101
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Yang M, Wang Y, Yin B, Zheng Q, Shi B, Jia Z. Association of soluble epoxide hydrolase 2 gene with the risk of non-syndromic cleft lip with or without cleft palate in western Han Chinese population. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2022; 40:279-284. [PMID: 38597007 PMCID: PMC9207791 DOI: 10.7518/hxkq.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/20/2022] [Indexed: 04/11/2024]
Abstract
OBJECTIVES This study aimed to explore the associations between soluble epoxide hydrolase 2 gene (EPHX2) variants and non-syndromic cleft lip with or without cleft palate (NSCL/P) in Chinese Han population. METHODS We recruited 159 NSCL/P cases from Chinese Han population and carried out targeted resequencing using the whole genome sequencing data of 542 healthy Chinese individuals from Novegene internal database as controls. We classified EPHX2 variants as common or rare according to their minor allele frequency and performed an association analysis for common variations and a burden analysis for rare variations. RESULTS The lowest P-value in NSCL/P was observed at rs57699806 (P=0.000 13, OR=2.849 and 95% CI: 1.691-4.800), followed by rs4732723 (P=0.006 50, OR=0.662 and 95%CI: 0.491-0.892), rs7829267 (P=0.009 20, OR=1.496 and 95%CI: 1.117-2.005), rs721619 (P=0.011 00, OR=1.474 and 95%CI: 1.098-1.980), and rs7816586 (P=0.040 00, OR=1.310 and 95%CI: 1.015-1.691). The odds ratios suggested the C allele at rs4732723 as a protective factor for NSCL/P and the reference alleles at other single nucleotide polymorphisms (SNPs) as the risk factors for NSCL/P. Burden analysis showed no statistical significance (P>0.05). CONCLUSIONS Through targeted resequencing, this study identified five SNPs named rs57699806, rs4732723, rs7829267, rs721619, and rs7816586 around the region of EPHX2 gene associated with NSCL/P in Chinese Han population. Four SNPs of rs57699806, rs4732723, rs7829267, and rs7816586 were first identified.
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Affiliation(s)
- Mengxi Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yiru Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qian Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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102
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Chimusa ER, Defo J. Dissecting Meta-Analysis in GWAS Era: Bayesian Framework for Gene/Subnetwork-Specific Meta-Analysis. Front Genet 2022; 13:838518. [PMID: 35664319 PMCID: PMC9159898 DOI: 10.3389/fgene.2022.838518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past decades, advanced high-throughput technologies have continuously contributed to genome-wide association studies (GWASs). GWAS meta-analysis has been increasingly adopted, has cross-ancestry replicability, and has power to illuminate the genetic architecture of complex traits, informing about the reliability of estimation effects and their variability across human ancestries. However, detecting genetic variants that have low disease risk still poses a challenge. Designing a meta-analysis approach that combines the effect of various SNPs within genes or genes within pathways from multiple independent population GWASs may be helpful in identifying associations with small effect sizes and increasing the association power. Here, we proposed ancMETA, a Bayesian graph-based framework, to perform the gene/pathway-specific meta-analysis by combining the effect size of multiple SNPs within genes, and genes within subnetwork/pathways across multiple independent population GWASs to deconvolute the interactions between genes underlying the pathogenesis of complex diseases across human populations. We assessed the proposed framework on simulated datasets, and the results show that the proposed model holds promise for increasing statistical power for meta-analysis of genetic variants underlying the pathogenesis of complex diseases. To illustrate the proposed meta-analysis framework, we leverage seven different European bipolar disorder (BD) cohorts, and we identify variants in the angiotensinogen (AGT) gene to be significantly associated with BD across all 7 studies. We detect a commonly significant BD-specific subnetwork with the ESR1 gene as the main hub of a subnetwork, associated with neurotrophin signaling (p = 4e−14) and myometrial relaxation and contraction (p = 3e−08) pathways. ancMETA provides a new contribution to post-GWAS methodologies and holds promise for comprehensively examining interactions between genes underlying the pathogenesis of genetic diseases and also underlying ethnic differences.
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103
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Burt CH. Challenging the utility of polygenic scores for social science: Environmental confounding, downward causation, and unknown biology. Behav Brain Sci 2022; 46:e207. [PMID: 35551690 PMCID: PMC9653522 DOI: 10.1017/s0140525x22001145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The sociogenomics revolution is upon us, we are told. Whether revolutionary or not, sociogenomics is poised to flourish given the ease of incorporating polygenic scores (or PGSs) as "genetic propensities" for complex traits into social science research. Pointing to evidence of ubiquitous heritability and the accessibility of genetic data, scholars have argued that social scientists not only have an opportunity but a duty to add PGSs to social science research. Social science research that ignores genetics is, some proponents argue, at best partial and likely scientifically flawed, misleading, and wasteful. Here, I challenge arguments about the value of genetics for social science and with it the claimed necessity of incorporating PGSs into social science models as measures of genetic influences. In so doing, I discuss the impracticability of distinguishing genetic influences from environmental influences because of non-causal gene-environment correlations, especially population stratification, familial confounding, and downward causation. I explain how environmental effects masquerade as genetic influences in PGSs, which undermines their raison d'être as measures of genetic propensity, especially for complex socially contingent behaviors that are the subject of sociogenomics. Additionally, I draw attention to the partial, unknown biology, while highlighting the persistence of an implicit, unavoidable reductionist genes versus environments approach. Leaving sociopolitical and ethical concerns aside, I argue that the potential scientific rewards of adding PGSs to social science are few and greatly overstated and the scientific costs, which include obscuring structural disadvantages and cultural influences, outweigh these meager benefits for most social science applications.
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Affiliation(s)
- Callie H Burt
- Department of Criminal Justice & Criminology, Center for Research on Interpersonal Violence (CRIV), Georgia State University, Atlanta, GA, USA ; www.callieburt.org
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104
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Chu X, Jiang M, Liu ZJ. Biomarker interaction selection and disease detection based on multivariate gain ratio. BMC Bioinformatics 2022; 23:176. [PMID: 35550010 PMCID: PMC9103137 DOI: 10.1186/s12859-022-04699-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Background Disease detection is an important aspect of biotherapy. With the development of biotechnology and computer technology, there are many methods to detect disease based on single biomarker. However, biomarker does not influence disease alone in some cases. It’s the interaction between biomarkers that determines disease status. The existing influence measure I-score is used to evaluate the importance of interaction in determining disease status, but there is a deviation about the number of variables in interaction when applying I-score. To solve the problem, we propose a new influence measure Multivariate Gain Ratio (MGR) based on Gain Ratio (GR) of single-variate, which provides us with multivariate combination called interaction. Results We propose a preprocessing verification algorithm based on partial predictor variables to select an appropriate preprocessing method. In this paper, an algorithm for selecting key interactions of biomarkers and applying key interactions to construct a disease detection model is provided. MGR is more credible than I-score in the case of interaction containing small number of variables. Our method behaves better with average accuracy \documentclass[12pt]{minimal}
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\begin{document}$$93.13\%$$\end{document}93.13% than I-score of \documentclass[12pt]{minimal}
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\begin{document}$$91.73\%$$\end{document}91.73% in Breast Cancer Wisconsin (Diagnostic) Dataset. Compared to the classification results \documentclass[12pt]{minimal}
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\begin{document}$$89.80\%$$\end{document}89.80% based on all predictor variables, MGR identifies the true main biomarkers and realizes the dimension reduction. In Leukemia Dataset, the experiment results show the effectiveness of MGR with the accuracy of \documentclass[12pt]{minimal}
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\begin{document}$$97.32\%$$\end{document}97.32% compared to I-score with accuracy \documentclass[12pt]{minimal}
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\begin{document}$$89.11\%$$\end{document}89.11%. The results can be explained by the nature of MGR and I-score mentioned above because every key interaction contains a small number of variables in Leukemia Dataset. Conclusions MGR is effective for selecting important biomarkers and biomarker interactions even in high-dimension feature space in which the interaction could contain more than two biomarkers. The prediction ability of interactions selected by MGR is better than I-score in the case of interaction containing small number of variables. MGR is generally applicable to various types of biomarker datasets including cell nuclei, gene, SNPs and protein datasets.
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Affiliation(s)
- Xiao Chu
- Academy of Mathematics and Systems Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Mao Jiang
- Academy of Mathematics and Systems Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhuo-Jun Liu
- Academy of Mathematics and Systems Science Chinese Academy of Sciences, Beijing, China
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105
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Genetically Adjusted Propensity Score Matching: A Comparison to Discordant MZ Twin Models. Twin Res Hum Genet 2022; 25:24-39. [PMID: 35506340 DOI: 10.1017/thg.2022.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Discordant monozygotic (MZ) twin methodologies are considered one of the foremost statistical approaches for estimating the influence of environmental factors on phenotypic variance. Limitations associated with the discordant MZ twin approach generates an inability to estimate particular relationships and adjust estimates for the confounding influence of gene-nonshared environment interactions. Recent advancements in molecular genetics, however, can provide the opportunity to address these limitations. The current study reviews an alternative technique, genetically adjusted propensity scores (GAPS) matching, that integrates observed genetic and environmental information to adjust for the confounding of these factors in nonkin individuals. Simulations and a real data example were used to compare the GAPS matching approach to the discordant MZ twin method. Although the results of the simulated comparisons demonstrated that the discordant MZ twin approach remains the more robust statistical technique to adjust for shared environmental and genetic factors, GAPS matching - under certain conditions - could represent a viable alternative when MZ twin samples are unavailable. Overall, the findings suggest that GAPS matching can potentially provide an alternative to the discordant MZ twin approach when limited variation exists between identical twin pairs. Moreover, the ability to adjust for gene-nonshared environment interactions represents a potential advancement associated with the GAPS approach. The limitations of the approach, as well as polygenic risk scores, are also discussed.
