1
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Oliver TRW, Chappell L, Sanghvi R, Deighton L, Ansari-Pour N, Dentro SC, Young MD, Coorens THH, Jung H, Butler T, Neville MDC, Leongamornlert D, Sanders MA, Hooks Y, Cagan A, Mitchell TJ, Cortes-Ciriano I, Warren AY, Wedge DC, Heer R, Coleman N, Murray MJ, Campbell PJ, Rahbari R, Behjati S. Clonal diversification and histogenesis of malignant germ cell tumours. Nat Commun 2022; 13:4272. [PMID: 35953478 PMCID: PMC9372159 DOI: 10.1038/s41467-022-31375-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 12/21/2022] Open
Abstract
Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.
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Affiliation(s)
- Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | | | | | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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2
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Gardner EJ, Neville MDC, Samocha KE, Barclay K, Kolk M, Niemi MEK, Kirov G, Martin HC, Hurles ME. Reduced reproductive success is associated with selective constraint on human genes. Nature 2022; 603:858-863. [PMID: 35322230 DOI: 10.1038/s41586-022-04549-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
Abstract
Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants1. Although genes under the strongest selective constraint are highly enriched for associations with Mendelian disorders, most of these genes are not associated with disease and therefore the nature of the selection acting on them is not known2. Here we show that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily owing to increased childlessness, with a stronger effect in males than in females. We present evidence that increased childlessness is probably mediated by genetically associated cognitive and behavioural traits, which may mean that male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. Although this genetic association may only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.
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Affiliation(s)
- Eugene J Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK.,Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Kaitlin E Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK
| | - Kieron Barclay
- Max Planck Institute for Demographic Research, Rostock, Germany.,Demography Unit, Department of Sociology, Stockholm University, Stockholm, Sweden.,Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Martin Kolk
- Demography Unit, Department of Sociology, Stockholm University, Stockholm, Sweden
| | - Mari E K Niemi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK
| | - George Kirov
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK.
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3
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Moore L, Cagan A, Coorens THH, Neville MDC, Sanghvi R, Sanders MA, Oliver TRW, Leongamornlert D, Ellis P, Noorani A, Mitchell TJ, Butler TM, Hooks Y, Warren AY, Jorgensen M, Dawson KJ, Menzies A, O'Neill L, Latimer C, Teng M, van Boxtel R, Iacobuzio-Donahue CA, Martincorena I, Heer R, Campbell PJ, Fitzgerald RC, Stratton MR, Rahbari R. The mutational landscape of human somatic and germline cells. Nature 2021; 597:381-386. [PMID: 34433962 DOI: 10.1038/s41586-021-03822-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022]
Abstract
Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.
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Affiliation(s)
- Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D C Neville
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rashesh Sanghvi
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Thomas R W Oliver
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Inivata, Cambridge, UK
| | - Ayesha Noorani
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mabel Teng
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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4
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Coorens THH, Moore L, Robinson PS, Sanghvi R, Christopher J, Hewinson J, Przybilla MJ, Lawson ARJ, Spencer Chapman M, Cagan A, Oliver TRW, Neville MDC, Hooks Y, Noorani A, Mitchell TJ, Fitzgerald RC, Campbell PJ, Martincorena I, Rahbari R, Stratton MR. Extensive phylogenies of human development inferred from somatic mutations. Nature 2021; 597:387-392. [PMID: 34433963 DOI: 10.1038/s41586-021-03790-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.
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Affiliation(s)
| | - Luiza Moore
- Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Philip S Robinson
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Joseph Christopher
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
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5
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Neville MDC, Kohze R, Erady C, Meena N, Hayden M, Cooper DN, Mort M, Prabakaran S. A platform for curated products from novel open reading frames prompts reinterpretation of disease variants. Genome Res 2021; 31:327-336. [PMID: 33468550 PMCID: PMC7849405 DOI: 10.1101/gr.263202.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022]
Abstract
Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in diverse regions of the genome, including in long noncoding RNAs, pseudogenes, 3' UTRs, 5' UTRs, and alternative reading frames of canonical protein coding exons. There is therefore a pressing need to evaluate the potential functional importance of these unannotated transcripts and proteins in biological pathways and human disease on a larger scale, rather than one at a time. In this study, we outline the creation of a valuable nORFs data set with experimental evidence of translation for the community, use measures of heritability and selection that reveal signals for functional importance, and show the potential implications for functional interpretation of genetic variants in nORFs. Our results indicate that some variants that were previously classified as being benign or of uncertain significance may have to be reinterpreted.
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Affiliation(s)
- Matthew D C Neville
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Robin Kohze
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Chaitanya Erady
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Narendra Meena
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Matthew Hayden
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
- St Edmund's College, University of Cambridge, Cambridge CB3 0BN, United Kingdom
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6
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Martin HC, Gardner EJ, Samocha KE, Kaplanis J, Akawi N, Sifrim A, Eberhardt RY, Tavares ALT, Neville MDC, Niemi MEK, Gallone G, McRae J, Wright CF, FitzPatrick DR, Firth HV, Hurles ME. The contribution of X-linked coding variation to severe developmental disorders. Nat Commun 2021; 12:627. [PMID: 33504798 PMCID: PMC7840967 DOI: 10.1038/s41467-020-20852-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.
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Affiliation(s)
- Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | | | | | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nadia Akawi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alejandro Sifrim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | | | - Ana Lisa Taylor Tavares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Genomics England, Queen Mary University of London, London, EC1M 6BQ, UK
| | | | - Mari E K Niemi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, FI-00014, Finland
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Jeremy McRae
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Caroline F Wright
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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7
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Neville MDC, Choi J, Lieberman J, Duan QL. Identification of deleterious and regulatory genomic variations in known asthma loci. Respir Res 2018; 19:248. [PMID: 30541564 PMCID: PMC6292105 DOI: 10.1186/s12931-018-0953-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/23/2018] [Indexed: 11/25/2022] Open
Abstract
Background Candidate gene and genome-wide association studies have identified hundreds of asthma risk loci. The majority of associated variants, however, are not known to have any biological function and are believed to represent markers rather than true causative mutations. We hypothesized that many of these associated markers are in linkage disequilibrium (LD) with the elusive causative variants. Methods We compiled a comprehensive list of 449 asthma-associated variants previously reported in candidate gene and genome-wide association studies. Next, we identified all sequence variants located within the 305 unique genes using whole-genome sequencing data from the 1000 Genomes Project. Then, we calculated the LD between known asthma variants and the sequence variants within each gene. LD variants identified were then annotated to determine those that are potentially deleterious and/or functional (i.e. coding or regulatory effects on the encoded transcript or protein). Results We identified 10,130 variants in LD (r2 > 0.6) with known asthma variants. Annotations of these LD variants revealed that several have potentially deleterious effects including frameshift, alternate splice site, stop-lost, and missense. Moreover, 24 of the LD variants have been reported to regulate gene expression as expression quantitative trait loci (eQTLs). Conclusions This study is proof of concept that many of the genetic loci previously associated with complex diseases such as asthma are not causative but represent markers of disease, which are in LD with the elusive causative variants. We hereby report a number of potentially deleterious and regulatory variants that are in LD with the reported asthma loci. These reported LD variants could account for the original association signals with asthma and represent the true causative mutations at these loci. Electronic supplementary material The online version of this article (10.1186/s12931-018-0953-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew D C Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada
| | - Jihoon Choi
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada
| | - Jonathan Lieberman
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada. .,School of Computing, Queen's University, 557 Goodwin Hall, Room 531, Kingston, ON, K7L 2N8, Canada.
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