1
|
Tsai CY, Hsu JSJ, Chen PL, Wu CC. Implementing next-generation sequencing for diagnosis and management of hereditary hearing impairment: a comprehensive review. Expert Rev Mol Diagn 2024:1-13. [PMID: 39194060 DOI: 10.1080/14737159.2024.2396866] [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: 06/14/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION Sensorineural hearing impairment (SNHI), a common childhood disorder with heterogeneous genetic causes, can lead to delayed language development and psychosocial problems. Next-generation sequencing (NGS) offers high-throughput screening and high-sensitivity detection of genetic etiologies of SNHI, enabling clinicians to make informed medical decisions, provide tailored treatments, and improve prognostic outcomes. AREAS COVERED This review covers the diverse etiologies of HHI and the utility of different NGS modalities (targeted sequencing and whole exome/genome sequencing), and includes HHI-related studies on newborn screening, genetic counseling, prognostic prediction, and personalized treatment. Challenges such as the trade-off between cost and diagnostic yield, detection of structural variants, and exploration of the non-coding genome are also highlighted. EXPERT OPINION In the current landscape of NGS-based diagnostics for HHI, there are both challenges (e.g. detection of structural variants and non-coding genome variants) and opportunities (e.g. the emergence of medical artificial intelligence tools). The authors advocate the use of technological advances such as long-read sequencing for structural variant detection, multi-omics analysis for non-coding variant exploration, and medical artificial intelligence for pathogenicity assessment and outcome prediction. By integrating these innovations into clinical practice, precision medicine in the diagnosis and management of HHI can be further improved.
Collapse
Affiliation(s)
- Cheng-Yu Tsai
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Jacob Shu-Jui Hsu
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
- Department of Otolaryngology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| |
Collapse
|
2
|
Adams DR, van Karnebeek CDM, Agulló SB, Faùndes V, Jamuar SS, Lynch SA, Pintos-Morell G, Puri RD, Shai R, Steward CA, Tumiene B, Verloes A. Addressing diagnostic gaps and priorities of the global rare diseases community: Recommendations from the IRDiRC diagnostics scientific committee. Eur J Med Genet 2024; 70:104951. [PMID: 38848991 DOI: 10.1016/j.ejmg.2024.104951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/05/2024] [Indexed: 06/09/2024]
Abstract
The International Rare Diseases Research Consortium (IRDiRC) Diagnostic Scientific Committee (DSC) is charged with discussion and contribution to progress on diagnostic aspects of the IRDiRC core mission. Specifically, IRDiRC goals include timely diagnosis, use of globally coordinated diagnostic pipelines, and assessing the impact of rare diseases on affected individuals. As part of this mission, the DSC endeavored to create a list of research priorities to achieve these goals. We present a discussion of those priorities along with aspects of current, global rare disease needs and opportunities that support our prioritization. In support of this discussion, we also provide clinical vignettes illustrating real-world examples of diagnostic challenges.
Collapse
Affiliation(s)
- David R Adams
- National Human Genome Research Institute, National Institutes of Health, USA.
| | - Clara D M van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam Gastro-enterology Endocrinology Metabolism, Amsterdam University Medical Centers, the Netherlands
| | - Sergi Beltran Agulló
- Centre Nacional d'Anàlisi Genòmica (CNAG), Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Spain
| | - Víctor Faùndes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Chile
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women's and Children's Hospital and Paediatrics ACP, Duke-NUS Medical School, Singapore; Singhealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | - Guillem Pintos-Morell
- Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital, Spain; MPS-Spain Patient Advocacy Organization, Spain
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, India
| | - Ruty Shai
- Pediatric Cancer Molecular Lab, Sheba Medical Center, Israel
| | | | - Biruté Tumiene
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Lithuania
| | - Alain Verloes
- Département de Génétique, CHU Paris - Hôpital Robert Debré, France
| |
Collapse
|
3
|
Lewis SA, Ruttenberg A, Iyiyol T, Kong N, Jin SC, Kruer MC. Potential clinical applications of advanced genomic analysis in cerebral palsy. EBioMedicine 2024; 106:105229. [PMID: 38970919 PMCID: PMC11282942 DOI: 10.1016/j.ebiom.2024.105229] [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: 02/15/2024] [Revised: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have been the primary methods for establishing new CP-gene relationships and providing a genetic etiology for individual patients, the cause of their condition remains unknown for many patients with CP. Recent advancements in genomic technologies offer additional opportunities to uncover variations in human genomes, transcriptomes, and epigenomes that have previously escaped detection. In this review, we outline the use of these state-of-the-art technologies to address the molecular diagnostic challenges experienced by individuals with CP. We also explore the importance of identifying a molecular etiology whenever possible, given the potential for genomic medicine to provide opportunities to treat patients with CP in new and more precise ways.
