NCM 2023 Houston: AmplideX PCR and nanopore sequencing for accessible carrier screening for any lab

Carrier screening (CS) aims to identify couples at risk for having a child with a severe genetic disorder. Although NGS is a widely used method, it fails to resolve many problematic genes, such as those with tandem repeats, copy number variation, pseudogenes, and structural variation. These genes require specialized techniques and only cover a fraction of carrier risk. We combined three innovations into a single workflow to address these shortcomings: novel short and long-range PCR enrichment, scalable any-length nanopore sequencing, and bioinformatic analysis software. The prototype assay panel interrogates 11 genes critical for CS representing ~70% of all pathogenic variants for a severe inherited disorder in at-risk couples compared to gene panels at least 15 times larger. Results on over 450 samples demonstrate that both challenging and conventional genes can be analyzed in an efficient, scalable single workflow with the potential to enable CS in any laboratory.