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Vaughn AH, Nielsen R. Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA. Mol Biol Evol 2024; 41:msae156. [PMID: 39078618 PMCID: PMC11321360 DOI: 10.1093/molbev/msae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 07/02/2024] [Accepted: 07/10/2024] [Indexed: 07/31/2024] Open
Abstract
We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.
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Affiliation(s)
- Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720, USA
- Center for GeoGenetics, University of Copenhagen, Copenhagen DK-1350, Denmark
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Porter LF, Saptarshi N, Fang Y, Rathi S, den Hollander AI, de Jong EK, Clark SJ, Bishop PN, Olsen TW, Liloglou T, Chavali VRM, Paraoan L. Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes. Clin Epigenetics 2019; 11:6. [PMID: 30642396 PMCID: PMC6332695 DOI: 10.1186/s13148-019-0608-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022] Open
Abstract
Background Age-related macular degeneration (AMD) is a degenerative disorder of the central retina and the foremost cause of blindness. The retinal pigment epithelium (RPE) is a primary site of disease pathogenesis. The genetic basis of AMD is relatively well understood; however, this knowledge is yet to yield a treatment for the most prevalent non-neovascular disease forms. Therefore, tissue-specific epigenetic mechanisms of gene regulation are of considerable interest in AMD. We aimed to identify differentially methylated genes associated with AMD in the RPE and differentiate local DNA methylation aberrations from global DNA methylation changes, as local DNA methylation changes may be more amenable to therapeutic manipulation. Methods Epigenome-wide association study and targeted gene expression profiling were carried out in RPE cells from eyes of human donors. We performed genome-wide DNA methylation profiling (Illumina 450k BeadChip array) on RPE cells from 44 human donor eyes (25 AMD and 19 normal controls). We validated the findings using bisulfite pyrosequencing in 55 RPE samples (30 AMD and 25 normal controls) including technical (n = 38) and independent replicate samples (n = 17). Long interspersed nucleotide element 1 (LINE-1) analysis was then applied to assess global DNA methylation changes in the RPE. RT-qPCR on independent donor RPE samples was performed to assess gene expression changes. Results Genome-wide DNA methylation profiling identified differential methylation of multiple loci including the SKI proto-oncogene (SKI) (p = 1.18 × 10−9), general transcription factor IIH subunit H4 (GTF2H4) (p = 7.03 × 10−7), and Tenascin X (TNXB) (p = 6.30 × 10−6) genes in AMD. Bisulfite pyrosequencing validated the differentially methylated locus cg18934822 in SKI, and cg22508626 within GTF2H4, and excluded global DNA methylation changes in the RPE in AMD. We further demonstrated the differential expression of SKI, GTF2H4, and TNXB in the RPE of independent AMD donors. Conclusions We report the largest genome-wide methylation analysis of RPE in AMD along with associated gene expression changes to date, for the first-time reaching genome-wide significance, and identified novel targets for functional and future therapeutic intervention studies. The novel differentially methylated genes SKI and GTF2H4 have not been previously associated with AMD, and regulate disease pathways implicated in AMD, including TGF beta signaling (SKI) and transcription-dependent DNA repair mechanisms (GTF2H4). Electronic supplementary material The online version of this article (10.1186/s13148-019-0608-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louise F Porter
- St Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK. .,Department of Eye and Vision Science, William Duncan Building, University of Liverpool, Liverpool, UK.