Collapse
Affiliation(s)
- Sara A Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States
| | - Andrew Ruttenberg
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tuğçe Iyiyol
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Nahyun Kong
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States; Programs in Neuroscience and Molecular & Cellular Biology, School of Life Sciences, Arizona State University, Tempe, AZ, United States.
| |
Collapse
|
4
|
Dyshlovoy SA, Paigin S, Afflerbach AK, Lobermeyer A, Werner S, Schüller U, Bokemeyer C, Schuh AH, Bergmann L, von Amsberg G, Joosse SA. Applications of Nanopore sequencing in precision cancer medicine. Int J Cancer 2024. [PMID: 39031959 DOI: 10.1002/ijc.35100] [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: 03/09/2024] [Revised: 04/25/2024] [Accepted: 06/25/2024] [Indexed: 07/22/2024]
Abstract
Oxford Nanopore Technologies sequencing, also referred to as Nanopore sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential for rapid, long read, and real-time DNA and RNA sequencing. This technology is currently making sequencing more accessible and affordable. In this comprehensive review, we explore its potential regarding precision cancer diagnostics and treatment. We encompass a critical analysis of clinical cases where Nanopore sequencing was successfully applied to identify point mutations, splice variants, gene fusions, epigenetic modifications, non-coding RNAs, and other pivotal biomarkers that defined subsequent treatment strategies. Additionally, we address the challenges of clinical applications of Nanopore sequencing and discuss the current efforts to overcome them.
Collapse
Affiliation(s)
- Sergey A Dyshlovoy
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie Paigin
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ann-Kristin Afflerbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabelle Lobermeyer
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Lina Bergmann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
5
|
Ong CT, Mody KT, Cavallaro AS, Yan Y, Nguyen LT, Shao R, Mitter N, Mahony TJ, Ross EM. Chromosome-Scale Genome Assembly of the Sheep-Biting Louse Bovicola ovis Using Nanopore Sequencing Data and Pore-C Analysis. Int J Mol Sci 2024; 25:7824. [PMID: 39063065 PMCID: PMC11276745 DOI: 10.3390/ijms25147824] [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: 06/10/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Bovicola ovis, commonly known as the sheep-biting louse, is an ectoparasite that adversely affects the sheep industry. Sheep louse infestation lowers the quality of products, including wool and leather, causing a loss of approximately AUD 123M per annum in Australia alone. The lack of a high-quality genome assembly for the sheep-biting louse, as well as any closely related livestock lice, has hindered the development of louse research and management control tools. In this study, we present the assembly of B. ovis with a genome size of ~123 Mbp based on a nanopore long-read sequencing library and Illumina RNA sequencing, complemented with a chromosome-level scaffolding using the Pore-C multiway chromatin contact dataset. Combining multiple alignment and gene prediction tools, a comprehensive annotation on the assembled B. ovis genome was conducted and recalled 11,810 genes as well as other genomic features including orf, ssr, rRNA and tRNA. A manual curation using alignment with the available closely related louse species, Pediculus humanus, increased the number of annotated genes to 16,024. Overall, this study reported critical genetic resources and biological insights for the advancement of sheep louse research and the development of sustainable control strategies in the sheep industry.
Collapse
Affiliation(s)
- Chian Teng Ong
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Karishma T. Mody
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Antonino S. Cavallaro
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Yakun Yan
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Loan T. Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Renfu Shao
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia;
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Neena Mitter
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Timothy J. Mahony
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Elizabeth M. Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| |
Collapse
|
6
|
Fahy S, O’Connor JA, Sleator RD, Lucey B. From Species to Genes: A New Diagnostic Paradigm. Antibiotics (Basel) 2024; 13:661. [PMID: 39061343 PMCID: PMC11274079 DOI: 10.3390/antibiotics13070661] [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: 06/02/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.
