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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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2
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Badwal AK, Singh S. A comprehensive review on the current status of CRISPR based clinical trials for rare diseases. Int J Biol Macromol 2024; 277:134097. [PMID: 39059527 DOI: 10.1016/j.ijbiomac.2024.134097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 07/03/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024]
Abstract
A considerable fraction of population in the world suffers from rare diseases. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its related Cas proteins offer a modern form of curative gene therapy for treating the rare diseases. Hereditary transthyretin amyloidosis, hereditary angioedema, duchenne muscular dystrophy and Rett syndrome are a few examples of such rare diseases. CRISPR/Cas9, for example, has been used in the treatment of β-thalassemia and sickle cell disease (Frangoul et al., 2021; Pavani et al., 2021) [1,2]. Neurological diseases such as Huntington's have also been focused in some studies involving CRISPR/Cas (Yang et al., 2017; Yan et al., 2023) [3,4]. Delivery of these biologicals via vector and non vector mediated methods depends on the type of target cells, characteristics of expression, time duration of expression, size of foreign genetic material etc. For instance, retroviruses find their applicability in case of ex vivo delivery in somatic cells due to their ability to integrate in the host genome. These have been successfully used in gene therapy involving X-SCID patients although, incidence of inappropriate activation has been reported. On the other hand, ex vivo gene therapy for β-thalassemia involved use of BB305 lentiviral vector for high level expression of CRISPR biological in HSCs. The efficacy and safety of these biologicals will decide their future application as efficient genome editing tools as they go forward in further stages of human clinical trials. This review focuses on CRISPR/Cas based therapies which are at various stages of clinical trials for treatment of rare diseases and the constraints and ethical issues associated with them.
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Affiliation(s)
- Amneet Kaur Badwal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali 160062, Punjab, India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali 160062, Punjab, India.
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3
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet 2024; 15:1374860. [PMID: 38510277 PMCID: PMC10951082 DOI: 10.3389/fgene.2024.1374860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
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Affiliation(s)
- Giulia Olivucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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5
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Sahın Vural G, Bolat H. Nanopore sequencing method for CTG18.1 expansion in TCF4 in late-onset Fuchs endothelial corneal dystrophy and a comparison of the structural features of cornea with first-degree relatives. Graefes Arch Clin Exp Ophthalmol 2024; 262:903-911. [PMID: 37747538 DOI: 10.1007/s00417-023-06243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND To evaluate the relationship between the number of trinucleotide repeats (TNR) in late-onset Fuchs corneal endothelial dystrophy (FCED) and to compare the endothelial properties of FCED, first-degree relatives, and controls. METHODS Blood samples were collected from FCEDs to determine TNR number. The FCED patients, first-degree relatives, and controls were examined with specular microscopy for central corneal thickness (CCT), endothelial cell density (ECD), pleomorphism and polymegatism, and with corneal topography for specific indicators such as (i) displacement of thinnest point of cornea, (ii) loss of isopachs, (iii) focal posterior surface depression towards anterior chamber. RESULTS This study included 92 patients with FCED, 92 first-degree relatives, and 96 controls. CCT was thickest in FCEDs (558.0 μm) (p < 0.05) while there was no difference between relatives (533.0 μm) and controls (530.4 μm) (p = 0.845). ECD was decreased in both FCED (2069.2 mm2) and relatives (2171.4 mm2) than controls (2822.9 mm2) (p < 0.05 in both). The presence of pleomorphism and polymegatism was significant in patients with FCED (93.4% and 93.4%, respectively), relatives (86.9% and 86.04%, respectively), and controls (8.33% and 1.04%, respectively) (p < 0.05). Specific topographic indicators differed among the groups (p < 0.05). The mean repeat number of the FCED patients was 17.48 ± 4.54 (12-25) times. The TNR number of FCED cases correlated with the relative CCT (p < 0.05, R = 0.615) and cell density (p = 0.009, R = -0.499). CONCLUSIONS A strong association between the corneal endothelium in relatives and TNR number of FCEDs was defined. Relatives tended to have fewer corneal endothelial cells, even though they did not have clinical findings.
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Affiliation(s)
- Gozde Sahın Vural
- Department of Ophthalmology, Balıkesir University Medicine Faculty, Balıkesir, Turkey.
- Department of Ophthalmology, Balıkesir University Medicine Faculty Hospital, Balıkesir, Turkey.
| | - Hilmi Bolat
- Department of Genetics, Balıkesir University Medicine Faculty, Balıkesir, Turkey
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Salomonsson SE, Maltos AM, Gill K, Aladesuyi Arogundade O, Brown KA, Sachdev A, Sckaff M, Lam KJK, Fisher IJ, Chouhan RS, Van Laar VS, Marley CB, McLaughlin I, Bankiewicz KS, Tsai YC, Conklin BR, Clelland CD. Validated assays for the quantification of C9orf72 human pathology. Sci Rep 2024; 14:828. [PMID: 38191789 PMCID: PMC10774390 DOI: 10.1038/s41598-023-50667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
A repeat expansion mutation in the C9orf72 gene is the leading known genetic cause of FTD and ALS. The C9orf72-ALS/FTD field has been plagued by a lack of reliable tools to monitor this genomic locus and its RNA and protein products. We have validated assays that quantify C9orf72 pathobiology at the DNA, RNA and protein levels using knock-out human iPSC lines as controls. Here we show that single-molecule sequencing can accurately measure the repeat expansion and faithfully report on changes to the C9orf72 locus in what has been a traditionally hard to sequence genomic region. This is of particular value to sizing and phasing the repeat expansion and determining changes to the gene locus after gene editing. We developed ddPCR assays to quantify two major C9orf72 transcript variants, which we validated by selective excision of their distinct transcriptional start sites. Using validated knock-out human iPSC lines, we validated 4 commercially available antibodies (of 9 tested) that were specific for C9orf72 protein quantification by Western blot, but none were specific for immunocytochemistry. We tested 15 combinations of antibodies against dipeptide repeat proteins (DPRs) across 66 concentrations using MSD immunoassay, and found two (against poly-GA and poly-GP) that yielded a 1.5-fold or greater signal increase in patient iPSC-motor neurons compared to knock-out control, and validated them in human postmortem and transgenic mouse brain tissue. Our validated DNA, RNA and protein assays are applicable to discovery research as well as clinical trials.
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Affiliation(s)
- S E Salomonsson
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - A M Maltos
- Gladstone Institutes, San Francisco, CA, USA
| | - K Gill
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - O Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - K A Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - A Sachdev
- Gladstone Institutes, San Francisco, CA, USA
| | - M Sckaff
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - K J K Lam
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - I J Fisher
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - R S Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - V S Van Laar
- Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA
- The Gene Therapy Institute, The Ohio State University, Columbus, OH, USA
| | - C B Marley
- Gladstone Institutes, San Francisco, CA, USA
| | | | - K S Bankiewicz
- Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA
- The Gene Therapy Institute, The Ohio State University, Columbus, OH, USA
| | - Y-C Tsai
- Pacific Biosciences, Menlo Park, CA, USA
| | - B R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - C D Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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7
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Ross JP, Akçimen F, Liao C, Kwan K, Phillips DE, Schmilovich Z, Spiegelman D, Genge A, Dupré N, Dion PA, Farhan SMK, Rouleau GA. Rare-variant and polygenic analyses of amyotrophic lateral sclerosis in the French-Canadian genome. Genet Med 2024; 26:100967. [PMID: 37638500 DOI: 10.1016/j.gim.2023.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
PURPOSE The genetic etiology of amyotrophic lateral sclerosis (ALS) includes few rare, large-effect variants and potentially many common, small-effect variants per case. The genetic risk liability for ALS might require a threshold comprised of a certain amount of variants. Here, we tested the degree to which risk for ALS was affected by rare variants in ALS genes, polygenic risk score, or both. METHODS 335 ALS cases and 356 controls from Québec, Canada were concurrently tested by microarray genotyping and targeted sequencing of ALS genes known at the time of study inception. ALS genome-wide association studies summary statistics were used to estimate an ALS polygenic risk score (PRS). Cases and controls were subdivided into rare-variant heterozygotes and non-heterozygotes. RESULTS Risk for ALS was significantly associated with PRS and rare variants independently in a logistic regression model. Although ALS PRS predicted a small amount of ALS risk overall, the effect was most pronounced between ALS cases and controls that were not heterozygous for a rare variant in the ALS genes surveyed. CONCLUSION Both PRS and rare variants in ALS genes impact risk for ALS. PRS for ALS is most informative when rare variants are not observed in ALS genes.
