Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing

Sci Rep. 2021 Nov 16;11(1):22372. doi: 10.1038/s41598-021-01749-7.

PMID: 34785703

Albina Nowak, Omer Murik, Tzvia Mann

Highlights: Long-read Oxford Nanopore sequencing technology can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.

Abstract

Background: The GLA gene has been reported to have over 900 variants. Fabry disease can be brought on by some intronic and copy number variants in GLA, which are not picked up by the traditional Sanger sequence.

Objective and methods: Using long-read Oxford Nanopore sequencing technology, the goal of this study was to design and validate a procedure for sequencing the GLA gene. Twelve Fabry patients underwent blinded analysis using a 13 kb PCR amplicon and a traditional Sanger sequence. To align the long-read data, minimap2 was used. To identify variants Nanopolish and Sniffles were used.

Results: Long-read sequencing also found every variant identified by Sanger, including a deep intronic variant. Sanger sequencing missed a deletion in one patient, but the new approach picked it up. With the use of intronic analysis, our long-read sequencing-based method successfully identified missense variants and an exonic deletion.

Conclusion: It is a reliable and affordable tool for Fabry disease screening and diagnosis.

Keywords: Fabry disease, GLA gene, nanopore sequencing