Collapse
Affiliation(s)
- Sinead Fahy
- Department of Microbiology, Mercy University Hospital, T12 WE28 Cork, Ireland;
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| | - James A. O’Connor
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| | - Roy D. Sleator
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| |
Collapse
|
7
|
Vormittag-Nocito E, Sukhanova M, Godley LA. The impact of next-generation sequencing for diagnosis and disease understanding of myeloid malignancies. Expert Rev Mol Diagn 2024; 24:591-600. [PMID: 39054632 DOI: 10.1080/14737159.2024.2383445] [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: 05/15/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
INTRODUCTION Defining the chromosomal and molecular changes associated with myeloid neoplasms (MNs) optimizes clinical care through improved diagnosis, prognosis, treatment planning, and patient monitoring. This review will concisely describe the techniques used to profile MNs clinically today, with descriptions of challenges and emerging approaches that may soon become standard-of-care. AREAS COVERED In this review, the authors discuss molecular assessment of MNs using non-sequencing techniques, including conventional cytogenetic analysis, fluorescence in situ hybridization, chromosomal genomic microarray testing; as well as DNA- or RNA-based next-generation sequencing (NGS) assays; and sequential monitoring via digital PCR or measurable residual disease assays. The authors explain why distinguishing somatic from germline alleles is critical for optimal management. Finally, they introduce emerging technologies, such as long-read, whole exome/genome, and single-cell sequencing, which are reserved for research purposes currently but will become clinical tests soon. EXPERT OPINION The authors describe challenges to the adoption of comprehensive genomic tests for those in resource-constrained environments and for inclusion into clinical trials. In the future, all aspects of patient care will likely be influenced by the adaptation of artificial intelligence and mathematical modeling, fueled by rapid advances in telecommunications.
Collapse
Affiliation(s)
- Erica Vormittag-Nocito
- Division of Genomics, Department of Pathology and the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madina Sukhanova
- Division of Genomics, Department of Pathology and the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lucy A Godley
- Division of Hematology/Oncology, Department of Medicine and the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
8
|
Kuroki Y, Hattori A, Matsubara K, Fukami M. Long-read next-generation sequencing for molecular diagnosis of pediatric endocrine disorders. Ann Pediatr Endocrinol Metab 2024; 29:156-160. [PMID: 38956752 PMCID: PMC11220396 DOI: 10.6065/apem.2448028.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/23/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advances in long-read next-generation sequencing (NGS) have enabled researchers to identify several pathogenic variants overlooked by short-read NGS, array-based comparative genomic hybridization, and other conventional methods. Long-read NGS is particularly useful in the detection of structural variants and repeat expansions. Furthermore, it can be used for mutation screening in difficultto- sequence regions, as well as for DNA-methylation analyses and haplotype phasing. This mini-review introduces the usefulness of long-read NGS in the molecular diagnosis of pediatric endocrine disorders.
Collapse
Affiliation(s)
- Yoko Kuroki
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Hattori
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keiko Matsubara
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| |
Collapse
|
9
|
Azevedo L, Amaro AP, Niza-Ribeiro J, Lopes-Marques M. Naturally occurring genetic diseases caused by de novo variants in domestic animals. Anim Genet 2024; 55:319-327. [PMID: 38323510 DOI: 10.1111/age.13403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024]
Abstract
With the advent of next-generation sequencing, an increasing number of cases of de novo variants in domestic animals have been reported in scientific literature primarily associated with clinically severe phenotypes. The emergence of new variants at each generation is a crucial aspect in understanding the pathology of early-onset diseases in animals and can provide valuable insights into similar diseases in humans. With the aim of collecting deleterious de novo variants in domestic animals, we searched the scientific literature and compiled reports on 42 de novo variants in 31 genes in domestic animals. No clear disease-associated phenotype has been established in humans for three of these genes (NUMB, ANKRD28 and KCNG1). For the remaining 28 genes, a strong similarity between animal and human phenotypes was recognized from available information in OMIM and OMIA, revealing the importance of comparative studies and supporting the use of domestic animals as natural models for human diseases, in line with the One Health approach.
Collapse
Affiliation(s)
- Luísa Azevedo
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Andreia P Amaro
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - João Niza-Ribeiro
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Population Studies Department, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- EPIUnit-Epidemiology Research Unit, ISPUP-Institute of Public Health of the University of Porto, Porto, Portugal
| | - Mónica Lopes-Marques
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| |
Collapse
|
10
|
Yeo K, Connell J, Bouras G, Smith E, Murphy W, Hodge JC, Krishnan S, Wormald PJ, Valentine R, Psaltis AJ, Vreugde S, Fenix KA. A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues. Arch Microbiol 2024; 206:248. [PMID: 38713383 PMCID: PMC11076400 DOI: 10.1007/s00203-024-03985-7] [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: 03/13/2024] [Accepted: 04/28/2024] [Indexed: 05/08/2024]
Abstract
Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina) in 26 HNC tumour tissues. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. We observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.131, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in relative abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (75% vs. 18.8%). FL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing.
