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Lassen FH, Venkatesh SS, Baya N, Hill B, Zhou W, Bloemendal A, Neale BM, Kessler BM, Whiffin N, Lindgren CM, Palmer DS. Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. CELL GENOMICS 2024; 4:100602. [PMID: 38944039 PMCID: PMC11293579 DOI: 10.1016/j.xgen.2024.100602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/11/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
The phenotypic impact of compound heterozygous (CH) variation has not been investigated at the population scale. We phased rare variants (MAF ∼0.001%) in the UK Biobank (UKBB) exome-sequencing data to characterize recessive effects in 175,587 individuals across 311 common diseases. A total of 6.5% of individuals carry putatively damaging CH variants, 90% of which are only identifiable upon phasing rare variants (MAF < 0.38%). We identify six recessive gene-trait associations (p < 1.68 × 10-7) after accounting for relatedness, polygenicity, nearby common variants, and rare variant burden. Of these, just one is discovered when considering homozygosity alone. Using longitudinal health records, we additionally identify and replicate a novel association between bi-allelic variation in ATP2C2 and an earlier age at onset of chronic obstructive pulmonary disease (COPD) (p < 3.58 × 10-8). Genetic phase contributes to disease risk for gene-trait pairs: ATP2C2-COPD (p = 0.000238), FLG-asthma (p = 0.00205), and USH2A-visual impairment (p = 0.0084). We demonstrate the power of phasing large-scale genetic cohorts to discover phenome-wide consequences of compound heterozygosity.
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Affiliation(s)
- Frederik H Lassen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Samvida S Venkatesh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Nikolas Baya
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Barney Hill
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Novo Nordisk Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Whiffin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK.
| | - Duncan S Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK.
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Lassen FH, Venkatesh SS, Baya N, Zhou W, Bloemendal A, Neale BM, Kessler BM, Whiffin N, Lindgren CM, Palmer DS. Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.29.23291992. [PMID: 37461573 PMCID: PMC10350147 DOI: 10.1101/2023.06.29.23291992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Exome-sequencing association studies have successfully linked rare protein-coding variation to risk of thousands of diseases. However, the relationship between rare deleterious compound heterozygous (CH) variation and their phenotypic impact has not been fully investigated. Here, we leverage advances in statistical phasing to accurately phase rare variants (MAF ~ 0.001%) in exome sequencing data from 175,587 UK Biobank (UKBB) participants, which we then systematically annotate to identify putatively deleterious CH coding variation. We show that 6.5% of individuals carry such damaging variants in the CH state, with 90% of variants occurring at MAF < 0.34%. Using a logistic mixed model framework, systematically accounting for relatedness, polygenic risk, nearby common variants, and rare variant burden, we investigate recessive effects in common complex diseases. We find six exome-wide significant (P < 1.68 × 10 - 7 ) and 17 nominally significant (P < 5.25 × 10 - 5 ) gene-trait associations. Among these, only four would have been identified without accounting for CH variation in the gene. We further incorporate age-at-diagnosis information from primary care electronic health records, to show that genetic phase influences lifetime risk of disease across 20 gene-trait combinations (FDR < 5%). Using a permutation approach, we find evidence for genetic phase contributing to disease susceptibility for a collection of gene-trait pairs, including FLG-asthma (P = 0.00205 ) and USH2A-visual impairment (P = 0.0084 ). Taken together, we demonstrate the utility of phasing large-scale genetic sequencing cohorts for robust identification of the phenome-wide consequences of compound heterozygosity.
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Affiliation(s)
- Frederik H. Lassen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Samvida S. Venkatesh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Nikolas Baya
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Wei Zhou
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola Whiffin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Population Health Health, Medical Sciences Division University of Oxford, Oxford, United Kingdom
| | - Duncan S. Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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Andersen YMF, Egeberg A, Balslev E, Jørgensen CLT, Szecsi PB, Stender S, Kaae J, Linneberg A, Gislason G, Skov L, Elias PM, Thyssen JP. Filaggrin loss-of-function mutations, atopic dermatitis and risk of actinic keratosis: results from two cross-sectional studies. J Eur Acad Dermatol Venereol 2017; 31:1038-1043. [PMID: 28213896 DOI: 10.1111/jdv.14172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/30/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Common loss-of-function mutations in filaggrin gene (FLG) represent a strong genetic risk factor for atopic dermatitis (AD). Homozygous mutation carriers typically display ichthyosis vulgaris (IV) and many have concomitant AD. Previously, homozygous, but not heterozygous, filaggrin gene mutations have been associated with squamous cell carcinomas. OBJECTIVE The first objective was to examine the association between FLG mutations and actinic keratosis (AK). The second objective was to investigate the occurrence of AK in patients with IV and AD, respectively. METHODS FLG mutation status in patients with AK was compared with controls from the general population. Furthermore, based on nationwide data from Danish registers, we compared the risk of AK in patients with IV, AD and psoriasis, respectively. RESULTS The prevalence of homozygous FLG mutations was significantly higher in the AK group (n = 4, 0.8%) in comparison with the control group (n = 18, 0.2%), whereas the prevalence of heterozygous FLG mutations was lower. In hospital registry data, patients with AD exhibited an increased risk of AK than did psoriasis controls (adjusted OR 1.46; [95% CI 1.12-1.90]), whereas no difference in risk was observed between patients with IV and AD. CONCLUSIONS This study indicates an increased susceptibility to AK in individuals with homozygous, but not heterozygous, FLG mutations and in patients with AD compared to psoriasis. Whether a reduction or absence of epidermal filaggrin could contribute to the susceptibility to AK in patients with IV and AD is unknown and additional research is needed to further explore this relationship.
