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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; 50:1039-1046. [PMID: 38733978 DOI: 10.1055/s-0044-1786756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [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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2
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Najafi P, Reimer C, Gilthorpe JD, Jacobsen KR, Ramløse M, Paul NF, Simianer H, Tetens J, Falker-Gieske C. Genomic evidence for the suitability of Göttingen Minipigs with a rare seizure phenotype as a model for human epilepsy. Neurogenetics 2024; 25:103-117. [PMID: 38383918 PMCID: PMC11076379 DOI: 10.1007/s10048-024-00750-2] [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: 11/29/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024]
Abstract
Epilepsy is a complex genetic disorder that affects about 2% of the global population. Although the frequency and severity of epileptic seizures can be reduced by a range of pharmacological interventions, there are no disease-modifying treatments for epilepsy. The development of new and more effective drugs is hindered by a lack of suitable animal models. Available rodent models may not recapitulate all key aspects of the disease. Spontaneous epileptic convulsions were observed in few Göttingen Minipigs (GMPs), which may provide a valuable alternative animal model for the characterisation of epilepsy-type diseases and for testing new treatments. We have characterised affected GMPs at the genome level and have taken advantage of primary fibroblast cultures to validate the functional impact of fixed genetic variants on the transcriptome level. We found numerous genes connected to calcium metabolism that have not been associated with epilepsy before, such as ADORA2B, CAMK1D, ITPKB, MCOLN2, MYLK, NFATC3, PDGFD, and PHKB. Our results have identified two transcription factor genes, EGR3 and HOXB6, as potential key regulators of CACNA1H, which was previously linked to epilepsy-type disorders in humans. Our findings provide the first set of conclusive results to support the use of affected subsets of GMPs as an alternative and more reliable model system to study human epilepsy. Further neurological and pharmacological validation of the suitability of GMPs as an epilepsy model is therefore warranted.
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Affiliation(s)
- Pardis Najafi
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Christian Reimer
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
- Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Höltystr. 10, 31535, Neustadt, Germany
| | - Jonathan D Gilthorpe
- Department of Integrative Medical Biology, Umeå University, 901 87, Umeå, Sweden
| | - Kirsten R Jacobsen
- Ellegaard Göttingen Minipigs A/S, Sorø Landevej 302, 4261, Dalmose, Denmark
| | - Maja Ramløse
- Ellegaard Göttingen Minipigs A/S, Sorø Landevej 302, 4261, Dalmose, Denmark
| | - Nora-Fabienne Paul
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Henner Simianer
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.
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3
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Raidt J, Loges NT, Olbrich H, Wallmeier J, Pennekamp P, Omran H. Primary ciliary dyskinesia. Presse Med 2023; 52:104171. [PMID: 37516247 DOI: 10.1016/j.lpm.2023.104171] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Primary ciliary dyskinesia (PCD, ORPHA:244) is a group of rare genetic disorders characterized by dysfunction of motile cilia. It is phenotypically and genetically heterogeneous, with more than 50 genes involved. Thanks to genetic, clinical, and functional characterization, immense progress has been made in the understanding and diagnosis of PCD. Nevertheless, it is underdiagnosed due to the heterogeneous phenotype and complexity of diagnosis. This review aims to help clinicians navigate this heterogeneous group of diseases. Here, we describe the broad spectrum of phenotypes associated with PCD and address pitfalls and difficult-to-interpret findings to avoid misinterpretation. METHOD Review of literature CONCLUSION: PCD diagnosis is complex and requires integration of history, clinical picture, imaging, functional and structural analysis of motile cilia and, if available, genetic analysis to make a definitive diagnosis. It is critical that we continue to expand our knowledge of this group of rare disorders to improve the identification of PCD patients and to develop evidence-based therapeutic approaches.
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Affiliation(s)
- Johanna Raidt
- Department of General Pediatrics, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany
| | - Niki Tomas Loges
- Department of General Pediatrics, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany
| | - Heike Olbrich
- Department of General Pediatrics, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany
| | - Julia Wallmeier
- Department of General Pediatrics, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany
| | - Petra Pennekamp
- Department of General Pediatrics, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany.
