NCM 2021: AmplideX PCR and nanopore sequencing deepens analysis and simplifies workflows for carrier screening

Sarah explained that current expanded carrier screening requires multiple methods and technologies, limiting access to only high-throughput sophisticated labs. Sarah’s team are exploring the combination of AmplideX long-range PCR technology with nanopore sequencing, that could potentially allow access to streamlined, combined, broad screening assays. In particular, they are researching how they might target and sequencing challenging genes of interest, and how they might combine these with conventional targets into one assay. Sarah explained that over half of the top ten carrier screening genes are intractable to conventional short-read sequencing; this may be due to repeat-rich sequences, or the presence of gene paralogs. Sarah presented three examples where long nanopore reads facilitated the accurate resolution of mutations in genes of interest, including: FMR1 repeat expansions, associated with Fragile X syndrome; analysis of the almost-identical SMN1 and SMN2 genes, associated with spinal muscular atrophy; and lastly CYP21A2, in which gene conversions, single nucleotide variations, large deletions, and variable copy number, are associated with congenital adrenal hyperplasia. ‘Bringing this all together, we were able to run a multi-sample, large amplicon panel on the [MinION] Mk1B, showing that this method has the potential to address real-world gaps in carrier screening’. Sarah highlighted how they successfully ran a 290-amplicon panel across 20 research samples, obtaining ~5x coverage for most amplicons, using a single MinION Flow Cell.