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Trégouët DA, Morange PE. Next-generation sequencing strategies in venous thromboembolism: in whom and for what purpose? J Thromb Haemost 2024; 22:1826-1834. [PMID: 38641321 DOI: 10.1016/j.jtha.2024.04.004] [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: 02/13/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
Abstract
This invited review follows the oral presentation "To Sequence or Not to Sequence, That Is Not the Question; But 'When, Who, Which and What For?' Is" given during the State of the Art session "Translational Genomics in Thrombosis: From OMICs to Clinics" of the International Society on Thrombosis and Haemostasis 2023 Congress. Emphasizing the power of next-generation sequencing technologies and the diverse strategies associated with DNA variant analysis, this review highlights the unresolved questions and challenges in their implementation both for the clinical diagnosis of venous thromboembolism and in translational research.
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Affiliation(s)
- David-Alexandre Trégouët
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale, Bordeaux Population Health Research Center, Unité Mixte de Recherche 1219, Bordeaux, France.
| | - Pierre-Emmanuel Morange
- Cardiovascular and Nutrition Research Center (Centre de Recherche en CardioVasculaire et Nutrition), Institut National de la Santé et de la Recherche Médicale, Institut National de Recherche pour l'agriculture, l' Alimentation et l'Environnement, Aix-Marseille University, Marseille, France
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2
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Matsumoto S, Uchiumi T, Ueyanagi Y, Noda N, Sakai A, Hotta T, Kato K, Ohga S, Kunisaki Y, Kang D. Long-range and real-time PCR identification of a large SERPINC1 deletion in a patient with antithrombin deficiency. Int J Hematol 2024:10.1007/s12185-024-03796-y. [PMID: 38801563 DOI: 10.1007/s12185-024-03796-y] [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: 01/25/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Congenital antithrombin (AT) or serpin C1 deficiency, caused by a SERPINC1 abnormality, is a high-risk factor for venous thrombosis. SERPINC1 is prone to genetic rearrangement, because it contains numerous Alu elements. In this study, a Japanese patient who developed deep vein thrombosis during pregnancy and exhibited low AT activity underwent SERPINC1 gene analysis using routine methods: long-range polymerase chain reaction (PCR) and real-time PCR. Sequencing using long-range PCR products revealed no pathological variants in SERPINC1 exons or exon-intron junctions, and all the identified variants were homozygous, suggesting a deletion in one SERPINC1 allele. Copy number quantification for each SERPINC1 exon using real-time PCR revealed half the number of exon 1 and 2 copies compared with controls. Moreover, a deletion region was deduced by quantifying the 5'-upstream region copy number of SERPINC1 for each constant region. Direct long-range PCR sequencing with primers for the 5'-end of each presumed deletion region revealed a large Alu-mediated deletion (∼13 kb) involving SERPINC1 exons 1 and 2. Thus, a large deletion was identified in SERPINC1 using conventional PCR methods.
