Long-Read Sequencing Emerging in Medical Genetics

Abstract

The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing repetitive regions, phasing of alleles and distinguishing highly homologous genomic regions. These limitations may significantly contribute to the diagnostic gap in patients with genetic disorders who have undergone standard NGS, like whole exome or even genome sequencing. Now, the emerging long-read sequencing (LRS) technologies may offer improvements in the characterization of genetic variation and regions that are difficult to assess with the prevailing NGS approaches. LRS has so far mainly been used to investigate genetic disorders with previously known or strongly suspected disease loci. While these targeted approaches already show the potential of LRS, it remains to be seen whether LRS technologies can soon enable true whole genome sequencing routinely. Ultimately, this could allow the de novo assembly of individual whole genomes used as a generic test for genetic disorders. In this article, we summarize the current LRS-based research on human genetic disorders and discuss the potential of these technologies to facilitate the next major advancements in medical genetics.

Molecular profiling for precision cancer therapies

“…Similar evaluations were also performed on pediatric pan-cancer cohorts to identify driver genes [40]. New sequencing approaches have extended the length of sequencing fragments to more than a few kilobases, thus improving the ability to detect complex structural alterations in the genome [41]. One study using genomic DNA from patients who had a variety of brain cancers was able to detect SNV, CNV, and methylation profiles simultaneously from a low-pass WGS approach using long-read sequencing [42].…”

A robust benchmark for germline structural variant detection

“…Conditions linked to SVs include autism, 1 schizophrenia, cardiovascular disease, 2 Huntington's Disease, and several other disorders. 3 Far fewer SVs exist in germline genomes relative to small variants, but SVs affect more base pairs and each SV may be more likely to impact phenotype. [4][5][6] While next generation sequencing technologies can detect many SVs, each technology and analysis method has different strengths and weaknesses.…”

Genomic Analysis of Carbapenemase-Producing Extensively Drug-Resistant Klebsiella pneumoniae Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding blaNDM-1 in South Africa

“…This is possibly associated with variations in the common genetic backbone of the bla NDM-1, supporting its versatility via a local horizontal transfer and subsequent evolution in their host by recombination events [72,73]. This reiterates the need for further circularization and annotation of the plasmid DNA using sequencing techniques that provide long-read sequences to offer insights into its evolution and spread [74]. Moreover, further larger epidemiological studies should be conducted in the province to trace the primary source(s) of their spread, possibly through frequent contact with healthcare workers and the movement of colonized patients among different healthcare settings [75,76].…”