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106
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Speed D, Kaphle A, Balding DJ. SNP-based heritability and selection analyses: Improved models and new results. Bioessays 2022; 44:e2100170. [PMID: 35279859 DOI: 10.1002/bies.202100170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 01/15/2023]
Abstract
Complex-trait genetics has advanced dramatically through methods to estimate the heritability tagged by SNPs, both genome-wide and in genomic regions of interest such as those defined by functional annotations. The models underlying many of these analyses are inadequate, and consequently many SNP-heritability results published to date are inaccurate. Here, we review the modelling issues, both for analyses based on individual genotype data and association test statistics, highlighting the role of a low-dimensional model for the heritability of each SNP. We use state-of-art models to present updated results about how heritability is distributed with respect to functional annotations in the human genome, and how it varies with allele frequency, which can reflect purifying selection. Our results give finer detail to the picture that has emerged in recent years of complex trait heritability widely dispersed across the genome. Confounding due to population structure remains a problem that summary statistic analyses cannot reliably overcome. Also see the video abstract here: https://youtu.be/WC2u03V65MQ.
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Affiliation(s)
- Doug Speed
- Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.,UCL Genetics Institute, University College London, London, UK
| | - Anubhav Kaphle
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics and Statistics, University of Melbourne, Victoria, Australia
| | - David J Balding
- UCL Genetics Institute, University College London, London, UK.,Melbourne Integrative Genomics, School of BioSciences and School of Mathematics and Statistics, University of Melbourne, Victoria, Australia
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107
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Machine learning approaches to explore digenic inheritance. Trends Genet 2022; 38:1013-1018. [DOI: 10.1016/j.tig.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/22/2022]
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108
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Chen YC, Tsai YJ, Wang CC, Ko PS, Su W, Su SL. Decisive gene strategy on osteoporosis: a comprehensive whole-literature-based approach for conclusive candidate gene targets. Aging (Albany NY) 2022; 14:3484-3528. [PMID: 35452412 PMCID: PMC9085221 DOI: 10.18632/aging.204026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
Purpose: Previous meta-analyses only examined the association between single gene polymorphisms and osteoporosis; there is no compilation of all gene loci that correlate with osteoporosis in the literature. In this study, we develop a new literature-based approach, a decisive gene strategy (DGS), to examine the sufficiency of the cumulative sample size for each gene locus and to assess whether a definite conclusion of the association between the gene locus and osteoporosis can be drawn. Methods: The DGS was used to search PubMed, Embase, and Cochrane databases for all meta-analyses that correlated gene polymorphisms with osteoporosis. Trial sequential analysis was employed to examine the sufficiency of the cumulative sample size. Finally, we assessed the importance of gene loci in osteoporosis based on whether there were enough sample sizes and the heterogeneity of the literature with the I2 value. Results: After excluding 169 irrelevant publications, 39 meta-analysis papers were obtained. Among Caucasians, in 17 gene loci, there were eight gene loci (e.g., vitamin D Receptor ApaI rs7975232) with sufficient cumulative sample size to confirm that they were unrelated to the disease. Among Asians, in 15 gene loci, four gene loci that had sufficient sample sizes were risk factors: VDR FokI rs2228570 (odds ratio (OR) = 1.44, 95% confidence interval (CI) = 1.22–1.70), TGF β1 rs1800470 (OR = 1.35, 95% CI = 1.10–1.65), IGF1 rs2288377 (OR = 1.44, 95% CI = 1.28–1.62), and IGF1 rs35767 (OR = 1.20, 95% CI = 1.06–1.36), respectively, whereas one gene locus, ESR2 RsaI rs1256049 (OR = 0.69, 95% CI = 0.59–0.81), was a protective factor. Conclusions: The DGS successfully identified five gene loci in osteoporosis that will apply to other diseases to find causal genes, which may contribute to further genetic therapy.
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Affiliation(s)
- Yueh-Chun Chen
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C
| | - Yu-Jui Tsai
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, R.O.C
| | - Chih-Chien Wang
- Department of Orthopedics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, R.O.C
| | - Pi-Shao Ko
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, R.O.C.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C
| | - Wen Su
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Taipei, Taiwan, R.O.C
| | - Sui-Lung Su
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C.,School of Public Health, National Defense Medical Center, Taipei, Taiwan, R.O.C
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109
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Tang M, Hou T, Tong X, Shen X, Zhang X, Wang T, Lu Q. Fast heritability estimation based on MINQUE and batch training. Brief Bioinform 2022; 23:6563939. [PMID: 35383355 DOI: 10.1093/bib/bbac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/20/2022] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
Abstract
Heritability, the proportion of phenotypic variance explained by genome-wide single nucleotide polymorphisms (SNPs) in unrelated individuals, is an important measure of the genetic contribution to human diseases and plays a critical role in studying the genetic architecture of human diseases. Linear mixed model (LMM) has been widely used for SNP heritability estimation, where variance component parameters are commonly estimated by using a restricted maximum likelihood (REML) method. REML is an iterative optimization algorithm, which is computationally intensive when applied to large-scale datasets (e.g. UK Biobank). To facilitate the heritability analysis of large-scale genetic datasets, we develop a fast approach, minimum norm quadratic unbiased estimator (MINQUE) with batch training, to estimate variance components from LMM (LMM.MNQ.BCH). In LMM.MNQ.BCH, the parameters are estimated by MINQUE, which has a closed-form solution for fast computation and has no convergence issue. Batch training has also been adopted in LMM.MNQ.BCH to accelerate the computation for large-scale genetic datasets. Through simulations and real data analysis, we demonstrate that LMM.MNQ.BCH is much faster than two existing approaches, GCTA and BOLT-REML.
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Affiliation(s)
- Mingsheng Tang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, No.56 Xin jian South Road, 030001 Shanxi, China
| | - Tingting Hou
- Department of Biostatistics, University of Florida, 2004 Mowry Road, 32611 FL, USA
| | - Xiaoran Tong
- Department of Biostatistics, University of Florida, 2004 Mowry Road, 32611 FL, USA
| | - Xiaoxi Shen
- Department of Biostatistics, University of Florida, 2004 Mowry Road, 32611 FL, USA
| | - Xuefen Zhang
- Social Medicine, School of Public Health, Shanxi Medical University,No.56 Xin jian South Road, 030001 Shanxi, China
| | - Tong Wang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, No.56 Xin jian South Road, 030001 Shanxi, China
| | - Qing Lu
- Department of Biostatistics, University of Florida, 2004 Mowry Road, 32611 FL, USA
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110
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Liu Y, Nazir MF, He S, Li H, Pan Z, Sun G, Dai P, Wang L, Du X. Deltapine 15 contributes to the genomic architecture of modern upland cotton cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1401-1411. [PMID: 35146550 DOI: 10.1007/s00122-022-04042-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Foundation parents play a critical role in the genetic constituents of the derived genotypes. Deltapine-15 (DLP-15), introduced to China in 1950, is one of the most commonly used parents for early breeding programs in China. However, the formation and inheritance patterns of genomic constituents have not been studied. Therefore, this study aimed at understanding and exploring the genomic architecture of 146 DLP-15 derived cultivars with a common foundation parent DLP-15. Population structure based on sequencing data clustered genotypes into two groups (G1 and G2) supported by principal component analysis. Further exploration led to the identification of Chr-A08 with significantly differentiated regions between two groups. Moreover, we identified genome-wide identity by descent (IBD) segments (840 segments) to understand the genomic inheritance pattern in DLP-15 derived cultivars, spanning the 20-95 Mb region on Chr-A08. Interestingly, Chr-A08 depicted a unique inheritance pattern from DLP-15 to its derived cultivars. IBD-segment-based haplotype analysis suggested significant differences among the two groups. Phenotypic trait association with DLP-derived haplotypes concerning Chr-A08 suggested a significant increase in yield and fiber quality. Furthermore, distinguished IBD segments overlapped with previously reported QTLs concerning fiber yield and quality. Our results systematically identified genomic signatures transmitted from the foundation parent DLP-15 to its derived cultivars and provided a basis for further exploiting excellent haplotypes associated with DLP-15.
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Affiliation(s)
- Yingfei Liu
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Mian Faisal Nazir
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China
| | - Shoupu He
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China
| | - Hongge Li
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoe Pan
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Panhong Dai
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liyuan Wang
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiongming Du
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China.
