Genetic Testing of Idiopathic Metabolic Disorders by Targeted Next-Generation Sequencing

摘要

INTRODUCTION: We describe a diagnostic genetic strategy regarding a 44 years old male, with an apparent hereditary metabolic disorder that affects muscles, liver and spleen. This patient also has an alteration in the lipid profile and epilepsy since childhood. The following possible diagnoses were excluded: Niemann-Pick disease, Lysosomal acid lipase deficiency, Sandhoff disease, Tay-Sachs disease, Mucopolysaccharidoses and Glycogen storage disease. METHODS: We performed mutation screening of 533 genes by next generation sequencing (NGS). Libraries were prepared using the Nextera Rapid Capture Target Enrichment (TruSight One kit, Illumina) and run on Illumina NextSeq500. After read alignment using BWA and variant calling using GATK, freebayes and samtools, variant annotation was done using an in-house developed pipeline. RESULTS: We detected four pathogenic mutations, in heterozygous state. From those, two are in the FMO3 gene (p.Glu158Lys and p.Val257Met) associated with Trimethylaminuria; other one in the HPD gene (p.Thr33Ala) associated with 4-Alpha-hydroxyphenylpyruvate hydroxylase deficiency and one in the LPL gene (p.Asn318Ser) associated with Familial Combined Hyperlipidemia. DISCUSSION: Analysis of a large number of candidate genes by NGS proved very useful in establishing the genetic cause of this patient's disease. Concerning the phenotype and the routine lab results, the mutations in the FMO3 and LPL genes were not considered. The mutation that most likely is causing the phenotype is the p.Thr33Ala in the HPD gene. This is being confirmed with additional biochemical tests. This study, which resulted from a close collaboration between the medical specialist and the molecular biology laboratory, highlights how NGS is transforming clinical genetic diagnosis.