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Affiliation(s)
- Jay P Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Calwing Liao
- Department of Medicine, Harvard Medical School, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Karina Kwan
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, QC, Canada
| | - Daniel E Phillips
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Biology, McGill University, Montréal, QC, Canada
| | - Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Dan Spiegelman
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Angela Genge
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Patrick A Dion
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sali M K Farhan
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.
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8
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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9
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Yu SY, Xi YL, Xu FQ, Zhang J, Liu YS. Application of long read sequencing in rare diseases: The longer, the better? Eur J Med Genet 2023; 66:104871. [PMID: 38832911 DOI: 10.1016/j.ejmg.2023.104871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 06/06/2024]
Abstract
Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.
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Affiliation(s)
- Si-Yan Yu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Lin Xi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Fu-Qiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China.
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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10
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Latallo MJ, Wang S, Dong D, Nelson B, Livingston NM, Wu R, Zhao N, Stasevich TJ, Bassik MC, Sun S, Wu B. Single-molecule imaging reveals distinct elongation and frameshifting dynamics between frames of expanded RNA repeats in C9ORF72-ALS/FTD. Nat Commun 2023; 14:5581. [PMID: 37696852 PMCID: PMC10495369 DOI: 10.1038/s41467-023-41339-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
C9ORF72 hexanucleotide repeat expansion is the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the accumulation of toxic dipeptide repeat (DPR) proteins like poly-GA, GP and GR, produced by the noncanonical translation of the expanded RNA repeats. However, how different DPRs are synthesized remains elusive. Here, we use single-molecule imaging techniques to directly measure the translation dynamics of different DPRs. Besides initiation, translation elongation rates vary drastically between different frames, with GP slower than GA and GR the slowest. We directly visualize frameshift events using a two-color single-molecule translation assay. The repeat expansion enhances frameshifting, but the overall frequency is low. There is a higher chance of GR-to-GA shift than in the reversed direction. Finally, the ribosome-associated protein quality control (RQC) factors ZNF598 and Pelota modulate the translation dynamics, and the repeat RNA sequence is important for invoking the RQC pathway. This study reveals that multiple translation steps modulate the final DPR production. Understanding repeat RNA translation is critically important to decipher the DPR-mediated pathogenesis and identify potential therapeutic targets in C9ORF72-ALS/FTD.
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Affiliation(s)
- Malgorzata J Latallo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shaopeng Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Daoyuan Dong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nathan M Livingston
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ning Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shuying Sun
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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11
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Akçimen F, Lopez ER, Landers JE, Nath A, Chiò A, Chia R, Traynor BJ. Amyotrophic lateral sclerosis: translating genetic discoveries into therapies. Nat Rev Genet 2023; 24:642-658. [PMID: 37024676 PMCID: PMC10611979 DOI: 10.1038/s41576-023-00592-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 04/08/2023]
Abstract
Recent advances in sequencing technologies and collaborative efforts have led to substantial progress in identifying the genetic causes of amyotrophic lateral sclerosis (ALS). This momentum has, in turn, fostered the development of putative molecular therapies. In this Review, we outline the current genetic knowledge, emphasizing recent discoveries and emerging concepts such as the implication of distinct types of mutation, variability in mutated genes in diverse genetic ancestries and gene-environment interactions. We also propose a high-level model to synthesize the interdependent effects of genetics, environmental and lifestyle factors, and ageing into a unified theory of ALS. Furthermore, we summarize the current status of therapies developed on the basis of genetic knowledge established for ALS over the past 30 years, and we discuss how developing treatments for ALS will advance our understanding of targeting other neurological diseases.
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Affiliation(s)
- Fulya Akçimen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Elia R Lopez
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute for Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R, Rome, Italy
- Azienda Ospedaliero Universitaria Citta' della Salute e della Scienza, Turin, Italy
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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12
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Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
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Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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13
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Wang S, Sun S. Translation dysregulation in neurodegenerative diseases: a focus on ALS. Mol Neurodegener 2023; 18:58. [PMID: 37626421 PMCID: PMC10464328 DOI: 10.1186/s13024-023-00642-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
RNA translation is tightly controlled in eukaryotic cells to regulate gene expression and maintain proteome homeostasis. RNA binding proteins, translation factors, and cell signaling pathways all modulate the translation process. Defective translation is involved in multiple neurological diseases including amyotrophic lateral sclerosis (ALS). ALS is a progressive neurodegenerative disorder and poses a major public health challenge worldwide. Over the past few years, tremendous advances have been made in the understanding of the genetics and pathogenesis of ALS. Dysfunction of RNA metabolisms, including RNA translation, has been closely associated with ALS. Here, we first introduce the general mechanisms of translational regulation under physiological and stress conditions and review well-known examples of translation defects in neurodegenerative diseases. We then focus on ALS-linked genes and discuss the recent progress on how translation is affected by various mutant genes and the repeat expansion-mediated non-canonical translation in ALS.
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Affiliation(s)
- Shaopeng Wang
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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14
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Calafatti M, Cocozza G, Limatola C, Garofalo S. Microglial crosstalk with astrocytes and immune cells in amyotrophic lateral sclerosis. Front Immunol 2023; 14:1223096. [PMID: 37564648 PMCID: PMC10410456 DOI: 10.3389/fimmu.2023.1223096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023] Open
Abstract
In recent years, biomedical research efforts aimed to unravel the mechanisms involved in motor neuron death that occurs in amyotrophic lateral sclerosis (ALS). While the main causes of disease progression were first sought in the motor neurons, more recent studies highlight the gliocentric theory demonstrating the pivotal role of microglia and astrocyte, but also of infiltrating immune cells, in the pathological processes that take place in the central nervous system microenvironment. From this point of view, microglia-astrocytes-lymphocytes crosstalk is fundamental to shape the microenvironment toward a pro-inflammatory one, enhancing neuronal damage. In this review, we dissect the current state-of-the-art knowledge of the microglial dialogue with other cell populations as one of the principal hallmarks of ALS progression. Particularly, we deeply investigate the microglia crosstalk with astrocytes and immune cells reporting in vitro and in vivo studies related to ALS mouse models and human patients. At last, we highlight the current experimental therapeutic approaches that aim to modulate microglial phenotype to revert the microenvironment, thus counteracting ALS progression.
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Affiliation(s)
- Matteo Calafatti
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Germana Cocozza
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Cristina Limatola
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
- Department of Physiology and Pharmacology, Sapienza University, Laboratory Affiliated to Istituto Pasteur, Rome, Italy
| | - Stefano Garofalo
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
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15
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Van't Spijker HM, Almeida S. How villains are made: The translation of dipeptide repeat proteins in C9ORF72-ALS/FTD. Gene 2023; 858:147167. [PMID: 36621656 PMCID: PMC9928902 DOI: 10.1016/j.gene.2023.147167] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
A hexanucleotide repeat expansion in the C9ORF72 gene is the most common genetic alteration associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These neurodegenerative diseases share genetic, clinical and pathological features. The mutation in C9ORF72 appears to drive pathogenesis through a combination of loss of C9ORF72 normal function and gain of toxic effects due to the repeat expansion, which result in aggregation prone expanded RNAs and dipeptide repeat (DPR) proteins. Studies in cellular and animal models indicate that the DPR proteins are the more toxic species. Thus, a large body of research has focused on identifying the cellular pathways most directly impacted by these toxic proteins, with the goal of characterizing disease pathogenesis and nominating potential targets for therapeutic development. The preventative block of the production of the toxic proteins before they can cause harm is a second strategy of intense focus. Despite the considerable amount of effort dedicated to this prophylactic approach, it is still unclear how the DPR proteins are synthesized from RNAs harboring repeat expansions. In this review, we summarize our current knowledge of the specific protein translation mechanisms shown to account for the synthesis of DPR proteins. We will then discuss how enhanced understanding of the composition of these toxic effectors could help in refining disease mechanisms, and paving the way to identify and design effective prophylactic therapies for C9ORF72 ALS-FTD.