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111
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Hébert F, Causeur D, Emily M. Omnibus testing approach for gene-based gene-gene interaction. Stat Med 2022; 41:2854-2878. [PMID: 35338506 DOI: 10.1002/sim.9389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 11/07/2022]
Abstract
Genetic interaction is considered as one of the main heritable component of complex traits. With the emergence of genome-wide association studies (GWAS), a collection of statistical methods dedicated to the identification of interaction at the SNP level have been proposed. More recently, gene-based gene-gene interaction testing has emerged as an attractive alternative as they confer advantage in both statistical power and biological interpretation. Most of the gene-based interaction methods rely on a multidimensional modeling of the interaction, thus facing a lack of robustness against the huge space of interaction patterns. In this paper, we study a global testing approaches to address the issue of gene-based gene-gene interaction. Based on a logistic regression modeling framework, all SNP-SNP interaction tests are combined to produce a gene-level test for interaction. We propose an omnibus test that takes advantage of (1) the heterogeneity between existing global tests and (2) the complementarity between allele-based and genotype-based coding of SNPs. Through an extensive simulation study, it is demonstrated that the proposed omnibus test has the ability to detect with high power the most common interaction genetic models with one causal pair as well as more complex genetic models where more than one causal pair is involved. On the other hand, the flexibility of the proposed approach is shown to be robust and improves power compared to single global tests in replication studies. Furthermore, the application of our procedure to real datasets confirms the adaptability of our approach to replicate various gene-gene interactions.
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Affiliation(s)
- Florian Hébert
- Department of Statistics and Computer Science, Institut Agro, CNRS, IRMAR, Univ Rennes, F-35000, Rennes, France
| | - David Causeur
- Department of Statistics and Computer Science, Institut Agro, CNRS, IRMAR, Univ Rennes, F-35000, Rennes, France
| | - Mathieu Emily
- Department of Statistics and Computer Science, Institut Agro, CNRS, IRMAR, Univ Rennes, F-35000, Rennes, France
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112
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Tang Y, You D, Yi H, Yang S, Zhao Y. IPRS: Leveraging Gene-Environment Interaction to Reconstruct Polygenic Risk Score. Front Genet 2022; 13:801397. [PMID: 35401709 PMCID: PMC8989431 DOI: 10.3389/fgene.2022.801397] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/08/2022] [Indexed: 12/30/2022] Open
Abstract
Background: Polygenic risk score (PRS) is widely regarded as a predictor of genetic susceptibility to disease, applied to individuals to predict the risk of disease occurrence. When the gene-environment (G×E) interaction is considered, the traditional PRS prediction model directly uses PRS to interact with the environment without considering the interactions between each variant and environment, which may lead to prediction performance and risk stratification of complex diseases are not promising. Methods: We developed a method called interaction PRS (iPRS), reconstructing PRS by leveraging G×E interactions. Two extensive simulations evaluated prediction performance, risk stratification, and calibration performance of the iPRS prediction model, and compared it with the traditional PRS prediction model. Real data analysis was performed using existing data from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial study to predict genetic susceptibility, pack-years of smoking history, and G×E interactions in patients with lung cancer. Results: Two extensive simulations indicated iPRS prediction model could improve the prediction performance of disease risk, the accuracy of risk stratification, and clinical calibration performance compared with the traditional PRS prediction model, especially when antagonism accounted for the majority of the interaction. PLCO real data analysis also suggested that the iPRS prediction model was superior to the PRS prediction model in predictive effect (p = 0.0205). Conclusion: IPRS prediction model could have a good application prospect in predicting disease risk, optimizing the screening of high-risk populations, and improving the clinical benefits of preventive interventions among populations.
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Affiliation(s)
- Yingdan Tang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dongfang You
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Honggang Yi
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Sheng Yang, ; Yang Zhao,
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Center of Biomedical Big Data and the Laboratory of Biomedical Big Data, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Sheng Yang, ; Yang Zhao,
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113
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Chen P, Michel AH, Zhang J. Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. Nat Commun 2022; 13:1490. [PMID: 35314699 PMCID: PMC8938418 DOI: 10.1038/s41467-022-29228-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/01/2022] [Indexed: 12/18/2022] Open
Abstract
Due to epistasis, the same mutation can have drastically different phenotypic consequences in different individuals. This phenomenon is pertinent to precision medicine as well as antimicrobial drug development, but its general characteristics are largely unknown. We approach this question by genome-wide assessment of gene essentiality polymorphism in 16 Saccharomyces cerevisiae strains using transposon insertional mutagenesis. Essentiality polymorphism is observed for 9.8% of genes, most of which have had repeated essentiality switches in evolution. Genes exhibiting essentiality polymorphism lean toward having intermediate numbers of genetic and protein interactions. Gene essentiality changes tend to occur concordantly among components of the same protein complex or metabolic pathway and among a group of over 100 mitochondrial proteins, revealing molecular machines or functional modules as units of gene essentiality variation. Most essential genes tolerate transposon insertions consistently among strains in one or more coding segments, delineating nonessential regions within essential genes.
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Affiliation(s)
- Piaopiao Chen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Agnès H Michel
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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114
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Zeng L, Moser S, Mirza-Schreiber N, Lamina C, Coassin S, Nelson CP, Annilo T, Franzén O, Kleber ME, Mack S, Andlauer TFM, Jiang B, Stiller B, Li L, Willenborg C, Munz M, Kessler T, Kastrati A, Laugwitz KL, Erdmann J, Moebus S, Nöthen MM, Peters A, Strauch K, Müller-Nurasyid M, Gieger C, Meitinger T, Steinhagen-Thiessen E, März W, Metspalu A, Björkegren JLM, Samani NJ, Kronenberg F, Müller-Myhsok B, Schunkert H. Cis-epistasis at the LPA locus and risk of cardiovascular diseases. Cardiovasc Res 2022; 118:1088-1102. [PMID: 33878186 PMCID: PMC8930071 DOI: 10.1093/cvr/cvab136] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
AIMS Coronary artery disease (CAD) has a strong genetic predisposition. However, despite substantial discoveries made by genome-wide association studies (GWAS), a large proportion of heritability awaits identification. Non-additive genetic effects might be responsible for part of the unaccounted genetic variance. Here, we attempted a proof-of-concept study to identify non-additive genetic effects, namely epistatic interactions, associated with CAD. METHODS AND RESULTS We tested for epistatic interactions in 10 CAD case-control studies and UK Biobank with focus on 8068 SNPs at 56 loci with known associations with CAD risk. We identified a SNP pair located in cis at the LPA locus, rs1800769 and rs9458001, to be jointly associated with risk for CAD [odds ratio (OR) = 1.37, P = 1.07 × 10-11], peripheral arterial disease (OR = 1.22, P = 2.32 × 10-4), aortic stenosis (OR = 1.47, P = 6.95 × 10-7), hepatic lipoprotein(a) (Lp(a)) transcript levels (beta = 0.39, P = 1.41 × 10-8), and Lp(a) serum levels (beta = 0.58, P = 8.7 × 10-32), while individual SNPs displayed no association. Further exploration of the LPA locus revealed a strong dependency of these associations on a rare variant, rs140570886, that was previously associated with Lp(a) levels. We confirmed increased CAD risk for heterozygous (relative OR = 1.46, P = 9.97 × 10-32) and individuals homozygous for the minor allele (relative OR = 1.77, P = 0.09) of rs140570886. Using forward model selection, we also show that epistatic interactions between rs140570886, rs9458001, and rs1800769 modulate the effects of the rs140570886 risk allele. CONCLUSIONS These results demonstrate the feasibility of a large-scale knowledge-based epistasis scan and provide rare evidence of an epistatic interaction in a complex human disease. We were directed to a variant (rs140570886) influencing risk through additive genetic as well as epistatic effects. In summary, this study provides deeper insights into the genetic architecture of a locus important for cardiovascular diseases.