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Affiliation(s)
- Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasushi Ueyanagi
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Nozomi Noda
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Atsuhiko Sakai
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Taeko Hotta
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuya Kunisaki
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Kashiigaoka Rehabilitation Hospital, Fukuoka, Japan
- Department of Medical Laboratory Science, Faculty of Health Sciences, Junshin Gakuen University, Fukuoka, Japan
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3
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Kumar KR, Cowley MJ, Davis RL. The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice. Semin Thromb Hemost 2024. [PMID: 38733978 DOI: 10.1055/s-0044-1786756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Affiliation(s)
- Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord Clinical School, University of Sydney, Concord, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
| | - Mark J Cowley
- School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
- Children's Cancer Institute, UNSW Sydney, Randwick, NSW, Australia
| | - Ryan L Davis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Neurogenetics Research Group, Kolling Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St Leonards, NSW, Australia
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4
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Zamora-Cánovas A, de la Morena-Barrio B, Marín-Quilez A, Sierra-Aisa C, Male C, Fernández-Mosteirin N, Trapero-Marugán M, Padilla J, Garrido-Rodriguez P, Sánchez-Fuentes A, Rodríguez-Alen A, Gómez-González PL, Revilla N, de la Morena-Barrio ME, Bastida JM, Corral J, Rivera J, Lozano ML. Targeted long-read sequencing identifies and characterizes structural variants in cases of inherited platelet disorders. J Thromb Haemost 2024; 22:851-859. [PMID: 38007062 DOI: 10.1016/j.jtha.2023.11.007] [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: 06/23/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Genetic diagnosis of inherited platelet disorders (IPDs) is mainly performed by high-throughput sequencing (HTS). These short-read-based sequencing methods sometimes fail to characterize the genetics of the disease. OBJECTIVES To evaluate nanopore long-read DNA sequencing for characterization of structural variants (SVs) in patients with IPDs. METHODS Four patients with a clinical and laboratory diagnosis of Glanzmann thrombasthenia (GT) (P1 and P2) and Hermansky-Pudlak syndrome (HPS) (P3 and P4) in whom HTS missed the underlying molecular cause were included. DNA was analyzed by both standard HTS and nanopore sequencing on a MinION device (Oxford Nanopore Technologies) after enrichment of DNA spanning regions covering GT and HPS genes. RESULTS In patients with GT, HTS identified only 1 heterozygous ITGB3 splice variant c.2301+1G>C in P2. In patients with HPS, a homozygous deletion in HPS5 was suspected in P3, and 2 heterozygous HPS3 variants, c.2464C>T (p.Arg822∗) and a deletion affecting 2 exons, were reported in P4. Nanopore sequencing revealed a complex SV affecting exons 2 to 6 in ITGB3 (deletion-inversion-duplication) in homozygosity in P1 and compound heterozygosity with the splice variant in P2. In the 2 patients with HPS, nanopore defined the length of the SVs, which were characterized at nucleotide resolution. This allowed the identification of repetitive Alu elements at the breakpoints and the design of specific polymerase chain reactions for family screening. CONCLUSION The nanopore technology overcomes the limitations of standard short-read sequencing techniques in SV characterization. Using nanopore, we characterized novel defects in ITGB3, HPS5, and HPS3, highlighting the utility of long-read sequencing as an additional diagnostic tool in IPDs.
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Affiliation(s)
- Ana Zamora-Cánovas
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Belén de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Ana Marín-Quilez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Cristina Sierra-Aisa
- Servicio de Hematología, Hospital Universitario Cruces, Baracaldo, Bilbao, Spain
| | - Christoph Male
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | | | | | - José Padilla
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Pedro Garrido-Rodriguez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Ana Sánchez-Fuentes
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Agustín Rodríguez-Alen
- Servicio de Hematología, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Toledo, Spain
| | - Pedro Luis Gómez-González
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Nuria Revilla
- Department of Hematology, Hospital Universitario Fundación Jiménez Díaz, Instituto Investigación Sanitaria FJD, Madrid, Spain
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - José María Bastida
- Departmento de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca, Universidad de Salamanca, Salamanca, Spain; On behalf of Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Spanish Society of Thrombosis and Haemostasis, Madrid, Spain
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain; On behalf of Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Spanish Society of Thrombosis and Haemostasis, Madrid, Spain.
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
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5
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Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ. The landscape of human SVA retrotransposons. Nucleic Acids Res 2023; 51:11453-11465. [PMID: 37823611 PMCID: PMC10681720 DOI: 10.1093/nar/gkad821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are evolutionarily young and still-active transposable elements (TEs) in the human genome. Several pathogenic SVA insertions have been identified that directly mutate host genes to cause neurodegenerative and other types of diseases. However, due to their sequence heterogeneity and complex structures as well as limitations in sequencing techniques and analysis, SVA insertions have been less well studied compared to other mobile element insertions. Here, we identified polymorphic SVA insertions from 3646 whole-genome sequencing (WGS) samples of >150 diverse populations and constructed a polymorphic SVA insertion reference catalog. Using 20 long-read samples, we also assembled reference and polymorphic SVA sequences and characterized the internal hexamer/variable-number-tandem-repeat (VNTR) expansions as well as differing SVA activity for SVA subfamilies and human populations. In addition, we developed a module to annotate both reference and polymorphic SVA copies. By characterizing the landscape of both reference and polymorphic SVA retrotransposons, our study enables more accurate genotyping of these elements and facilitate the discovery of pathogenic SVA insertions.
