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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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2
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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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3
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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4
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Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
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Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
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5
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Birnbaum R. Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities. Transl Psychiatry 2023; 13:402. [PMID: 38123544 PMCID: PMC10733427 DOI: 10.1038/s41398-023-02689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Tandem repeats (TRs) are prevalent throughout the genome, constituting at least 3% of the genome, and often highly polymorphic. The high mutation rate of TRs, which can be orders of magnitude higher than single-nucleotide polymorphisms and indels, indicates that they are likely to make significant contributions to phenotypic variation, yet their contribution to schizophrenia has been largely ignored by recent genome-wide association studies (GWAS). Tandem repeat expansions are already known causative factors for over 50 disorders, while common tandem repeat variation is increasingly being identified as significantly associated with complex disease and gene regulation. The current review summarizes key background concepts of tandem repeat variation as pertains to disease risk, elucidating their potential for schizophrenia association. An overview of next-generation sequencing-based methods that may be applied for TR genome-wide identification is provided, and some key methodological challenges in TR analyses are delineated.
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Affiliation(s)
- Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Rafehi H, Bennett MF, Bahlo M. Detection and discovery of repeat expansions in ataxia enabled by next-generation sequencing: present and future. Emerg Top Life Sci 2023; 7:349-359. [PMID: 37733280 PMCID: PMC10754322 DOI: 10.1042/etls20230018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Hereditary cerebellar ataxias are a heterogenous group of progressive neurological disorders that are disproportionately caused by repeat expansions (REs) of short tandem repeats (STRs). Genetic diagnosis for RE disorders such as ataxias are difficult as the current gold standard for diagnosis is repeat-primed PCR assays or Southern blots, neither of which are scalable nor readily available for all STR loci. In the last five years, significant advances have been made in our ability to detect STRs and REs in short-read sequencing data, especially whole-genome sequencing. Given the increasing reliance of genomics in diagnosis of rare diseases, the use of established RE detection pipelines for RE disorders is now a highly feasible and practical first-step alternative to molecular testing methods. In addition, many new pathogenic REs have been discovered in recent years by utilising WGS data. Collectively, genomes are an important resource/platform for further advancements in both the discovery and diagnosis of REs that cause ataxia and will lead to much needed improvement in diagnostic rates for patients with hereditary ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters. Emerg Top Life Sci 2023; 7:ETLS20230075. [PMID: 38088823 PMCID: PMC10754335 DOI: 10.1042/etls20230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over more than three decades, more than 60 monogenic human disorders have been found to be caused by tandem-repeat mutations. These monogenic tandem-repeat disorders include Huntington's disease, a variety of ataxias, amyotrophic lateral sclerosis and frontotemporal dementia, as well as many other neurodegenerative diseases. Furthermore, tandem-repeat disorders can include fragile X syndrome, related fragile X disorders, as well as other neurological and psychiatric disorders. However, these monogenic tandem-repeat disorders, which were discovered via their dominant or recessive modes of inheritance, may represent the 'tip of the iceberg' with respect to tandem-repeat contributions to human disorders. A previous proposal that tandem repeats may contribute to the 'missing heritability' of various common polygenic human disorders has recently been supported by a variety of new evidence. This includes genome-wide studies that associate tandem-repeat mutations with autism, schizophrenia, Parkinson's disease and various types of cancers. In this article, I will discuss how tandem-repeat mutations and polymorphisms could contribute to a wide range of common disorders, along with some of the many major challenges of tandem-repeat biology and medicine. Finally, I will discuss the potential of tandem repeats to be therapeutically targeted, so as to prevent and treat an expanding range of human disorders.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
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Jadhav B, Garg P, van Vugt JJFA, Ibanez K, Gagliardi D, Lee W, Shadrina M, Mokveld T, Dolzhenko E, Martin-Trujillo A, Gies SL, Rocca C, Barbosa M, Jain M, Lahiri N, Lachlan K, Houlden H, Paten B, Veldink J, Tucci A, Sharp AJ. A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.03.23289461. [PMID: 37205357 PMCID: PMC10187445 DOI: 10.1101/2023.05.03.23289461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
GC-rich tandem repeat expansions (TREs) are often associated with DNA methylation, gene silencing and folate-sensitive fragile sites and underlie several congenital and late-onset disorders. Through a combination of DNA methylation profiling and tandem repeat genotyping, we identified 24 methylated TREs and investigated their effects on human traits using PheWAS in 168,641 individuals from the UK Biobank, identifying 156 significant TRE:trait associations involving 17 different TREs. Of these, a GCC expansion in the promoter of AFF3 was linked with a 2.4-fold reduced probability of completing secondary education, an effect size comparable to several recurrent pathogenic microdeletions. In a cohort of 6,371 probands with neurodevelopmental problems of suspected genetic etiology, we observed a significant enrichment of AFF3 expansions compared to controls. With a population prevalence that is at least 5-fold higher than the TRE that causes fragile X syndrome, AFF3 expansions represent a significant cause of neurodevelopmental delay.