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Affiliation(s)
- Y M F Andersen
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark.,Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - A Egeberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark.,Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - E Balslev
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - C L T Jørgensen
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - P B Szecsi
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - S Stender
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - J Kaae
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - A Linneberg
- Research Centre for Prevention and Health, the Capital Region of Denmark, Copenhagen, Denmark.,Department of Clinical Experimental Research, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - G Gislason
- Department of Cardiology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - L Skov
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - P M Elias
- Dermatology Service, Veterans Affairs Medical Center, and Department of Dermatology, UCSF, San Francisco, CA, USA
| | - J P Thyssen
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
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Kaae J, Szecsi PB, Meldgaard M, Espersen MLM, Stender S, Johansen JD, Bandier J, Thyssen JP, Menné T, Nielsen SL, Høgdall E, Balslev E, Skov L. Individuals with complete filaggrin deficiency may have an increased risk of squamous cell carcinoma. Br J Dermatol 2016; 170:1380-1. [PMID: 24641578 DOI: 10.1111/bjd.12911] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- J Kaae
- Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, 2900-Hellerup, Denmark.
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Abstract
Background Many genetic variants have been identified in the human genome. The functional effects of a single variant have been intensively studied. However, the joint effects of multiple variants in the same genes have been largely ignored due to their complexity or lack of data. This paper uses HMMvar, a hidden Markov model based approach, to investigate the combined effect of multiple variants from the 1000 Genomes Project. Two tumor suppressor genes, TP53 and phosphatase and tensin homolog (PTEN), are also studied for the joint effect of compensatory indel variants. Results Results show that there are cases where the joint effect of having multiple variants in the same genes is significantly different from that of a single variant. The deleterious effect of a single indel variant can be alleviated by their compensatory indels in TP53 and PTEN. Compound mutations in two genes, β-MHC and MyBP-C, leading to severer cardiovascular disease compared to single mutations, are also validated. Conclusions This paper extends the functionality of HMMvar, a tool for assigning a quantitative score to a variant, to measure not only the deleterious effect of a single variant but also the joint effect of multiple variants. HMMvar is the first tool that can predict the functional effects of both single and general multiple variations on proteins. The precomputed scores for multiple variants from the 1000 Genomes Project and the HMMvar package are available at https://bioinformatics.cs.vt.edu/zhanglab/HMMvar/
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Affiliation(s)
- Mingming Liu
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| | - Layne T Watson
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. .,Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. .,Department of Aerospace and Ocean Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| | - Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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Komova EG, Shintyapina AB, Makarova SI, Ivanov MK, Chekryga EA, Kaznacheeva LF, Vavilin VA. Filaggrin Mutations in a Western Siberian Population and Their Association with Atopic Dermatitis in Children. Genet Test Mol Biomarkers 2014; 18:791-6. [DOI: 10.1089/gtmb.2014.0247] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Elena G. Komova
- Institute for Molecular Biology and Biophysics, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
- Joint-Stock Company Vector-Best, Novosibirsk, Russia
| | - Alexandra B. Shintyapina
- Institute for Molecular Biology and Biophysics, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Svetlana I. Makarova
- Institute for Molecular Biology and Biophysics, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | | | - Elena A. Chekryga
- Regional Allergodermatological Center of the State Children's City Clinical Hospital No. 1, Novosibirsk, Russia
| | - Larisa F. Kaznacheeva
- Regional Allergodermatological Center of the State Children's City Clinical Hospital No. 1, Novosibirsk, Russia
| | - Valentin A. Vavilin
- Institute for Molecular Biology and Biophysics, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
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