Oxford Nanopore sequencing technology used to develop an assay for comprehensive variant analysis in spinal muscular atrophy (SMA)

In a preprint released today, Hall et al. describe a method of comprehensive and accurate detection of the genetic variation linked to SMA that shows future potential for early screening and treatment

Oxford Nanopore sequencing technology has been used to develop a sequencing assay and customised analysis pipeline for the comprehensive and accurate detection of variation at the specific chromosomal location associated with SMA. This finding could make early screening and faster treatment more accessible for SMA, a debilitating genetic disorder characterised by the loss of motor neurons that causes muscle wasting and weakness.

In a preprint publication released today, a team led by Al Jalila Children's Specialty Hospital in the United Arab Emirates and Asuragen outline the method they developed, optimised, and evaluated to amplify both short and long targets covering key regions of the SMN1 and SMN2 genes. When followed by any-length nanopore sequencing and analysis using a variant calling model, this method was able to identify single nucleotide variants (SNVs), indels and copy number variants (CNVs) with greater than 97% accuracy. It was evaluated using more than 750 samples.

Spinal muscular atrophy (SMA) is a common recessive disorder with potentially life-threatening outcomes, however recently novel gene therapy treatments have been approved for patients by the US FDA. These treatments are extremely costly so a rapid and accurate method for screening and genetic diagnostics is therefore now essential for timely patient treatment.

In this recent preprint, scientists carried out genetic screening on 1,252 healthy Emirati babies and found about 1.5% cent of the Emirati population to be carriers, so a widely available and low-cost screening method could have a significant health economic impact as well.

The pathogenic variants responsible for SMA are in two genes, which have high sequence similarity (99.9%). Understanding the variants in the genes SMN1 and SMN2, is key for diagnosis and predicting disease severity in SMA. Due to the high homology of these two genes, current genetic diagnostic methods either require complex analytical approaches, or are limited to identifying CNVs only. This means the results can be difficult to interpret or provide an incomplete picture.

In this new study, the team used Oxford Nanopore’s portable, real-time sequencing device, the MinION Mk1B, which can potentially be used at point of care and easily scaled. The workflow for this method takes less than 48 hours for a 24-sample batch, and less than 72 hours for 96 samples with the cost estimated to be less than $20 per samples (excluding PCR). This study is proof of concept that this method is cost-effective and scalable and it shows potential for broad, global implementation.

The preprint can be accessed in full here.