Nanopore sequencing medically relevant ‘dark’ genomic regions

Abstract

Clinical sequencing ‘dark’ genomic regions using short-read technology is challenging due to high homology, low complexity, and repetitive sequences. Amongst medically relevant ‘dark’ genomic regions, Survival Motor Neuron 1 gene (SMN1) variation leads to spinal muscular atrophy (SMA), a common cause of pediatric genetic disease. SMN1 has >99.9% identity to its paralog SMN2 on 5q13 with innumerable segmental duplications, inversions, and gene conversions, resulting in copy number variation (CNVs) for 95% of SMA cases. Current clinical laboratory diagnosis of SMA relies on molecular characterization of SMN1/2 using up to 5-differentiating nucleotides to identify CNVs, and long-range PCR with Sanger sequencing for single nucleotide variation (SNV) detection. The ability to resolve complex genetic events in homologous regions with improved Oxford Nanopore basecalling and long-read chemistry inspired us to develop a rapid clinical method and novel bioinformatics workflow exploiting anchor kmers to accurately detect SMN1/2 CNVs and SNVs in SMA individuals. Our future aim is to translate an Oxford Nanopore WGS workflow that can reliably cover ‘dark’ genomic regions for SMA and other genetic conditions into the clinical laboratory.

Biography

Devin Oglesbee is a Consultant in the Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology at the Mayo Clinic, USA. He also holds the positions of Associate Professor of Medical Genetics and Associate Professor of Laboratory Medicine and Pathology.