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Affiliation(s)
- Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, 80636 Munich, Germany
| | - Sylvain Moser
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Nazanin Mirza-Schreiber
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Groby Rd, Leicester LE3 9QP, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Tarmo Annilo
- Estonian Genome Center, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, 14186 Stockholm, Sweden
| | - Marcus E Kleber
- Medizinische Klinik V (Nephrologie, Hypertensiologie, Rheumatologie, Endokrinologie, Diabetologie), Medizinische Fakultät Mannheim der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Salome Mack
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Till F M Andlauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Beibei Jiang
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Barbara Stiller
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, 80636 Munich, Germany
| | - Ling Li
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, 80636 Munich, Germany
| | - Christina Willenborg
- Institute for Cardiogenetics and University Heart Center Luebeck, University of Lübeck, 23562 Lübeck, Germany
| | - Matthias Munz
- Institute for Cardiogenetics and University Heart Center Luebeck, University of Lübeck, 23562 Lübeck, Germany
- Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
- Charité – University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Dental and Craniofacial Sciences, Department of Periodontology and Synoptic Dentistry, 14197 Berlin, Germany
| | - Thorsten Kessler
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, 80636 Munich, Germany
- Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Partner Site Munich Heart Alliance, 80636 Munich, Germany
| | - Adnan Kastrati
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, 80636 Munich, Germany
- Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Partner Site Munich Heart Alliance, 80636 Munich, Germany
| | - Karl-Ludwig Laugwitz
- Medizinische Klinik, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics and University Heart Center Luebeck, University of Lübeck, 23562 Lübeck, Germany
- Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, 45147 Essen, Germany
- Centre for Urbane Epidemiology, University Hospital Essen, 45147 Essen, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, 53012 Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, 81377 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, 81377 Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, 81377 Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55101 Mainz, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, 81377 Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Winfried März
- Medizinische Klinik V (Nephrologie, Hypertensiologie, Rheumatologie, Endokrinologie, Diabetologie), Medizinische Fakultät Mannheim der Universität Heidelberg, 69120 Heidelberg, Germany
- Synlab Akademie, Synlab Holding Deutschland GmbH, Mannheim und Augsburg, 86156 Augsburg, Germany
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, 14186 Stockholm, Sweden
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Groby Rd, Leicester LE3 9QP, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Munich Cluster of Systems Biology, SyNergy, 81377 Munich, Germany
- Department of Health Data Science, University of Liverpool, Liverpool L69 3BX, UK
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, 80636 Munich, Germany
- Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Partner Site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
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Gong H, Rehman F, Li Z, Liu J, Yang T, Liu J, Li H, Hu Z, Ma Q, Wu Z, A B, Yang M, Gao H, Zhi H, Qu H, Di D, Wang Y. Discrimination of Geographical Origins of Wolfberry ( Lycium barbarum L.) Fruits Using Stable Isotopes, Earth Elements, Free Amino Acids, and Saccharides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2984-2997. [PMID: 35179024 DOI: 10.1021/acs.jafc.1c06207] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To develop sophisticated approaches for distinguishing goji origins, 325 wolfberry fruit samples of a certain cultivar, plant age, drying method, and collection season were gathered from 26 producing areas across Northwest China in 2017 and 2018. We employed 49 indices, including stable isotopes, earth elements, soluble amino acids, and saccharides, to identify the regions of origin of these goji fruits. Analysis of variance (ANOVA) and heritability analysis were used to assess the effects of the environment (producing areas), cultivar, plant age, drying process, and collection season. Samples from the same place can be classified and partially discriminated using principal component analysis (PCA). We were able to distinguish fruits produced in Zhongning County from those produced in the other five producing provinces using orthogonal projection to latent structure-discriminant analysis (OPLS-DA). Calcium (Ca), manganese (Mn), ornithine (Orn), cystine (Cys-Cys), glutamate (Glu), phenylalanine (Phe), phosphoserine (Ps), serine (Ser), lysine (Lys), taurine (Tau), proline (Pro), and tyrosine (Tyr) indices were chosen using S-plots and heritability analysis, and their repeatability was established with samples collected in 2018. The indices selected in this study can distinguish goji berries produced in Zhongning County from fruits originating from five other Provinces with high repeatability, which was validated with various cultivars, drying methods, harvest seasons, and plant ages and with heritability analysis.
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Affiliation(s)
- Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Zhong Li
- Bairuiyuan Company, Yinchuan 750000, P. R. China
| | - Jianfei Liu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, P. R. China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Juan Liu
- Zhongning County Goji Industry Development Service Bureau, Zhongwei 755100, Ningxia, P. R. China
| | - Haoran Li
- Zhongning County Goji Industry Development Service Bureau, Zhongwei 755100, Ningxia, P. R. China
| | - Zhongqing Hu
- Zhongning County Goji Industry Development Service Bureau, Zhongwei 755100, Ningxia, P. R. China
| | - Qihu Ma
- Beijing TongRenTang Health-Pharmaceutical (Ningxia) Co., Ltd., Yinchuan 750000, Ningxia, P. R. China
| | - Zhigeng Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Biao A
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Meizhen Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, P. R. China
| | - Hui Zhi
- School of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Hongxia Qu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Duolong Di
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, P. R. China
- Center of Resource Chemical and New Material, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Qingdao 266100, P. R. China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
- Gannan Normal University, Ganzhou, Jinagxi 341000, P. R. China
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116
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Kamani T, Charkhchi P, Zahedi A, Akbari MR. Genetic susceptibility to hereditary non-medullary thyroid cancer. Hered Cancer Clin Pract 2022; 20:9. [PMID: 35255942 PMCID: PMC8900298 DOI: 10.1186/s13053-022-00215-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
Non-medullary thyroid cancer (NMTC) is the most common type of thyroid cancer. With the increasing incidence of NMTC in recent years, the familial form of the disease has also become more common than previously reported, accounting for 5-15% of NMTC cases. Familial NMTC is further classified as non-syndromic and the less common syndromic FNMTC. Although syndromic NMTC has well-known genetic risk factors, the gene(s) responsible for the vast majority of non-syndromic FNMTC cases are yet to be identified. To date, several candidate genes have been identified as susceptibility genes in hereditary NMTC. This review summarizes genetic predisposition to non-medullary thyroid cancer and expands on the role of genetic variants in thyroid cancer tumorigenesis and the level of penetrance of NMTC-susceptibility genes.
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Affiliation(s)
- Tina Kamani
- Women's College Research Institute, University of Toronto, 76 Grenville St. Room 6421, Toronto, ON, M5S 1B2, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, University of Toronto, 76 Grenville St. Room 6421, Toronto, ON, M5S 1B2, Canada
| | - Afshan Zahedi
- Women's College Research Institute, University of Toronto, 76 Grenville St. Room 6421, Toronto, ON, M5S 1B2, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, University of Toronto, 76 Grenville St. Room 6421, Toronto, ON, M5S 1B2, Canada. .,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5T 3M7, Canada.
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117
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Harley IT, Sawalha AH. Systemic lupus erythematosus as a genetic disease. Clin Immunol 2022; 236:108953. [PMID: 35149194 PMCID: PMC9167620 DOI: 10.1016/j.clim.2022.108953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus is the prototypical systemic autoimmune disease, as it is characterized both by protean multi-organ system manifestations and by the uniform presence of pathogenic autoantibodies directed against components of the nucleus. Prior to the modern genetic era, the diverse clinical manifestations of SLE suggested to many that SLE patients were unlikely to share a common genetic risk basis. However, modern genetic studies have revealed that SLE usually arises when an environmental exposure occurs in an individual with a collection of genetic risk variants passing a liability threshold. Here, we summarize the current state of the field aimed at: (1) understanding the genetic architecture of this complex disease, (2) synthesizing how this genetic risk architecture impacts cellular and molecular disease pathophysiology, (3) providing illustrative examples that highlight the rich complexity of the pathobiology of this prototypical autoimmune disease and (4) communicating this complex etiopathogenesis to patients.
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Affiliation(s)
- Isaac T.W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA,Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA,Rocky Mountain Regional Veteran’s Administration Medical Center (VAMC), Medicine Service, Rheumatology Section, Aurora, CO, USA,Corresponding author at: Isaac TW Harley, MD, PhD, MS, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Barbara Davis Center, Mail Stop B115, 1775 Aurora Court, Aurora, CO 80045, USA, (I.T.W. Harley)
| | - Amr H. Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Corresponding author at: Amr H. Sawalha, MD, University of Pittsburgh, 7123 Rangos Research Center, 4401 Penn Avenue, Pittsburgh, PA 15224, USA, (A.H. Sawalha)
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118
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Hu T, Yang F, He K, Ying J, Cui H. Association of mental health with the risk of coronary artery disease in patients with diabetes: A mendelian randomization study. Nutr Metab Cardiovasc Dis 2022; 32:703-709. [PMID: 35144858 DOI: 10.1016/j.numecd.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND AND AIMS Observational studies have shown an association between mental health and coronary artery disease (CAD) in patients with diabetes. Nevertheless, whether these associations are causal is still unknown. In this two-sample Mendelian randomization (MR) study, we aimed to assess the causality between mental health and CAD in patients with diabetes. METHODS AND RESULTS Single-nucleotide polymorphisms (SNPs) associated with: depression (807,553 individuals), anxiety (83,556 individuals) and neuroticism (329,821 individuals) were identified from the largest genome-wide association studies (GWAS). Summary-level data for CAD were extracted from the recently published GWAS of 15,666 diabetic patients (3968 CAD cases and 11,696 controls). The inverse-variance weighted (IVW) method was used for the main analysis. Sensitivity analyses included weighted median, maximum likelihood, and the MR-Egger method. Genetic liability to depression was significantly associated with a higher risk of CAD in patients with diabetes (odds ratio [OR], 1.286; 95%CI,1.018-1.621;p = 0.035). For anxiety and neuroticism, no causal association with CAD in patients with diabetes was observed. Consistent results were obtained in most sensitivity analyses. CONCLUSIONS This MR study provides genetic evidence that depression is a potential risk factor for CAD in patients with diabetes. However, anxiety and neuroticism were not causally associated with CAD in patients with diabetes. Mental health treatments should be enhanced to prevent CAD in patients with diabetes.
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Affiliation(s)
- Teng Hu
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China; Cardiology Center, Ningbo First Hospital, Ningbo, Zhejiang, 315010, China
| | - Fangkun Yang
- Cardiology Center, Ningbo First Hospital, Ningbo, Zhejiang, 315010, China; School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Kewan He
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China; Cardiology Center, Ningbo First Hospital, Ningbo, Zhejiang, 315010, China
| | - Jiajun Ying
- Cardiology Center, Ningbo First Hospital, Ningbo, Zhejiang, 315010, China; School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Hanbin Cui
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China; Cardiology Center, Ningbo First Hospital, Ningbo, Zhejiang, 315010, China.
