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Jat KR, Faruq M, Jindal S, Bari S, Soni A, Sharma P, Mathews S, Shamim U, Ahuja V, Uppilli B, Yadav SC, Lodha R, Arava SK, Kabra SK. Genetics of 67 patients of suspected primary ciliary dyskinesia from India. Clin Genet 2024; 106:650-658. [PMID: 39004944 DOI: 10.1111/cge.14590] [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: 03/25/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
Data are limited on the genetic profile of primary ciliary dyskinesia (PCD) from developing countries. Here, we report one of the first study on genetic profile of patients with suspected PCD from India. In this prospective cross-sectional study, we enrolled 162 children with suspected PCD. We recorded clinical features, relevant laboratory tests for PCD and performed whole exome sequencing (WES). We are reporting 67 patients here who had positive variant/s on WES. We had 117 variants in 40 genes among 67 patients. Among the 108 unique variants, 33 were categorized as pathogenic or likely pathogenic (P/LP). We had nine novel variants in out cohort. The 29 definite PCD cases, diagnosed by composite reference standards, had variants in 16 genes namely LRRC6/DNAAF11 (5), DNAH5 (3), CCDC39 (3), HYDIN (3), DNAH11 (2), CCDC40 (2), CCDC65 (2) and one each DNAAF3, DNAAF2, CFAP300, RPGR, CCDC103, CCDC114, SPAG1, DNAI1, and DNAH14. To conclude, we identified 108 unique variants in 40 genes among 67 patients. The common genes involved in definite cases of PCD in Indian patients were LRRC6, DNAH5, CCDC39, and HYDIN. Our findings suggest a need to develop a separate genetic panel for PCD in the Indian population.
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Affiliation(s)
- Kana Ram Jat
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shishir Jindal
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Shreya Bari
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Akshita Soni
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Pooja Sharma
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Susi Mathews
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Uzma Shamim
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vanshika Ahuja
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Subhash C Yadav
- Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sudheer K Arava
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sushil K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Fleming A, Galey M, Briggs L, Edwards M, Hogg C, John S, Wilkinson S, Quinn E, Rai R, Burgoyne T, Rogers A, Patel MP, Griffin P, Muller S, Carr SB, Loebinger MR, Lucas JS, Shah A, Jose R, Mitchison HM, Shoemark A, Miller DE, Morris-Rosendahl DJ. Combined approaches, including long-read sequencing, address the diagnostic challenge of HYDIN in primary ciliary dyskinesia. Eur J Hum Genet 2024; 32:1074-1085. [PMID: 38605126 PMCID: PMC11369241 DOI: 10.1038/s41431-024-01599-7] [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: 12/11/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Primary ciliary dyskinesia (PCD), a disorder of the motile cilia, is now recognised as an underdiagnosed cause of bronchiectasis. Accurate PCD diagnosis comprises clinical assessment, analysis of cilia and the identification of biallelic variants in one of 50 known PCD-related genes, including HYDIN. HYDIN-related PCD is underdiagnosed due to the presence of a pseudogene, HYDIN2, with 98% sequence homology to HYDIN. This presents a significant challenge for Short-Read Next Generation Sequencing (SR-NGS) and analysis, and many diagnostic PCD gene panels do not include HYDIN. We have used a combined approach of SR-NGS with bioinformatic masking of HYDIN2, and state-of-the-art long-read Nanopore sequencing (LR_NGS), together with analysis of respiratory cilia including transmission electron microscopy and immunofluorescence to address the underdiagnosis of HYDIN as a cause of PCD. Bioinformatic masking of HYDIN2 after SR-NGS facilitated the detection of biallelic HYDIN variants in 15 of 437 families, but compromised the detection of copy number variants. Supplementing testing with LR-NGS detected HYDIN deletions in 2 families, where SR-NGS had detected a single heterozygous HYDIN variant. LR-NGS was also able to confirm true homozygosity in 2 families when parental testing was not possible. Utilising a combined genomic diagnostic approach, biallelic HYDIN variants were detected in 17 families from 242 genetically confirmed PCD cases, comprising 7% of our PCD cohort. This represents the largest reported HYDIN cohort to date and highlights previous underdiagnosis of HYDIN-associated PCD. Moreover this provides further evidence for the utility of LR-NGS in diagnostic testing, particularly for regions of high genomic complexity.
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Affiliation(s)
- Andrew Fleming
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington and Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Lizi Briggs
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Matthew Edwards
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Claire Hogg
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Shibu John
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Sam Wilkinson
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Ellie Quinn
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Ranjit Rai
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Tom Burgoyne
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Andy Rogers
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Mitali P Patel
- Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, W1W 7FF, UK
| | - Paul Griffin
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Steven Muller
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Siobhan B Carr
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Michael R Loebinger
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
- Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, SO16 6YD, UK
| | - Anand Shah
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- MRC Centre of Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Ricardo Jose
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, W1W 7FF, UK
| | - Amelia Shoemark
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington and Seattle Children's Hospital, Seattle, WA, 98105, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Deborah J Morris-Rosendahl
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, SW3 6NP, UK.
- National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.
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