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Fore R, Boehme J, Li K, Westra J, Tintle N. Multi-Set Testing Strategies Show Good Behavior When Applied to Very Large Sets of Rare Variants. Front Genet 2020; 11:591606. [PMID: 33240333 PMCID: PMC7680887 DOI: 10.3389/fgene.2020.591606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/05/2020] [Indexed: 12/22/2022] Open
Abstract
Gene-based tests of association (e.g., variance components and burden tests) are now common practice for analyses attempting to elucidate the contribution of rare genetic variants on common disease. As sequencing datasets continue to grow in size, the number of variants within each set (e.g., gene) being tested is also continuing to grow. Pathway-based methods have been used to allow for the initial aggregation of gene-based statistical evidence and then the subsequent aggregation of evidence across the pathway. This “multi-set” approach (first gene-based test, followed by pathway-based) lacks thorough exploration in regard to evaluating genotype–phenotype associations in the age of large, sequenced datasets. In particular, we wonder whether there are statistical and biological characteristics that make the multi-set approach optimal vs. simply doing all gene-based tests? In this paper, we provide an intuitive framework for evaluating these questions and use simulated data to affirm us this intuition. A real data application is provided demonstrating how our insights manifest themselves in practice. Ultimately, we find that when initial subsets are biologically informative (e.g., tending to aggregate causal genetic variants within one or more subsets, often genes), multi-set strategies can improve statistical power, with particular gains in cases where causal variants are aggregated in subsets with less variants overall (high proportion of causal variants in the subset). However, we find that there is little advantage when the sets are non-informative (similar proportion of causal variants in the subsets). Our application to real data further demonstrates this intuition. In practice, we recommend wider use of pathway-based methods and further exploration of optimal ways of aggregating variants into subsets based on emerging biological evidence of the genetic architecture of complex disease.
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Affiliation(s)
- Ruby Fore
- Department of Biostatistics, Brown University, Providence, RI, United States
| | - Jaden Boehme
- Department of Mathematics, Oregon State University, Corvallis, OR, United States
| | - Kevin Li
- Department of Mathematics, School of Arts and Sciences, Columbia University, New York, NY, United States
| | - Jason Westra
- Department of Mathematics and Statistics, Dordt University, Sioux Center, IA, United States
| | - Nathan Tintle
- Department of Mathematics and Statistics, Dordt University, Sioux Center, IA, United States
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Bianchi M, Alisi A, Fabrizi M, Vallone C, Ravà L, Giannico R, Vernocchi P, Signore F, Manco M. Maternal Intake of n-3 Polyunsaturated Fatty Acids During Pregnancy Is Associated With Differential Methylation Profiles in Cord Blood White Cells. Front Genet 2019; 10:1050. [PMID: 31708974 PMCID: PMC6824245 DOI: 10.3389/fgene.2019.01050] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
A healthy diet during pregnancy is pivotal for the offspring health at birth and later in life. N-3 polyunsaturated fatty acids (n-3 PUFAs) are not endogenously produced in humans and are exclusively derived from the diet. They are pivotal for the fetus growth and neuronal development and seem beneficial in reducing the risk of cardiometabolic diseases and preventing later allergic disorders in the offspring by modulating the inflammatory immune response. In the present study, we investigated the association between maternal intakes of n-3PUFAs, profiled on maternal erythrocyte membranes at pregnancy term, and offspring DNA methylation on cord blood mononuclear cells in a sample of 118 mother–newborn pairs randomly drawn from the “Feeding fetus’ low-grade inflammation and insulin-resistance” study cohort. N-3 PUFA content on erythrocyte membranes is a validated biomarker to measure objectively medium term intake of n-3 PUFAs. Based on distribution of n-3 PUFA in the whole cohort of mothers, we identified mothers with low (n-3 PUFA concentration <25th percentile), medium (n-3 PUFAs between 25th and 75th percentiles), and high n-3 PUFA content (>75th percentile). The HumanMethylation450 BeadChip (Illumina) was used for the epigenome-wide association study using the Infinium Methylation Assay. The overall DNA methylation level was not different between the three groups while there was significant difference in methylation levels at certain sites. Indeed, 8,503 sites had significantly different methylations between low and high n-3 PUFA groups, 12,716 between low and medium n-3 PUFA groups, and 18,148 between high and medium n-3 PUFA groups. We found differentially methylated genes that belong prevalently to pathways of signal transduction, metabolism, downstream signaling of G protein-coupled receptors, and gene expression. Within these pathways, we identified four differentially methylated genes, namely, MSTN, IFNA13, ATP8B3, and GABBR2, that are involved in the onset of insulin resistance and adiposity, innate immune response, phospholipid translocation across cell membranes, and mechanisms of addiction to high fat diet, alcohol, and sweet taste. In conclusion, findings of this preliminary investigation suggest that maternal intake of n-3 PUFAs during pregnancy has potential to influence the offspring DNA methylation. Validation of results in a larger cohort and investigation of biological significance and impact on the phenotype are warranted.