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Wainschtein P, Jain D, Zheng Z, Cupples LA, Shadyab AH, McKnight B, Shoemaker BM, Mitchell BD, Psaty BM, Kooperberg C, Liu CT, Albert CM, Roden D, Chasman DI, Darbar D, Lloyd-Jones DM, Arnett DK, Regan EA, Boerwinkle E, Rotter JI, O'Connell JR, Yanek LR, de Andrade M, Allison MA, McDonald MLN, Chung MK, Fornage M, Chami N, Smith NL, Ellinor PT, Vasan RS, Mathias RA, Loos RJF, Rich SS, Lubitz SA, Heckbert SR, Redline S, Guo X, Chen YDI, Laurie CA, Hernandez RD, McGarvey ST, Goddard ME, Laurie CC, North KE, Lange LA, Weir BS, Yengo L, Yang J, Visscher PM. Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data. Nat Genet 2022; 54:263-273. [PMID: 35256806 PMCID: PMC9119698 DOI: 10.1038/s41588-021-00997-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022]
Abstract
Analyses of data from genome-wide association studies on unrelated individuals have shown that, for human traits and diseases, approximately one-third to two-thirds of heritability is captured by common SNPs. However, it is not known whether the remaining heritability is due to the imperfect tagging of causal variants by common SNPs, in particular whether the causal variants are rare, or whether it is overestimated due to bias in inference from pedigree data. Here we estimated heritability for height and body mass index (BMI) from whole-genome sequence data on 25,465 unrelated individuals of European ancestry. The estimated heritability was 0.68 (standard error 0.10) for height and 0.30 (standard error 0.10) for body mass index. Low minor allele frequency variants in low linkage disequilibrium (LD) with neighboring variants were enriched for heritability, to a greater extent for protein-altering variants, consistent with negative selection. Our results imply that rare variants, in particular those in regions of low linkage disequilibrium, are a major source of the still missing heritability of complex traits and disease.
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Affiliation(s)
- Pierrick Wainschtein
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Benjamin M Shoemaker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Christine M Albert
- Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular, Brigham and Women's Hospital, Boston, MA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dan Roden
- Departments of Medicine, Pharmacology and Bioinformatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawood Darbar
- Department of Medicine, University of Illinois-Chicago, Chicago, IL, USA
| | | | - Donna K Arnett
- Dean's Office, College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Eric Boerwinkle
- Health Science Center, University of Texas, Houston, TX, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Matthew A Allison
- Department of Family Medicine, University of California San Diego, La Jolla, CA, USA
| | - Merry-Lynn N McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mina K Chung
- Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nathalie Chami
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Institute for Child Health and Development, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas L Smith
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Patrick T Ellinor
- Harvard Medical School, Boston, MA, USA
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA, USA
- Sections of Preventive Medicine and Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Divisions of Allergy and Clinical Immunology and General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Institute for Child Health and Development, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Steven A Lubitz
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Susan R Heckbert
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Y -D Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Stephen T McGarvey
- International Health Institute, Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Michael E Goddard
- Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology and Carolina Center of Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Loic Yengo
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- School of Life Sciences, Westlake University, Hangzhou Zhejiang, China.
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
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120
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Mularo AJ, Bernal XE, DeWoody JA. Dominance can increase genetic variance after a population bottleneck: a synthesis of the theoretical and empirical evidence. J Hered 2022; 113:257-271. [PMID: 35143665 DOI: 10.1093/jhered/esac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on two theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.
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Affiliation(s)
- Andrew J Mularo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ximena E Bernal
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
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121
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Bourrat P. Unifying heritability in evolutionary theory. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2022; 91:201-210. [PMID: 34968803 DOI: 10.1016/j.shpsa.2021.10.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/25/2021] [Accepted: 10/30/2021] [Indexed: 06/14/2023]
Abstract
Despite being widely used in both biology and psychology as if it were a single notion, heritability is not a unified concept. This is also true in evolutionary theory, in which the word 'heritability' has at least two technical definitions that only partly overlap. These yield two approaches to heritability: the 'variance approach' and the 'regression approach.' In this paper, I aim to unify these two approaches. After presenting them, I argue that a general notion of heritability ought to satisfy two desiderata-'general applicability' and 'separability of the causes of resemblance.' I argue that neither the variance nor the regression approach satisfies these two desiderata concomitantly. From there, I develop a general definition of heritability that relies on the distinction between intrinsic and extrinsic properties. I show that this general definition satisfies the two desiderata. I then illustrate the potential usefulness of this general definition in the context of microbiome research.
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Affiliation(s)
- Pierrick Bourrat
- Macquarie University, Department of Philosophy, North Ryde, NSW 2109, Australia; The University of Sydney, Department of Philosophy & Charles Perkins Centre, Camperdown, NSW 2006, Australia.
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122
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Ropers HH, van Karnebeek CD. Rare diseases: human genome research is coming home. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006210. [PMID: 35332074 PMCID: PMC8958923 DOI: 10.1101/mcs.a006210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
After a long and largely disappointing detour, Genome Research has reidentified Rare Diseases as a major opportunity for improving health care and a clue to understanding gene and genome function. In this Special Issue of CSH Molecular Case Studies on Rare Diseases, several invited Perspectives, numerous Case Reports, and this Editorial itself address recent breakthroughs as well as unsolved problems in this wide field. These range from exciting prospects for gap-free diagnostic whole-genome sequencing to persisting problems related to identifying and distinguishing pathogenic and benign variants; and from the good news that soon, the United Kingdom will no longer be the only country to have introduced whole-genome sequencing into health care to the sobering conclusion that in many countries the clinical infrastructure for bringing Genome Medicine to the patient is still lacking. With less than 5000 genes firmly implicated in disease, the identification of at least twice as many disease genes is a major challenge, and the elucidation of their function is an even larger task. But given the renewed interest in rare diseases, their importance for health care, and the vast and growing spectrum of concepts and methods for studying them, the future of Human Genome Research is bright.
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Affiliation(s)
- Hans-Hilger Ropers
- Max Planck Institute for Molecular Genetics, Berlin D-14195, and Institute of Human Genetics, University Medicine, Mainz D-55131, Germany
| | - Clara D. van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam University Medical Centers, NL-1105 AZ Amsterdam, The Netherlands
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123
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An adaptive combination method for Cauchy variable based on optimal threshold. J Genet 2022. [DOI: 10.1007/s12041-021-01351-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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124
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Ogbunugafor CB. The mutation effect reaction norm (mu-rn) highlights environmentally dependent mutation effects and epistatic interactions. Evolution 2022; 76:37-48. [PMID: 34989399 DOI: 10.1111/evo.14428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022]
Abstract
Since the modern synthesis, the fitness effects of mutations and epistasis have been central yet provocative concepts in evolutionary and population genetics. Studies of how the interactions between parcels of genetic information can change as a function of environmental context have added a layer of complexity to these discussions. Here I introduce the "mutation effect reaction norm" (Mu-RN), a new instrument through which one can analyze the phenotypic consequences of mutations and interactions across environmental contexts. It embodies the fusion of measurements of genetic interactions with the reaction norm, a classic depiction of the performance of genotypes across environments. I demonstrate the utility of the Mu-RN through the signature of a "compensatory ratchet" mutation that undermines reverse evolution of antimicrobial resistance. More broadly, I argue that the mutation effect reaction norm may help us resolve the dynamism and unpredictability of evolution, with implications for theoretical biology, genetic modification technology, and public health. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
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125
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Monaco AP. The selfish environment meets the selfish gene: Coevolution and inheritance of RNA and DNA pools: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools. Bioessays 2022; 44:e2100239. [PMID: 34985131 DOI: 10.1002/bies.202100239] [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: 10/09/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 11/07/2022]
Abstract
Throughout evolution, there has been interaction and exchange between RNA pools in the environment, and DNA and RNA pools of eukaryotic organisms. Metagenomic and metatranscriptomic sequencing of invertebrate hosts and their microbiota has revealed a rich evolutionary history of RNA virus shuttling between species. Horizontal transfer adapted the RNA pool for successful future interactions which lead to zoonotic transmission and detrimental RNA viral pandemics like SARS-CoV2. In eukaryotes, noncoding RNA (ncRNA) is an established mechanism derived from prokaryotes to defend against viral attack through innate immunity and regulation of host-derived mRNA. Transgenerational inheritance of ncRNA is evidence for feedforward adaptive immunity and epigenetically encoded environmental change across generations, which may explain the ''missing heritability'' of common disease. Causal graph theory and the Price Equation can model epigenetic inheritance involving dynamic internal and external RNA pools. Experimental designs should include metatranscriptomic analyses to understand how ncRNA responds to rapidly changing environmental conditions, within and between organisms, and across generations.