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Affiliation(s)
- Heleen M Van't Spijker
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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16
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Zou J, Wang F, Gong Z, Wang R, Chen S, Zhang H, Sun R, Gao C, Li W, Shang J, Zhang J. A Chinese SCA36 pedigree analysis of NOP56 expansion region based on long-read sequencing. Front Genet 2023; 14:1110307. [PMID: 37051597 PMCID: PMC10083286 DOI: 10.3389/fgene.2023.1110307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/15/2023] [Indexed: 03/28/2023] Open
Abstract
Introduction: Spinocerebellar ataxias 36 (SCA36) is the neurodegenerative disease caused by the GGCCTG Hexanucleotide repeat expansions in NOP56, which is too long to sequence using short-read sequencing. Single molecule real time (SMRT) sequencing can sequence across disease-causing repeat expansion. We report the first long-read sequencing data across the expansion region in SCA36.Methods: We collected and described the clinical manifestations and imaging features of Han Chinese pedigree with three generations of SCA36. Also, we focused on structural variation analysis for intron 1 of the NOP56 gene by SMRT sequencing in the assembled genome.Results: The main clinical features of this pedigree are late-onset ataxia symptoms, with a presymptomatic presence of affective and sleep disorders. In addition, the results of SMRT sequencing showed the specific repeat expansion region and demonstrated that the region was not composed of single GGCCTG hexanucleotides and there were random interruptions.Discussion: We extended the phenotypic spectrum of SCA36. We applied SMRT sequencing to reveal the correlation between genotype and phenotype of SCA36. Our findings indicated that long-read sequencing is well suited to characterize known repeat expansion.
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Affiliation(s)
- Jinlong Zou
- Department of Neurology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Fengyu Wang
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Zhenping Gong
- Department of Neurology, Xinxiang Medical University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Runrun Wang
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Shuai Chen
- Department of Neurology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Haohan Zhang
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ruihua Sun
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Chenhao Gao
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Wei Li
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Junkui Shang
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Jiewen Zhang
- Department of Neurology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Department of Neurology, Xinxiang Medical University, Henan Provincial People’s Hospital, Zhengzhou, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Jiewen Zhang,
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17
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Malekshoar M, Azimi SA, Kaki A, Mousazadeh L, Motaei J, Vatankhah M. CRISPR-Cas9 Targeted Enrichment and Next-Generation Sequencing for Mutation Detection. J Mol Diagn 2023; 25:249-262. [PMID: 36841425 DOI: 10.1016/j.jmoldx.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/08/2023] [Accepted: 01/27/2023] [Indexed: 02/27/2023] Open
Abstract
Despite the rapid application of next-generation sequencing (NGS) technologies, target sequencing in regions of the genome is often required to diagnose many genetic diseases. Target enrichment can be an effective factor in reducing the cost of sequencing and the duration of sequencing. Recently, several clustered system regularly interspaced short palindromic repeats (CRISPR)-based methods (amplification-free sequencing) have been developed to target enrichment in combination with one of the NGS platforms. CRISPR-based target enrichment strategies act as an auxiliary tool to improve NGS analytical performance, thereby indirectly facilitating nucleic acid detection. The direct DNA cleavage approach by CRISPR-Cas at genome-specific sites enhances the possibility of separating native large fragments from disease-related genomic regions. The CRISPR-Cas can isolate the target region without any amplification; subsequently, long-read sequencing technologies were also implemented. These methods, as promising tools, have the ability to assess genetic and epigenetic composition for clinical application and treatment responses in cancer precision medicine. By modifying CRISPR-based enrichment protocols, it was possible to identify different types of mutations, including structural variants, short tandem repeats, fusion genes, and mobile elements. The Cas9 can specifically eliminate wild-type sequences, and it also enables the enrichment and detection of small amounts of tumor DNA fragments among the highly heterogeneous fragments of wild-type DNA.
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Affiliation(s)
- Mehrdad Malekshoar
- Anesthesiology, Critical Care and Pain Management Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sajad Ataei Azimi
- Department of Hematology-Oncology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arastoo Kaki
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Leila Mousazadeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamshid Motaei
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Vatankhah
- Anesthesiology, Critical Care and Pain Management Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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18
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Abstract
The options for prenatal genetic testing have evolved rapidly in the past decade, and advances in sequencing technology now allow genetic diagnoses to be made down to the single-base-pair level, even before the birth of the child. This offers women the opportunity to obtain information regarding the foetus, thereby empowering them to make informed decisions about their pregnancy. As genetic testing becomes increasingly available to women, clinician knowledge and awareness of the options available to women is of great importance. Additionally, comprehensive pretest and posttest genetic counselling about the advantages, pitfalls and limitations of genetic testing should be provided to all women. This review article aims to cover the range of genetic tests currently available in prenatal screening and diagnosis, their current applications and limitations in clinical practice as well as what the future holds for prenatal genetics.
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Affiliation(s)
- Karen Mei Xian Lim
- Department of Obstetrics and Gynaecology, National University Health System, Singapore
| | - Aniza Puteri Mahyuddin
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University Health System, Singapore,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Correspondence: A/Prof Mahesh Choolani, Head and Senior Consultant, Department of Obstetrics and Gynaecology, National University Health System, NUHS Tower Block, Level 12, 1E Kent Ridge Road, 119228, Singapore. E-mail:
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19
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Udine E, Jain A, van Blitterswijk M. Advances in sequencing technologies for amyotrophic lateral sclerosis research. Mol Neurodegener 2023; 18:4. [PMID: 36635726 PMCID: PMC9838075 DOI: 10.1186/s13024-022-00593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
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.
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Affiliation(s)
- Evan Udine
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Angita Jain
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Center for Clinical and Translational Sciences, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL, 32224, USA.
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20
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Kaivola K, Pirinen M, Laaksovirta H, Jansson L, Rautila O, Launes J, Hokkanen L, Lahti J, Eriksson JG, Strandberg TE, FinnGen, Tienari PJ. C9orf72 hexanucleotide repeat allele tagging SNPs: Associations with ALS risk and longevity. Front Genet 2023; 14:1087098. [PMID: 36936421 PMCID: PMC10014923 DOI: 10.3389/fgene.2023.1087098] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/23/2023] [Indexed: 03/05/2023] Open
Abstract
C9orf72 hexanucleotide repeat expansion is a common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The C9orf72 locus may harbor residual risk outside the hexanucleotide repeat expansion, but the evidence is conflicting. Here, we first compared 683 unrelated amyotrophic lateral sclerosis cases and 3,196 controls with Finnish ancestry to find best single nucleotide polymorphisms that tag the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles. Rs2814707 was the best tagging single nucleotide polymorphisms for intermediate-length alleles with ≥7 repeats (p = 5 × 10-307) and rs139185008 for the hexanucleotide repeat expansion (p = 7 × 10-114) as well as alleles with ≥20 repeats. rs139185008*C associated with amyotrophic lateral sclerosis after removing cases with the hexanucleotide repeat expansion, especially in the subpopulation homozygous for the rs2814707*T (p = 0.0002, OR = 5.06), which supports the concept of residual amyotrophic lateral sclerosis risk at the C9orf72 haplotypes other than the hexanucleotide repeat expansion. We then leveraged Finnish biobank data to test the effects of rs2814707*T and rs139185008*C on longevity after removing individuals with amyotrophic lateral sclerosis / frontotemporal dementia diagnoses. In the discovery cohort (n = 230,006), the frequency of rs139185008*C heterozygotes decreased significantly with age in the comparisons between 50 and 80 years vs. >80 years (p = 0.0005) and <50 years vs. >80 years (p = 0.0001). The findings were similar but less significant in a smaller replication cohort (2-sided p = 0.037 in 50-80 years vs. >80 years and 0.061 in <50 years vs. >80 years). Analysis of the allele frequencies in 5-year bins demonstrated that the decrease of rs139185008*C started after the age of 70 years. The hexanucleotide repeat expansion tagging single nucleotide polymorphisms decreasing frequency with age suggests its' association with age-related diseases probably also outside amyotrophic lateral sclerosis / frontotemporal dementia.
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Affiliation(s)
- Karri Kaivola
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- *Correspondence: Karri Kaivola,
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Hannu Laaksovirta
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Lilja Jansson
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Osma Rautila
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Jyrki Launes
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Laura Hokkanen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Johan G. Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of General Practice and Primary Healthcare, University of Helsinki, Helsinki, Finland
| | - Timo E. Strandberg
- University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- University of Oulu, Center for Life Course Health Research, Oulu, Finland
| | | | - Pentti J. Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
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21
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Taylor A, Barros D, Gobet N, Schuepbach T, McAllister B, Aeschbach L, Randall E, Trofimenko E, Heuchan E, Barszcz P, Ciosi M, Morgan J, Hafford-Tear N, Davidson A, Massey T, Monckton D, Jones L, network REGISTRYH, Xenarios I, Dion V. Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing. NAR Genom Bioinform 2022; 4:lqac089. [PMID: 36478959 PMCID: PMC9719798 DOI: 10.1093/nargab/lqac089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022] Open
Abstract
Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington's disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington's disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and in the development of novel therapies.