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Affiliation(s)
- Marzia Bianchi
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Alisi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Fabrizi
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gynecology, Misericordia Hospital, Grosseto, Italy
| | - Lucilla Ravà
- Clinical Epidemiology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Riccardo Giannico
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gynecology, Misericordia Hospital, Grosseto, Italy
| | - Melania Manco
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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Tremblay BL, Guénard F, Lamarche B, Pérusse L, Vohl MC. Familial resemblances in human whole blood transcriptome. BMC Genomics 2018; 19:300. [PMID: 29703154 PMCID: PMC5921553 DOI: 10.1186/s12864-018-4698-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/18/2018] [Indexed: 12/31/2022] Open
Abstract
Background Considering the implication of gene expression in the susceptibility of chronic diseases and the familial clustering of chronic diseases, the study of familial resemblances in gene expression levels is then highly relevant. Few studies have considered the contribution of both genetic and common environmental effects to familial resemblances in whole blood gene expression levels. The objective is to quantify the contribution of genetic and common environmental effects in the familial resemblances of whole blood genome-wide gene expression levels. We also make comparisons with familial resemblances in blood leukocytes genome-wide DNA methylation levels in the same cohort in order to further investigate biological mechanisms. Results Maximal heritability, genetic heritability, and common environmental effect were computed for all probes (20.6%, 15.6%, and 5.0% respectively) and for probes showing a significant familial effect (78.1%, 60.1%, and 18.0% respectively). Pairwise phenotypic correlations between gene expression and DNA methylation levels adjusted for blood cell heterogeneity were computed for probes showing significant familial effect. A total of 78 probe pairs among the 7,618,401 possible pairs passed Bonferroni correction (corrected P-value = 6.56 × 10− 9). Significant genetic correlations between gene expression and DNA methylation levels were found for 25 probe pairs (absolute genetic correlation of 0.97). Conclusions Familial resemblances in gene expression levels were mainly attributable to genetic factors, but common environmental effect also played a role especially in probes showing a significant familial effect. Probes and CpG sites with familial effect seem to be under a strong shared genetic control. Electronic supplementary material The online version of this article (10.1186/s12864-018-4698-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bénédicte L Tremblay
- Institute of Nutrition and Functional Foods (INAF), Laval University, Pavillon des Services, 2440 Hochelaga Blvd, Quebec City, QC G1V 0A6, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Pavillon des Services, 2440 Hochelaga Blvd, Quebec City, QC G1V 0A6, Canada
| | - Benoît Lamarche
- Institute of Nutrition and Functional Foods (INAF), Laval University, Pavillon des Services, 2440 Hochelaga Blvd, Quebec City, QC G1V 0A6, Canada
| | - Louis Pérusse
- CHU de Québec Research Center - Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec City, QC G1V 4G2, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Pavillon des Services, 2440 Hochelaga Blvd, Quebec City, QC G1V 0A6, Canada. .,CHU de Québec Research Center - Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec City, QC G1V 4G2, Canada.