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Schlüter A, Vélez-Santamaría V, Verdura E, Rodríguez-Palmero A, Ruiz M, Fourcade S, Planas-Serra L, Launay N, Guilera C, Martínez JJ, Homedes-Pedret C, Albertí-Aguiló MA, Zulaika M, Martí I, Troncoso M, Tomás-Vila M, Bullich G, García-Pérez MA, Sobrido-Gómez MJ, López-Laso E, Fons C, Del Toro M, Macaya A, Beltran S, Gutiérrez-Solana LG, Pérez-Jurado LA, Aguilera-Albesa S, de Munain AL, Casasnovas C, Pujol A. ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization. Genome Med 2023; 15:68. [PMID: 37679823 PMCID: PMC10486091 DOI: 10.1186/s13073-023-01214-2] [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: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions. Nevertheless, there is still an urgent need for sensitive, fast algorithms to maximise WES/WGS diagnostic yield in rare disease patients. Most tools devoted to this aim take advantage of patient phenotype information for prioritization of genomic data, although are often limited by incomplete gene-phenotype knowledge stored in biomedical databases and a lack of proper benchmarking on real-world patient cohorts. METHODS We developed ClinPrior, a novel method for the analysis of WES/WGS data that ranks candidate causal variants based on the patient's standardized phenotypic features (in Human Phenotype Ontology (HPO) terms). The algorithm propagates the data through an interactome network-based prioritization approach. This algorithm was thoroughly benchmarked using a synthetic patient cohort and was subsequently tested on a heterogeneous prospective, real-world series of 135 families affected by hereditary spastic paraplegia (HSP) and/or cerebellar ataxia (CA). RESULTS ClinPrior successfully identified causative variants achieving a final positive diagnostic yield of 70% in our real-world cohort. This includes 10 novel candidate genes not previously associated with disease, 7 of which were functionally validated within this project. We used the knowledge generated by ClinPrior to create a specific interactome for HSP/CA disorders thus enabling future diagnoses as well as the discovery of novel disease genes. CONCLUSIONS ClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses.