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Affiliation(s)
- Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Eric W Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Antuan Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Natalie I Ho
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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6
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Cuenca-Guardiola J, Morena-Barrio BDL, Navarro-Manzano E, Stevens J, Ouwehand WH, Gleadall NS, Corral J, Fernández-Breis JT. Detection and annotation of transposable element insertions and deletions on the human genome using nanopore sequencing. iScience 2023; 26:108214. [PMID: 37953943 PMCID: PMC10638045 DOI: 10.1016/j.isci.2023.108214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/28/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Repetitive sequences represent about 45% of the human genome. Some are transposable elements (TEs) with the ability to change their position in the genome, creating genetic variability both as insertions or deletions, with potential pathogenic consequences. We used long-read nanopore sequencing to identify TE variants in the genomes of 24 patients with antithrombin deficiency. We identified 7 344 TE insertions and 3 056 TE deletions, 2 926 were not previously described in publicly available databases. The insertions affected 3 955 genes, with 6 insertions located in exons, 3 929 in introns, and 147 in promoters. Potential functional impact was evaluated with gene annotation and enrichment analysis, which suggested a strong relationship with neuron-related functions and autism. We conclude that this study encourages the generation of a complete map of TEs in the human genome, which will be useful for identifying new TEs involved in genetic disorders.
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Affiliation(s)
- Javier Cuenca-Guardiola
- Departamento de Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, IMIB-Pascual Parrilla, Facultad de Informática, Campus de Espinardo, Murcia 30100, Spain
| | - Belén de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-III, Ronda de Garay S/N, Murcia 30003, Spain
| | - Esther Navarro-Manzano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-III, Ronda de Garay S/N, Murcia 30003, Spain
| | - Jonathan Stevens
- Department of Haematology, University of Cambridge, CB2 0PT, Cambridge Biomedical Campus, Cambridge, Cambridge, England, UK
- Blood and Transplant, National Health Service (NHS), CB2 0QQ, Cambridge Biomedical Campus, Cambridge, England, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, CB2 0PT, Cambridge Biomedical Campus, Cambridge, Cambridge, England, UK
- Blood and Transplant, National Health Service (NHS), CB2 0QQ, Cambridge Biomedical Campus, Cambridge, England, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Cambridge Heart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge, England CB2 0AY, UK
- University College London Hospitals, NHS Foundation Trust, London, England, UK
| | - Nicholas S Gleadall
- Department of Haematology, University of Cambridge, CB2 0PT, Cambridge Biomedical Campus, Cambridge, Cambridge, England, UK
- Blood and Transplant, National Health Service (NHS), CB2 0QQ, Cambridge Biomedical Campus, Cambridge, England, UK
| | - Javier Corral
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-III, Ronda de Garay S/N, Murcia 30003, Spain
| | - Jesualdo Tomás Fernández-Breis
- Departamento de Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, IMIB-Pascual Parrilla, Facultad de Informática, Campus de Espinardo, Murcia 30100, Spain
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7
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Sanchis-Juan A, Megy K, Stephens J, Armirola Ricaurte C, Dewhurst E, Low K, French CE, Grozeva D, Stirrups K, Erwood M, McTague A, Penkett CJ, Shamardina O, Tuna S, Daugherty LC, Gleadall N, Duarte ST, Hedrera-Fernández A, Vogt J, Ambegaonkar G, Chitre M, Josifova D, Kurian MA, Parker A, Rankin J, Reid E, Wakeling E, Wassmer E, Woods CG, Raymond FL, Carss KJ. Genome sequencing and comprehensive rare-variant analysis of 465 families with neurodevelopmental disorders. Am J Hum Genet 2023; 110:1343-1355. [PMID: 37541188 PMCID: PMC10432178 DOI: 10.1016/j.ajhg.2023.07.007] [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: 03/13/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023] Open
Abstract
