Long-read sequencing in deciphering human genetics to a greater depth

Midha, Mohit; Wu, Mengchu; Chiu, King-Wah

doi:10.1007/s00439-019-02064-y

Cited by 78 publications

(63 citation statements)

References 126 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Typical RNA-seq read lengths are <200 bp, and such short reads are often unable to resolve the full-length sequence of RNA transcripts and determine specific isoforms [39]. In contrast, long-read sequencing is exceptionally useful in comprehensive characterization of RNA isoforms [40].…”

Section: Novel Approaches To Detect Alternative Splicing Eventsmentioning

confidence: 99%

The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease

Aísa-Marín

García-Arroyo

Mirra

et al. 2021

IJMS

View full text Add to dashboard Cite

Alternative splicing of mRNA is an essential mechanism to regulate and increase the diversity of the transcriptome and proteome. Alternative splicing frequently occurs in a tissue- or time-specific manner, contributing to differential gene expression between cell types during development. Neural tissues present extremely complex splicing programs and display the highest number of alternative splicing events. As an extension of the central nervous system, the retina constitutes an excellent system to illustrate the high diversity of neural transcripts. The retina expresses retinal specific splicing factors and produces a large number of alternative transcripts, including exclusive tissue-specific exons, which require an exquisite regulation. In fact, a current challenge in the genetic diagnosis of inherited retinal diseases stems from the lack of information regarding alternative splicing of retinal genes, as a considerable percentage of mutations alter splicing or the relative production of alternative transcripts. Modulation of alternative splicing in the retina is also instrumental in the design of novel therapeutic approaches for retinal dystrophies, since it enables precision medicine for specific mutations.

show abstract

Section: Novel Approaches To Detect Alternative Splicing Eventsmentioning

confidence: 99%

The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease

Aísa-Marín

García-Arroyo

Mirra

et al. 2021

IJMS

View full text Add to dashboard Cite

show abstract

“…While this initial report only provided "sequence fingerprints" 5 base pairs in length, the technology has no theoretical maximum on read length, and currently read lengths upward of 2 million base pairs have been reported (Payne, Holmes, Rakyan, & Loose, 2019). Pacific Biosciences and Oxford Nanopore are the leading platforms for long read sequencing, and both platforms utilize polymerases for reading sequence information, although in slightly different ways (Midha, Wu, & Chiu, 2019). The biggest advantage of long-read sequencing for RNA is the ability to detect unique isoforms rather than having to infer isoform usage from smaller junctions.…”

Section: Commentary Background Informationmentioning

confidence: 99%

Preparation of Mammalian Nascent RNA for Long Read Sequencing

Reimer

Neugebauer

2020

CP Molecular Biology

View full text Add to dashboard Cite

Long read sequencing technologies now allow high-quality sequencing of RNAs (or their cDNAs) that are hundreds to thousands of nucleotides long. Long read sequences of nascent RNA provide single-nucleotide-resolution information about co-transcriptional RNA processing events-e.g., splicing, folding, and base modifications. Here, we describe how to isolate nascent RNA from mammalian cells through subcellular fractionation of chromatinassociated RNA, as well as how to deplete poly(A) + RNA and rRNA, and, finally, how to generate a full-length cDNA library for use on long read sequencing platforms. This approach allows for an understanding of coordinated splicing status across multi-intron transcripts by revealing patterns of splicing or other RNA processing events that cannot be gained from traditional short read RNA sequencing.

show abstract

“…However, the fragmented nature of these assemblies limits downstream biological inferences. Other genome sequencing technologies, for example longread technologies (Jung et al 2019;Midha et al 2019), are becoming increasingly available and affordable and promise 'high-quality' genome assemblies (Phillippy 2017).…”

Section: Understanding Species Ecosystems and Communities Using Genomentioning

confidence: 99%

Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage

Inwood¹,

Aotearoa²,

McLaughlin³

et al. 2020

NZJE

View full text Add to dashboard Cite

In the past few years genetic technologies springing from advances in DNA sequencing (so-called high-throughput sequencing), and/or from CRISPR/Cas9 gene editing, have been proposed as being useful in bioheritage research. The potential scope for the use of these genetic technologies in bioheritage is vast, including enabling the recovery of threatened species, engineering proxies of extinct species and genetically controlling pests. While these technologies are often complex, they provide new opportunities that may help support New Zealand's beleaguered flora and fauna, and thus warrant scientific examination. Here we discuss these genetic technologies, focussing on scientific benefits and risks of each. We also acknowledge the social, cultural, ethical and regulatory constraints on their use, with emphasis on the importance of partnership with tangata whenua to determine when, whether or how these technologies should be used in enhancing New Zealand's bioheritage. We hope this will provide source material to support future decision making around the use of new genetic technologies in bioheritage.

show abstract

Long-read sequencing in deciphering human genetics to a greater depth

Cited by 78 publications

References 126 publications

The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease

The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease

Preparation of Mammalian Nascent RNA for Long Read Sequencing

Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage

Contact Info

Product

Resources

About