Recent research has uncovered an important role for de novo variation in neurodevelopmental disorders. Using aggregated data from 9,246 families with autism spectrum disorder, intellectual disability, or developmental delay, we found that ∼1/3 of de novo variants are independently present as standing variation in the Exome Aggregation Consortium's cohort of 60,706 adults, and these de novo variants do not contribute to neurodevelopmental risk. We further used a loss-of-function (LoF)-intolerance metric, pLI, to identify a subset of LoF-intolerant genes containing the observed signal of associated de novo protein-truncating variants (PTVs) in neurodevelopmental disorders. LoF-intolerant genes also carry a modest excess of inherited PTVs, although the strongest de novo–affected genes contribute little to this excess, thus suggesting that the excess of inherited risk resides in lower-penetrant genes. These findings illustrate the importance of population-based reference cohorts for the interpretation of candidate pathogenic variants, even for analyses of complex diseases and de novo variation.
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Autism and Developmental Disabilities Monitoring Network Surveillance Year 2010 Principal Investigators. Prevalence of autism spectrum disorder among children aged 8 years-autism and developmental disabilities monitoring network, 11 sites, United States, 2010. MMWR Surveill. Summ. 63, 1–21 (2014).
Lee, S.H. et al. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat. Genet. 45, 984–994 (2013).
Gaugler, T. et al. Most genetic risk for autism resides with common variation. Nat. Genet. 46, 881–885 (2014).
Klei, L. et al. Common genetic variants, acting additively, are a major source of risk for autism. Mol. Autism 3, 9 (2012).
De Rubeis, S. et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515, 209–215 (2014).
Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014).
Iossifov, I. et al. De novo gene disruptions in children on the autistic spectrum. Neuron 74, 285–299 (2012).
Neale, B.M. et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485, 242–245 (2012).
O'Roak, B.J. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246–250 (2012).
Sanders, S.J. et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237–241 (2012).
Reichenberg, A. et al. Discontinuity in the genetic and environmental causes of the intellectual disability spectrum. Proc. Natl. Acad. Sci. USA 113, 1098–1103 (2016).
de Ligt, J. et al. Diagnostic exome sequencing in persons with severe intellectual disability. N. Engl. J. Med. 367, 1921–1929 (2012).
Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature 519, 223–228 (2015).
Rauch, A. et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380, 1674–1682 (2012).
Robinson, E.B. et al. Autism spectrum disorder severity reflects the average contribution of de novo and familial influences. Proc. Natl. Acad. Sci. USA 111, 15161–15165 (2014).
Samocha, K.E. et al. A framework for the interpretation of de novo mutation in human disease. Nat. Genet. 46, 944–950 (2014).
Robinson, E.B. et al. Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population. Nat. Genet. 48, 552–555 (2016).
Bellus, G.A. et al. Achondroplasia is defined by recurrent G380R mutations of FGFR3. Am. J. Hum. Genet. 56, 368–373 (1995).
Kimura, M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61, 893–903 (1969).
Coulondre, C., Miller, J.H., Farabaugh, P.J. & Gilbert, W. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274, 775–780 (1978).
Haukka, J., Suvisaari, J. & Lönnqvist, J. Fertility of patients with schizophrenia, their siblings, and the general population: a cohort study from 1950 to 1959 in Finland. Am. J. Psychiatry 160, 460–463 (2003).
Laursen, T.M. & Munk-Olsen, T. Reproductive patterns in psychotic patients. Schizophr. Res. 121, 234–240 (2010).
Power, R.A. et al. Fecundity of patients with schizophrenia, autism, bipolar disorder, depression, anorexia nervosa, or substance abuse vs their unaffected siblings. JAMA Psychiatry 70, 22–30 (2013).
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
Fromer, M. et al. De novo mutations in schizophrenia implicate synaptic networks. Nature 506, 179–184 (2014).
Homsy, J. et al. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science 350, 1262–1266 (2015).
Zaidi, S. et al. De novo mutations in histone-modifying genes in congenital heart disease. Nature 498, 220–223 (2013).
Przyborowski, J. & Wilenski, H. Homogeneity of results in testing samples from Poisson series: with an application to testing clover seed for dodder. Biometrika 31, 313–323 (1940).