Collapse
Affiliation(s)
- Kenny Yeo
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia.
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.
| | - James Connell
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - George Bouras
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Eric Smith
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - William Murphy
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - John-Charles Hodge
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Otolaryngology, Head and Neck Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Suren Krishnan
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Otolaryngology, Head and Neck Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Peter-John Wormald
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Rowan Valentine
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Alkis James Psaltis
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Sarah Vreugde
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Kevin Aaron Fenix
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia.
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.
| |
Collapse
|
11
|
Morita S, Nomura S, Azuma K, Chida-Nagai A, Furutani Y, Inai K, Inoue T, Niimi Y, Iizuka Y, Tsutsumi Y, Ishizaki R, Yamagishi H, Kawamata T, Akagawa H. Functional characterization of variants found in Japanese patients with hereditary hemorrhagic telangiectasia. Clin Genet 2024; 105:543-548. [PMID: 38225712 DOI: 10.1111/cge.14483] [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: 11/10/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant form of vascular dysplasia. Genetic diagnosis is made by identifying loss-of-function variants in genes, such as ENG and ACVRL1. However, the causal mechanisms of various variants of unknown significance remains unclear. In this study, we analyzed 12 Japanese patients from 11 families who were clinically diagnosed with HHT. Sequencing analysis identified 11 distinct variants in ACVRL1 and ENG. Three of the 11 were truncating variants, leading to a definitive diagnosis, whereas the remaining eight were splice-site and missense variants that required functional analyses. In silico splicing analyses demonstrated that three variants, c.526-3C > G and c.598C > G in ACVRL1, and c.690-1G > A in ENG, caused aberrant splicing, as confirmed by a minigene assay. The five remaining missense variants were p.Arg67Gln, p.Ile256Asn, p.Leu285Pro, and p.Pro424Leu in ACVRL and p.Pro165His in ENG. Nanoluciferase-based bioluminescence analyses demonstrated that these ACVRL1 variants impaired cell membrane trafficking, resulting in the loss of bone morphogenetic protein 9 (BMP9) signal transduction. In contrast, the ENG mutation impaired BMP9 signaling despite normal cell membrane expression. The updated functional analysis methods performed in this study will facilitate effective genetic testing and appropriate medical care for patients with HHT.
Collapse
Affiliation(s)
- Shuhei Morita
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Shunsuke Nomura
- Department of Neurosurgery, Tokyo Women's Medical University Yachiyo Medical center, Yachiyo, Japan
- Krembil Brain Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Kenko Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Ayako Chida-Nagai
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Kei Inai
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Tatsuya Inoue
- Department of Neurosurgery, St. Luke's International Hospital, Tokyo, Japan
| | - Yasunari Niimi
- Department of Neuroendovascular Therapy, St. Luke's International Hospital, Tokyo, Japan
| | - Yuo Iizuka
- Department of Neuroradiology, Kashiwa Tanaka Hospital, Kashiwa, Japan
| | - Yoshiyuki Tsutsumi
- Department of Radiology, National Center for Child Health and Development, Tokyo, Japan
| | - Reina Ishizaki
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Yamagishi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| |
Collapse
|
12
|
Luo Y, Zhang J, Ni M, Mei Z, Ye Q, Guo B, Fang L, Feng D, Wang L, Yan J, Wang G. Pilot validation of on-field STR typing and human identity testing by MinION nanopore sequencing. Electrophoresis 2024; 45:885-896. [PMID: 38356010 DOI: 10.1002/elps.202300234] [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: 10/16/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
Nanopore sequencing technology has broad application prospects in forensic medicine due to its small size, portability, fast speed, real-time result analysis capabilities, single-molecule sequencing abilities, and simple operation. Here, we demonstrate for the first time that nanopore sequencing platforms can be used to identify individuals in the field. Through scientific and reasonable design, a nanopore MinION MK1B device and other auxiliary devices are integrated into a portable detection box conducive to individual identification at the accident site. Individual identification of 12 samples could be completed within approximately 24 h by jointly detecting 23 short tandem repeat (STR) loci. Through double-blinded experiments, the genotypes of 49 samples were successfully determined, and the accuracy of the STR genotyping was verified by the gold standard. Specifically, the typing success rate for 1150 genotypes was 95.3%, and the accuracy rate was 86.87%. Although this study focused primarily on demonstrating the feasibility of full-process testing, it can be optimistically predicted that further improvements in bioinformatics workflows and nanopore sequencing technology will help enhance the feasibility of Oxford Nanopore Technologies equipment for real-time individual identification at accident sites.