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4
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Baker EK, Han J, Langley WA, Reott MA, Hallinan BE, Hopkin RJ, Zhang W. RNA sequencing reveals a complete picture of a homozygous missense variant in a patient with VPS13D movement disorder: a case report and review of the literature. Mol Genet Genomics 2023:10.1007/s00438-023-02044-y. [PMID: 37340120 DOI: 10.1007/s00438-023-02044-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: 10/11/2022] [Accepted: 06/04/2023] [Indexed: 06/22/2023]
Abstract
RNA sequencing (RNA-seq) is a complementary diagnostic tool to exome sequencing (ES), only recently clinically available to undiagnosed patients post-ES, that provides functional information on variants of unknown significance (VUS) by evaluating its effect on RNA transcription. ES became clinically available in the early 2010s and promised an agnostic platform for patients with a neurological disease, especially for those who believed to have a genetic etiology. However, the massive data generated by ES pose challenges in variant interpretation, especially for rare missense, synonymous, and deep intronic variants that may have a splicing effect. Without functional study and/or family segregation analysis, these rare variants would be likely interpreted as VUS which is difficult for clinicians to use in clinical care. Clinicians are able to assess the VUS for phenotypic overlap, but this additional information alone is usually not enough to re-classify a variant. Here, we report a case of a 14-month-old male who presented to clinic with a history of seizures, nystagmus, cerebral palsy, oral aversion, global developmental delay, and poor weight gain requiring gastric tube placement. ES revealed a previously unreported homozygous missense VUS, c.7406A > G p.(Asn2469Ser), in VPS13D. This variant has not been previously reported in genome aggregation database (gnomAD), ClinVar, or in any peer-reviewed published literature. By RNA-seq, we demonstrated that this variant mainly impacts splicing and results in a frameshift and early termination. It is expected to generate either a truncated protein, p.(Val2468fs*19), or no protein from this transcript due to nonsense-mediated mRNA decay leading to VPS13D deficiency. To our knowledge, this is the first case utilizing RNA-seq to further functionally characterize a homozygous novel missense VUS in VPS13D and confirm its impact on splicing. This confirmed pathogenicity gave the diagnosis of VPS13D movement disorder to this patient. Therefore, clinicians should consider utilizing RNA-seq to clarify VUS by evaluating its effect on RNA transcription.
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Affiliation(s)
- Elizabeth K Baker
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jingfen Han
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
| | | | | | - Barbara E Hallinan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Neurology, Cincinnati Children's Hospital Medicine, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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5
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Cook DE, Venkat A, Yelizarov D, Pouliot Y, Chang PC, Carroll A, De La Vega FM. A deep-learning-based RNA-seq germline variant caller. BIOINFORMATICS ADVANCES 2023; 3:vbad062. [PMID: 37416509 PMCID: PMC10320079 DOI: 10.1093/bioadv/vbad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Summary RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci and identifying gene fusion events. Although RNA-seq can detect germline variants, the complexities of variable transcript abundance, target capture and amplification introduce challenging sources of error. Here, we extend DeepVariant, a deep-learning-based variant caller, to learn and account for the unique challenges presented by RNA-seq data. Our DeepVariant RNA-seq model produces highly accurate variant calls from RNA-sequencing data, and outperforms existing approaches such as Platypus and GATK. We examine factors that influence accuracy, how our model addresses RNA editing events and how additional thresholding can be used to facilitate our models' use in a production pipeline. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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6
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Salik D, Richert B, Smits G. Clinical and molecular diagnosis of genodermatoses: Review and perspectives. J Eur Acad Dermatol Venereol 2023; 37:488-500. [PMID: 36502512 DOI: 10.1111/jdv.18769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
Genodermatoses are a complex and heterogeneous group of genetic skin disorders characterized by variable expression and clinical and genetic heterogeneity, rendering their diagnosis challenging. DNA-based techniques, like whole-exome sequencing, can establish a diagnosis in 50% of cases. RNA-sequencing is emerging as an attractive tool that can obtain information regarding gene expression while integrating functional genomic data with regard to the interpretation of variants. This increases the diagnostic rate by an additional 10-15%. In the present review, we detail the clinical steps involved in the diagnosis of genodermatoses, as well as the current DNA-based technologies available to clinicians. Herein, the intention is to facilitate a better understanding of the possibilities and limitations of these diagnostic technologies. In addition, this review could guide dermatologists through new emerging techniques, such as RNA-sequencing and its applications to familiarizing them with future techniques. Currently, this multi-omics approach is likely the best strategy designed to promote the diagnosis of patients with genodermatoses and discover new skin disease genes that could result in novel targeted therapies.
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Affiliation(s)
- Deborah Salik
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Bertrand Richert
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics Université Libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
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7
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Čelešnik H, Potočnik U. Blood-Based mRNA Tests as Emerging Diagnostic Tools for Personalised Medicine in Breast Cancer. Cancers (Basel) 2023; 15:1087. [PMID: 36831426 PMCID: PMC9954278 DOI: 10.3390/cancers15041087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Molecular diagnostic tests help clinicians understand the underlying biological mechanisms of their patients' breast cancer (BC) and facilitate clinical management. Several tissue-based mRNA tests are used routinely in clinical practice, particularly for assessing the BC recurrence risk, which can guide treatment decisions. However, blood-based mRNA assays have only recently started to emerge. This review explores the commercially available blood mRNA diagnostic assays for BC. These tests enable differentiation of BC from non-BC subjects (Syantra DX, BCtect), detection of small tumours <10 mm (early BC detection) (Syantra DX), detection of different cancers (including BC) from a single blood sample (multi-cancer blood test Aristotle), detection of BC in premenopausal and postmenopausal women and those with high breast density (Syantra DX), and improvement of diagnostic outcomes of DNA testing (variant interpretation) (+RNAinsight). The review also evaluates ongoing transcriptomic research on exciting possibilities for future assays, including blood transcriptome analyses aimed at differentiating lymph node positive and negative BC, distinguishing BC and benign breast disease, detecting ductal carcinoma in situ, and improving early detection further (expression changes can be detected in blood up to eight years before diagnosing BC using conventional approaches, while future metastatic and non-metastatic BC can be distinguished two years before BC diagnosis).