Picoraro, J.A. & Chung, W.K. Delineation of new disorders and phenotypic expansion of known disorders through whole exome sequencing. Curr. Genet. Med. Rep. 3, 209–218 (2015).
Krumm, N. et al. Excess of rare, inherited truncating mutations in autism. Nat. Genet. 47, 582–588 (2015).
Purcell, S.M. et al. A polygenic burden of rare disruptive mutations in schizophrenia. Nature 506, 185–190 (2014).
Singh, T. et al. Rare schizophrenia risk variants are enriched in genes shared with neurodevelopmental disorders. Preprint at http://biorxiv.org/content/early/2016/08/16/069344 (2016).
Akawi, N. et al. Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families. Nat. Genet. 47, 1363–1369 (2015).
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17, 405–424 (2015).
Tan, A., Abecasis, G.R. & Kang, H.M. Unified representation of genetic variants. Bioinformatics 31, 2202–2204 (2015).
McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069–2070 (2010).
Buxbaum, J.D. et al. The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders. Neuron 76, 1052–1056 (2012).
Fischbach, G.D. & Lord, C. The Simons Simplex Collection: a resource for identification of autism genetic risk factors. Neuron 68, 192–195 (2010).
Ben-David, E. & Shifman, S. Combined analysis of exome sequencing points toward a major role for transcription regulation during brain development in autism. Mol. Psychiatry 18, 1054–1056 (2013).
Takata, A., Ionita-Laza, I., Gogos, J.A., Xu, B. & Karayiorgou, M. De novo synonymous mutations in regulatory elements contribute to the genetic etiology of autism and schizophrenia. Neuron 89, 940–947 (2016).
Lelieveld, S.H. et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat. Neurosci. 19, 1194–1196 (2016).
Sanders, S.J. et al. Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 87, 1215–1233 (2015).
We thank all of the members of the ATGU and the laboratory of D.P.W. for assistance in this endeavor. We thank the families who took part in the Simons Simplex Collection study and the Simons Variation in Individuals Project, as well as the clinicians who collected data at each of the study sites. The authors would like to thank the Exome Aggregation Consortium and the groups that provided exome variant data for comparison. A full list of contributing groups can be found on the ExAC website (see URLs). We also greatly thank A. Byrnes, R. Fine, D. Fronk, A. Martin, C. Nichols, N. Radd, K. Satterstrom, and E. Wigdor for their insightful contributions. Finally, we acknowledge G.A. Barnard for inspiring us to write in a more conversational tone similar to that in his seminal 1947 paper (Biometrika 34, 123–138, 1947). This work was supported by NIH grants U01MH100233, U01MH100209, U01MH100229, and U01MH100239 to the Autism Sequencing Consortium (ASC), and R56 MH097849 and R01 MH097849 to the Population-based Autism Genetics and Environment Study (PAGES). M.J.D., J.A.K., and K.E.S. were supported by grants from the Simons Foundation Autism Research Initiative (SFARI 342292 and a subaward from the Simons Center for the Social Brain at MIT). M.L. and D.G.M.'s work on the ExAC project was funded by U54DK105566 and R01 GM104371 from the National Institutes of Health. K.S. was funded by T32 HG002295/HG/NHGRI. E.B.R. was funded by National Institutes of Mental Health Grant 1K01MH099286 and NARSAD Young Investigator grant 22379.
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 Recurrence rate is a function of allele frequency and reference-population size.
Expected number of discovered class 2 de novo variants by size of the reference dataset, partitioned based on the number of copies of the variant currently present in ExAC. The number of de novo variants found in the standing population is a function of the sample size of the reference dataset and the current estimated allele count (AC).
The proportion of de novo variants across each cohort split between class 1 (left) and class 2 (right) when using the non-psychiatric version of ExAC (See Figure 2A for the results using the full version of ExAC). Removing the 15,330 exomes from the psychiatric cohorts did not change the enrichment of CpG variants among class 2nonpsych de novo variants (P < 10-20). Error bars represent 95% confidence intervals. ID/DD, intellectual disability / developmental delay; ASD, autism spectrum disorder.
Supplementary Figure 3 Partitioning the rate of de novo variants per exome on the basis of class 1, class 2, and pLI, by using the nonpsychiatric version of ExAC.