Collapse
Affiliation(s)
- Yuan Luo
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Jiarong Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
| | - Zhusong Mei
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Qiao Ye
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Bingqian Guo
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Longmei Fang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Dongyun Feng
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Lu Wang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Guangyun Wang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| |
Collapse
|
13
|
Mallett AJ, Ingles J, Goranitis I, Stark Z. Implementation of reimbursement for genomic testing in Australia: early successes and the pathway ahead. Intern Med J 2024; 54:531-534. [PMID: 38578038 DOI: 10.1111/imj.16369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 02/18/2024] [Indexed: 04/06/2024]
Affiliation(s)
- Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Queensland, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Jodie Ingles
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research and University of New South Wales, Sydney, New South Wales, Australia
| | - Ilias Goranitis
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Economics of Genomics and Precision Medicine Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| |
Collapse
|
14
|
Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
Collapse
Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
| | | |
Collapse
|
15
|
Mahmoud M, Harting J, Corbitt H, Chen X, Jhangiani SN, Doddapaneni H, Meng Q, Han T, Lambert C, Zhang S, Baybayan P, Henno G, Shen H, Hu J, Han Y, Riegler C, Metcalf G, Henno G, Chinn IK, Eberle MA, Kingan S, Farinholt T, Carvalho CM, Gibbs RA, Kronenberg Z, Muzny D, Sedlazeck FJ. Closing the gap: Solving complex medically relevant genes at scale. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24304179. [PMID: 38562723 PMCID: PMC10984040 DOI: 10.1101/2024.03.14.24304179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Comprehending the mechanism behind human diseases with an established heritable component represents the forefront of personalized medicine. Nevertheless, numerous medically important genes are inaccurately represented in short-read sequencing data analysis due to their complexity and repetitiveness or the so-called 'dark regions' of the human genome. The advent of PacBio as a long-read platform has provided new insights, yet HiFi whole-genome sequencing (WGS) cost remains frequently prohibitive. We introduce a targeted sequencing and analysis framework, Twist Alliance Dark Genes Panel (TADGP), designed to offer phased variants across 389 medically important yet complex autosomal genes. We highlight TADGP accuracy across eleven control samples and compare it to WGS. This demonstrates that TADGP achieves variant calling accuracy comparable to HiFi-WGS data, but at a fraction of the cost. Thus, enabling scalability and broad applicability for studying rare diseases or complementing previously sequenced samples to gain insights into these complex genes. TADGP revealed several candidate variants across all cases and provided insight into LPA diversity when tested on samples from rare disease and cardiovascular disease cohorts. In both cohorts, we identified novel variants affecting individual disease-associated genes (e.g., IKZF1, KCNE1). Nevertheless, the annotation of the variants across these 389 medically important genes remains challenging due to their underrepresentation in ClinVar and gnomAD. Consequently, we also offer an annotation resource to enhance the evaluation and prioritization of these variants. Overall, we can demonstrate that TADGP offers a cost-efficient and scalable approach to routinely assess the dark regions of the human genome with clinical relevance.
Collapse
Affiliation(s)
- Medhat Mahmoud
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Xiao Chen
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Harsha Doddapaneni
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Qingchang Meng
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Tina Han
- Twist Bioscience, South San Francisco, USA
| | | | - Siyuan Zhang
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Geoff Henno
- Pacific Biosciences, Menlo Park, California, USA
| | - Hua Shen
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Jianhong Hu
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Yi Han
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | | | - Ginger Metcalf
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Geoff Henno
- Pacific Biosciences, Menlo Park, California, USA
| | - Ivan K. Chinn
- Department of Pediatrics, Section of Immunology Allergy and Rheumatology, Center for Human Immunobiology, Texas Children’s Hospital and Baylor College of Medicine, Houston, Texas, USA
| | | | - Sarah Kingan
- Pacific Biosciences, Menlo Park, California, USA
| | | | | | - Richard A. Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | | | - Donna Muzny
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
| |
Collapse
|
16
|
Cho JW, Cao J, Hemberg M. Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome Biol 2024; 25:65. [PMID: 38459554 PMCID: PMC10921788 DOI: 10.1186/s13059-024-03201-1] [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: 11/03/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to study both mutational and transcriptomic profiles, but as most studies have been conducted on model systems, little is known about cancer evolution in human patients. Hence, a better understanding of cancer evolution could have important implications for treatment strategies. RESULTS Here, we analyze cancer evolution and clonal selection by jointly considering mutational and transcriptomic profiles of single cells acquired from tumor biopsies from 49 lung cancer samples and 51 samples with chronic myeloid leukemia. Comparing the two profiles, we find that each clone is associated with a preferred transcriptional state. For metastasis and drug resistance, we find that the number of mutations affecting related genes increases as the clone evolves, while changes in gene expression profiles are limited. Surprisingly, we find that mutations affecting ligand-receptor interactions with the tumor microenvironment frequently emerge as clones acquire drug resistance. CONCLUSIONS Our results show that lung cancer and chronic myeloid leukemia maintain a high clonal and transcriptional diversity, and we find little evidence in favor of clonal sweeps. This suggests that for these cancers selection based solely on growth rate is unlikely to be the dominating driving force during cancer evolution.
