De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes

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Megalencephaly-capillary malformation (MCAP) and megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndromes are sporadic overgrowth disorders associated with markedly enlarged brain size and other recognizable features1,2,3,4,5. We performed exome sequencing in 3 families with MCAP or MPPH, and our initial observations were confirmed in exomes from 7 individuals with MCAP and 174 control individuals, as well as in 40 additional subjects with megalencephaly, using a combination of Sanger sequencing, restriction enzyme assays and targeted deep sequencing. We identified de novo germline or postzygotic mutations in three core components of the phosphatidylinositol 3-kinase (PI3K)-AKT pathway. These include 2 mutations in AKT3, 1 recurrent mutation in PIK3R2 in 11 unrelated families with MPPH and 15 mostly postzygotic mutations in PIK3CA in 23 individuals with MCAP and 1 with MPPH. Our data highlight the central role of PI3K-AKT signaling in vascular, limb and brain development and emphasize the power of massively parallel sequencing in a challenging context of phenotypic and genetic heterogeneity combined with postzygotic mosaicism.

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Figure 1: Craniofacial appearance and magnetic resonance imaging (MRI) of the three index subjects.
Figure 2: PIP3 levels in lymphoblastoid cell lines derived from an unaffected control (WT), an individual with Cowden disease (GM10080) and four individuals with megalencephaly.
Figure 3: Distribution of alterations in AKT3, PIK3R2 and PIK3CA.

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We wish to thank all of the children and families in this study, their referring physicians and the M-CM Network (see URLs) for their help with this project over many years. We thank the members of the Northwest Genomics Center and the McGill University and Genome Quebec Innovation Centre for their excellent technical assistance. We also thank the Finding of Rare Disease Genes (FORGE) Canada Consortium, especially J. Marcadier for her contribution to the infrastructure.

This work was funded by the US National Institutes of Health under National Institute of Neurological Disorders and Stroke (NINDS) grant NS058721 (to W.B.D.), National Institute of Child Health & Human Development (NICHD) grant HD36657 and National Institute of General Medical Sciences (NIGMS) grant 5-T32-GM08243 (to J.M.G.), the Government of Canada (to FORGE) through Genome Canada, the Canadian Institutes of Health Research (CIHR) and the Ontario Genomics Institute (OGI-049). Additional funding was provided to FORGE by Genome Quebec and Genome British Columbia. J.-B.R. is supported by a Banting Postdoctoral Fellowship from the CIHR. K.M.B. is supported by a Clinical Investigatorship Award from the CIHR Institute of Genetics. The laboratory of M.O. is funded by Cancer Research UK (CR-UK), the Medical Research Council (UK) and Leukaemia Lymphoma Research (UK). M.O. is a Senior CR-UK Research Fellow.

We would like to thank the Simons Foundation Autism Research Initiative (SFARI) for providing control exome data (grant 191889 to J.S.). We also thank the NIEHS Environmental Genome Project (contract HHSN273200800010C) and the NHLBI GO Exome Sequencing Project and its ongoing studies—Lung GO (HL-102923), Broad GO (HL-102925), Seattle GO (HL-102926), Heart GO (HL-103010) and the Women's Health Institute (WHI; HL-102924) Sequencing Projects—for providing exome variant calls for comparison.

Author information

J.-B.R., G.M.M., K.M.B. and W.B.D. designed the study. J.-B.R., B.J.O. and J.S.-O. designed and performed the genetics experiments. M.B., T.W., C.T.S. and T.R.W. contributed to the genetics experiments. J.-B.R., J.A.S. and B.J.O. performed the bioinformatics experiments. D.A. performed the experiments in lymphoblastoid cell lines. G.M.M., R.L.C., K.W.G., S.M.N., B.A., C.M.A., L.A., O.C., C.C., B.A.D., A.M.I., J.L.L., A.E.L., G.M.S.M., W.S.M., J.D.R., A.K.S., T.L.-S., G.U., R.W., B.Z., J.M.G., K.M.B. and W.B.D. recruited and evaluated the study subjects. H.E.B., N.A.K. and C.L.B. provided administrative support and recruited the study subjects. J.M., D.E.B., M.O., J.S., K.M.B. and W.B.D. supervised the study. J.-B.R., G.M.M. and W.B.D. wrote the manuscript.

Correspondence to William B Dobyns.

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The authors declare no competing financial interests.

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Membership of the Steering Committee for the Consortium is provided in the Supplementary Note.

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Supplementary Figures 1–5, Supplementary Tables 1–12 and Supplementary Note (PDF 1017 kb)

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