Christos Proukakis - Detection of GBA missense mutations and other variants using the Oxford Nanopore MinION
London Calling 2018
Mutations in GBA cause Gaucher disease when biallelic, and are strong risk factors for Parkinson’s disease when heterozygous. GBA analysis is complicated by the presence of a nearby pseudogene. Here we present a method for sequencing GBA, using an amplicon including all coding regions and introns, on the Oxford Nanopore MinION, enabling a fast and comprehensive assessment. For illustration we successfully sequenced DNA samples from 17 individuals, including patients with Parkinson’s and Gaucher disease, in a study combining earlier and current nanopore chemistry. We initially compared different aligners (Graphmap and NGMLR), and used Nanopolish and Sniffles to call variants, and NanoOK for quality metrics. Many samples had previously known mutations, including the common p.N409S (N370S) and p.L483P (L444P). We detected these, mostly in a blinded fashion, and other causative mutations in Gaucher patients. In a sample with the complex RecNciI allele, we detected an additional coding SNP, and a 55-base pair deletion in data aligned by NGMLR. We haplotyped all samples using Whatshap and confirmed compound heterozygosity where relevant. False positives were fewer with NGMLR, and easily identified and filtered. We demonstrate the potential of the MinION to analyse this difficult gene, with the added advantage of phasing and intronic analysis.