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Affiliation(s)
- Anthony P Monaco
- Office of the President, Ballou Hall, Tufts University, Medford, Massachusetts, USA
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126
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Arends D, Kärst S, Heise S, Korkuc P, Hesse D, Brockmann GA. Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line. Genetics 2021; 220:6428544. [PMID: 34791189 PMCID: PMC8733443 DOI: 10.1093/genetics/iyab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022] Open
Abstract
While direct additive and dominance effects on complex traits have been mapped repeatedly, additional genetic factors contributing to the heterogeneity of complex traits have been scarcely investigated. To assess genetic background effects, we investigated transmission ratio distortions (TRDs) of alleles from parent to offspring using an advanced intercross line (AIL) of an initial cross between the mouse inbred strains C57BL/6NCrl (B6N) and BFMI860-12 [Berlin Fat Mouse Inbred (BFMI)]. A total of 341 males of generation 28 and their respective 61 parents and 66 grandparents were genotyped using Mega Mouse Universal Genotyping Arrays. TRDs were investigated using allele transmission asymmetry tests, and pathway overrepresentation analysis was performed. Sequencing data were used to test for overrepresentation of nonsynonymous SNPs (nsSNPs) in TRD regions. Genetic incompatibilities were tested using the Bateson–Dobzhansky–Muller two-locus model. A total of 62 TRD regions were detected, many in close proximity to the telocentric centromere. TRD regions contained 44.5% more nsSNPs than randomly selected regions (182 vs 125.9 ± 17.0, P < 1 × 10−4). Testing for genetic incompatibilities between TRD regions identified 29 genome-wide significant incompatibilities between TRD regions [P(BF) < 0.05]. Pathway overrepresentation analysis of genes in TRD regions showed that DNA methylation, epigenetic regulation of RNA, and meiotic/meiosis regulation pathways were affected independent of the parental origin of the TRD. Paternal BFMI TRD regions showed overrepresentation in the small interfering RNA biogenesis and in the metabolism of lipids and lipoproteins. Maternal B6N TRD regions harbored genes involved in meiotic recombination, cell death, and apoptosis pathways. The analysis of genes in TRD regions suggests the potential distortion of protein–protein interactions influencing obesity and diabetic retinopathy as a result of disadvantageous combinations of allelic variants in Aass, Pgx6, and Nme8. Using an AIL significantly improves the resolution at which we can investigate TRD. Our analysis implicates distortion of protein–protein interactions as well as meiotic drive as the underlying mechanisms leading to the observed TRD in our AIL. Furthermore, genes with large amounts of nsSNPs located in TRD regions are more likely to be involved in pathways that are related to the phenotypic differences between the parental strains. Genes in these TRD regions provide new targets for investigating genetic adaptation, protein–protein interactions, and determinants of complex traits such as obesity.
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Affiliation(s)
- Danny Arends
- Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Stefan Kärst
- Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Sebastian Heise
- Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Paula Korkuc
- Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Deike Hesse
- Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Gudrun A Brockmann
- Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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127
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Ghosh Dasgupta M, Abdul Bari MP, Shanmugavel S, Dharanishanthi V, Muthupandi M, Kumar N, Chauhan SS, Kalaivanan J, Mohan H, Krutovsky KV, Rajasugunasekar D. Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis. Genomics 2021; 113:4276-4292. [PMID: 34785351 DOI: 10.1016/j.ygeno.2021.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 06/20/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
Globally, Eucalyptus plantations occupy 22 million ha area and is one of the preferred hardwood species due to their short rotation, rapid growth, adaptability and wood properties. In this study, we present results of GWAS in parents and 100 hybrids of Eucalyptus tereticornis × E. grandis using 762 genes presumably involved in wood formation. Comparative analysis between parents predicted 32,202 polymorphic SNPs with high average read depth of 269-562× per individual per nucleotide. Seventeen wood related traits were phenotyped across three diverse environments and GWAS was conducted using 13,610 SNPs. A total of 45 SNP-trait associations were predicted across two locations. Seven large effect markers were identified which explained more than 80% of phenotypic variation for fibre area. This study has provided an array of candidate genes which may govern fibre morphology in this genus and has predicted potential SNPs which can guide future breeding programs in tropical Eucalyptus.
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Affiliation(s)
| | | | | | | | - Muthusamy Muthupandi
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, India
| | - Naveen Kumar
- Institute of Wood Science and Technology, 18(th) Cross Malleshwaram, Bangalore 560 003, India
| | - Shakti Singh Chauhan
- Institute of Wood Science and Technology, 18(th) Cross Malleshwaram, Bangalore 560 003, India
| | | | - Haritha Mohan
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, India
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany; Center for Integrated Breeding Research, George-August University of Göttingen, 37075 Göttingen, Germany; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia; Laboratory of Population Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, USA
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128
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Crkvenjakov R, Heng HH. Further illusions: On key evolutionary mechanisms that could never fit with Modern Synthesis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 169-170:3-11. [PMID: 34767862 DOI: 10.1016/j.pbiomolbio.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
In the light of illusions of the Modern Synthesis (MS) listed by Noble (2021a), its key concept, that gradual accumulation of gene mutations within microevolution leads to macroevolution, requires reexamination. In this article, additional illusions of the MS are identified as being caused by the absence of system information and correct history. First, the MS lacks distinction among the two basic types of information: genome-defined system and gene-defined parts-information, as its treatment was based mostly on gene information. In contrast, it is argued here that system information is maintained by species-specific karyotype code, and macroevolution is based on the whole genome information package rather than on specific genes. Linking the origin of species with system information shows that the creation and accumulation of the latter in evolution is the fundamental question omitted from the MS. Second, modern evidence eliminates the MS's preferred theory that present evolutionary events can be linearly extrapolated to the past to reconstruct Life's history, wrongly assuming that most of the fossil record supports the gradual change while ignoring the true karyotype/genome patterns. Furthermore, stasis, as the most prominent pattern of the deep history of Life, remains a puzzle to the MS, but can be explained by the mechanism of karyotype-preservation-via-sex. Consequently, the concept of system-information is smoothly integrated into the two-phased evolutionary model that paleontology requires (Eldredge and Gould, 1972). Finally, research on genome-level causation of evolution, which does not fit the MS, is summarized. The availability of alternative concepts further illustrates that it is time to depart from the MS.
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Affiliation(s)
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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129
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Otyama PI, Chamberlin K, Ozias-Akins P, Graham MA, Cannon EKS, Cannon SB, MacDonald GE, Anglin NL. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). G3-GENES GENOMES GENETICS 2021; 12:6423989. [PMID: 34751378 DOI: 10.1093/g3journal/jkab382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022]
Abstract
The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here we employ genome-wide association approaches on a recently genotyped collection of 787 plant introduction accessions in the USDA peanut core collection, plus selected improved cultivars, to discover markers associated with the natural variation in fatty acid composition, and to explain the genetic control of fatty acid composition in seed oils. Overall, 251 single nucleotide polymorphisms (SNPs) had significant trait associations with the measured fatty acid components. Twelve SNPs were associated with two or three different traits. Of these loci with apparent pleiotropic effects, 10 were associated with both oleic (C18:1) and linoleic acid (C18:2) content at different positions in the genome. In all 10 cases, the favorable allele had an opposite effect-increasing and lowering the concentration, respectively, of oleic and linoleic acid. The other traits with pleiotropic variant control were palmitic (C16:0), behenic (C22:0), lignoceric (C24:0), gadoleic (C20:1), total saturated, and total unsaturated fatty acid content. One hundred (100) of the significantly associated SNPs were located within 1000 kbp of 55 genes with fatty acid biosynthesis functional annotations. These genes encoded, among others: ACCase carboxyl transferase subunits, and several fatty acid synthase II enzymes. With the exception of gadoleic (C20:1) and lignoceric (C24:0) acid content, which occur at relatively low abundance in cultivated peanut, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7,682 pairwise SNP interactions affecting the relative abundance of fatty acid components in the seed oil. Of these, 627 SNP pairs had at least one SNP within 1000 kbp of a gene with fatty acid biosynthesis functional annotation. We evaluated 168 candidate genes underlying these SNP interactions. Functional enrichment and protein-to-protein interactions supported significant interactions (p-value < 1.0E-16) among the genes evaluated. These results show the complex nature of the biology and genes underlying the variation in seed oil fatty acid composition and contribute to an improved genotype-to-phenotype map for fatty acid variation in peanut seed oil.
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Affiliation(s)
- Paul I Otyama
- Interdepartmental Genetics and Genomics, Iowa State University, Ames, IA 50011, USA.,Agronomy Department, Iowa State University, Ames, IA 50011, USA.,ORISE Postdoctoral Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Kelly Chamberlin
- USDA-Agricultural Research Service, Stillwater, OK 740752714, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics and Department of Horticulture, University of Georgia, Tifton, GA 31793-5766, USA
| | - Michelle A Graham
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Steven B Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | | | - Noelle L Anglin
- USDA-ARS Small Grains and Potato Research Laboratory, Aberdeen, ID 83210, USA
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Zimoń M, Huang Y, Trasta A, Halavatyi A, Liu JZ, Chen CY, Blattmann P, Klaus B, Whelan CD, Sexton D, John S, Huber W, Tsai EA, Pepperkok R, Runz H. Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake. Nat Commun 2021; 12:6411. [PMID: 34741066 PMCID: PMC8571362 DOI: 10.1038/s41467-021-26761-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 10/09/2021] [Indexed: 12/27/2022] Open
Abstract
Complex traits are characterized by multiple genes and variants acting simultaneously on a phenotype. However, studying the contribution of individual pairs of genes to complex traits has been challenging since human genetics necessitates very large population sizes, while findings from model systems do not always translate to humans. Here, we combine genetics with combinatorial RNAi (coRNAi) to systematically test for pairwise additive effects (AEs) and genetic interactions (GIs) between 30 lipid genome-wide association studies (GWAS) genes. Gene-based burden tests from 240,970 exomes show that in carriers with truncating mutations in both, APOB and either PCSK9 or LPL ("human double knock-outs") plasma lipid levels change additively. Genetics and coRNAi identify overlapping AEs for 12 additional gene pairs. Overlapping GIs are observed for TOMM40/APOE with SORT1 and NCAN. Our study identifies distinct gene pairs that modulate plasma and cellular lipid levels primarily via AEs and nominates putative drug target pairs for improved lipid-lowering combination therapies.
