, Raphael Bernier2, Jay Shendure1 &EvanE.Eichler1,5 It is well established that autism spectrum disorders (ASD) have a per generation, in close agreement with our previous observations4, strong genetic component; however, for at least 70% of cases, the yet in general, higher than previous studies, indicating increased underlying genetic cause is unknown1. Under the hypothesis that sensitivity (Supplementary Table 2 and Supplementary Table 4)7. de novo mutations underlie a substantial fraction of the risk for We also observed complex classes of de novo mutation including: five developing ASD in families with no previous history of ASD or cases of multiple mutations in close proximity; two events consistent related phenotypes—so-called sporadic or simplex families2,3—we with paternal germline mosaicism (that is, where both siblings con- sequenced all coding regions of the genome (the exome) for tained a de novo event observed in neither parent); and nine events parent–child trios exhibiting sporadic ASD, including 189 new showing a weak minor allele profile consistent with somatic mosaicism trios and 20 that were previously reported4. Additionally, we also (Supplementary Table 3 and Supplementary Figs 2 and 3). sequenced the exomes of 50 unaffected siblings corresponding to Of the severe de novo events, 28% (33 of 120) are predicted to these new (n 5 31) and previously reported trios (n 5 19)4, for a truncate the protein. The distribution of synonymous, missense and total of 677 individual exomes from 209 families. Here we show nonsense changes corresponds well with a random mutation model7 that de novo point mutations are overwhelmingly paternal in (Supplementary Fig. 4 and Supplementary Table 2). However, the origin (4:1 bias) and positively correlated with paternal age, con- difference in nonsense rates between de novo and rare singleton events sistent with the modest increased risk for children of older fathers (not present in 1,779 other exomes) is striking (4:1) and suggests to develop ASD5. Moreover, 39% (49 of 126) of the most severe or strong selection against new nonsense events (Fisher’s exact test, disruptive de novo mutations map to a highly interconnected P , 0.0001). In contrast with a recent report8, we find no significant b-catenin/chromatin remodelling protein network ranked signifi- difference in mutation rate between affected and unaffected indivi- cantly for autism candidate genes. In proband exomes, recurrent duals; however, we do observe a trend towards increased non- protein-altering mutations were observed in two genes: CHD8 and synonymous rates in probands, consistent with the findings of ref. 9 NTNG1. Mutation screening of six candidate genes in 1,703 ASD (Supplementary Tables 1 and 2). probands identified additional de novo, protein-altering muta- Given the association of ASD with increased paternal age5 and our tions in GRIN2B, LAMC3 and SCN1A. Combined with copy previous observations4, we used molecular cloning, read-pair informa- number variant (CNV) data, these results indicate extreme locus tion, and obligate carrier status to identify informative markers linked heterogeneity but also provide a target for future discovery, to 51 de novo events and observed a marked paternal bias (41:10; diagnostics and therapeutics. binomial P , 1.4 3 1025; Fig. 1a and Supplementary Tables 3 and 5). We selected 189 autism trios from the Simons Simplex Collection This provides strong direct evidence that the germline mutation rate in (SSC)6, which included males significantly impaired with autism and protein-coding regions is, on average, substantially higher in males. A intellectual disability (n 5 47), a female sample set (n 5 56) of which similar finding was recently reported for de novo CNVs10. In addition, 26 were cognitively impaired, and samples chosen at random from the we observe that the number of de novo events is positively correlated remaining males in the collection (n 5 86) (Supplementary Table 1 with increasing paternal age (Spearman’s rank correlation 5 0.19; and Supplementary Fig. 1). In general, we excluded samples known to P , 0.008; Fig. 1b). Together, these observations are consistent with carry large de novo CNVs2. Exome sequencing was performed as the hypothesis that the modest increased risk for children of older described previously4, but with an expanded target definition (see fathers to develop ASD5 is the result of an increased mutation rate. Methods). We achieved sufficient coverage for both parents and child