Despite significant progress in unraveling the genetic causes of neurodevelopmental disorders (NDDs), a substantial proportion of individuals with NDDs remain without a genetic diagnosis after microarray and/or exome sequencing. Here, we aimed to assess the power of short-read genome sequencing (GS), complemented with long-read GS, to identify causal variants in participants with NDD from the National Institute for Health and Care Research (NIHR) BioResource project. Short-read GS was conducted on 692 individuals (489 affected and 203 unaffected relatives) from 465 families. Additionally, long-read GS was performed on five affected individuals who had structural variants (SVs) in technically challenging regions, had complex SVs, or required distal variant phasing. Causal variants were identified in 36% of affected individuals (177/489), and a further 23% (112/489) had a variant of uncertain significance after multiple rounds of re-analysis. Among all reported variants, 88% (333/380) were coding nuclear SNVs or insertions and deletions (indels), and the remainder were SVs, non-coding variants, and mitochondrial variants. Furthermore, long-read GS facilitated the resolution of challenging SVs and invalidated variants of difficult interpretation from short-read GS. This study demonstrates the value of short-read GS, complemented with long-read GS, in investigating the genetic causes of NDDs. GS provides a comprehensive and unbiased method of identifying all types of variants throughout the nuclear and mitochondrial genomes in individuals with NDD.
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Affiliation(s)
- Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jonathan Stephens
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Camila Armirola Ricaurte
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Eleanor Dewhurst
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kayyi Low
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Detelina Grozeva
- Department of Medical Genetics, University of Cambridge, Cambridge, UK; Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Kathleen Stirrups
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Marie Erwood
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Amy McTague
- Molecular Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Christopher J Penkett
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Olga Shamardina
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Salih Tuna
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Louise C Daugherty
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nicholas Gleadall
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sofia T Duarte
- Hospital Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisbon, Portugal
| | | | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Gautam Ambegaonkar
- Child Development Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Manali Chitre
- Clinical Medical School, University of Cambridge, Cambridge, UK
| | | | - Manju A Kurian
- Molecular Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alasdair Parker
- Clinical Medical School, University of Cambridge, Cambridge, UK; Child Development Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Evan Reid
- Cambridge Institute for Medical Research and Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Emma Wakeling
- North West Thames Regional Genetics Service, Harrow, UK
| | - Evangeline Wassmer
- Neurology Department, Birmingham Women and Children's Hospital, Birmingham, UK
| | - C Geoffrey Woods
- Clinical Medical School, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - F Lucy Raymond
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK.
| | - Keren J Carss
- Department of Haematology, University of Cambridge, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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8
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Pfaff AL, Bubb VJ, Quinn JP, Koks S. A Genome-Wide Screen for the Exonisation of Reference SINE-VNTR-Alus and Their Expression in CNS Tissues of Individuals with Amyotrophic Lateral Sclerosis. Int J Mol Sci 2023; 24:11548. [PMID: 37511314 PMCID: PMC10380656 DOI: 10.3390/ijms241411548] [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: 06/22/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The hominid-specific retrotransposon SINE-VNTR-Alu (SVA) is a composite element that has contributed to the genetic variation between individuals and influenced genomic structure and function. SVAs are involved in modulating gene expression and splicing patterns, altering mRNA levels and sequences, and have been associated with the development of disease. We evaluated the genome-wide effects of SVAs present in the reference genome on transcript sequence and expression in the CNS of individuals with and without the neurodegenerative disorder Amyotrophic Lateral Sclerosis (ALS). This study identified SVAs in the exons of 179 known transcripts, several of which were expressed in a tissue-specific manner, as well as 92 novel exonisation events occurring in the motor cortex. An analysis of 65 reference genome SVAs polymorphic for their presence/absence in the ALS consortium cohort did not identify any elements that were significantly associated with disease status, age at onset, and survival. However, there were transcripts, such as transferrin and HLA-A, that were differentially expressed between those with or without disease, and expression levels were associated with the genotype of proximal SVAs. This study demonstrates the functional consequences of several SVA elements altering mRNA splicing patterns and expression levels in tissues of the CNS.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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de la Morena-Barrio B, Palomo Á, Padilla J, Martín-Fernández L, Rojo-Carrillo JJ, Cifuentes R, Bravo-Pérez C, Garrido-Rodríguez P, Miñano A, Rubio AM, Pagán J, Llamas M, Vicente V, Vidal F, Lozano ML, Corral J, de la Morena-Barrio ME. Impact of genetic structural variants in factor XI deficiency: identification, accurate characterization, and inferred mechanism by long-read sequencing. J Thromb Haemost 2023; 21:1779-1788. [PMID: 36940803 DOI: 10.1016/j.jtha.2023.03.009] [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: 12/23/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