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Aslibekyan S, Ruiz-Narváez EA. The State of Cardiovascular Genomics: Abundant Data, Limited Information. REVISTA ESPANOLA DE CARDIOLOGIA (ENGLISH ED.) 2017; 70:696-698. [PMID: 28400104 PMCID: PMC5821493 DOI: 10.1016/j.rec.2017.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States.
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Situación actual en genómica cardiovascular: muchos datos, poca información. Rev Esp Cardiol (Engl Ed) 2017. [DOI: 10.1016/j.recesp.2017.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Epigenetic changes in blood leukocytes following an omega-3 fatty acid supplementation. Clin Epigenetics 2017; 9:43. [PMID: 28450971 PMCID: PMC5405524 DOI: 10.1186/s13148-017-0345-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/14/2017] [Indexed: 12/24/2022] Open
Abstract
Background Omega-3 polyunsaturated fatty acids (n-3 FAs) have several beneficial effects on cardiovascular (CV) disease risk factors. These effects on CV risk profile may be mediated by several factors, including epigenetic modifications. Our objective is to investigate, using genome-wide DNA methylation analyses, methylation changes following an n-3 FA supplementation in overweight and obese subjects and to identify specific biological pathways potentially altered by the supplementation. Results Blood leukocytes genome-wide DNA methylation profiles of 36 overweight and obese subjects before and after a 6-week supplementation with 3 g of n-3 FAs were compared using GenomeStudio software. After supplementation, 308 CpG sites, assigned to 231 genes, were differentially methylated (FDR-corrected Diffscore ≥│13│~ P ≤ 0.05). Using Ingenuity Pathway Analysis system, a total of 55 pathways were significantly overrepresented following supplementation. Among these pathways, 16 were related to inflammatory and immune response, lipid metabolism, type 2 diabetes, and cardiovascular signaling. Changes in methylation levels of CpG sites within AKT3, ATF1, HDAC4, and IGFBP5 were correlated with changes in plasma triglyceride and glucose levels as well as with changes in the ratio of total cholesterol/HDL-cholesterol following the supplementation. Conclusions These data provide key differences in blood leukocytes DNA methylation profiles of subjects following an n-3 FA supplementation, which brings new, potential insights on metabolic pathways underlying the effects of n-3 FAs on CV health. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0345-3) contains supplementary material, which is available to authorized users.
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Suravajhala P, Kogelman LJA, Kadarmideen HN. Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. Genet Sel Evol 2016; 48:38. [PMID: 27130220 PMCID: PMC4850674 DOI: 10.1186/s12711-016-0217-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/16/2016] [Indexed: 02/06/2023] Open
Abstract
In the past years, there has been a remarkable development of high-throughput omics (HTO) technologies such as genomics, epigenomics, transcriptomics, proteomics and metabolomics across all facets of biology. This has spearheaded the progress of the systems biology era, including applications on animal production and health traits. However, notwithstanding these new HTO technologies, there remains an emerging challenge in data analysis. On the one hand, different HTO technologies judged on their own merit are appropriate for the identification of disease-causing genes, biomarkers for prevention and drug targets for the treatment of diseases and for individualized genomic predictions of performance or disease risks. On the other hand, integration of multi-omic data and joint modelling and analyses are very powerful and accurate to understand the systems biology of healthy and sustainable production of animals. We present an overview of current and emerging HTO technologies each with a focus on their applications in animal and veterinary sciences before introducing an integrative systems genomics framework for analysing and integrating multi-omic data towards improved animal production, health and welfare. We conclude that there are big challenges in multi-omic data integration, modelling and systems-level analyses, particularly with the fast emerging HTO technologies. We highlight existing and emerging systems genomics approaches and discuss how they contribute to our understanding of the biology of complex traits or diseases and holistic improvement of production performance, disease resistance and welfare.
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Affiliation(s)
- Prashanth Suravajhala
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, Denmark
| | - Lisette J A Kogelman
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, Denmark
| | - Haja N Kadarmideen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, Denmark.