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Affiliation(s)
- Alysha S Taylor
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Dinis Barros
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Nastassia Gobet
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Thierry Schuepbach
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Newbiologix, Ch. De la corniche 6-8, 1066 Epalinges, Switzerland
| | - Branduff McAllister
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lorene Aeschbach
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Emma L Randall
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Evgeniya Trofimenko
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Eleanor R Heuchan
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Paula Barszcz
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Joanne Morgan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | | | - Alice E Davidson
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - Thomas H Massey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Darren G Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | | | - Ioannis Xenarios
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
- Health2030 Genome Center, Ch des Mines 14, 1202 Genève, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
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22
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Conlin LK, Aref-Eshghi E, McEldrew DA, Luo M, Rajagopalan R. Long-read sequencing for molecular diagnostics in constitutional genetic disorders. Hum Mutat 2022; 43:1531-1544. [PMID: 36086952 PMCID: PMC9561063 DOI: 10.1002/humu.24465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
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Affiliation(s)
- Laura K. Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Deborah A. McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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23
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Meijboom KE, Abdallah A, Fordham NP, Nagase H, Rodriguez T, Kraus C, Gendron TF, Krishnan G, Esanov R, Andrade NS, Rybin MJ, Ramic M, Stephens ZD, Edraki A, Blackwood MT, Kahriman A, Henninger N, Kocher JPA, Benatar M, Brodsky MH, Petrucelli L, Gao FB, Sontheimer EJ, Brown RH, Zeier Z, Mueller C. CRISPR/Cas9-mediated excision of ALS/FTD-causing hexanucleotide repeat expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro. Nat Commun 2022; 13:6286. [PMID: 36271076 PMCID: PMC9587249 DOI: 10.1038/s41467-022-33332-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/13/2022] [Indexed: 12/25/2022] Open
Abstract
A GGGGCC24+ hexanucleotide repeat expansion (HRE) in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), fatal neurodegenerative diseases with no cure or approved treatments that substantially slow disease progression or extend survival. Mechanistic underpinnings of neuronal death include C9ORF72 haploinsufficiency, sequestration of RNA-binding proteins in the nucleus, and production of dipeptide repeat proteins. Here, we used an adeno-associated viral vector system to deliver CRISPR/Cas9 gene-editing machineries to effectuate the removal of the HRE from the C9ORF72 genomic locus. We demonstrate successful excision of the HRE in primary cortical neurons and brains of three mouse models containing the expansion (500-600 repeats) as well as in patient-derived iPSC motor neurons and brain organoids (450 repeats). This resulted in a reduction of RNA foci, poly-dipeptides and haploinsufficiency, major hallmarks of C9-ALS/FTD, making this a promising therapeutic approach to these diseases.
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Affiliation(s)
- Katharina E. Meijboom
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Abbas Abdallah
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Nicholas P. Fordham
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Hiroko Nagase
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Tomás Rodriguez
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Carolyn Kraus
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Tania F. Gendron
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Gopinath Krishnan
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Rustam Esanov
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Nadja S. Andrade
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Matthew J. Rybin
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Melina Ramic
- grid.26790.3a0000 0004 1936 8606Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Zachary D. Stephens
- grid.66875.3a0000 0004 0459 167XDepartment of Quantitative Health Sciences. Mayo Clinic, Rochester, MN 55905 USA
| | - Alireza Edraki
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Meghan T. Blackwood
- grid.168645.80000 0001 0742 0364Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Aydan Kahriman
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Nils Henninger
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Jean-Pierre A. Kocher
- grid.66875.3a0000 0004 0459 167XDepartment of Quantitative Health Sciences. Mayo Clinic, Rochester, MN 55905 USA
| | - Michael Benatar
- grid.26790.3a0000 0004 1936 8606Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael H. Brodsky
- grid.168645.80000 0001 0742 0364Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Leonard Petrucelli
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Fen-Biao Gao
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Erik J. Sontheimer
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Robert H. Brown
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Zane Zeier
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| | - Christian Mueller
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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24
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Machine learning predicts translation initiation sites in neurologic diseases with nucleotide repeat expansions. PLoS One 2022; 17:e0256411. [PMID: 35648796 PMCID: PMC9159584 DOI: 10.1371/journal.pone.0256411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
A number of neurologic diseases associated with expanded nucleotide repeats, including an inherited form of amyotrophic lateral sclerosis, have an unconventional form of translation called repeat-associated non-AUG (RAN) translation. It has been speculated that the repeat regions in the RNA fold into secondary structures in a length-dependent manner, promoting RAN translation. Repeat protein products are translated, accumulate, and may contribute to disease pathogenesis. Nucleotides that flank the repeat region, especially ones closest to the initiation site, are believed to enhance translation initiation. A machine learning model has been published to help identify ATG and near-cognate translation initiation sites; however, this model has diminished predictive power due to its extensive feature selection and limited training data. Here, we overcome this limitation and increase prediction accuracy by the following: a) capture the effect of nucleotides most critical for translation initiation via feature reduction, b) implement an alternative machine learning algorithm better suited for limited data, c) build comprehensive and balanced training data (via sampling without replacement) that includes previously unavailable sequences, and d) split ATG and near-cognate translation initiation codon data to train two separate models. We also design a supplementary scoring system to provide an additional prognostic assessment of model predictions. The resultant models have high performance, with ~85-88% accuracy, exceeding that of the previously published model by >18%. The models presented here are used to identify translation initiation sites in genes associated with a number of neurologic repeat expansion disorders. The results confirm a number of sites of translation initiation upstream of the expanded repeats that have been found experimentally, and predict sites that are not yet established.
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25
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Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biol 2022; 23:108. [PMID: 35484600 PMCID: PMC9052667 DOI: 10.1186/s13059-022-02670-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
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Affiliation(s)
- Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,School of Life Sciences, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA. .,Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA.
| | - Alex Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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26
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Duan X, Pan M, Fan S. Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data. BMC Genomics 2022; 23:324. [PMID: 35461238 PMCID: PMC9034514 DOI: 10.1186/s12864-022-08548-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/11/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Structural variants (SVs) play a crucial role in gene regulation, trait association, and disease in humans. SV genotyping has been extensively applied in genomics research and clinical diagnosis. Although a growing number of SV genotyping methods for long reads have been developed, a comprehensive performance assessment of these methods has yet to be done. RESULTS Based on one simulated and three real SV datasets, we performed an in-depth evaluation of five SV genotyping methods, including cuteSV, LRcaller, Sniffles, SVJedi, and VaPoR. The results show that for insertions and deletions, cuteSV and LRcaller have similar F1 scores (cuteSV, insertions: 0.69-0.90, deletions: 0.77-0.90 and LRcaller, insertions: 0.67-0.87, deletions: 0.74-0.91) and are superior to other methods. For duplications, inversions, and translocations, LRcaller yields the most accurate genotyping results (0.84, 0.68, and 0.47, respectively). When genotyping SVs located in tandem repeat region or with imprecise breakpoints, cuteSV (insertions and deletions) and LRcaller (duplications, inversions, and translocations) are better than other methods. In addition, we observed a decrease in F1 scores when the SV size increased. Finally, our analyses suggest that the F1 scores of these methods reach the point of diminishing returns at 20× depth of coverage. CONCLUSIONS We present an in-depth benchmark study of long-read SV genotyping methods. Our results highlight the advantages and disadvantages of each genotyping method, which provide practical guidance for optimal application selection and prospective directions for tool improvement.