BACKGROUND Congenital factor XI (FXI) deficiency is a probably underestimated coagulopathy that confers antithrombotic protection. Characterization of genetic defects in F11 is mainly focused on the identification of single-nucleotide variants and small insertion/deletions because they represent up to 99% of the alterations accounting for factor deficiency, with only 3 gross gene defects of structural variants (SVs) having been described. OBJECTIVES To identify and characterize the SVs affecting F11. METHODS The study was performed in 93 unrelated subjects with FXI deficiency recruited in Spanish hospitals over a period of 25 years (1997-2022). F11 was analyzed by next-generation sequencing, multiplex ligand probe amplification, and long-read sequencing. RESULTS Our study identified 30 different genetic variants. Interestingly, we found 3 SVs, all heterozygous: a complex duplication affecting exons 8 and 9, a tandem duplication of exon 14, and a large deletion affecting the whole gene. Nucleotide resolution obtained by long-read sequencing revealed Alu repetitive elements involved in all breakpoints. The large deletion was probably generated de novo in the paternal allele during gametogenesis, and despite affecting 30 additional genes, no syndromic features were described. CONCLUSION SVs may account for a high proportion of F11 genetic defects implicated in the molecular pathology of congenital FXI deficiency. These SVs, likely caused by a nonallelic homologous recombination involving repetitive elements, are heterogeneous in both type and length and may be de novo. These data support the inclusion of methods to detect SVs in this disorder, with long-read-based methods being the most appropriate because they detect all SVs and achieve adequate nucleotide resolution.
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Affiliation(s)
- Belén de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ángeles Palomo
- Servicio de Hematología y Hemoterapia del centro Materno-Infantil del Hospital Regional Universitario Carlos de Haya, Málaga, Spain
| | - José Padilla
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Laura Martín-Fernández
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José Rojo-Carrillo
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Rosa Cifuentes
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Carlos Bravo-Pérez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Pedro Garrido-Rodríguez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Antonia Miñano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ana María Rubio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Pagán
- Servicio de Medicina Interna, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - María Llamas
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Vicente Vicente
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Francisco Vidal
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - María Luisa Lozano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
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Cifuentes R, Padilla J, de la Morena-Barrio ME, de la Morena-Barrio B, Bravo-Pérez C, Garrido-Rodríguez P, Llamas M, Miñano A, Vicente V, Lozano ML, Corral J. Usefulness and Limitations of Multiple Ligation-Dependent Probe Amplification in Antithrombin Deficiency. Int J Mol Sci 2023; 24:ijms24055023. [PMID: 36902454 PMCID: PMC10002544 DOI: 10.3390/ijms24055023] [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: 02/10/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) identifies genetic structural variants in SERPINC1 in 5% of cases with antithrombin deficiency (ATD), the most severe congenital thrombophilia. Our aim was to unravel the utility and limitations of MLPA in a large cohort of unrelated patients with ATD (N = 341). MLPA identified 22 structural variants (SVs) causing ATD (6.5%). MLPA did not detect SVs affecting introns (four cases), and the diagnosis was inaccurate in two cases according to long-range PCR or nanopore sequencing. MLPA was used to detect possible hidden SVs in 61 cases with type I deficiency with single nucleotide variations (SNVs) or small insertion/deletion (INDEL). One case had a false deletion of exon 7, as the 29-bp deletion affected an MLPA probe. We evaluated 32 variants affecting MLPA probes: 27 SNVs and 5 small INDELs. In three cases, MLPA gave false-positive results, all diagnosed as deletions of the affected exon: a small INDEL complex, and two SNVs affecting MLPA probes. Our study confirms the utility of MLPA to detect SVs in ATD, but also shows some limitations in detecting intronic SVs. MLPA renders imprecise and false-positive results for genetic defects which affect MLPA probes. Our results encourage the validation of MLPA results.