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Richardson TG, Timpson NJ, Campbell C, Gaunt TR. A pathway-centric approach to rare variant association analysis. Eur J Hum Genet 2016; 25:123-129. [PMID: 27577545 PMCID: PMC5136291 DOI: 10.1038/ejhg.2016.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 05/18/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Current endeavours in rare variant analysis are typically underpowered when investigating association signals from individual genes. We undertook an approach to rare variant analysis which utilises biological pathway information to analyse functionally relevant genes together. Conventional filtering approaches for rare variant analysis are based on variant consequence and are therefore confined to coding regions of the genome. Therefore, we undertook a novel approach to this process by obtaining functional annotations from the Combined Annotation Dependent Depletion (CADD) tool, which allowed potentially deleterious variants from intronic regions of genes to be incorporated into analyses. This work was undertaken using whole-genome sequencing data from the UK10K project. Rare variants from the KEGG pathway for arginine and proline metabolism were collectively associated with systolic blood pressure (P=3.32x10-5) based on analyses using the optimal sequence kernel association test. Variants along this pathway also showed evidence of replication using imputed data from the Avon Longitudinal Study of Parents and Children cohort (P=0.02). Subsequent analyses found that the strength of evidence diminished when analysing genes in this pathway individually, suggesting that they would have been overlooked in a conventional gene-based analysis. Future studies that adopt similar approaches to investigate polygenic effects should yield value in better understanding the genetic architecture of complex disease.
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Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK.
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Cordell HJ. Summary of results and discussions from the gene-based tests group at Genetic Analysis Workshop 18. Genet Epidemiol 2014; 38 Suppl 1:S44-8. [PMID: 25112187 PMCID: PMC4305206 DOI: 10.1002/gepi.21824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
I present a summary of the results and discussions held within the working group on gene-based tests at Genetic Analysis Workshop 18 (GAW18). The main focus of interest in our working group was modeling the action of combinations or "groups" of genetic variants, with a group of variants most often defined as a set of single-nucleotide polymorphisms lying within a known gene. Some contributions investigated the performance of previously proposed methods (particularly rare variant collapsing or burden-type methods) for addressing this question, applied to the GAW18 data, and other contributions developed novel approaches and addressed novel questions. Most approaches were successful in detecting significant effects at MAP4 in the simulated data. No other genetic effects were consistently detected across different analyses. Low power was noted, particularly for those methods that restricted analysis to purely the subset of unrelated individuals.
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Affiliation(s)
- Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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Paterson AD. Drinking from the Holy Grail: analysis of whole-genome sequencing from the Genetic Analysis Workshop 18. Genet Epidemiol 2014; 38 Suppl 1:S1-4. [PMID: 25112182 DOI: 10.1002/gepi.21818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Genetic Analysis Workshops distribute real and simulated human genetic data to allow the development and comparison of methods to detect genetic variants and genes related to biological traits; the results are then presented and discussed at a biennial meeting. The data made available for Genetic Analysis Workshop 18 (GAW18) included whole-genome sequence data for odd-numbered autosomes from 20 large Mexican American pedigrees selected through probands with type 2 diabetes. Real and simulated blood pressure phenotype data were provided to allow the comparison of methods to detect variants and genes associated with blood pressure. Some of the complexity present in the data includes related individuals, repeated quantitative trait outcomes, covariates, medication effects, pharmacokinetic effects, missing data, admixed population, and imputed genotypes. A wide range of analytic approaches were applied to the data. Contributions that focused only on a subset of up to 155 unrelated subjects from the pedigrees were faced with low power. One recommendation for future analysis is the use of the provided null phenotype to allow comparison of type I error across methods. Collaboration between statistical geneticists and molecular biologists or bioinformaticians would provide helpful input to place variants in genes for gene-based association tests.
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Affiliation(s)
- Andrew D Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Divisions of Epidemiology and Biostatistics, Dalla Lana School of Public Health, Department of Psychiatry, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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