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Affiliation(s)
- Xiaoke Duan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438 China
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Mingpei Pan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438 China
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438 China
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27
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Marsili L, Duque KR, Bode RL, Kauffman MA, Espay AJ. Uncovering Essential Tremor Genetics: The Promise of Long-Read Sequencing. Front Neurol 2022; 13:821189. [PMID: 35401394 PMCID: PMC8983820 DOI: 10.3389/fneur.2022.821189] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/25/2022] [Indexed: 12/23/2022] Open
Abstract
Long-read sequencing (LRS) technologies have been recently introduced to overcome intrinsic limitations of widely-used next-generation sequencing (NGS) technologies, namely the sequencing limited to short-read fragments (150–300 base pairs). Since its introduction, LRS has permitted many successes in unraveling hidden mutational mechanisms. One area in clinical neurology in need of rethinking as it applies to genetic mechanisms is essential tremor (ET). This disorder, among the most common in neurology, is a syndrome often exhibiting an autosomal dominant pattern of inheritance whose large phenotypic spectrum suggest a multitude of genetic etiologies. Exome sequencing has revealed the genetic etiology only in rare ET families (FUS, SORT1, SCN4A, NOS3, KCNS2, HAPLN4/BRAL2, and USP46). We hypothesize that a reason for this shortcoming may be non-classical genetic mechanism(s) underpinning ET, among them trinucleotide, tetranucleotide, or pentanucleotide repeat disorders. In support of this hypothesis, trinucleotide (e.g., GGC repeats in NOTCH2NLC) and pentanucleotide repeat disorders (e.g., ATTTC repeats in STARD7) have been revealed as pathogenic in patients with a past history of what has come to be referred to as “ET plus,” bilateral hand tremor associated with epilepsy and/or leukoencephalopathy. A systematic review of LRS in neurodegenerative disorders showed that 10 of the 22 (45%) genetic etiologies ascertained by LRS include tremor in their phenotypic spectrum, suggesting that future clinical applications of LRS for tremor disorders may uncover genetic subtypes of familial ET that have eluded NGS, particularly those with associated leukoencephalopathy or family history of epilepsy. LRS provides a pathway for potentially uncovering novel genes and genetic mechanisms, helping narrow the large proportion of “idiopathic” ET.
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Affiliation(s)
- Luca Marsili
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Kevin R. Duque
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Rachel L. Bode
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Marcelo A. Kauffman
- Consultorio y Laboratorio de Neurogenética, Centro Universitario de Neurología José María Ramos Mejía, Buenos Aires, Argentina
| | - Alberto J. Espay
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Alberto J. Espay
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28
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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29
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Detecting MUC1 Variants in Patients Clinicopathologically Diagnosed With Having Autosomal Dominant Tubulointerstitial Kidney Disease. Kidney Int Rep 2022; 7:857-866. [PMID: 35497811 PMCID: PMC9039432 DOI: 10.1016/j.ekir.2021.12.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction Autosomal dominant tubulointerstitial kidney disease (ADTKD)-MUC1 is predominantly caused by frameshift mutations owing to a single-base insertion into the variable number tandem repeat (VNTR) region in MUC1. Because of the complexity of the variant hotspot, identification using short-read sequencers (SRSs) is challenging. Although recent studies have revealed the usefulness of long-read sequencers (LRSs), the prevalence of MUC1 variants in patients with clinically suspected ADTKD remains unknown. We aimed to clarify this prevalence and the genetic characteristics and clinical manifestations of ADTKD-MUC1 in a Japanese population using an SRS and an LRS. Methods From January 2015 to December 2019, genetic analysis was performed using an SRS in 48 patients with clinically suspected ADTKD. Additional analyses were conducted using an LRS in patients with negative SRS results. Results Short-read sequencing results revealed MUC1 variants in 1 patient harboring a cytosine insertion in the second repeat unit of the VNTR region; however, deeper VNTR regions could not be read by the SRS. Therefore, we conducted long-read sequencing analysis of 39 cases and detected MUC1 VNTR variants in 8 patients (in total, 9 patients from unrelated families). With the inclusion of family-affected patients (n = 31), the median age at the development of end-stage kidney disease (ESKD) was 45 years (95% CI: 40–40 years). Conclusion In Japan, the detection rate of MUC1 variants in patients with clinically suspected ADTKD was 18.8%. More than 20% of patients with negative SRS results had MUC1 variants detected by an LRS.
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30
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Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 2022; 32:1-27. [PMID: 34965938 PMCID: PMC8744678 DOI: 10.1101/gr.269530.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans. TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference genomes but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be "insertions" within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools, and challenges for further discoveries of disease-causing TR instabilities and understanding their biological and pathological impacts-a vista that is about to expand.
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Affiliation(s)
- Terence Gall-Duncan
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nozomu Sato
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Ryan K C Yuen
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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31
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Abramzon Y, Dewan R, Cortese A, Resnick S, Ferrucci L, Houlden H, Traynor BJ. Investigating RFC1 expansions in sporadic amyotrophic lateral sclerosis. J Neurol Sci 2021; 430:118061. [PMID: 34537679 PMCID: PMC9014296 DOI: 10.1016/j.jns.2021.118061] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
A homozygous AAGGG repeat expansion within the RFC1 gene was recently described as a common cause of CANVAS syndrome. We examined 1069 sporadic ALS patients for the presence of this repeat expansion. We did not discover any carriers of the homozygous AAGGG expansion in our ALS cohort, indicating that this form of RFC1 repeat expansions is not a common cause of sporadic ALS. However, our study did identify a novel repeat conformation and further expanded on the highly polymorphic nature of the RFC1 locus.
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Affiliation(s)
- Yevgenya Abramzon
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London WC1N 1PJ, UK.
| | - Ramita Dewan
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Andrea Cortese
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Susan Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London WC1N 1PJ, UK; Neurology Department, Johns Hopkins University, Baltimore, MD 21205, USA
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Rostalski H, Korhonen V, Kuulasmaa T, Solje E, Krüger J, Gen F, Kaivola K, Eide PK, Lambert JC, Julkunen V, Tienari PJ, Remes AM, Leinonen V, Hiltunen M, Haapasalo A. A Novel Genetic Marker for the C9orf72 Repeat Expansion in the Finnish Population. J Alzheimers Dis 2021; 83:1325-1332. [PMID: 34397416 DOI: 10.3233/jad-210599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND C9orf72 repeat expansion (C9exp) is the most common genetic cause underlying frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). However, detection of the C9exp requires elaborative methods. OBJECTIVE Identification of C9exp carriers from genotyped cohorts could be facilitated by using single nucleotide polymorphisms (SNPs) as markers for the C9exp. METHODS We elucidated the potential of the previously described Finnish risk haplotype, defined by the SNP rs3849942, to identify potential C9exp carriers among 218,792 Finns using the FinnGen database. The haplotype approach was first tested in an idiopathic normal pressure hydrocephalus (iNPH) patient cohort (European Alzheimer's Disease DNA BioBank) containing C9exp carriers by comparing intermediate (15-30) and full-length (> 60 repeats) C9exp carriers (n = 41) to C9exp negative patients (< 15 repeats, n = 801). RESULTS In this analysis, rs3849942 was associated with carriership of C9exp (OR 8.44, p < 2×10-15), while the strongest association was found with rs139185008 (OR 39.4, p < 5×10-18). Unbiased analysis of rs139185008 in FinnGen showed the strongest association with FTLD (OR 4.38, 3×10-15) and motor neuron disease ALS (OR 5.19, 3×10-21). rs139185008 was the top SNP in all diseases (iNPH, FTLD, ALS), and further showed a strong association with ALS in the UK Biobank (p = 9.0×10-8). CONCLUSION Our findings suggest that rs139185008 is a useful marker to identify potential C9exp carriers in the genotyped cohorts and biobanks originating from Finland.