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Bai J, Qu Y, OuYang S, Jiao H, Wang Y, Li J, Huang W, Zhao Y, Peng X, Wang D, Jin Y, Wang H, Song F. Novel Alu-mediated deletions of the SMN1 gene were identified by ultra-long read sequencing technology in patients with spinal muscular atrophy. Neuromuscul Disord 2023; 33:382-390. [PMID: 37023488 DOI: 10.1016/j.nmd.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by biallelic variants of the survival motor neuron 1 (SMN1) gene. In this study, our aim was to make a molecular diagnosis in two patients with SMA carrying only one SMN1 copy number. Using ultra-long read sequencing (Ultra-LRS), 1415 bp deletion and 3348 bp deletion of the SMN1 gene were identified in patient 1 and the father of patient 2, respectively. Ultra-LRS revealed two novel deletions, starting from the SMN1 promoter to intron 1. It also accurately provided the location of the deletion breakpoints in the SMN1 gene: chr5 g.70,924,798-70,926,212 for a 1415 bp deletion; chr5 g.70,922,695-70,926,042 for a 3348 bp deletion. By analyzing the breakpoint junctions, we identified that these genomic sequences were composed of Alu sequences, including AluJb, AluYm1, AluSq, and AluYm1, indicating that Alu-mediated rearrangements are a mechanism of SMN1 deletion events. In addition, full-length SMN1 transcripts and SMN protein in patient 1 were significantly decreased (p < 0.01), suggesting that a 1415 bp deletion that included the transcription and translation initiation sites of the SMN1 gene had severe consequences for SMN expression. Ultra-LRS can easily distinguish highly homozygous genes compared to other detection technologies, which is useful for detecting SMN1 intragenic mutations, to quickly discover structural rearrangements and to precisely present the breakpoint positions.
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Cuenca-Guardiola J, de la Morena-Barrio B, García JL, Sanchis-Juan A, Corral J, Fernández-Breis JT. Improvement of large copy number variant detection by whole genome nanopore sequencing. J Adv Res 2022:S2090-1232(22)00241-7. [PMID: 36323370 PMCID: PMC10403694 DOI: 10.1016/j.jare.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such as next-generation short read sequencing or PCR assays, are limited in their capabilities to detect or characterize structural variants. However, the existing software for nanopore sequencing data analysis still reports incomplete variant sets, which also contain erroneous calls, a considerable obstacle for the molecular diagnosis or accurate genotyping of populations. METHODS We compared multiple factors affecting variant calling, such as reference genome version, aligner (minimap2, NGMLR, and lra) choice, and variant caller combinations (Sniffles, CuteSV, SVIM, and NanoVar), to find the optimal group of tools for calling large (>50 kb) deletions and duplications, using data from seven patients exhibiting gross gene defects on SERPINC1 and from a reference variant set as the control. The goal was to obtain the most complete, yet reasonably specific group of large variants using a single cell of PromethION sequencing, which yielded lower depth coverage than short-read sequencing. We also used a custom method for the statistical analysis of the coverage value to refine the resulting datasets. RESULTS We found that for large deletions and duplications (>50 kb), the existing software performed worse than for smaller ones, in terms of both sensitivity and specificity, and newer tools had not improved this. Our novel software, disCoverage, could polish variant callers' results, improving specificity by up to 62% and sensitivity by 15%, the latter requiring other data or samples. CONCLUSION We analyzed the current situation of >50-kb copy number variants with nanopore sequencing, which could be improved. The methods presented in this work could help to identify the known deletions and duplications in a set of patients, while also helping to filter out erroneous calls for these variants, which might aid the efforts to characterize a not-yet well-known fraction of genetic variability in the human genome.
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