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Affiliation(s)
- Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Valentina Vélez-Santamaría
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
| | - Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Unit, Pediatrics Department, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Nathalie Launay
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Cristina Guilera
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Juan José Martínez
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Christian Homedes-Pedret
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
- Neurology Department, Hospital Universitari General de Catalunya, Barcelona, Spain
| | - M Antonia Albertí-Aguiló
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
| | - Miren Zulaika
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
| | - Itxaso Martí
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Donostia University Hospital, University of the Basque Country (UPV-EHU), San Sebastian, Spain
| | - Mónica Troncoso
- Pediatric Neurology Department, Central Campus, Hospital Clínico San Borja Arriarán, Universidad de Chile, Santiago, Chile
| | - Miguel Tomás-Vila
- Neuropediatrics Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG) - Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - M Asunción García-Pérez
- Pediatric Neurology Unit, Pediatrics Department, Hospital Universitario Fundación Alcorcón, Madrid, Spain
| | - María-Jesús Sobrido-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Coruña Institute of Biomedical Research (INIBIC), A Coruña, Spain
- Hospital Clínico Universitario, A Coruña, Spain
| | - Eduardo López-Laso
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Unit, Pediatrics Department, Reina Sofía University Hospital, Córdoba, Spain
- Maimonides Institute For Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
| | - Carme Fons
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Sant Joan de Déu University Hospital, Member of the ERN EpiCARE, Barcelona, Spain
- Sant Joan de Déu Research Institute, (IRSJD), Barcelona, Spain
| | - Mireia Del Toro
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alfons Macaya
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG) - Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Facultat de Biologia, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, 08028, Spain
| | - Luis G Gutiérrez-Solana
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Children's University Hospital Niño Jesús, Madrid, Spain
| | - Luis A Pérez-Jurado
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Genetics Service, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergio Aguilera-Albesa
- Pediatric Neurology Unit, Pediatrics Department, Navarra Health Service, Pamplona, Spain
- Navarrabiomed, Biomedical Research Center, Pamplona, Spain
| | - Adolfo López de Munain
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- Neurology Department, Donostia University Hospital, San Sebastian, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain.
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain.
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10
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Wang X, Huang M, Budowle B, Ge J. TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads. Front Genet 2023; 14:1227176. [PMID: 37533432 PMCID: PMC10390829 DOI: 10.3389/fgene.2023.1227176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.
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Affiliation(s)
- Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
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11
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Vockley J, Aartsma-Rus A, Cohen JL, Cowsert LM, Howell RR, Yu TW, Wasserstein MP, Defay T. Whole-genome sequencing holds the key to the success of gene-targeted therapies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:19-29. [PMID: 36453229 DOI: 10.1002/ajmg.c.32017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/12/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
Rare genetic disorders affect as many as 3%-5% of all babies born. Approximately 10,000 such disorders have been identified or hypothesized to exist. Treatment is supportive except in a limited number of instances where specific therapies exist. Development of new therapies has been hampered by at least two major factors: difficulty in diagnosing diseases early enough to enable treatment before irreversible damage occurs, and the high cost of developing new drugs and getting them approved by regulatory agencies. Whole-genome sequencing (WGS) techniques have become exponentially less expensive and more rapid since the beginning of the human genome project, such that return of clinical data can now be achieved in days rather than years and at a cost that is comparable to other less expansive genetic testing. Thus, it is likely that WGS will ultimately become a mainstream, first-tier NBS technique at least for those disorders without appropriate high-throughput functional tests. However, there are likely to be several steps in the evolution to this end. The clinical implications of these advances are profound but highlight the bottlenecks in drug development that still limit transition to treatments. This article summarizes discussions arising from a recent National Institute of Health conference on nucleic acid therapy, with a focus on the impact of WGS in the identification of diagnosis and treatment of rare genetic disorders.
