A Streamlined PCR/Nanopore Sequencing Carrier Screening Panel for Cystic Fibrosis, Spinal Muscular Atrophy, and Fragile X Syndrome
Cystic Fibrosis (CF), Spinal Muscular Atrophy (SMA), and Fragile X Syndrome (FXS) are three of the most common inherited genetic disorders, each with high carrier rates that often require distinct genotyping methods. We developed a prototype assay comprised of novel PCR enrichment and Nanopore sequencing to simultaneously detect SNV/indels, copy number variation, and repeat sizing in a unified workflow, without the need for manual analysis. The assay utilizes amplicon read depth and machine learning models to automate and streamline identification of key genetic variants specific to each disease. Assay performance was evaluated with a cohort of 94 cell-line and 207 whole blood samples for all three genes resulting in 96-100% accuracy for each variant class.
Authors: Jon Kemppainen, Pranesh Rao, Julie R Thibert, Walairat Laosinchai-Wolf, Ryan Routsong, Ted Markulin, Monica Roberts, Bradley Martin, Bryan Killinger, Chris Fraher, Gary J Latham, and Bradley Hall