Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutations.
Two megalencephaly (MEG) syndromes, megalencephaly-capillary malformation (MCAP) and megalencephaly-polymicrogyriapolydactyly-hydrocephalus (MPPH), have recently been defined on the basis of physical and neuroimaging features. Subsequently, exome sequencing of ten MEG cases identified de-novo postzygotic mutations in PIK3CA which cause MCAP and de-novo mutations in AKT and PIK3R2 which cause MPPH. Here we present findings from exome sequencing three unrelated megalencephaly patients which identified a causal PIK3CA mutation in two cases and a causal PIK3R2 mutation in the third case. However, our patient with the PIK3R2 mutation which is considered to cause MPPH has a marked bifrontal band heterotopia which is a feature of MCAP. Furthermore, one of our patients with a PIK3CA mutation lacks syndactyly/polydactyly which is a characteristic of MCAP. These findings suggest that the overlap between MCAP and MPPH may be greater than the available studies suggest. In addition, the PIK3CA mutation in one of our patients could not be detected using standard exome analysis because the mutation was observed at a low frequency consistent with somatic mosaicism. We have therefore investigated several alternative methods of exome analysis and demonstrate that alteration of the initial allele frequency spectrum (AFS), used as a prior for variant calling in samtools, had the greatest power to detect variants with low mutant allele frequencies in our 3 MEG exomes and in simulated data. We therefore recommend non-default settings of the AFS in combination with stringent quality control when searching for causal mutation(s) that could have low levels of mutant reads due to post-zygotic mutation.
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom ; Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom.
William J
WJ
Tapper
UHS NHS Foundation Trust and Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom.
Nicola
N
Foulds
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom ; Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom.
Nicholas C P
NC
Cross
Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom ; Department of Genetics, School of Sciences, University of Navarra, Pamplona, Spain.
Paula
P
Aranaz
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom ; Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom.
Joannah
J
Score
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom ; Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom.
Claire
C
Hidalgo-Curtis
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom ; Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom.
David O
DO
Robinson
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom.
Jane
J
Gibson
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom.
Sarah
S
Ennis
UHS NHS Foundation Trust and Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom.
I Karen
IK
Temple
Department of Human Genetics and Genomic medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom.
Andrew
A
Collins
D002196:Capillaries / Q000002:abnormalities / Q000473:pathology; D058534:Class I Phosphatidylinositol 3-Kinases; D059472:Exome / Q000235:genetics*; D017809:Fatal Outcome; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005838:Genotype; D006801:Humans; D006849:Hydrocephalus / Q000235:genetics / Q000473:pathology; D007223:Infant; D008297:Male; D058627:Megalencephaly / Q000235:genetics* / Q000473:pathology; D009154:Mutation; D010641:Phenotype; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D017689:Polydactyly / Q000235:genetics / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D051057:Proto-Oncogene Proteins c-akt / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D013576:Syndactyly / Q000235:genetics / Q000473:pathology; D013577:Syndrome; D054079:Vascular Malformations / Q000235:genetics / Q000473:pathology
D019869:Phosphatidylinositol 3-Kinases; C560566:phosphoinositol-3 kinase regulatory subunit 2, human; D058534:Class I Phosphatidylinositol 3-Kinases; C484760:PIK3CA protein, human; D051057:Proto-Oncogene Proteins c-akt