Within each grouping, the rate is shown for ID/DD (left), ASD (middle), and unaffected ASD siblings (right) with the number of individuals labeled in the legend. (a) Rate of de novo synonymous variants per exome partitioned into class 2nonpsych (middle) and class 1nonpsych (right). No significant difference was observed for any grouping of de novo synonymous variants. (b) Rate of de novo PTVs per exome partitioned into class 2nonpsych (middle) and class 1nonpsych (right). Only class 1nonpsych de novo PTVs in ID/DD and ASD show association when compared to unaffected ASD siblings. (c) Rate of de novo PTVs partitioned into class 1nonpsych de novo PTVs in pLI ≥0.9 genes (right), and the class 1nonpsych de novo PTVs in pLI <0.9 genes (middle). For all such analyses, the rate ratio and significance were calculated by comparing the rate for ID/DD and ASD to the rate in unaffected ASD siblings using a two-sided Poisson exact test for synonymous variants and one-sided for the remainder (Supplemental Note). Error bars represent 95% confidence intervals throughout (a) – (c). ID/DD, intellectual disability / developmental delay; ASD, autism spectrum disorder; PTV, protein truncating variant; pLI, probability of loss-of-function intolerance; NS, not significant.
Singleton synonymous variants discovered in the joint called set was ordered by VQSLOD in descending order (i.e. higher confident variants first) and then binned into percentiles. The red line marks the GATK-defined VQSR cut off (-1.49) and the blue line marks where VQSR was moved (-1.724) to achieve 1:1 transmission rate of synonymous variants.
Supplementary Figures 1–4, Supplementary Tables 3–5, 7–21, 23–25, 27–30 and 32–34, and Supplementary Note (PDF 1747 kb)
ASD and unaffected ASD sibling de novo variants. All 5,856 de novo variants in 3,982 individuals with ASD and 2,545 de novo variants in 2,078 unaffected siblings. Each row in the file represents one de novo variant in an individual. Descriptions of the column names are in the second tab. (XLSX 1915 kb)
ID/DD de novo variants. All 1,692 de novo variants in 1,284 individuals with ID/DD14-17. As with Supplementary Table 1, each row in the file represents one de novo variant in an individual. As noted in the DDD study, some de novo variants were observed in multiple unrelated individuals14. As with Supplementary Table 1, column name descriptions are in the second tab. (XLSX 398 kb)
Congenital heart disease and schizophrenia de novo variants. All 1,281 de novo variants in 362 individuals with congenital heart disease, and 640 de novo variants in 617 individuals with schizophrenia. As with Supplementary Tables 1 and 2, each row in the file represents one de novo variant in an individual. Likewise, descriptions of the column names are in the second tab. (XLSX 478 kb)
Gene summary statistics. Counts of class 1 de novo PTVs, transmitted and untransmitted singleton PTVs absent from ExAC, and singleton PTVs absent from ExAC from 404 cases and 3,654 controls grouped by gene. In total, there are 9,637 genes with at least one PTV from these categories. Descriptions of the column names are in the second tab. (XLSX 544 kb)
Transmitted and untransmitted PTVs from 4,319 ASD trios. All singleton, LofTee high-confidence PTVs absent from ExAC that were transmitted or untransmitted in 4,319 trios with ASD. Descriptions of the columns are found in the second tab. (XLSX 144 kb)
PTVs from Swedish case-control study. All singleton, LofTee high-confidence PTVs absent from ExAC that were present in 404 cases and 3,654 controls from Sweden. Descriptions of the columns are found in the second tab. (XLSX 88 kb)
About this article
Cite this article
Kosmicki, J., Samocha, K., Howrigan, D. et al. Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples. Nat Genet 49, 504–510 (2017). https://doi.org/10.1038/ng.3789
Operative list of genes associated with autism and neurodevelopmental disorders based on database review
Molecular and Cellular Neuroscience (2021)
An X‐linked syndrome with severe neurodevelopmental delay, hydrocephalus, and early lethality caused by a missense variation in the OTUD5 gene
Clinical Genetics (2021)
De novo loss-of-function variants in X-linked MED12 are associated with Hardikar syndrome in females
Genetics in Medicine (2021)
Human Genetics and Genomics Advances (2021)
Роль естественных процессов старения в возникновении и патогенезе болезней, связанных с аномальным накоплением белковых агрегатов