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Affiliation(s)
- Helena Čelešnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
- Department for Science and Research, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
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8
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Körner MB, Velluva A, Bundalian L, Radtke M, Lin CC, Zacher P, Bartolomaeus T, Kirstein AS, Mrestani A, Scholz N, Platzer K, Teichmann AC, Hentschel J, Langenhan T, Lemke JR, Garten A, Abou Jamra R, Le Duc D. Altered gene expression profiles impair the nervous system development in individuals with 15q13.3 microdeletion. Sci Rep 2022; 12:13507. [PMID: 35931711 PMCID: PMC9356015 DOI: 10.1038/s41598-022-17604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
The 15q13.3 microdeletion has pleiotropic effects ranging from apparently healthy to severely affected individuals. The underlying basis of the variable phenotype remains elusive. We analyzed gene expression using blood from three individuals with 15q13.3 microdeletion and brain cortex tissue from ten mice Df[h15q13]/+. We assessed differentially expressed genes (DEGs), protein–protein interaction (PPI) functional modules, and gene expression in brain developmental stages. The deleted genes’ haploinsufficiency was not transcriptionally compensated, suggesting a dosage effect may contribute to the pathomechanism. DEGs shared between tested individuals and a corresponding mouse model show a significant overlap including genes involved in monogenic neurodevelopmental disorders. Yet, network-wide dysregulatory effects suggest the phenotype is not caused by a single critical gene. A significant proportion of blood DEGs, silenced in adult brain, have maximum expression during the prenatal brain development. Based on DEGs and their PPI partners we identified altered functional modules related to developmental processes, including nervous system development. We show that the 15q13.3 microdeletion has a ubiquitous impact on the transcriptome pattern, especially dysregulation of genes involved in brain development. The high phenotypic variability seen in 15q13.3 microdeletion could stem from an increased vulnerability during brain development, instead of a specific pathomechanism.
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Affiliation(s)
- Marek B Körner
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany.,Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Akhil Velluva
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Linnaeus Bundalian
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Pia Zacher
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.,Epilepsy Center Kleinwachau, 01454, Radeberg, Germany
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Anna S Kirstein
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103, Leipzig, Germany
| | - Achmed Mrestani
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany.,Department of Neurology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Nicole Scholz
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | | | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Tobias Langenhan
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Antje Garten
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany. .,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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9
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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: 6] [Impact Index Per Article: 3.0] [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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10
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Targeted RNAseq Improves Clinical Diagnosis of Very Early-Onset Pediatric Immune Dysregulation. J Pers Med 2022; 12:jpm12060919. [PMID: 35743704 PMCID: PMC9224647 DOI: 10.3390/jpm12060919] [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: 04/28/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
Despite increased use of whole exome sequencing (WES) for the clinical analysis of rare disease, overall diagnostic yield for most disorders hovers around 30%. Previous studies of mRNA have succeeded in increasing diagnoses for clearly defined disorders of monogenic inheritance. We asked if targeted RNA sequencing could provide similar benefits for primary immunodeficiencies (PIDs) and very early-onset inflammatory bowel disease (VEOIBD), both of which are difficult to diagnose due to high heterogeneity and variable severity. We performed targeted RNA sequencing of a panel of 260 immune-related genes for a cohort of 13 patients (seven suspected PID cases and six VEOIBD) and analyzed variants, splicing, and exon usage. Exonic variants were identified in seven cases, some of which had been previously prioritized by exome sequencing. For four cases, allele specific expression or lack thereof provided additional insights into possible disease mechanisms. In addition, we identified five instances of aberrant splicing associated with four variants. Three of these variants had been previously classified as benign in ClinVar based on population frequency. Digenic or oligogenic inheritance is suggested for at least two patients. In addition to validating the use of targeted RNA sequencing, our results show that rare disease research will benefit from incorporating contributing genetic factors into the diagnostic approach.
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11
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Peymani F, Farzeen A, Prokisch H. RNA sequencing role and application in clinical diagnostic. Pediatr Investig 2022; 6:29-35. [PMID: 35382420 PMCID: PMC8960934 DOI: 10.1002/ped4.12314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
Although whole-exome sequencing and whole-genome sequencing has tremendously improved our understanding of the genetic etiology of human disorders, about half of the patients still do not receive a molecular diagnosis. The high fraction of variants with uncertain significance and the challenges of interpretation of noncoding variants have urged scientists to implement RNA sequencing (RNA-seq) in the diagnostic approach as a high throughput assay to complement genomic data with functional evidence. RNA-seq data can be used to identify aberrantly spliced genes, detect allele-specific expression, and identify gene expression outliers. Amongst eight studies utilizing RNA-seq, a mean diagnostic uplift of 15% has been reported. Here, we provide an overview of how RNA-seq has been implemented to aid in identifying the causal variants of Mendelian disorders.
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Affiliation(s)
- Fatemeh Peymani
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre MunichNeuherbergGermany
| | - Aiman Farzeen
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre MunichNeuherbergGermany
| | - Holger Prokisch
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre MunichNeuherbergGermany
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