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Affiliation(s)
- Hannah Rostalski
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ville Korhonen
- Neurocenter, Neurosurgery, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Teemu Kuulasmaa
- Institute of Biomedicine, Yliopistonranta 1E, University of Eastern Finland, Kuopio, Finland
| | - Eino Solje
- Institute of Clinical Medicine - Neurology, University of Eastern Finland.,Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Johanna Krüger
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland.,Medical Research Center (MRC), Oulu University Hospital, Oulu, Finland
| | - Finn Gen
- Department of Neurology, Helsinki University Hospital and Translational Immunology Program, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Karri Kaivola
- Department of Neurology, Helsinki University Hospital and Translational Immunology Program, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Per Kristian Eide
- Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liés au vieillissement, Lille, France
| | - Valtteri Julkunen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland.,Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Pentti J Tienari
- Department of Neurology, Helsinki University Hospital and Translational Immunology Program, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Anne M Remes
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland.,Medical Research Center (MRC), Oulu University Hospital, Oulu, Finland
| | - Ville Leinonen
- Neurocenter, Neurosurgery, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, Yliopistonranta 1E, University of Eastern Finland, Kuopio, Finland
| | - Annakaisa Haapasalo
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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Su Y, Fan L, Shi C, Wang T, Zheng H, Luo H, Zhang S, Hu Z, Fan Y, Dong Y, Yang J, Mao C, Xu Y. Deciphering Neurodegenerative Diseases Using Long-Read Sequencing. Neurology 2021; 97:423-433. [PMID: 34389649 PMCID: PMC8408508 DOI: 10.1212/wnl.0000000000012466] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/23/2021] [Indexed: 11/15/2022] Open
Abstract
Neurodegenerative diseases exhibit chronic progressive lesions in the central and peripheral nervous systems with unclear causes. The search for pathogenic mutations in human neurodegenerative diseases has benefited from massively parallel short-read sequencers. However, genomic regions, including repetitive elements, especially with high/low GC content, are far beyond the capability of conventional approaches. Recently, long-read single-molecule DNA sequencing technologies have emerged and enabled researchers to study genomes, transcriptomes, and metagenomes at unprecedented resolutions. The identification of novel mutations in unresolved neurodegenerative disorders, the characterization of causative repeat expansions, and the direct detection of epigenetic modifications on naive DNA by virtue of long-read sequencers will further expand our understanding of neurodegenerative diseases. In this article, we review and compare 2 prevailing long-read sequencing technologies, Pacific Biosciences and Oxford Nanopore Technologies, and discuss their applications in neurodegenerative diseases.
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Affiliation(s)
- Yun Su
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Liyuan Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Tai Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Huimin Zheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Haiyang Luo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Yu Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Yali Dong
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P. R. China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China .,Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, P. R. China.,Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan, P. R. China
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34
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Reyes CJ, Laabs BH, Schaake S, Lüth T, Ardicoglu R, Rakovic A, Grütz K, Alvarez-Fischer D, Jamora RD, Rosales RL, Weyers I, König IR, Brüggemann N, Klein C, Dobricic V, Westenberger A, Trinh J. Brain Regional Differences in Hexanucleotide Repeat Length in X-Linked Dystonia-Parkinsonism Using Nanopore Sequencing. NEUROLOGY-GENETICS 2021; 7:e608. [PMID: 34250228 PMCID: PMC8265576 DOI: 10.1212/nxg.0000000000000608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
Objective Our study investigated the presence of regional differences in hexanucleotide repeat number in postmortem brain tissues of 2 patients with X-linked dystonia-parkinsonism (XDP), a combined dystonia-parkinsonism syndrome modified by a (CCCTCT)n repeat within the causal SINE-VNTR-Alu retrotransposon insertion in the TAF1 gene. Methods Genomic DNA was extracted from blood and postmortem brain samples, including the basal ganglia and cortex from both patients and from the cerebellum, midbrain, and pituitary gland from 1 patient. Repeat sizing was performed using fragment analysis, small-pool PCR-based Southern blotting, and Oxford nanopore sequencing. Results The basal ganglia (p < 0.001) and cerebellum (p < 0.001) showed higher median repeat numbers and higher degrees of repeat instability compared with blood. Conclusions Somatic repeat instability may predominate in brain regions selectively affected in XDP, thereby hinting at its potential role in disease manifestation and modification.
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Affiliation(s)
- Charles Jourdan Reyes
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Björn-Hergen Laabs
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Theresa Lüth
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Raphaela Ardicoglu
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Aleksandar Rakovic
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Karen Grütz
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Daniel Alvarez-Fischer
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Roland Dominic Jamora
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Raymond L Rosales
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Imke Weyers
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Inke R König
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Valerija Dobricic
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Ana Westenberger
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
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Chintalaphani SR, Pineda SS, Deveson IW, Kumar KR. An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics. Acta Neuropathol Commun 2021; 9:98. [PMID: 34034831 PMCID: PMC8145836 DOI: 10.1186/s40478-021-01201-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease. They have an established role in more than 40 different phenotypes including the myotonic dystrophies, Fragile X syndrome, Huntington's disease, the hereditary cerebellar ataxias, amyotrophic lateral sclerosis and frontotemporal dementia. MAIN BODY STR expansions are difficult to detect and may explain unsolved diseases, as highlighted by recent findings including: the discovery of a biallelic intronic 'AAGGG' repeat in RFC1 as the cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS); and the finding of 'CGG' repeat expansions in NOTCH2NLC as the cause of neuronal intranuclear inclusion disease and a range of clinical phenotypes. However, established laboratory techniques for diagnosis of repeat expansions (repeat-primed PCR and Southern blot) are cumbersome, low-throughput and poorly suited to parallel analysis of multiple gene regions. While next generation sequencing (NGS) has been increasingly used, established short-read NGS platforms (e.g., Illumina) are unable to genotype large and/or complex repeat expansions. Long-read sequencing platforms recently developed by Oxford Nanopore Technology and Pacific Biosciences promise to overcome these limitations to deliver enhanced diagnosis of repeat expansion disorders in a rapid and cost-effective fashion. CONCLUSION We anticipate that long-read sequencing will rapidly transform the detection of short tandem repeat expansion disorders for both clinical diagnosis and gene discovery.
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Affiliation(s)
- Sanjog R. Chintalaphani
- School of Medicine, University of New South Wales, Sydney, 2052 Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Brain and Mind Centre, University of Sydney, Camperdown, NSW 2050 Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Faculty of Medicine, St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010 Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Molecular Medicine Laboratory and Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW 2137 Australia
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Cerebellar ataxia, neuropathy, vestibular areflexia syndrome: genetic and clinical insights. Curr Opin Neurol 2021; 34:556-564. [PMID: 34227574 DOI: 10.1097/wco.0000000000000961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW This review aims to summarise the present cerebellar ataxia, neuropathy, vestibular ataxia syndrome (CANVAS) literature, providing both clinical and genetic insights that might facilitate the timely clinical and genetic diagnosis of this disease. RECENT FINDINGS Recent advancements in the range of the clinical features of CANVAS have aided the development of a broader, more well-defined clinical diagnostic criteria. Additionally, the identification of a biallelic repeat expansion in RFC1 as the cause of CANVAS and a common cause of late-onset ataxia has opened the door to the potential discovery of a pathogenic mechanism, which in turn, may lead to therapeutic advancements and improved patient care. SUMMARY The developments in the clinical and genetic understanding of CANVAS will aid the correct and timely diagnosis of CANVAS, which continues to prove challenging within the clinic. The insights detailed within this review will raise the awareness of the phenotypic spectrum and currently known genetics. We also speculate on the future directions of research into CANVAS.
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DeJesus-Hernandez M, Aleff RA, Jackson JL, Finch NA, Baker MC, Gendron TF, Murray ME, McLaughlin IJ, Harting JR, Graff-Radford NR, Oskarsson B, Knopman DS, Josephs KA, Boeve BF, Petersen RC, Fryer JD, Petrucelli L, Dickson DW, Rademakers R, Ebbert MTW, Wieben ED, van Blitterswijk M. Long-read targeted sequencing uncovers clinicopathological associations for C9orf72-linked diseases. Brain 2021; 144:1082-1088. [PMID: 33889947 PMCID: PMC8105038 DOI: 10.1093/brain/awab006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 11/14/2022] Open
Abstract
To examine the length of a hexanucleotide expansion in C9orf72, which represents the most frequent genetic cause of frontotemporal lobar degeneration and motor neuron disease, we employed a targeted amplification-free long-read sequencing technology: No-Amp sequencing. In our cross-sectional study, we assessed cerebellar tissue from 28 well-characterized C9orf72 expansion carriers. We obtained 3507 on-target circular consensus sequencing reads, of which 814 bridged the C9orf72 repeat expansion (23%). Importantly, we observed a significant correlation between expansion sizes obtained using No-Amp sequencing and Southern blotting (P = 5.0 × 10-4). Interestingly, we also detected a significant survival advantage for individuals with smaller expansions (P = 0.004). Additionally, we uncovered that smaller expansions were significantly associated with higher levels of C9orf72 transcripts containing intron 1b (P = 0.003), poly(GP) proteins (P = 1.3 × 10- 5), and poly(GA) proteins (P = 0.005). Thorough examination of the composition of the expansion revealed that its GC content was extremely high (median: 100%) and that it was mainly composed of GGGGCC repeats (median: 96%), suggesting that expanded C9orf72 repeats are quite pure. Taken together, our findings demonstrate that No-Amp sequencing is a powerful tool that enables the discovery of relevant clinicopathological associations, highlighting the important role played by the cerebellar size of the expanded repeat in C9orf72-linked diseases.
