1
|
Miyake N. Identifying novel disease genes and revealing the pathomechanism of monogenic diseases. Pediatr Int 2024; 66:e15760. [PMID: 38641939 DOI: 10.1111/ped.15760] [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: 09/05/2023] [Revised: 01/06/2024] [Accepted: 02/27/2024] [Indexed: 04/21/2024]
Abstract
Diseases are caused by genetic and/or environmental factors. It is important to understand the pathomechanism of monogenic diseases that are caused only by genetic factors, especially prenatal- or childhood-onset diseases for pediatricians. Identifying "novel" disease genes and elucidating how genomic changes lead to human phenotypes would develop new therapeutic approaches for rare diseases for which no fundamental cure has yet been established. Genomic analysis has evolved along with the development of analytical techniques, from Sanger sequencing (first-generation sequencing) to techniques such as comparative genomic hybridization, massive parallel short-read sequencing (using a next-generation sequencer or second-generation sequencer) and long-read sequencing (using a next-next generation sequencer or third-generation sequencer). I have been researching human genetics using conventional and new technologies, together with my mentors and numerous collaborators, and have identified genes responsible for more than 60 diseases. Here, an overview of genomic analyses of monogenic diseases that aims to identify novel disease genes, and several examples using different approaches depending on the disease characteristics are presented.
Collapse
Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| |
Collapse
|
2
|
Soo CC, Brandenburg JT, Nebel A, Tollman S, Berkman L, Ramsay M, Choudhury A. Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community. Commun Biol 2023; 6:328. [PMID: 36973338 PMCID: PMC10043003 DOI: 10.1038/s42003-023-04636-1] [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: 10/18/2021] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Cognitive function is an indicator for global physical and mental health, and cognitive impairment has been associated with poorer life outcomes and earlier mortality. A standard cognition test, adapted to a rural-dwelling African community, and the Oxford Cognition Screen-Plus were used to capture cognitive performance as five continuous traits (total cognition score, verbal episodic memory, executive function, language, and visuospatial ability) for 2,246 adults in this population of South Africans. A novel common variant, rs73485231, reached genome-wide significance for association with episodic memory using data for ~14 million markers imputed from the H3Africa genotyping array data. Window-based replication of previously implicated variants and regions of interest support the discovery of African-specific associated variants despite the small population size and low allele frequency. This African genome-wide association study identifies suggestive associations with general cognition and domain-specific cognitive pathways and lays the groundwork for further genomic studies on cognition in Africa.
Collapse
Affiliation(s)
- Cassandra C Soo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Almut Nebel
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa Berkman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, MA, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
3
|
Schobers G, Schieving JH, Yntema HG, Pennings M, Pfundt R, Derks R, Hofste T, de Wijs I, Wieskamp N, van den Heuvel S, Galbany JC, Gilissen C, Nelen M, Brunner HG, Kleefstra T, Kamsteeg EJ, Willemsen MAAP, Vissers LELM. Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications. Genome Med 2022; 14:66. [PMID: 35710456 PMCID: PMC9204949 DOI: 10.1186/s13073-022-01069-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background Approximately two third of patients with a rare genetic disease remain undiagnosed after exome sequencing (ES). As part of our post-test counseling procedures, patients without a conclusive diagnosis are advised to recontact their referring clinician to discuss new diagnostic opportunities in due time. We performed a systematic study of genetically undiagnosed patients 5 years after their initial negative ES report to determine the efficiency of diverse reanalysis strategies. Methods We revisited a cohort of 150 pediatric neurology patients originally enrolled at Radboud University Medical Center, of whom 103 initially remained genetically undiagnosed. We monitored uptake of physician-initiated routine clinical and/or genetic re-evaluation (ad hoc re-evaluation) and performed systematic reanalysis, including ES-based resequencing, of all genetically undiagnosed patients (systematic re-evaluation). Results Ad hoc re-evaluation was initiated for 45 of 103 patients and yielded 18 diagnoses (including 1 non-genetic). Subsequent systematic re-evaluation identified another 14 diagnoses, increasing the diagnostic yield in our cohort from 31% (47/150) to 53% (79/150). New genetic diagnoses were established by reclassification of previously identified variants (10%, 3/31), reanalysis with enhanced bioinformatic pipelines (19%, 6/31), improved coverage after resequencing (29%, 9/31), and new disease-gene associations (42%, 13/31). Crucially, our systematic study also showed that 11 of the 14 further conclusive genetic diagnoses were made in patients without a genetic diagnosis that did not recontact their referring clinician. Conclusions We find that upon re-evaluation of undiagnosed patients, both reanalysis of existing ES data as well as resequencing strategies are needed to identify additional genetic diagnoses. Importantly, not all patients are routinely re-evaluated in clinical care, prolonging their diagnostic trajectory, unless systematic reanalysis is facilitated. We have translated our observations into considerations for systematic and ad hoc reanalysis in routine genetic care. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01069-z.
Collapse
Affiliation(s)
- Gaby Schobers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Jolanda H Schieving
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje Pennings
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilse de Wijs
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nienke Wieskamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michèl A A P Willemsen
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| |
Collapse
|
4
|
Taylor JP, Malhotra A, Burns NJ, Clause AR, Brown CM, Burns BT, Chandrasekhar A, Schlachetzki Z, Bennett M, Thorpe E, Taft RJ, Perry DL, Coffey AJ. A clinical laboratory's experience using GeneMatcher - building stronger gene-disease relationships. Hum Mutat 2022; 43:765-771. [PMID: 35181961 DOI: 10.1002/humu.24356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/08/2022]
Abstract
The use of whole-genome sequencing (WGS) has accelerated the pace of gene discovery and highlighted the need for open and collaborative data sharing in the search for novel disease genes and variants. GeneMatcher (GM) is designed to facilitate connections between researchers, clinicians, health-care providers and others to help in the identification of additional patients with variants in the same candidate disease genes. The Illumina Clinical Services Laboratory offers a WGS test for patients with suspected rare and undiagnosed genetic disease and regularly submits potential candidate genes to GM to strengthen gene-disease relationships. We describe our experience with GM, including criteria for evaluation of candidate genes, and our workflow for the submission and review process. We have made 69 submissions, 36 of which are currently active. Ten per cent of submissions have resulted in publications, with an additional 14 submissions part of ongoing collaborations and expected to result in a publication. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Julie P Taylor
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Alka Malhotra
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Nicole J Burns
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Amanda R Clause
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Carolyn M Brown
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Brendan T Burns
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Anjana Chandrasekhar
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Zina Schlachetzki
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Maren Bennett
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| |
Collapse
|