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Joyce KE, Onabanjo E, Brownlow S, Nur F, Olupona K, Fakayode K, Sroya M, Thomas GA, Ferguson T, Redhead J, Millar CM, Cooper N, Layton DM, Boardman-Pretty F, Caulfield MJ, Shovlin CL. Whole genome sequences discriminate hereditary hemorrhagic telangiectasia phenotypes by non-HHT deleterious DNA variation. Blood Adv 2022; 6:3956-3969. [PMID: 35316832 PMCID: PMC9278305 DOI: 10.1182/bloodadvances.2022007136] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 11/20/2022] Open
Abstract
The abnormal vascular structures of hereditary hemorrhagic telangiectasia (HHT) often cause severe anemia due to recurrent hemorrhage, but HHT causal genes do not predict the severity of hematological complications. We tested for chance inheritance and clinical associations of rare deleterious variants in which loss-of-function causes bleeding or hemolytic disorders in the general population. In double-blinded analyses, all 104 patients with HHT from a single reference center recruited to the 100 000 Genomes Project were categorized on new MALO (more/as-expected/less/opposite) sub-phenotype severity scales, and whole genome sequencing data were tested for high impact variants in 75 HHT-independent genes encoding coagulation factors, or platelet, hemoglobin, erythrocyte enzyme, and erythrocyte membrane constituents. Rare variants (all gnomAD allele frequencies <0.003) were identified in 56 (75%) of these 75 HHT-unrelated genes. Deleteriousness assignments by Combined Annotation Dependent Depletion (CADD) scores >15 were supported by gene-level mutation significance cutoff scores. CADD >15 variants were identified in 38/104 (36.5%) patients with HHT, found for 1 in 10 patients within platelet genes; 1 in 8 within coagulation genes; and 1 in 4 within erythrocyte hemolytic genes. In blinded analyses, patients with greater hemorrhagic severity that had been attributed solely to HHT vessels had more CADD-deleterious variants in platelet (Spearman ρ = 0.25; P = .008) and coagulation (Spearman ρ = 0.21; P = .024) genes. However, the HHT cohort had 60% fewer deleterious variants in platelet and coagulation genes than expected (Mann-Whitney test P = .021). In conclusion, patients with HHT commonly have rare variants in genes of relevance to their phenotype, offering new therapeutic targets and opportunities for informed, personalized medicine strategies.
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Affiliation(s)
- Katie E. Joyce
- Imperial College School of Medicine, Imperial College, London, United Kingdom
- Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, United Kingdom
| | - Ebun Onabanjo
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Sheila Brownlow
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Fadumo Nur
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Kike Olupona
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Kehinde Fakayode
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Manveer Sroya
- Department of Surgery and Cancer, Imperial College, London, United Kingdom
| | | | - Teena Ferguson
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Julian Redhead
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Carolyn M. Millar
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College, London, United Kingdom
| | - Nichola Cooper
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College, London, United Kingdom
| | - D. Mark Layton
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College, London, United Kingdom
| | | | - Mark J. Caulfield
- Genomics England Research Consortium, Genomics England, London, United Kingdom
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom; and
| | | | - Claire L. Shovlin
- Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, United Kingdom
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
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