Collapse
Affiliation(s)
- Jae-Won Cho
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jingyi Cao
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Hemberg
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
17
|
Geo JA, Ameen R, Al Shemmari S, Thomas J. Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine. Med Princ Pract 2024; 33:215-231. [PMID: 38442703 PMCID: PMC11175610 DOI: 10.1159/000538176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
HLA typing serves as a standard practice in hematopoietic stem cell transplantation to ensure compatibility between donors and recipients, preventing the occurrence of allograft rejection and graft-versus-host disease. Conventional laboratory methods that have been widely employed in the past few years, including sequence-specific primer PCR and sequencing-based typing (SBT), currently face the risk of becoming obsolete. This risk stems not only from the extensive diversity within HLA genes but also from the rapid advancement of next-generation sequencing and third-generation sequencing technologies. Third-generation sequencing systems like single-molecule real-time (SMRT) sequencing and Oxford Nanopore (ONT) sequencing have the capability to analyze long-read sequences that span entire intronic-exonic regions of HLA genes, effectively addressing challenges related to HLA ambiguity and the phasing of multiple short-read fragments. The growing dominance of these advanced sequencers in HLA typing is expected to solidify further through ongoing refinements, cost reduction, and error rate minimization. This review focuses on hematopoietic stem cell transplantation (HSCT) and explores prospective advancements and application of HLA DNA typing techniques. It explores how the adoption of third-generation sequencing technologies can revolutionize the field by offering improved accuracy, reduced ambiguity, and enhanced assessment of compatibility in HSCT. Embracing these cutting-edge technologies is essential to advancing the success rates and outcomes of hematopoietic stem cell transplantation. This review underscores the importance of staying at the forefront of HLA typing techniques to ensure the best possible outcomes for patients undergoing HSCT.
Collapse
Affiliation(s)
- Jeethu Anu Geo
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Reem Ameen
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Salem Al Shemmari
- Department of Medicine, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Jibu Thomas
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
| |
Collapse
|
18
|
Behrens YL, Pietzsch S, Antić Ž, Zhang Y, Bergmann AK. The landscape of cytogenetic and molecular genetic methods in diagnostics for hematologic neoplasia. Best Pract Res Clin Haematol 2024; 37:101539. [PMID: 38490767 DOI: 10.1016/j.beha.2024.101539] [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: 12/05/2023] [Accepted: 01/28/2024] [Indexed: 03/17/2024]
Abstract
Improvements made during the last decades in the management of patients with hematologic neoplasia have resulted in increase of overall survival. These advancements have become possible through progress in our understanding of genetic basis of different hematologic malignancies and their role in the current risk-adapted treatment protocols. In this review, we provide an overview of current cytogenetic and molecular genetic methods, commonly used in the genetic characterization of hematologic malignancies, describe the current developments in the cytogenetic and molecular diagnostics, and give an outlook into their future development. Furthermore, we give a brief overview of the most important public databases and guidelines for sequence variant interpretation.
Collapse
Affiliation(s)
- Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Stefan Pietzsch
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany.
| |
Collapse
|
19
|
Porubsky D, Eichler EE. A 25-year odyssey of genomic technology advances and structural variant discovery. Cell 2024; 187:1024-1037. [PMID: 38290514 DOI: 10.1016/j.cell.2024.01.002] [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: 10/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
This perspective focuses on advances in genome technology over the last 25 years and their impact on germline variant discovery within the field of human genetics. The field has witnessed tremendous technological advances from microarrays to short-read sequencing and now long-read sequencing. Each technology has provided genome-wide access to different classes of human genetic variation. We are now on the verge of comprehensive variant detection of all forms of variation for the first time with a single assay. We predict that this transition will further transform our understanding of human health and biology and, more importantly, provide novel insights into the dynamic mutational processes shaping our genomes.