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Affiliation(s)
- Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | | | - Jennifer L Cohen
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Lex M Cowsert
- National Phenylketonuria Alliance, Eau Claire, Wisconsin, USA
| | - R Rodney Howell
- Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Timothy W Yu
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York, USA
| | - Thomas Defay
- Alexion AstraZeneca Rare Diseases, Boston, Massachusetts, USA
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12
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Handra J, Elbert A, Gazzaz N, Moller-Hansen A, Hyunh S, Lee HK, Boerkoel P, Alderman E, Anderson E, Clarke L, Hamilton S, Hamman R, Hughes S, Ip S, Langlois S, Lee M, Li L, Mackenzie F, Patel MS, Prentice LM, Sangha K, Sato L, Seath K, Seppelt M, Swenerton A, Warnock L, Zambonin JL, Boerkoel CF, Chin HL, Armstrong L. The practice of genomic medicine: A delineation of the process and its governing principles. Front Med (Lausanne) 2023; 9:1071348. [PMID: 36714130 PMCID: PMC9877428 DOI: 10.3389/fmed.2022.1071348] [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: 10/16/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Genomic medicine, an emerging medical discipline, applies the principles of evolution, developmental biology, functional genomics, and structural genomics within clinical care. Enabling widespread adoption and integration of genomic medicine into clinical practice is key to achieving precision medicine. We delineate a biological framework defining diagnostic utility of genomic testing and map the process of genomic medicine to inform integration into clinical practice. This process leverages collaboration and collective cognition of patients, principal care providers, clinical genomic specialists, laboratory geneticists, and payers. We detail considerations for referral, triage, patient intake, phenotyping, testing eligibility, variant analysis and interpretation, counseling, and management within the utilitarian limitations of health care systems. To reduce barriers for clinician engagement in genomic medicine, we provide several decision-making frameworks and tools and describe the implementation of the proposed workflow in a prototyped electronic platform that facilitates genomic care. Finally, we discuss a vision for the future of genomic medicine and comment on areas for continued efforts.
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Affiliation(s)
- Julia Handra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Adrienne Elbert
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Nour Gazzaz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ashley Moller-Hansen
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Stephanie Hyunh
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Pierre Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Emily Alderman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Erin Anderson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Lorne Clarke
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Sara Hamilton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Ronnalea Hamman
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Shevaun Hughes
- Clinical Research Informatics, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Simon Ip
- Process & Systems Improvement, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Mary Lee
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Laura Li
- Breakthrough Genomics, Irvine, CA, United States
| | - Frannie Mackenzie
- Women’s Health Research Institute, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Millan S. Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Leah M. Prentice
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Laura Sato
- Process & Systems Improvement, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Kimberly Seath
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Margaret Seppelt
- Process & Systems Improvement, Provincial Health Services Authority, Vancouver, BC, Canada
| | - Anne Swenerton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Lynn Warnock
- Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Jessica L. Zambonin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Cornelius F. Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Hui-Lin Chin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada,Khoo Teck Puat-National University Children’s Medical Institute, National University Hospital, Singapore, Singapore,*Correspondence: Hui-Lin Chin,
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Provincial Medical Genetics Program, British Columbia Women’s Hospital and Health Centre, Vancouver, BC, Canada
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13
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Méreaux JL, Davoine CS, Coutelier M, Guillot-Noël L, Castrioto A, Charles P, Coarelli G, Ewenczyk C, Klebe S, Heinzmann A, Méneret A, Fauret-Amsellem AL, de Sainte Agathe JM, Brice A, Durr A. Fast and reliable detection of repeat expansions in spinocerebellar ataxia using exomes. J Med Genet 2023:jmg-2022-108924. [PMID: 36599645 DOI: 10.1136/jmg-2022-108924] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/20/2022] [Indexed: 01/06/2023]
Abstract
Usually, molecular diagnosis of spinocerebellar ataxia is based on a step-by-step approach with targeted sizing of four repeat expansions accounting for most dominant cases, then targeted sequencing of other genes. Nowadays, genome sequencing allows detection of most pathogenic variants in a single step. The ExpansionHunter tool can detect expansions in short-read genome sequencing data. Recent studies have shown that ExpansionHunter can also be used to identify repeat expansions in exome sequencing data. We tested ExpansionHunter on spinocerebellar ataxia exomes in a research context as a second-line analysis, after exclusion of main CAG repeat expansions in half of the probands. First, we confirmed the detection of expansions in seven known expansion carriers and then, after targeted analysis of ATXN1, 2, 3 and 7, CACNA1A, TBP, ATN1, NOP56, AR and HTT in 498 exomes, we found 22 additional pathogenic expansions. Comparison with capillary migration sizing in 247 individuals and confirmation of all expanded alleles detected by ExpansionHunter demonstrated that for these loci, sensitivity and specificity reached 100%. ExpansionHunter detected but underestimated the repeat size for larger expansions, and the normal alleles distribution at each locus should be taken into account to detect expansions. Exome combined with ExpansionHunter is reliable to detect repeat expansions in selected loci as first-line analysis in spinocerebellar ataxia.
