Long-read sequencing and adaptive sampling solve complex diagnostic conundrums | LC 25

Biography

Prof. Sebastian Lunke is the Head of Division of Genetics and Genomics at the Victorian Clinical Genetics Services. His team oversees the development and delivery of clinically accredited genetics and genomics laboratories in Australia, with a strong focus on translating novel technologies into clinical practice. He is also a co-lead of the Translational Genomics Research Group at the Murdoch Children’s Research Institute.

Abstract

Short-read sequencing remains the dominant application in clinical genomics and continues to improve its ability to resolve more complex variant types, such as structural variants and repeat expansions. It is often, however, able to provide only indicative information regarding the true variant and may not be clinically accredited. Orthogonal assays are therefore frequently required for confirmation and full resolution. These can be highly customised, expensive and labour-intensive, and often still do not provide the required answers.

We explored the utility of nanopore long-read sequencing and adaptive sampling across 30 complex diagnostic cases, encompassing structural variants, repeat expansions, high-homology regions, transposon insertions, copy number variants, imprinting disorders, and phasing of de novo variants in recessive genes.

Long-read sequencing confirmed or clarified suspected complex variants in over 90% of cases, resulting in high-confidence clinical diagnosis. In one case, a combination of short- and long-read data was required to show that a de novo variant in TTN was in trans with a second pathogenic variant 150 kb downstream. Utilisation of adaptive sampling had the further advantage of dynamically targeting unique variants, resulting in a time- and cost-efficient solution.

Adaptive sampling long-read sequencing is a fast and cost-effective approach to orthogonally confirm a wide range of complex clinical variants. It has the potential to replace a variety of traditional custom assays while resolving previously unaddressed challenges such as long-distance phasing of de novo and variants in recessive genes and variant-specific imprinting analysis.