Collapse
Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
20
|
Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [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: 01/18/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
Collapse
Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
21
|
Latham KE. Preimplantation genetic testing: A remarkable history of pioneering, technical challenges, innovations, and ethical considerations. Mol Reprod Dev 2024; 91:e23727. [PMID: 38282313 DOI: 10.1002/mrd.23727] [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: 10/11/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
Preimplantation genetic testing (PGT) has emerged as a powerful companion to assisted reproduction technologies. The origins and history of PGT are reviewed here, along with descriptions of advances in molecular assays and sampling methods, their capabilities, and their applications in preventing genetic diseases and enhancing pregnancy outcomes. Additionally, the potential for increasing accuracy and genome coverage is considered, as well as some of the emerging ethical and legislative considerations related to the expanding capabilities of PGT.
Collapse
Affiliation(s)
- Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing, Michigan, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
22
|
Zheng X, Lee J. Imputation-Based HLA Typing with GWAS SNPs. Methods Mol Biol 2024; 2809:127-143. [PMID: 38907895 DOI: 10.1007/978-1-0716-3874-3_9] [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] [Indexed: 06/24/2024]
Abstract
SNP-based imputation approaches for human leukocyte antigen (HLA) typing take advantage of the haplotype structure within the major histocompatibility complex (MHC) region. These methods predict HLA classical alleles using dense SNP genotypes, commonly found on array-based platforms used in genome-wide association studies (GWAS). The analysis of HLA classical alleles can be conducted on current SNP datasets at no additional cost. Here, we describe the workflow of HIBAG, an imputation method with attribute bagging, to infer a sample's HLA classical alleles using SNP data. Two examples are offered to demonstrate the functionality using public HLA and SNP data from the latest release of the 1000 Genomes project: genotype imputation using pre-built classifiers in a GWAS, and model training to create a new prediction model. The GPU implementation facilitates model building, making it hundreds of times faster compared to the single-threaded implementation.
Collapse
Affiliation(s)
- Xiuwen Zheng
- Genomics Research Center, AbbVie Inc., North Chicago, IL, USA.
| | - John Lee
- Genomics Research Center, AbbVie Inc., North Chicago, IL, USA
| |
Collapse
|
23
|
Owusu R, Savarese M. Long-read sequencing improves diagnostic rate in neuromuscular disorders. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2023; 42:123-128. [PMID: 38406378 PMCID: PMC10883326 DOI: 10.36185/2532-1900-394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 02/27/2024]
Abstract
Massive parallel sequencing methods, such as exome, genome, and targeted DNA sequencing, have aided molecular diagnosis of genetic diseases in the last 20 years. However, short-read sequencing methods still have several limitations, such inaccurate genome assembly, the inability to detect large structural variants, and variants located in hard-to-sequence regions like highly repetitive areas. The recently emerged PacBio single-molecule real-time (SMRT) and Oxford nanopore technology (ONT) long-read sequencing (LRS) methods have been shown to overcome most of these technical issues, leading to an increase in diagnostic rate. LRS methods are contributing to the detection of repeat expansions in novel disease-causing genes (e.g., ABCD3, NOTCH2NLC and RILPL1 causing an Oculopharyngodistal myopathy or PLIN4 causing a Myopathy with rimmed ubiquitin-positive autophagic vacuolation), of structural variants (e.g., in DMD), and of single nucleotide variants in repetitive regions (TTN and NEB). Moreover, these methods have simplified the characterization of the D4Z4 repeats in DUX4, facilitating the diagnosis of Facioscapulohumeral muscular dystrophy (FSHD). We review recent studies that have used either ONT or PacBio SMRT sequencing methods and discuss different types of variants that have been detected using these approaches in individuals with neuromuscular disorders.
