Utility of clinical high-depth next generation sequencing for somatic variant detection in the PIK3CA-related overgrowth spectrum.
Next-generation sequencing (NGS) has revolutionized the approach of studying sequence variation, and has been well described in the clinical laboratory setting for the detection of constitutional alterations, as well as somatic tumor-associated variants. It is increasingly recognized that post-zygotic somatic alteration can be associated with congenital phenotypic abnormalities. Variation within the PI3K/AKT/mTOR pathway, including PIK3CA, has been described in somatic overgrowth syndromes and vascular malformations. Detection of PIK3CA somatic alteration is challenging because of low variant allele frequency (VAF) along with the need to assay involved tissue, thus necessitating a highly sensitive methodology. Here we describe the utility of target hybrid capture coupled with NGS for the identification of somatic variation in the PIK3CA-related overgrowth spectrum (PROS) among 14 patients submitted for clinical testing. Assay detection of low allelic fraction variation is coverage dependent with >90% sensitivity at 400× unique read depth for VAF of 10%, and approaching 100% at 1000×. Average read depth among the patient dataset across PIK3CA coding regions was 788.4. The diagnostic yield among this cohort was 71%, including the detection of two PIK3CA alterations novel in the setting of PROS. This report expands the mutational scope and phenotypic attributes of PROS disorders.
Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
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Hucthagowder
Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
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Shenoy
Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
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Corliss
Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
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Vigh-Conrad
Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
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Storer
Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA.
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Grange
Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.|Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
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Cottrell
D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D058534:Class I Phosphatidylinositol 3-Kinases; D015331:Cohort Studies; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods; D006130:Growth Disorders / Q000175:diagnosis / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007223:Infant; D008297:Male; D009154:Mutation; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D019869:Phosphatidylinositol 3-Kinases; D058534:Class I Phosphatidylinositol 3-Kinases; C484760:PIK3CA protein, human
NGS; PIK3CA; PROS; next-generation sequencing; overgrowth; somatic