Advances in sequencing technologies for amyotrophic lateral sclerosis research

Abstract

Amyotrophic lateral sclerosis (ALS) is caused by upper and lower motor neuron loss and has a fairly rapid disease progression, leading to fatality in an average of 2-5 years after symptom onset. Numerous genes have been implicated in this disease; however, many cases remain unexplained. Several technologies are being used to identify regions of interest and investigate candidate genes. Initial approaches to detect ALS genes include, among others, linkage analysis, Sanger sequencing, and genome-wide association studies. More recently, next-generation sequencing methods, such as whole-exome and whole-genome sequencing, have been introduced. While those methods have been particularly useful in discovering new ALS-linked genes, methodological advances are becoming increasingly important, especially given the complex genetics of ALS. Novel sequencing technologies, like long-read sequencing, are beginning to be used to uncover the contribution of repeat expansions and other types of structural variation, which may help explain missing heritability in ALS. In this review, we discuss how popular and/or upcoming methods are being used to discover ALS genes, highlighting emerging long-read sequencing platforms and their role in aiding our understanding of this challenging disease.

The First Insight into the Hereditary Fusion Gene Landscape of Amyotrophic Lateral Sclerosis

“…More recently, the discovery of genes associated with ASL has been shifted to next-generation sequencing, such as whole-genome sequencing (WGS) and RNA-Seq. Many WGS studies have confirmed previous findings and identified many common and rare variants associated with ASL 15,16 .…”

“…More recently, the discovery of genes associated with ASL has been shifted to next-generation sequencing, such as whole-genome sequencing (WGS) and RNA-Seq. Many WGS studies have confirmed previous findings and identified many common and rare variants associated with ASL 15, 16 . Brown et al have performed RNA-Seq analysis on the ASL postmortem cortex samples of NYGC ALS Consortium and found that TDP-43 loss resulted from retrotransposon and ALS-risk SNPs drive mis-splicing and depletion of UNC13A 17, 18 .…”

“…The First Insight into the Hereditary Fusion Gene Landscape of ASL Supplemental Materials NYGC ALS Consortium Hemali Phatnani 5 , Justin Kwan 6 , Dhruv Sareen 7,8 , James R. Broach9, Zachary Simmons 10 , Ximena Arcila-Londono 11 , Edward B. Lee 12 , Vivianna M. Van Deerlin 12 , Neil A. Shneider 13 , Ernest Fraenkel 1 , Lyle W. Ostrow 14 , Frank Baas 15,16 , Noah Zaitlen 17 , James D. Berry 18,19 , Andrea Malaspina 19,20,21 , Pietro Fratta 22 , Gregory A. Cox 23 , Leslie M. Thompson 24,25 Johns Hopkins School of Medicine, Baltimore, MD, USA. 15 Department of Neurogenetics, Academic Medical Centre, Amsterdam, The Netherlands. 16 Leiden University Medical Center, Leiden, The Netherlands.…”

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity

“…However, efforts to include unique molecular identifiers within the Iso-Seq protocol have been described [ 54 ]. With improvements such as depletion-based strategies of unwanted overexpressed transcripts, [ 55 ] concatenation workflows like PB_FLIC-Seq, and sequencing platform upgrades such as the Revio that offer larger SMRT Cell capacity, [ 56 ] Iso-Seq provides a new area of investigation focusing on alternative splicing and isoform differences in comparator and disease tissues that may control phenotypic presentation.…”

Unraveling metagenomics through long-read sequencing: a comprehensive review

“…Additionally, the integration of phi29 DNA polymerase has played a role in slowing DNA translocation and further reducing the error rate in ONT [ 15 ]. Although these accuracies still fall slightly short compared to SRS, PacBio's latest LRS technology iteration, Revio, has reached an impressive accuracy level of 99.9%, placing it on par with SRS [ 16 ].…”