Work

Editorial: Long-read sequencing—Pitfalls, benefits and success stories

Year: 2023

Type: editorial

Abstract: Editorial on the Research Topic Long-read sequencing -Pitfalls, benefits and success stories Long-read sequencing is an approach that holds promise to obtain genomic information for the first time in its entirety, accurately and resolved by haplotypes.In recent years the accuracy of long-read sequencing techniques, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), has significantly improved.Already, long-read sequencing can be used to reach an unprecedented genetic resolution (Garg, 2021), e.g. by covering previously inaccessible genomic regions or entire RNA transcripts in individual reads.Hence, long-read sequencing is a game changer in genetic research for many fields.Advancements in sequencing technology require major, simultaneous algorithmic developments, for example, in the context of base calling, variant calling and assembly.The latest ONT Q20+ and PacBio high fidelity (HiFi) protocols have revolutionized sequencing by producing reads with lengths in the order of tens of kilobases up to megabases and with base accuracies exceeding 99% (Logsdon et al., 2020).While the HiFi technology produces relatively more accurate sequences than ONT, ONT can generate ultra-long reads and is scalable from portable devices to benchtop sequencers.The key requirement of both technologies is high molecular weight DNA.Rapidly decreasing sequencing costs have fueled the generation of increasing amounts of genomic data for biodiversity applications and human health (De Coster et al., 2021;Miller et al., 2021).An example is the implementation of next-generation sequencing (NGS) into clinical practice for diagnosis, prognosis, and therapy selection in various medical fields, of which oncology has been a pioneer (Berger and Mardis, 2018).Undoubtedly, challenges still exist, such as input material requirements and establishing robust data analysis methods.Further, extensive method development and benchmarking are needed and ongoing to fully unlock the potential of long reads for these and other applications (Amarasinghe et al., 2020).

Source: Frontiers in Genetics

DOI: 10.3389/fgene.2022.1114542

Authors: Inken Wohlers, Shilpa Garg, Jayne Y. Hehir-Kwa

Institutions: University of Lübeck, University of Copenhagen, Technical University of Denmark, Princess Máxima Center

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,295

Funder: Novo Nordisk Fonden