| | - Neil Saptarshi
- Department of Eye and Vision Science, William Duncan Building, University of Liverpool, Liverpool, UK
| | - Yongxiang Fang
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Sonika Rathi
- Department of Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simon J Clark
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul N Bishop
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | | | | | - Venkata R M Chavali
- Department of Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Luminita Paraoan
- Department of Eye and Vision Science, William Duncan Building, University of Liverpool, Liverpool, UK
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Wen X, Liu Y, Yan Q, Liang M, Tang M, Liu R, Pan J, Liu Q, Chen T, Guo S, Liang J, Lu L, Ding X, Chen W, Wei L. Association of IGFN1 variant with polypoidal choroidal vasculopathy. J Gene Med 2018; 20:e3007. [PMID: 29323771 DOI: 10.1002/jgm.3007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Polypoidal choroidal vasculopathy (PCV) and neovascular age-related macular degeneration (nAMD) share a similar phenotype but are different in their clinical manifestations, responses to treatment and prognosis. Whether PCV is a subtype of AMD or a distinct entity from nAMD remains unknown. Therefore, we performed a whole-exome sequencing based association analysis to compare the genetic architecture of PCV and nAMD in Han Chinese. METHODS Whole-exome sequencing analysis was performed on 21 nAMD cases, 20 PCV cases and 20 healthy controls. As a follow-up validation, 145 nAMD cases, 160 PCV cases and 193 controls were genotyped using the Sequenom MassARRAY platform (Sequenom, San Diego, CA, USA). RESULTS A novel variant, c.6196A>G in the IGFN1 gene, was significantly associated with only PCV (combined p = 7.1 × 10-11 , odds ratio = 9.44), but not with nAMD (combined p = 0.683, odds ratio = 1.30). The minor allele G conferred an increased risk of PCV. CONCLUSIONS The findings of the present study indicate that, although some of the susceptibility loci are shared between PCV and nAMD, a unique genetic signature may decide the pathogenesis of PCV.
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Affiliation(s)
- Xiaofeng Wen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yu Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Qi Yan
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Minling Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Miao Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Ran Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jianying Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiuhui Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Tingting Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shixin Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Juanran Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Xu X. Fighting blinding fundus diseases: China on the way! Acta Ophthalmol 2016; 94:319-20. [PMID: 27217065 DOI: 10.1111/aos.13091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lambert NG, ElShelmani H, Singh MK, Mansergh FC, Wride MA, Padilla M, Keegan D, Hogg RE, Ambati BK. Risk factors and biomarkers of age-related macular degeneration. Prog Retin Eye Res 2016; 54:64-102. [PMID: 27156982 DOI: 10.1016/j.preteyeres.2016.04.003] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/01/2016] [Accepted: 04/12/2016] [Indexed: 02/03/2023]
Abstract
A biomarker can be a substance or structure measured in body parts, fluids or products that can affect or predict disease incidence. As age-related macular degeneration (AMD) is the leading cause of blindness in the developed world, much research and effort has been invested in the identification of different biomarkers to predict disease incidence, identify at risk individuals, elucidate causative pathophysiological etiologies, guide screening, monitoring and treatment parameters, and predict disease outcomes. To date, a host of genetic, environmental, proteomic, and cellular targets have been identified as both risk factors and potential biomarkers for AMD. Despite this, their use has been confined to research settings and has not yet crossed into the clinical arena. A greater understanding of these factors and their use as potential biomarkers for AMD can guide future research and clinical practice. This article will discuss known risk factors and novel, potential biomarkers of AMD in addition to their application in both academic and clinical settings.
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Affiliation(s)
- Nathan G Lambert
- Ambati Lab, John A. Moran Eye Center, 65 Mario Capecchi Drive, Salt Lake City, UT, USA; Department of Ophthalmology & Visual Sciences, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT, USA.
| | - Hanan ElShelmani
- Ocular Development and Neurobiology Research Group, Zoology Department, School of Natural Sciences, University of Dublin, Trinity College, Dublin 2, Ireland.
| | - Malkit K Singh
- Ambati Lab, John A. Moran Eye Center, 65 Mario Capecchi Drive, Salt Lake City, UT, USA; Department of Ophthalmology & Visual Sciences, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT, USA.
| | - Fiona C Mansergh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Michael A Wride
- Ocular Development and Neurobiology Research Group, Zoology Department, School of Natural Sciences, University of Dublin, Trinity College, Dublin 2, Ireland.
| | - Maximilian Padilla
- Ambati Lab, John A. Moran Eye Center, 65 Mario Capecchi Drive, Salt Lake City, UT, USA; Department of Ophthalmology & Visual Sciences, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT, USA.
| | - David Keegan
- Mater Misericordia Hospital, Eccles St, Dublin 7, Ireland.
| | - Ruth E Hogg
- Centre for Experimental Medicine, Institute of Clinical Science Block A, Grosvenor Road, Belfast, Co.Antrim, Northern Ireland, UK.
| | - Balamurali K Ambati
- Ambati Lab, John A. Moran Eye Center, 65 Mario Capecchi Drive, Salt Lake City, UT, USA; Department of Ophthalmology & Visual Sciences, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT, USA.
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