Examination of faeces for bacterial pathogens.

Abstract

<h3>Objective</h3> To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms. <h3>Methods</h3> We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. <h3>Results</h3> Using ES, we discovered individuals with known pathogenic SNVs in <i>GBA</i> (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and <i>LRRK2</i> (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in <i>GBA</i> and <i>LRRK2</i>. Based on aCGH, we additionally discovered cases with an <i>SNCA</i> duplication and heterozygous intragenic <i>GBA</i> deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the <i>PRKN</i> locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. <h3>Conclusions</h3> Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for <i>SNCA</i> and <i>PRKN</i> CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.