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Affiliation(s)
- Magdalena Zimoń
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Yunfeng Huang
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Anthi Trasta
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility (ALMF), European Molecular Biological Laboratory, Heidelberg, Germany
| | - Jimmy Z. Liu
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Chia-Yen Chen
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Psychiatric and Neurodevelopmental Genetics Unit, Mass General Hospital, Boston, MA USA
| | - Peter Blattmann
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany ,grid.508389.f0000 0004 6414 2411Idorsia Pharmaceuticals Ltd, Basel, Switzerland
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Christopher D. Whelan
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - David Sexton
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Sally John
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Ellen A. Tsai
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Rainer Pepperkok
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany ,Advanced Light Microscopy Facility (ALMF), European Molecular Biological Laboratory, Heidelberg, Germany
| | - Heiko Runz
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
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131
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Hansen TF, Pélabon C. Evolvability: A Quantitative-Genetics Perspective. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-011121-021241] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The concept of evolvability emerged in the early 1990s and soon became fashionable as a label for different streams of research in evolutionary biology. In evolutionary quantitative genetics, evolvability is defined as the ability of a population to respond to directional selection. This differs from other fields by treating evolvability as a property of populations rather than organisms or lineages and in being focused on quantification and short-term prediction rather than on macroevolution. While the term evolvability is new to quantitative genetics, many of the associated ideas and research questions have been with the field from its inception as biometry. Recent research on evolvability is more than a relabeling of old questions, however. New operational measures of evolvability have opened possibilities for understanding adaptation to rapid environmental change, assessing genetic constraints, and linking micro- and macroevolution.
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Affiliation(s)
- Thomas F. Hansen
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Christophe Pélabon
- Center for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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132
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Bairos-Novak KR, Hoogenboom MO, van Oppen MJH, Connolly SR. Coral adaptation to climate change: Meta-analysis reveals high heritability across multiple traits. GLOBAL CHANGE BIOLOGY 2021; 27:5694-5710. [PMID: 34482591 DOI: 10.1111/gcb.15829] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic climate change is a rapidly intensifying selection pressure on biodiversity across the globe and, particularly, on the world's coral reefs. The rate of adaptation to climate change is proportional to the amount of phenotypic variation that can be inherited by subsequent generations (i.e., narrow-sense heritability, h2 ). Thus, traits that have higher heritability (e.g., h2 > 0.5) are likely to adapt to future conditions faster than traits with lower heritability (e.g., h2 < 0.1). Here, we synthesize 95 heritability estimates across 19 species of reef-building corals. Our meta-analysis reveals low heritability (h2 < 0.25) of gene expression metrics, intermediate heritability (h2 = 0.25-0.50) of photochemistry, growth, and bleaching, and high heritability (h2 > 0.50) for metrics related to survival and immune responses. Some of these values are higher than typically observed in other taxa, such as survival and growth, while others were more comparable, such as gene expression and photochemistry. There was no detectable effect of temperature on heritability, but narrow-sense heritability estimates were generally lower than broad-sense estimates, indicative of significant non-additive genetic variation across traits. Trait heritability also varied depending on coral life stage, with bleaching and growth in juveniles generally having lower heritability compared to bleaching and growth in larvae and adults. These differences may be the result of previous stabilizing selection on juveniles or may be due to constrained evolution resulting from genetic trade-offs or genetic correlations between growth and thermotolerance. While we find no evidence that heritability decreases under temperature stress, explicit tests of the heritability of thermal tolerance itself-such as coral thermal reaction norm shape-are lacking. Nevertheless, our findings overall reveal high trait heritability for the majority of coral traits, suggesting corals may have a greater potential to adapt to climate change than has been assumed in recent evolutionary models.
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Affiliation(s)
- Kevin R Bairos-Novak
- College of Science and Engineering and ARCCOE for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Mia O Hoogenboom
- College of Science and Engineering and ARCCOE for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Sean R Connolly
- College of Science and Engineering and ARCCOE for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Smithsonian Tropical Research Institute, Panama City, Panama
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133
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Fisch GS. Associating complex traits with genetic variants: polygenic risk scores, pleiotropy and endophenotypes. Genetica 2021; 150:183-197. [PMID: 34677750 DOI: 10.1007/s10709-021-00138-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022]
Abstract
Genotype-phenotype causal modeling has evolved significantly since Johannsen's and Wright's original designs were published. The development of genomewide assays to interrogate and detect possible causal variants associated with complex traits has expanded the scope of genotype-phenotype research considerably. Clusters of causal variants discovered by genomewide assays and associated with complex traits have been used to develop polygenic risk scores to predict clinical diagnoses of multidimensional human disorders. However, genomewide investigations have met with many challenges to their research designs and statistical complexities which have hindered the reliability and validity of their predictions. Findings linked to differences in heritability estimates between causal clusters and complex traits among unrelated individuals remain a research area of some controversy. Causal models developed from case-control studies as opposed to experiments, as well as other issues concerning the genotype-phenotype causal model and the extent to which various forms of pleiotropy and the concept of the endophenotype add to its complexity, will be reviewed.
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Affiliation(s)
- Gene S Fisch
- Paul H. Chook Dept. of CIS & Statistics, CUNY/Baruch College, New York, NY, USA.
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134
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McMahon A, Lewis E, Buniello A, Cerezo M, Hall P, Sollis E, Parkinson H, Hindorff LA, Harris LW, MacArthur JA. Sequencing-based genome-wide association studies reporting standards. CELL GENOMICS 2021; 1:100005. [PMID: 34870259 PMCID: PMC8637874 DOI: 10.1016/j.xgen.2021.100005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome sequencing has recently become a viable genotyping technology for use in genome-wide association studies (GWASs), offering the potential to analyze a broader range of genome-wide variation, including rare variants. To survey current standards, we assessed the content and quality of reporting of statistical methods, analyses, results, and datasets in 167 exome- or genome-wide-sequencing-based GWAS publications published from 2014 to 2020; 81% of publications included tests of aggregate association across multiple variants, with multiple test models frequently used. We observed a lack of standardized terms and incomplete reporting of datasets, particularly for variants analyzed in aggregate tests. We also find a lower frequency of sharing of summary statistics compared with array-based GWASs. Reporting standards and increased data sharing are required to ensure sequencing-based association study data are findable, interoperable, accessible, and reusable (FAIR). To support that, we recommend adopting the standard terminology of sequencing-based GWAS (seqGWAS). Further, we recommend that single-variant analyses be reported following the same standards and conventions as standard array-based GWASs and be shared in the GWAS Catalog. We also provide initial recommended standards for aggregate analyses metadata and summary statistics.
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Affiliation(s)
- Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK,Corresponding author
| | - Elizabeth Lewis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK,Corresponding author
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura W. Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jacqueline A.L. MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK,BHF Data Science Centre, Health Data Research UK, London, UK
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135
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Metabolomics for Crop Breeding: General Considerations. Genes (Basel) 2021; 12:genes12101602. [PMID: 34680996 PMCID: PMC8535592 DOI: 10.3390/genes12101602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner.
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136
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Singh RS. Decoding 'Unnecessary Complexity': A Law of Complexity and a Concept of Hidden Variation Behind "Missing Heritability" in Precision Medicine. J Mol Evol 2021; 89:513-526. [PMID: 34341835 PMCID: PMC8327892 DOI: 10.1007/s00239-021-10023-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/20/2021] [Indexed: 01/06/2023]
Abstract
The high hopes for the Human Genome Project and personalized medicine were not met because the relationship between genotypes and phenotypes turned out to be more complex than expected. In a previous study we laid the foundation of a theory of complexity and showed that because of the blind nature of evolution, and molecular and historical contingency, cells have accumulated unnecessary complexity, complexity beyond what is necessary and sufficient to describe an organism. Here we provide empirical evidence and show that unnecessary complexity has become integrated into the genome in the form of redundancy and is relevant to molecular evolution of phenotypic complexity. Unnecessary complexity creates uncertainty between molecular and phenotypic complexity, such that phenotypic complexity (CP) is higher than molecular complexity (CM), which is higher than DNA complexity (CD). The qualitative inequality in complexity is based on the following hierarchy: CP > CM > CD. This law-like relationship holds true for all complex traits, including complex diseases. We present a hypothesis of two types of variation, namely open and closed (hidden) systems, show that hidden variation provides a hitherto undiscovered "third source" of phenotypic variation, beside genotype and environment, and argue that "missing heritability" for some complex diseases is likely to be a case of "diluted heritability". There is a need for radically new ways of thinking about the principles of genotype-phenotype relationship. Understanding how cells use hidden, pathway variation to respond to stress can shed light on why two individuals who share the same risk factors may not develop the same disease, or how cancer cells escape death.
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Affiliation(s)
- Rama S Singh
- Department of Biology, and Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada.