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Affiliation(s)
| | - Ross A Aleff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jazmyne L Jackson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Ian J McLaughlin
- Pacific Biosciences of California, Inc., Menlo Park, CA 94025, USA
| | - John R Harting
- Pacific Biosciences of California, Inc., Menlo Park, CA 94025, USA
| | | | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - David S Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Keith A Josephs
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bradley F Boeve
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ 85259, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Mark T W Ebbert
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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van der Ende EL, Jackson JL, White A, Seelaar H, van Blitterswijk M, Van Swieten JC. Unravelling the clinical spectrum and the role of repeat length in C9ORF72 repeat expansions. J Neurol Neurosurg Psychiatry 2021; 92:502-509. [PMID: 33452054 PMCID: PMC8053328 DOI: 10.1136/jnnp-2020-325377] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022]
Abstract
Since the discovery of the C9orf72 repeat expansion as the most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis, it has increasingly been associated with a wider spectrum of phenotypes, including other types of dementia, movement disorders, psychiatric symptoms and slowly progressive FTD. Prompt recognition of patients with C9orf72-associated diseases is essential in light of upcoming clinical trials. The striking clinical heterogeneity associated with C9orf72 repeat expansions remains largely unexplained. In contrast to other repeat expansion disorders, evidence for an effect of repeat length on phenotype is inconclusive. Patients with C9orf72-associated diseases typically have very long repeat expansions, containing hundreds to thousands of GGGGCC-repeats, but smaller expansions might also have clinical significance. The exact threshold at which repeat expansions lead to neurodegeneration is unknown, and discordant cut-offs between laboratories pose a challenge for genetic counselling. Accurate and large-scale measurement of repeat expansions has been severely hindered by technical difficulties in sizing long expansions and by variable repeat lengths across and within tissues. Novel long-read sequencing approaches have produced promising results and open up avenues to further investigate this enthralling repeat expansion, elucidating whether its length, purity, and methylation pattern might modulate clinical features of C9orf72-related diseases.
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Affiliation(s)
- Emma L van der Ende
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Adrianna White
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA.,Department of Biology, University of North Florida, Jacksonville, Florida, USA
| | - Harro Seelaar
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA.,Department of Biology, University of North Florida, Jacksonville, Florida, USA
| | - John C Van Swieten
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
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Barp A, Mosca L, Sansone VA. Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders. Diagnostics (Basel) 2021; 11:diagnostics11040701. [PMID: 33919863 PMCID: PMC8070835 DOI: 10.3390/diagnostics11040701] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of “unknown significance” can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain “not genetically defined”. In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss “facilitations and hurdles” of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of “therapeutic offer”.
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
- Correspondence:
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
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40
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Perrone F, Cacace R, van der Zee J, Van Broeckhoven C. Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases. Genome Med 2021; 13:59. [PMID: 33853652 PMCID: PMC8048219 DOI: 10.1186/s13073-021-00878-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the molecular etiology of neurodegenerative brain diseases (NBD) has substantially increased over the past three decades. Early genetic studies of NBD families identified rare and highly penetrant deleterious mutations in causal genes that segregate with disease. Large genome-wide association studies uncovered common genetic variants that influenced disease risk. Major developments in next-generation sequencing (NGS) technologies accelerated gene discoveries at an unprecedented rate and revealed novel pathways underlying NBD pathogenesis. NGS technology exposed large numbers of rare genetic variants of uncertain significance (VUS) in coding regions, highlighting the genetic complexity of NBD. Since experimental studies of these coding rare VUS are largely lacking, the potential contributions of VUS to NBD etiology remain unknown. In this review, we summarize novel findings in NBD genetic etiology driven by NGS and the impact of rare VUS on NBD etiology. We consider different mechanisms by which rare VUS can act and influence NBD pathophysiology and discuss why a better understanding of rare VUS is instrumental for deriving novel insights into the molecular complexity and heterogeneity of NBD. New knowledge might open avenues for effective personalized therapies.
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Affiliation(s)
- Federica Perrone
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
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41
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Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of "unknown significance" can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain "not genetically defined". In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss "facilitations and hurdles" of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of "therapeutic offer".
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
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42
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Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR. CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. PLoS One 2021; 16:e0241253. [PMID: 33830997 PMCID: PMC8031414 DOI: 10.1371/journal.pone.0241253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 11/29/2022] Open
Abstract
A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read sequencing technologies, such as Oxford Nanopore's MinION, enable direct measurement of complex loci without introducing many of the biases inherent to short-read methods, though they suffer from relatively lower throughput. This limitation has motivated recent efforts to develop amplification-free strategies to target and enrich loci of interest for subsequent sequencing with long reads. Here, we present CaBagE, a method for target enrichment that is efficient and useful for sequencing large, structurally complex targets. The CaBagE method leverages the stable binding of Cas9 to its DNA target to protect desired fragments from digestion with exonuclease. Enriched DNA fragments are then sequenced with Oxford Nanopore's MinION long-read sequencing technology. Enrichment with CaBagE resulted in a median of 116X coverage (range 39-416) of target loci when tested on five genomic targets ranging from 4-20kb in length using healthy donor DNA. Four cancer gene targets were enriched in a single reaction and multiplexed on a single MinION flow cell. We further demonstrate the utility of CaBagE in two ALS patients with C9orf72 short tandem repeat expansions to produce genotype estimates commensurate with genotypes derived from repeat-primed PCR for each individual. With CaBagE there is a physical enrichment of on-target DNA in a given sample prior to sequencing. This feature allows adaptability across sequencing platforms and potential use as an enrichment strategy for applications beyond sequencing. CaBagE is a rapid enrichment method that can illuminate regions of the 'hidden genome' underlying human disease.
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Affiliation(s)
- Amelia D. Wallace
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Thomas A. Sasani
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jordan Swanier
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Brooke L. Gates
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Jeff Greenland
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Brent S. Pedersen
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Katherine E. Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Aaron R. Quinlan
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biomedical Informatics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
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Bakhtiari M, Park J, Ding YC, Shleizer-Burko S, Neuhausen SL, Halldórsson BV, Stefánsson K, Gymrek M, Bafna V. Variable number tandem repeats mediate the expression of proximal genes. Nat Commun 2021; 12:2075. [PMID: 33824302 PMCID: PMC8024321 DOI: 10.1038/s41467-021-22206-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Variable number tandem repeats (VNTRs) account for significant genetic variation in many organisms. In humans, VNTRs have been implicated in both Mendelian and complex disorders, but are largely ignored by genomic pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks to genotype a VNTR in 18 seconds on 55X whole genome data, while maintaining high accuracy. We use adVNTR-NN to genotype 10,264 VNTRs in 652 GTEx individuals. Associating VNTR length with gene expression in 46 tissues, we identify 163 "eVNTRs". Of the 22 eVNTRs in blood where independent data is available, 21 (95%) are replicated in terms of significance and direction of association. 49% of the eVNTR loci show a strong and likely causal impact on the expression of genes and 80% have maximum effect size at least 0.3. The impacted genes are involved in diseases including Alzheimer's, obesity and familial cancers, highlighting the importance of VNTRs for understanding the genetic basis of complex diseases.
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Affiliation(s)
- Mehrdad Bakhtiari
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jonghun Park
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yuan-Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | | | | | - Melissa Gymrek
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA.
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Zamyatin A, Avdeyev P, Liang J, Sharma A, Chen C, Lukyanchikova V, Alexeev N, Tu Z, Alekseyev MA, Sharakhov IV. Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis. Gigascience 2021; 10:giab017. [PMID: 33718948 PMCID: PMC7957348 DOI: 10.1093/gigascience/giab017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. FINDINGS In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis. CONCLUSION The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.
