De novo mutations and Autism redux

In articles published online by Nature, Professors Stephan Sanders and colleagues and Brian J. O’Roak his colleagues reported additional evidence that rare mutations contribute to risk for Autism. By analyzing genetic material from parents who had children with Autism, the researchers were able to focus on differences in specific genes, what changed from one generation to the next. One team, working in the research lab of Professor Matthew State at Yale University, found strikingly unusual matches for a specific mutation at SCN2A. The other team, under the direction of Professor Evan Eichler at the University of Washington, found several candidates (including SCN1A) and a strong (4 to 1) relationship for older fathers.

These findings do not explain the cause of Autism completely. Not all cases have these specific mutations. But the results add to the mounting body of evidence about de novo mutations as a general area of research. To see earlier posts on EBD Blog on this topic, simply enter “de novo” into the search box at the top right.

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

Stephan J. Sanders, Michael T. Murtha, Abha R. Gupta, John D. Murdoch, Melanie J. Raubeson, A. Jeremy Willsey, A. Gulhan Ercan-Sencicek, Nicholas M. DiLullo, Neelroop N. Parikshak, Jason L. Stein, Michael F. Walker, Gordon T. Ober, Nicole A. Teran, Youeun Song, Paul El-Fishawy, Ryan C. Murtha, Murim Choi, John D. Overton, Robert D. Bjornson, Nicholas J. Carriero, Kyle A. Meyer, Kaya Bilguvar, Shrikant M. Mane, Nenad Šestan, Richard P. Lifton, Murat Günel, Kathryn Roeder, Daniel H. Geschwind, Bernie Devlin & Matthew W. State
Nature (2012) doi:10.1038/nature10945
Received 09 September 2011 Accepted 14 February 2012 Published online 04 April 2012

Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, ? subunit), a result that is highly unlikely by chance.

Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J.,… State, M. W. (2012). De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature, 484. Advance online publication doi:10.1038/nature10945.

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Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure & Evan E. Eichler
Nature (2012) doi:10.1038/nature10989
Received 08 September 2011 Accepted 23 February 2012 Published online 04 April 2012

It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown1. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes—so-called sporadic or simplex families,—we sequenced all coding regions of the genome (the exome) for parent–child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD5. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected ?-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.

O’Roak, B. J., Vives, L., Girigajan, S., Karakoc, E., Krumm, N., Coe, B. P.,…Eicher, E. E. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature, 484. Advance online publication doi:10.1038/nature10989

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