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Lancet Neurol. 2015 Dec;14(12):1182-95. doi: 10.1016/S1474-4422(15)00278-1. Epub 2015 Oct 29.

Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study.

Author information

1
Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA. Electronic address: gmirzaa@uw.edu.
2
Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy.
3
Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA.
4
Department of Neurology and Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
5
Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.
6
Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
7
Division of Medical Genetics, University of Missouri, St Louis, MO, USA.
8
Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA.
9
Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
10
Department of Pediatrics, Shimada Ryoiku Center Hachioji, Tokyo, Japan.
11
Genetics Department, Permanente Medical Group, San Francisco, CA, USA.
12
Centre National de Génotypage, Evry, France.
13
Plateforme de Bioinformatique Paris-Descartes, Institut Imagine, Paris, France.
14
Genetics and Molecular Pathology, Women's and Children's Hospital, North Adelaide, SA, Australia.
15
Division of Genetics, Birth Defects and Metabolism, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA.
16
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
17
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
18
Department of Pediatrics, Division of Genetics, University of California, San Francisco, CA, USA.
19
Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals, Headington, UK.
20
South Australian Clinical Genetics Service, Women's and Children's Hospital/SA Pathology, North Adelaide, SA, Australia; Discipline of Pediatrics, University of Adelaide, Adelaide, Australia.
21
Pôle de biologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; IGBMC, Translational Medicine and Neurogenetics Department, Illkirch, France.
22
Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.
23
Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy; IRCCS Stella Maris Foundation, Pisa, Italy. Electronic address: renzo.guerrini@meyer.it.

Abstract

BACKGROUND:

Bilateral perisylvian polymicrogyria (BPP), the most common form of regional polymicrogyria, causes the congenital bilateral perisylvian syndrome, featuring oromotor dysfunction, cognitive impairment, and epilepsy. The causes of BPP are heterogeneous, but only a few genetic causes have been reported. The aim of this study was to identify additional genetic causes of BPP and characterise their frequency in this population.

METHODS:

Children (aged ≤18 years) with polymicrogyria were enrolled into our research programme from July, 1980, to October, 2015, at two centres (Florence, Italy, and Seattle, WA, USA). We obtained samples (blood and saliva) throughout this period at both centres and did whole-exome sequencing on DNA from eight trios (two parents and one affected child) with BPP in 2014. After the identification of mosaic PIK3R2 mutations in two of these eight children, we performed targeted screening of PIK3R2 by two methods in a cohort of 118 children with BPP. First, we performed targeted sequencing of the entire PIK3R2 gene by single molecule molecular inversion probes (smMIPs) on 38 patients with BPP with normal to large head size. Second, we did amplicon sequencing of the recurrent PIK3R2 mutation (Gly373Arg) in 80 children with various types of polymicrogyria including BPP. One additional patient had clinical whole-exome sequencing done independently, and was included in this study because of the phenotypic similarity to our cohort.

FINDINGS:

We identified a mosaic mutation (Gly373Arg) in a regulatory subunit of the PI3K-AKT-mTOR pathway, PIK3R2, in two children with BPP. Of the 38 patients with BPP and normal to large head size who underwent targeted next-generation sequencing by smMIPs, we identified constitutional and mosaic PIK3R2 mutations in 17 additional children. In parallel, one patient had the recurrent PIK3R2 mutation identified by clinical whole-exome sequencing. Seven of these 20 patients had BPP alone, and 13 had BPP in association with features of the megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome. 19 patients had the same mutation (Gly373Arg), and one had a nearby missense mutation (Lys376Glu). Mutations were constitutional in 12 patients and mosaic in eight patients. In patients with mosaic mutations, we noted substantial variation in alternate (mutant) allele levels, ranging from ten (3%) of 377 reads to 39 (37%) of 106 reads, equivalent to 5-73% of cells analysed. Levels of mosaicism varied from undetectable to 37 (17%) of 216 reads in blood-derived DNA compared with 2030 (29%) of 6889 reads to 275 (43%) of 634 reads in saliva-derived DNA.

INTERPRETATION:

Constitutional and mosaic mutations in the PIK3R2 gene are associated with developmental brain disorders ranging from BPP with a normal head size to the MPPH syndrome. The phenotypic variability and low-level mosaicism, which challenge conventional molecular methods, have important implications for genetic testing and counselling.

FUNDING:

US National Institutes of Health.

Comment in

PMID:
26520804
PMCID:
PMC4672724
DOI:
10.1016/S1474-4422(15)00278-1
[Indexed for MEDLINE]
Free PMC Article

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