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Affiliation(s)
- Anton Zamyatin
- Computer Technologies Laboratory, ITMO University, Kronverkskiy Prospekt 49-A, Saint Petersburg 197101, Russia
| | - Pavel Avdeyev
- Department of Mathematics, The George Washington University, 801 22nd Street NW, Washington, DC 20052, USA
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
| | - Atashi Sharma
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Chujia Chen
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Institute of Cytology and Genetics the Siberian Division of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Kronverkskiy Prospekt 49-A, Saint Petersburg 197101, Russia
| | - Zhijian Tu
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Max A Alekseyev
- Department of Mathematics, The George Washington University, 801 22nd Street NW, Washington, DC 20052, USA
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
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Schmitz A, Pinheiro Marques J, Oertig I, Maharjan N, Saxena S. Emerging Perspectives on Dipeptide Repeat Proteins in C9ORF72 ALS/FTD. Front Cell Neurosci 2021; 15:637548. [PMID: 33679328 PMCID: PMC7930069 DOI: 10.3389/fncel.2021.637548] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is a hexanucleotide expansion in the chromosome 9 open reading frame 72 gene (C9ORF72). This hexanucleotide expansion consists of GGGGCC (G4C2) repeats that have been implicated to lead to three main modes of disease pathology: loss of function of the C9ORF72 protein, the generation of RNA foci, and the production of dipeptide repeat proteins (DPRs) through repeat-associated non-AUG (RAN) translation. Five different DPRs are currently known to be formed: glycine-alanine (GA) and glycine-arginine (GR) from the sense strand, proline-alanine (PA), and proline-arginine (PR) from the antisense strand, and glycine-proline (GP) from both strands. The exact contribution of each DPR to disease pathology is currently under intense scrutiny and is still poorly understood. However, recent advances in both neuropathological and cellular studies have provided us with clues enabling us to better understand the effect of individual DPRs on disease pathogenesis. In this review, we compile the current knowledge of specific DPR involvement on disease development and highlight recent advances, such as the impact of arginine-rich DPRs on nucleolar protein quality control, the correlation of poly-GR with neurodegeneration, and the possible involvement of chimeric DPR species. Further, we discuss recent findings regarding the mechanisms of RAN translation, its modulators, and other promising therapeutic options.
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Affiliation(s)
- Alexander Schmitz
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - João Pinheiro Marques
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Irina Oertig
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Niran Maharjan
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Smita Saxena
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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Blondal T, Gamba C, Møller Jagd L, Su L, Demirov D, Guo S, Johnston CM, Riising EM, Wu X, Mikkelsen MJ, Szabova L, Mouritzen P. Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing. Methods 2021; 191:68-77. [PMID: 33582298 DOI: 10.1016/j.ymeth.2021.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/12/2020] [Accepted: 02/02/2021] [Indexed: 01/02/2023] Open
Abstract
Validation of CRISPR-Cas9 editing typically explores the immediate vicinity of the gene editing site and distal off-target sequences, which has led to the conclusion that CRISPR-Cas9 editing is very specific. However, an increasing number of studies suggest that on-target unintended editing events like deletions and insertions are relatively frequent but unfortunately often missed in the validation of CRISPR-Cas9 editing. The deletions may be several kilobases-long and only affect one allele. The gold standard in molecular validation of gene editing is direct sequencing of relatively short PCR amplicons. This approach allows the detection of small editing events but fails in detecting large rearrangements, in particular when only one allele is affected. Detection of large rearrangements requires that an extended region is analyzed and the characterization of events may benefit from long-read sequencing. Here we implemented Xdrop™, a new microfluidic technology that allows targeted enrichment of long regions (~100 kb) using just a single standard PCR primer set. Sequencing of the enriched CRISPR-Cas9 gene-edited region in four cell lines on long- and short-read sequencing platforms unravelled unknown and unintended genome editing events. The analysis revealed accidental kilobases-large insertions in three of the cell lines, which remained undetected using standard procedures. We also applied the targeted enrichment approach to identify the integration site of a transgene in a mouse line. The results demonstrate the potential of this technology in gene editing validation as well as in more classic transgenics.
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Affiliation(s)
| | | | | | - Ling Su
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Ludmila Szabova
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, MD, USA
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47
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Koriath CAM, Kenny J, Ryan NS, Rohrer JD, Schott JM, Houlden H, Fox NC, Tabrizi SJ, Mead S. Genetic testing in dementia - utility and clinical strategies. Nat Rev Neurol 2021; 17:23-36. [PMID: 33168964 DOI: 10.1038/s41582-020-00416-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Techniques for clinical genetic testing in dementia disorders have advanced rapidly but remain to be more widely implemented in practice. A positive genetic test offers a precise molecular diagnosis, can help members of an affected family to determine personal risk, provides a basis for reproductive choices and can offer options for clinical trials. The likelihood of identifying a specific genetic cause of dementia depends on the clinical condition, the age at onset and family history. Attempts to match phenotypes to single genes are mostly inadvisable owing to clinical overlap between the dementias, genetic heterogeneity, pleiotropy and concurrent mutations. Currently, the appropriate genetic test in most cases of dementia is a next-generation sequencing gene panel, though some conditions necessitate specific types of test such as repeat expansion testing. Whole-exome and whole-genome sequencing are becoming financially feasible but raise or exacerbate complex issues such as variants of uncertain significance, secondary findings and the potential for re-analysis in light of new information. However, the capacity for data analysis and counselling is already restricting the provision of genetic testing. Patients and their relatives need to be given reliable information to enable them to make informed choices about tests, treatments and data sharing; the ability of patients with dementia to make decisions must be considered when providing this information.
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Affiliation(s)
| | - Joanna Kenny
- South West Thames Regional Genetics Service, London, UK
| | - Natalie S Ryan
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Jonathan D Rohrer
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Jonathan M Schott
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London, UK
| | - Nick C Fox
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, UK.
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48
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Liu Q, Tong Y, Wang K. Genome-wide detection of short tandem repeat expansions by long-read sequencing. BMC Bioinformatics 2020; 21:542. [PMID: 33371889 PMCID: PMC7768641 DOI: 10.1186/s12859-020-03876-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR), or "microsatellite", is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific repeat expansions may be associated with human diseases. Long-read sequencing coupled with bioinformatics tools enables the estimation of repeat counts for STRs. However, with the exception of a few well-known disease-relevant STRs, normal ranges of repeat counts for most STRs in human populations are not well known, preventing the prioritization of STRs that may be associated with human diseases. RESULTS In this study, we extend a computational tool RepeatHMM to infer normal ranges of 432,604 STRs using 21 long-read sequencing datasets on human genomes, and build a genomic-scale database called RepeatHMM-DB with normal repeat ranges for these STRs. Evaluation on 13 well-known repeats show that the inferred repeat ranges provide good estimation to repeat ranges reported in literature from population-scale studies. This database, together with a repeat expansion estimation tool such as RepeatHMM, enables genomic-scale scanning of repeat regions in newly sequenced genomes to identify disease-relevant repeat expansions. As a case study of using RepeatHMM-DB, we evaluate the CAG repeats of ATXN3 for 20 patients with spinocerebellar ataxia type 3 (SCA3) and 5 unaffected individuals, and correctly classify each individual. CONCLUSIONS In summary, RepeatHMM-DB can facilitate prioritization and identification of disease-relevant STRs from whole-genome long-read sequencing data on patients with undiagnosed diseases. RepeatHMM-DB is incorporated into RepeatHMM and is available at https://github.com/WGLab/RepeatHMM .
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yao Tong
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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49
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Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V. Massively multiplex single-molecule oligonucleosome footprinting. eLife 2020; 9:59404. [PMID: 33263279 PMCID: PMC7735760 DOI: 10.7554/elife.59404] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/24/2020] [Indexed: 01/10/2023] Open
Abstract
Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across human epigenomic domains. Our analyses suggest that chromatin is comprised of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution and offers up new avenues for modeling and visualizing higher order chromatin structure.
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Affiliation(s)
- Nour J Abdulhay
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States
| | - Colin P McNally
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States
| | - Laura J Hsieh
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States
| | | | - Aidan Keith
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States
| | - Laurel S Estes
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States
| | - Mehran Karimzadeh
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States.,Vector Institute, Toronto, United States
| | | | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States.,Bakar Computational Health Sciences Institute, San Francisco, United States
| | - Geeta J Narlikar
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States
| | - Vijay Ramani
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States.,Bakar Computational Health Sciences Institute, San Francisco, United States
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50
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Burgio G, Teboul L. Anticipating and Identifying Collateral Damage in Genome Editing. Trends Genet 2020; 36:905-914. [PMID: 33039248 PMCID: PMC7658041 DOI: 10.1016/j.tig.2020.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.
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Affiliation(s)
- Gaëtan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, ACT 2603, Australia.
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK.
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