Genome Research (https://genome.org) publishes a special issue highlighting advances in long-read sequencing applications in biology and medicine.
In this first of two Special Issues guest-edited by Dr. Ana Conesa, Dr. Alexander Hoischen, and Dr. Fritz Sedlazeck, Genome Research publishes a diverse collection of research and review articles highlighting novel applications and developments in long-read sequencing (LRS). Papers in this issue focus on original research offering novel biological and clinical insights gained using long-read DNA and RNA sequencing technologies and other long molecule approaches. The issue offers significant advances in long-read sequencing analysis, including novel methods for genome assembly and annotation, characterization of complex structural variation, quantifying DNA and RNA modification, full-length mRNA isoform resolution, vaccine and gene therapy vector quality control, and bacterial outbreak tracing. Several of the studies are highlighted below.
LRS technologies are expanding our understanding of rare diseases and impacting diagnostic potential of germline testing in the clinic, including characterization of disease-relevant complex genomic rearrangements and structural variants (SVs) (Bilgrav Saether et al. 2024, de Groot et al. 2024, Eisfeldt et al. 2024a, Eisfeldt et al. 2024b, Guitart et al. 2024, Gustafson et al. 2024, Hiatt et al. 2024), cancer-related variants (Gulsuner et al. 2024), aberrant splicing Pacholewska et al. 2024), and transcriptional features linked to tumor progression (Lee et al. 2024).
New telomere-to-telomere and chromosome-level assemblies using long-read sequencing are presented. Several studies highlight the advancements in accuracy and read length in driving telomere-to-telomere and chromosome-level assembly-based analysis methods in humans and various non-human, non-model, and plant species and provide valuable resources to the genomics community, including a new rat reference genome assembly (Li et al. 2024), as well as insights into genome structure and evolution (Byerly et al. 2024, Gardner et al. 2024, Kamath et al. 2024, Volarić et al. 2024). Koren et al. (2024) generated human, tomato, and maize genome assemblies using only Oxford Nanopore Technologies’ long-read sequencing data demonstrating the value of a single-instrument approach for constructing high quality de novo genome assemblies.
Novel long-read sequencing data approaches are presented, including tools enabling visualization of clinically or biologically relevant variant types (De Coster et al. 2024; Zhou et al. 2024; Tesi et al. 2024) and chromatin structure and methylation (Gocuk et al. 2024; Jha et al. 2024, Teng et al. 2024). Additionally, increased read-throughput and lowering costs are enabling large-scale studies to capture transcriptome variability, including in the house mouse brain (Zhang et al. 2024) and multiple other tissues (Adams and Vollmers 2024).
This issue also reviews targeted sequencing strategies that leverage existing long-read technologies (Iyer et al. 2024), the specific challenges involved in identifying and quantifying mRNA terminal ends with LRS technologies (Calvo-Roitberg et al. 2024), and advances in single-cell and spatial long-read sequencing (Belchikov et al. 2024).
This special issue provides important insights into how advances in long-read sequencing technology are driving impactful scientific discoveries in numerous areas of biology and medicine, technological advances for studying complex regions of the genome, and reflects the broad interest and discoveries in genome science enabled by this technology. A second issue of LRS related studies is planned to be published early next year.
Source – Eurekalert
Related Posts
Genome Research (https://genome.org) publishes a special issue highlighting advances in long-read sequencing applications in biology and medicine.
In this first of two Special Issues guest-edited by Dr. Ana Conesa, Dr. Alexander Hoischen, and Dr. Fritz Sedlazeck, Genome Research publishes a diverse collection of research and review articles highlighting novel applications and developments in long-read sequencing (LRS). Papers in this issue focus on original research offering novel biological and clinical insights gained using long-read DNA and RNA sequencing technologies and other long molecule approaches. The issue offers significant advances in long-read sequencing analysis, including novel methods for genome assembly and annotation, characterization of complex structural variation, quantifying DNA and RNA modification, full-length mRNA isoform resolution, vaccine and gene therapy vector quality control, and bacterial outbreak tracing. Several of the studies are highlighted below.
LRS technologies are expanding our understanding of rare diseases and impacting diagnostic potential of germline testing in the clinic, including characterization of disease-relevant complex genomic rearrangements and structural variants (SVs) (Bilgrav Saether et al. 2024, de Groot et al. 2024, Eisfeldt et al. 2024a, Eisfeldt et al. 2024b, Guitart et al. 2024, Gustafson et al. 2024, Hiatt et al. 2024), cancer-related variants (Gulsuner et al. 2024), aberrant splicing Pacholewska et al. 2024), and transcriptional features linked to tumor progression (Lee et al. 2024).
New telomere-to-telomere and chromosome-level assemblies using long-read sequencing are presented. Several studies highlight the advancements in accuracy and read length in driving telomere-to-telomere and chromosome-level assembly-based analysis methods in humans and various non-human, non-model, and plant species and provide valuable resources to the genomics community, including a new rat reference genome assembly (Li et al. 2024), as well as insights into genome structure and evolution (Byerly et al. 2024, Gardner et al. 2024, Kamath et al. 2024, Volarić et al. 2024). Koren et al. (2024) generated human, tomato, and maize genome assemblies using only Oxford Nanopore Technologies’ long-read sequencing data demonstrating the value of a single-instrument approach for constructing high quality de novo genome assemblies.
Novel long-read sequencing data approaches are presented, including tools enabling visualization of clinically or biologically relevant variant types (De Coster et al. 2024; Zhou et al. 2024; Tesi et al. 2024) and chromatin structure and methylation (Gocuk et al. 2024; Jha et al. 2024, Teng et al. 2024). Additionally, increased read-throughput and lowering costs are enabling large-scale studies to capture transcriptome variability, including in the house mouse brain (Zhang et al. 2024) and multiple other tissues (Adams and Vollmers 2024).
This issue also reviews targeted sequencing strategies that leverage existing long-read technologies (Iyer et al. 2024), the specific challenges involved in identifying and quantifying mRNA terminal ends with LRS technologies (Calvo-Roitberg et al. 2024), and advances in single-cell and spatial long-read sequencing (Belchikov et al. 2024).
This special issue provides important insights into how advances in long-read sequencing technology are driving impactful scientific discoveries in numerous areas of biology and medicine, technological advances for studying complex regions of the genome, and reflects the broad interest and discoveries in genome science enabled by this technology. A second issue of LRS related studies is planned to be published early next year.
Source – Eurekalert
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