The adoption of whole exome sequencing (WES) and whole genome sequencing (WGS) using short-read next-generation sequencing (NGS) platforms have contributed to the molecular diagnosis of rare genetic diseases and novel gene discovery at an unprecedented rate, although only 25-50% of tested patients are ultimately solved. WES involves the simultaneous sequencing of short fragments of the coding genome and immediate splice sites, while WGS has the potential to sequence both coding and non-coding regions; this results in a 10-15% increase in diagnostic yield. Although WES is currently implemented in medical genetics practice, with the use of WGS in only specific situations, a proportion of patients remain unsolved, precluding comprehensive clinical management and their prioritization for possible therapeutic options.
In recent years “Long Read Sequencing” (LRS) technologies have emerged, using the commercially available platforms from Oxford Nanopore Technologies (ONT) (based on changes in ionic current as DNA passes through a membrane-embedded nanopore) and Pacific Biosciences (single-molecule real-time DNA sequencing in zero-mode waveguides). These instruments have the capability of generating sequence reads in the kilo- to mega-base range.
Both platforms have been applied to complete gaps (8%) in the reference human genome 20 years after its draft release. Despite historically lower throughput and per-base accuracy, compared to short-read chemistries, the use of LRS in the research setting has shown several advantages with respect to WES/WGS, particularly for the detection of larger structural rearrangements/CNVs, epigenetic profiles, the annotation of transcript isoforms, and identification of noncoding variants.
The direct (PCR-free) sequencing of DNA and RNA modifications makes LRS a multi-omics technology impacting genomics, epigenomics, and transcriptomic.
This themed edition welcomes articles addressing the following long-read sequencing subjects:
- identification and characterization of structural variants (>50bp) that are refractory to detection by short-read sequencing and cytogenetic arrays
- improved resolution of genome regions with challenging genomic architecture (repetitive elements, segmental duplications, repeat expansions, regions of polymorphic structural variation)
- ultrarapid sequencing and interpretation in a critical care setting
- identification and characterization of complex chromothriptic events
- assessment by Targeted Long Read Sequencing (T-LRS) of missing heritability, including the identification of a second pathogenic mutation in patients with presumed autosomal recessive disorders- the configuration of phased haplotypes from long read datasets
- detection of native DNA and RNA modifications directly from sequence reads
- phased sequencing of methylation patterns in individuals with Imprinting Disorders
- detection of coding and non-coding variants causing Imprinting Disorders
- identification of trans-acting variants in mothers of children with MLID (Multi Locus Imprinting Disorder)
- capturing a comprehensive set of transcript isoforms for interpretation of the pathological mechanism of rare disease
- detection of aberrant splicing events
The adoption of whole exome sequencing (WES) and whole genome sequencing (WGS) using short-read next-generation sequencing (NGS) platforms have contributed to the molecular diagnosis of rare genetic diseases and novel gene discovery at an unprecedented rate, although only 25-50% of tested patients are ultimately solved. WES involves the simultaneous sequencing of short fragments of the coding genome and immediate splice sites, while WGS has the potential to sequence both coding and non-coding regions; this results in a 10-15% increase in diagnostic yield. Although WES is currently implemented in medical genetics practice, with the use of WGS in only specific situations, a proportion of patients remain unsolved, precluding comprehensive clinical management and their prioritization for possible therapeutic options.
In recent years “Long Read Sequencing” (LRS) technologies have emerged, using the commercially available platforms from Oxford Nanopore Technologies (ONT) (based on changes in ionic current as DNA passes through a membrane-embedded nanopore) and Pacific Biosciences (single-molecule real-time DNA sequencing in zero-mode waveguides). These instruments have the capability of generating sequence reads in the kilo- to mega-base range.
Both platforms have been applied to complete gaps (8%) in the reference human genome 20 years after its draft release. Despite historically lower throughput and per-base accuracy, compared to short-read chemistries, the use of LRS in the research setting has shown several advantages with respect to WES/WGS, particularly for the detection of larger structural rearrangements/CNVs, epigenetic profiles, the annotation of transcript isoforms, and identification of noncoding variants.
The direct (PCR-free) sequencing of DNA and RNA modifications makes LRS a multi-omics technology impacting genomics, epigenomics, and transcriptomic.
This themed edition welcomes articles addressing the following long-read sequencing subjects:
- identification and characterization of structural variants (>50bp) that are refractory to detection by short-read sequencing and cytogenetic arrays
- improved resolution of genome regions with challenging genomic architecture (repetitive elements, segmental duplications, repeat expansions, regions of polymorphic structural variation)
- ultrarapid sequencing and interpretation in a critical care setting
- identification and characterization of complex chromothriptic events
- assessment by Targeted Long Read Sequencing (T-LRS) of missing heritability, including the identification of a second pathogenic mutation in patients with presumed autosomal recessive disorders- the configuration of phased haplotypes from long read datasets
- detection of native DNA and RNA modifications directly from sequence reads
- phased sequencing of methylation patterns in individuals with Imprinting Disorders
- detection of coding and non-coding variants causing Imprinting Disorders
- identification of trans-acting variants in mothers of children with MLID (Multi Locus Imprinting Disorder)
- capturing a comprehensive set of transcript isoforms for interpretation of the pathological mechanism of rare disease
- detection of aberrant splicing events