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Affiliation(s)
- Jean-Loup Méreaux
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claire-Sophie Davoine
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marie Coutelier
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Léna Guillot-Noël
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Anna Castrioto
- Department of Neurology, University Hospital Centre Grenoble Alpes, Grenoble, France
| | - Perrine Charles
- Genetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Giulia Coarelli
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claire Ewenczyk
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Stephan Klebe
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Anna Heinzmann
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Méneret
- Neurology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Anne-Laure Fauret-Amsellem
- Molecular and Cellular Neurogenetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean-Madeleine de Sainte Agathe
- Molecular and Cellular Neurogenetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alexis Brice
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alexandra Durr
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
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14
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Koczwara KE, Lake NJ, DeSimone AM, Lek M. Neuromuscular disorders: finding the missing genetic diagnoses. Trends Genet 2022; 38:956-971. [PMID: 35908999 DOI: 10.1016/j.tig.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022]
Abstract
Neuromuscular disorders (NMDs) are a wide-ranging group of diseases that seriously affect the quality of life of affected individuals. The development of next-generation sequencing revolutionized the diagnosis of NMD, enabling the discovery of hundreds of NMD genes and many more pathogenic variants. However, the diagnostic yield of genetic testing in NMD cohorts remains incomplete, indicating a large number of genetic diagnoses are not identified through current methods. Fortunately, recent advancements in sequencing technologies, analytical tools, and high-throughput functional screening provide an opportunity to circumvent current challenges. Here, we discuss reasons for missing genetic diagnoses in NMD, how emerging technologies and tools can overcome these hurdles, and examine future approaches to improving diagnostic yields in NMD.
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Affiliation(s)
- Katherine E Koczwara
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Nicole J Lake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alec M DeSimone
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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15
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Chiu R, Rajan-Babu IS, Birol I, Friedman JM. Linked-read sequencing for detecting short tandem repeat expansions. Sci Rep 2022; 12:9352. [PMID: 35672336 PMCID: PMC9174224 DOI: 10.1038/s41598-022-13024-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection. We also devised a novel algorithm using BLRS barcodes for distance estimation and evaluated its application for STR genotyping. Both approaches were designed for genotyping large expansions (> 1 kb) that cannot be sized accurately by existing methods. Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an important limitation of BLRS, BLRS is an effective strategy for genotyping many other STR loci.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
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16
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Sharpe JL, Harper NS, West RJH. Identification and Monitoring of Nucleotide Repeat Expansions Using Southern Blotting in Drosophila Models of C9orf72 Motor Neuron Disease and Frontotemporal Dementia. Bio Protoc 2022; 12:e4424. [PMID: 35813024 PMCID: PMC9183971 DOI: 10.21769/bioprotoc.4424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/29/2022] Open
Abstract
Repeat expansion diseases, including fragile X syndrome, Huntington's disease, and C9orf72-related motor neuron disease and frontotemporal dementia, are a group of disorders associated with polymorphic expansions of tandem repeat nucleotide sequences. These expansions are highly repetitive and often hundreds to thousands of repeats in length, making accurate identification and determination of repeat length via PCR or sequencing challenging. Here we describe a protocol for monitoring repeat length in Drosophila models carrying 1,000 repeat C9orf72-related dipeptide repeat transgenes using Southern blotting. This protocol has been used regularly to check the length of these lines for over 100 generations with robust and repeatable results and can be implemented for monitoring any repeat expansion in Drosophila.