Using sequence read-depth methods in 122 of the 189 families, we to call genotypes for, on average, 29.5 megabases (Mb) of haploid scanned ASD probands for either de novo CNVs or rare (,1% of exome coding sequence (Supplementary Table 1). In addition, we controls), inherited CNVs. Individual events were validated by either performed copy number analysis on 122 of these families, using a array CGH or genotyping array (see Methods). We identified 76 events combination of the exome data, array comparative genomic hybrid- in 53 individuals, including six de novo (median size 467 kilobases ization (CGH), and genotyping arrays, thereby providing a more com- (kb)) and 70 inherited (median size 155 kb) CNVs (Supplementary prehensive view of rare variation. Table 6). These include disruptions of EHMT1 (Kleefstra’s syndrome, In the 189 new probands, we validated 248 de novo events, 225 single Online Mendelian Inheritance in Man (OMIM) accession 610253), nucleotide variants (SNVs), 17 small insertions/deletions (indels), and CNTNAP4 (reported in children with developmental delay and aut- six CNVs (Supplementary Table 2). These included 181 non- ism11) and the 16p11.2 duplication (OMIM 611913) associated with synonymous changes, of which 120 were classified as severe based developmental delay, bipolar disorder and schizophrenia. on sequence conservation and/or biochemical properties (Methods We performed a multivariate analysis on non-verbal IQ (NVIQ), and Supplementary Table 3). The observed point mutation rate in verbal IQ (VIQ) and the load of ‘extreme’ de novo mutations—where coding sequence was ,1.3 events per trio or 2.17 3 1028 per base extreme is defined as point mutations that truncate proteins, intersect 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA. 2Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA. 3Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA. 4Santa Fe Institute, Santa Fe, New Mexico 87501, USA. 5Howard Hughes Medical Institute, Seattle, Washington 98195, USA. 246 | NATURE | VOL 485 | 10 MAY 2012 ©2012 Macmillan Publishers Limited. All rights reserved LETTER RESEARCH a b c 140 120 A A T T 80 100 T T 41 10 Non-verbal IQ A G paternal maternal 40 60 Paternal age (months) A G events events 250 350 450 550 T 012 3+ 20 012+ Number of de novo coding mutations Number of extreme de novo mutations d Chr18: 40000000 40500000 41000000 41500000 Cases Controls 18q12.3 SETBP1 SLC14A2 EPG5 SLC14A1 SIGLEC15 Figure 1 | De novo mutation events in autism spectrum disorder. mutation events (0, n 5 138; 1, n 5 41; 21, n 5 10), both with and without a, Haplotype phasing using informative markers shows a strong parent-of- CNVs (Supplementary Discussion). d, Browser images showing CNVs origin bias with 41 of 51 de novo events occurring on the paternally inherited identified in the del(18)(q12.2q21.1) syndrome region. The truncating point haplotype. Arrows represent sequence reads from paternal (blue) or maternal mutation in SETBP1 occurs within the critical region, identifying the likely (red) haplotypes. b, c, Box and whisker plots for 189 SSC probands. b,The causative locus. Each red (deletion) and green (duplication) line represents an paternal estimated age at conception versus the number of observed de novo identified CNV in cases (solid lines) versus controls (dashed lines), with point mutations (0, n 5 53; 1, n 5 65; 2, n 5 44; 31, n 5 27). c, Decreased non- arrowheads showing point mutation. verbal IQ is significantly associated with an increasing number of extreme Mendelian or ASD loci (n 5 57), or de novo CNVs that intersect genes The de novo mutations included truncating events in syndromic (n 5 5) (Fig. 1c and Supplementary Discussion). NVIQ, but not VIQ, intellectual disability genes (MBD5 (mental retardation, autosomal decreased significantly (P , 0.01) with increased number of events. dominant 1, OMIM 156200), RPS6KA3 (Coffin–Lowry syndrome, Covariant analysis of the samples with CNV data showed that this OMIM 303600) and DYRK1A (the Down’s syndrome candidate finding was strengthened, but not exclusively driven, by the presence gene, OMIM 600855)), and missense variants in loci associated with of either de novo or rare CNVs (Supplementary Fig. 5). syndromic ASD, including CHD7, PTEN (macrocephaly/autism Among the de novo events, we identified 62 top ASD risk con- syndrome, OMIM 605309) and TSC2 (tuberous sclerosis complex, tributing mutations based on the deleteriousness of the
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