Collapse
Affiliation(s)
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- University of Helsinki, Faculty of Medicine, Helsinki, Finland
| |
Collapse
|
24
|
Oakley J, Hill M, Giess A, Tanguy M, Elgar G. Long read sequencing characterises a novel structural variant, revealing underactive AKR1C1 with overactive AKR1C2 as a possible cause of severe chronic fatigue. J Transl Med 2023; 21:825. [PMID: 37978513 PMCID: PMC10655400 DOI: 10.1186/s12967-023-04711-5] [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: 09/04/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Causative genetic variants cannot yet be found for many disorders with a clear heritable component, including chronic fatigue disorders like myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). These conditions may involve genes in difficult-to-align genomic regions that are refractory to short read approaches. Structural variants in these regions can be particularly hard to detect or define with short reads, yet may account for a significant number of cases. Long read sequencing can overcome these difficulties but so far little data is available regarding the specific analytical challenges inherent in such regions, which need to be taken into account to ensure that variants are correctly identified. Research into chronic fatigue disorders faces the additional challenge that the heterogeneous patient populations likely encompass multiple aetiologies with overlapping symptoms, rather than a single disease entity, such that each individual abnormality may lack statistical significance within a larger sample. Better delineation of patient subgroups is needed to target research and treatment. METHODS We use nanopore sequencing in a case of unexplained severe fatigue to identify and fully characterise a large inversion in a highly homologous region spanning the AKR1C gene locus, which was indicated but could not be resolved by short-read sequencing. We then use GC-MS/MS serum steroid analysis to investigate the functional consequences. RESULTS Several commonly used bioinformatics tools are confounded by the homology but a combined approach including visual inspection allows the variant to be accurately resolved. The DNA inversion appears to increase the expression of AKR1C2 while limiting AKR1C1 activity, resulting in a relative increase of inhibitory GABAergic neurosteroids and impaired progesterone metabolism which could suppress neuronal activity and interfere with cellular function in a wide range of tissues. CONCLUSIONS This study provides an example of how long read sequencing can improve diagnostic yield in research and clinical care, and highlights some of the analytical challenges presented by regions containing tandem arrays of genes. It also proposes a novel gene associated with a novel disease aetiology that may be an underlying cause of complex chronic fatigue. It reveals biomarkers that could now be assessed in a larger cohort, potentially identifying a subset of patients who might respond to treatments suggested by the aetiology.
Collapse
Affiliation(s)
| | - Martin Hill
- Department of Steroids and Proteofactors, Institute of Endocrinology, Národni 8, 11694, Prague, Czech Republic
| | - Adam Giess
- Scientific Research and Development, Genomics England, London, UK
| | - Mélanie Tanguy
- Scientific Research and Development, Genomics England, London, UK
| | - Greg Elgar
- Scientific Research and Development, Genomics England, London, UK.
| |
Collapse
|
25
|
Chang W, Hao M, Qiu J, Sherman BT, Imamichi T. Discovery of a Novel Intron in US10/US11/US12 of HSV-1 Strain 17. Viruses 2023; 15:2144. [PMID: 38005822 PMCID: PMC10675037 DOI: 10.3390/v15112144] [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: 09/13/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Herpes Simplex Virus type 1 (HSV-1) infects humans and causes a variety of clinical manifestations. Many HSV-1 genomes have been sequenced with high-throughput sequencing technologies and the annotation of these genome sequences heavily relies on the known genes in reference strains. Consequently, the accuracy of reference strain annotation is critical for future research and treatment of HSV-1 infection. In this study, we analyzed RNA-Seq data of HSV-1 from NCBI databases and discovered a novel intron in the overlapping coding sequence (CDS) of US10 and US11, and the 3' UTR of US12 in strain 17, a commonly used HSV-1 reference strain. To comprehensively understand the shared US10/US11/US12 intron structure, we used US11 as a representative and surveyed all US11 gene sequences from the NCBI nt/nr database. A total of 193 high-quality US11 sequences were obtained, of which 186 sequences have a domain of uninterrupted tandemly repeated RXP (Arg-X-Pro) in the C-terminus half of the protein. In total, 97 of the 186 sequences encode US11 protein with the same length of the mature US11 in strain 17:26 of them have the same structure of US11 and can be spliced as in strain 17; 71 of them have transcripts that are the same as mature US11 mRNA in strain 17. In total, 76 US11 gene sequences have either canonical or known noncanonical intron border sequences and may be spliced like strain 17 and obtain mature US11 CDS with the same length. If not spliced, they will have extra RXP repeats. A tandemly repeated RXP domain was proposed to be essential for US11 to bind with RNA and other host factors. US10 protein sequences from the same strains have also been studied. The results of this study show that even a frequently used reference organism may have errors in widely used databases. This study provides accurate annotation of the US10, US11, and US12 gene structure, which will build a more solid foundation to study expression regulation of the function of these genes.
Collapse
Affiliation(s)
- Weizhong Chang
- Laboratory of Human Retrovirology and Lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (M.H.); (J.Q.); (B.T.S.); (T.I.)
| | | | | | | | | |
Collapse
|