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Affiliation(s)
- Joanne L. Sharpe
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
,Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
,Neuroscience Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Nikki S. Harper
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Ryan J. H. West
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
,Neuroscience Institute, The University of Sheffield, Sheffield, United Kingdom
,
*For correspondence:
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17
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Guan W, Shan J, Gao M, Guo J, Wu D, Zhang Q, Wang J, Chen R, Du B, Zhu L, He G. Bulked Segregant RNA Sequencing Revealed Difference Between Virulent and Avirulent Brown Planthoppers. FRONTIERS IN PLANT SCIENCE 2022; 13:843227. [PMID: 35498688 PMCID: PMC9047503 DOI: 10.3389/fpls.2022.843227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most devastating insect pests of rice (Oryza sativa L.), but BPH populations have varying degrees of virulence to rice varieties carrying different resistance genes. To help efforts to characterize these variations we applied bulked segregant RNA sequencing (BSR-seq) to identify differentially expressed genes (DEGs) and genetic loci associated with BPH virulence to YHY15 rice plants carrying the resistance gene Bph15. BPHs that are highly virulent or avirulent to these plants were selected from an F2 population to form two contrasting bulks, and BSR-seq identified 751 DEGs between the bulks. Genes associated with carbohydrate, amino acid and nucleotide metabolism, the endocrine system, and signal transduction were upregulated in the avirulent insects when they fed on these plants. The results also indicated that shifts in lipid metabolism and digestive system pathways were crucial for the virulent BPHs' adaptation to the resistant rice. We identified 24 single-nucleotide polymorphisms (SNPs) in 21 genes linked with BPH virulence. Possible roles of genes apparently linked to BPH virulence are discussed. Our results provide potentially valuable information for further studies of BPH virulence mechanisms and development of robust control strategies.
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18
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Schuler BA, Nelson ET, Koziura M, Cogan JD, Hamid R, Phillips JA. Lessons learned: next-generation sequencing applied to undiagnosed genetic diseases. J Clin Invest 2022; 132:e154942. [PMID: 35362483 PMCID: PMC8970663 DOI: 10.1172/jci154942] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rare genetic disorders, when considered together, are relatively common. Despite advancements in genetics and genomics technologies as well as increased understanding of genomic function and dysfunction, many genetic diseases continue to be difficult to diagnose. The goal of this Review is to increase the familiarity of genetic testing strategies for non-genetics providers. As genetic testing is increasingly used in primary care, many subspecialty clinics, and various inpatient settings, it is important that non-genetics providers have a fundamental understanding of the strengths and weaknesses of various genetic testing strategies as well as develop an ability to interpret genetic testing results. We provide background on commonly used genetic testing approaches, give examples of phenotypes in which the various genetic testing approaches are used, describe types of genetic and genomic variations, cover challenges in variant identification, provide examples in which next-generation sequencing (NGS) failed to uncover the variant responsible for a disease, and discuss opportunities for continued improvement in the application of NGS clinically. As genetic testing becomes increasingly a part of all areas of medicine, familiarity with genetic testing approaches and result interpretation is vital to decrease the burden of undiagnosed disease.
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Affiliation(s)
- Bryce A. Schuler
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Erica T. Nelson
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary Koziura
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joy D. Cogan
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rizwan Hamid
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John A. Phillips
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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19
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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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20
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Rajan-Babu IS, Peng JJ, Chiu R, Li C, Mohajeri A, Dolzhenko E, Eberle MA, Birol I, Friedman JM. Correction to: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions. Genome Med 2021; 13:151. [PMID: 34517885 PMCID: PMC8439056 DOI: 10.1186/s13073-021-00961-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada. .,Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK.
| | - Junran J Peng
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada
| | | | | | - Chenkai Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Arezoo Mohajeri
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| | | | | | - Inanc Birol
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
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Chiu R, Rajan-Babu IS, Friedman JM, Birol I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol 2021; 22:224. [PMID: 34389037 PMCID: PMC8361843 DOI: 10.1186/s13059-021-02447-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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