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137
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Yu QY, Lu TP, Hsiao TH, Lin CH, Wu CY, Tzeng JY, Hsiao CK. An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data. Front Genet 2021; 12:709555. [PMID: 34567069 PMCID: PMC8456116 DOI: 10.3389/fgene.2021.709555] [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: 05/14/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic studies have been a major approach to elucidating disease etiology and to exploring potential targets for treatments of many complex diseases. Statistical analyses in these studies often face the challenges of multiplicity, weak signals, and the nature of dependence among genetic markers. This situation becomes even more complicated when multi-omics data are available. To integrate the data from different platforms, various integrative analyses have been adopted, ranging from the direct union or intersection operation on sets derived from different single-platform analysis to complex hierarchical multi-level models. The former ignores the biological relationship between molecules while the latter can be hard to interpret. We propose in this study an integrative approach that combines both single nucleotide variants (SNVs) and copy number variations (CNVs) in the same genomic unit to co-localize the concurrent effect and to deal with the sparsity due to rare variants. This approach is illustrated with simulation studies to evaluate its performance and is applied to low-density lipoprotein cholesterol and triglyceride measurements from Taiwan Biobank. The results show that the proposed method can more effectively detect the collective effect from both SNVs and CNVs compared to traditional methods. For the biobank analysis, the identified genetic regions including the gene VNN2 could be novel and deserve further investigation.
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Affiliation(s)
- Qi-You Yu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ching-Heng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Yun Wu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Statistics, University of Pennsylvania, Philadelphia, PA, United States
| | - Jung-Ying Tzeng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States
| | - Chuhsing Kate Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
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138
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Sharma S, Pinson SRM, Gealy DR, Edwards JD. Genomic prediction and QTL mapping of root system architecture and above-ground agronomic traits in rice (Oryza sativa L.) with a multitrait index and Bayesian networks. G3 (BETHESDA, MD.) 2021; 11:jkab178. [PMID: 34568907 PMCID: PMC8496310 DOI: 10.1093/g3journal/jkab178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022]
Abstract
Root system architecture (RSA) is a crucial factor in resource acquisition and plant productivity. Roots are difficult to phenotype in the field, thus new tools for predicting phenotype from genotype are particularly valuable for plant breeders aiming to improve RSA. This study identifies quantitative trait loci (QTLs) for RSA and agronomic traits in a rice (Oryza sativa) recombinant inbred line (RIL) population derived from parents with contrasting RSA traits (PI312777 × Katy). The lines were phenotyped for agronomic traits in the field, and separately grown as seedlings on agar plates which were imaged to extract RSA trait measurements. QTLs were discovered from conventional linkage analysis and from a machine learning approach using a Bayesian network (BN) consisting of genome-wide SNP data and phenotypic data. The genomic prediction abilities (GPAs) of multi-QTL models and the BN analysis were compared with the several standard genomic prediction (GP) methods. We found GPAs were improved using multitrait (BN) compared to single trait GP in traits with low to moderate heritability. Two groups of individuals were selected based on GPs and a modified rank sum index (GSRI) indicating their divergence across multiple RSA traits. Selections made on GPs did result in differences between the group means for numerous RSA. The ranking accuracy across RSA traits among the individual selected RILs ranged from 0.14 for root volume to 0.59 for lateral root tips. We conclude that the multitrait GP model using BN can in some cases improve the GPA of RSA and agronomic traits, and the GSRI approach is useful to simultaneously select for a desired set of RSA traits in a segregating population.
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Affiliation(s)
- Santosh Sharma
- Dale Bumpers National Rice Research Center, United States Department of Agriculture—Agricultural Research Service, Stuttgart, AR 72160, USA
| | - Shannon R M Pinson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture—Agricultural Research Service, Stuttgart, AR 72160, USA
| | - David R Gealy
- Dale Bumpers National Rice Research Center, United States Department of Agriculture—Agricultural Research Service, Stuttgart, AR 72160, USA
| | - Jeremy D Edwards
- Dale Bumpers National Rice Research Center, United States Department of Agriculture—Agricultural Research Service, Stuttgart, AR 72160, USA
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139
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Visscher PM, Yengo L, Cox NJ, Wray NR. Discovery and implications of polygenicity of common diseases. Science 2021; 373:1468-1473. [PMID: 34554790 PMCID: PMC9945947 DOI: 10.1126/science.abi8206] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The sequencing of the human genome has allowed the study of the genetic architecture of common diseases: the number of genomic variants that contribute to risk of disease and their joint frequency and effect size distribution. Common diseases are polygenic, with many loci contributing to phenotype, and the cumulative burden of risk alleles determines individual risk in conjunction with environmental factors. Most risk loci occur in noncoding regions of the genome regulating cell- and context-specific gene expression. Although the effect sizes of most risk alleles are small, their cumulative effects in individuals, quantified as a polygenic (risk) score, can identify people at increased risk of disease, thereby facilitating prevention or early intervention.
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Affiliation(s)
- Peter M. Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia,Corresponding author.
| | - Loic Yengo
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Nancy J. Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia,Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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140
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Almahboob A, Alroqi A, Almohizea MI. Nasopharyngeal cancer in monozygotic twins: A case report and review of the role of genetics and the environment. Int J Surg Case Rep 2021; 87:106371. [PMID: 34547666 PMCID: PMC8455980 DOI: 10.1016/j.ijscr.2021.106371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 12/04/2022] Open
Abstract
Introduction and importance Nasopharyngeal carcinoma (NPC) is considered a rare malignant head and neck tumour. However, the importance of genetics and environmental factors in the epidemiology of NPC is still unclear. Twins represent an excellent study population for genetic epidemiology; this is especially true of monozygotic-type twins because they are genetically identical. The difference in cancer occurrence between monozygotic twins is typically interpreted as a result of possible environmental factors. Case presentation and clinical discussion We present the first case report of monozygotic twins with NPC. The twins' significant features are homogenous presentation, tumour location (both left-sided) and identical histology; therefore, the prognoses may be similar. Environmental factors could not be addressed in these twins because they shared the same background, and at the same time, they had no potential known contributing factors. Conclusion Having one of the twins affected is a strong and easily recognisable risk factor for developing NPC in the other. This strong association suggests the need for regular screening of the second twin for early diagnosis of NPC. The importance of genetics and environmental factors in the epidemiology of NPC is still unclear. Having one of the twins affected is a strong and easily recognisable risk factor for developing Nasopharyngeal carcinoma in the other. This strong association suggests the need for regular screening of the second twin for early diagnosis of Nasopharyngeal carcinoma.
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Affiliation(s)
- Ayshah Almahboob
- Department of Otolaryngology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
| | - Ahmad Alroqi
- Department of Otolaryngology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed I Almohizea
- Department of Otolaryngology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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141
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Ahmed H, Alarabi L, El-Sappagh S, Soliman H, Elmogy M. Genetic variations analysis for complex brain disease diagnosis using machine learning techniques: opportunities and hurdles. PeerJ Comput Sci 2021; 7:e697. [PMID: 34616886 PMCID: PMC8459785 DOI: 10.7717/peerj-cs.697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVES This paper presents an in-depth review of the state-of-the-art genetic variations analysis to discover complex genes associated with the brain's genetic disorders. We first introduce the genetic analysis of complex brain diseases, genetic variation, and DNA microarrays. Then, the review focuses on available machine learning methods used for complex brain disease classification. Therein, we discuss the various datasets, preprocessing, feature selection and extraction, and classification strategies. In particular, we concentrate on studying single nucleotide polymorphisms (SNP) that support the highest resolution for genomic fingerprinting for tracking disease genes. Subsequently, the study provides an overview of the applications for some specific diseases, including autism spectrum disorder, brain cancer, and Alzheimer's disease (AD). The study argues that despite the significant recent developments in the analysis and treatment of genetic disorders, there are considerable challenges to elucidate causative mutations, especially from the viewpoint of implementing genetic analysis in clinical practice. The review finally provides a critical discussion on the applicability of genetic variations analysis for complex brain disease identification highlighting the future challenges. METHODS We used a methodology for literature surveys to obtain data from academic databases. Criteria were defined for inclusion and exclusion. The selection of articles was followed by three stages. In addition, the principal methods for machine learning to classify the disease were presented in each stage in more detail. RESULTS It was revealed that machine learning based on SNP was widely utilized to solve problems of genetic variation for complex diseases related to genes. CONCLUSIONS Despite significant developments in genetic diseases in the past two decades of the diagnosis and treatment, there is still a large percentage in which the causative mutation cannot be determined, and a final genetic diagnosis remains elusive. So, we need to detect the variations of the genes related to brain disorders in the early disease stages.
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Affiliation(s)
- Hala Ahmed
- Information Technology Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Louai Alarabi
- Department of Computer Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shaker El-Sappagh
- Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Information Systems Department, Faculty of Computers and Artificial Intelligence, Benha University, Benha, Egypt
| | - Hassan Soliman
- Information Technology Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Mohammed Elmogy
- Information Technology Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
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142
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Gupta PK. GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers. Bioessays 2021; 43:e2100109. [PMID: 34486143 DOI: 10.1002/bies.202100109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
Abstract
The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.
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Affiliation(s)
- Pushpendra K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University Meerut, Meerut, Uttar Pradesh, India
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143
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Inferring multilayer interactome networks shaping phenotypic plasticity and evolution. Nat Commun 2021; 12:5304. [PMID: 34489412 PMCID: PMC8421358 DOI: 10.1038/s41467-021-25086-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution.
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144
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Wood ZT, Wiegardt AK, Barton KL, Clark JD, Homola JJ, Olsen BJ, King BL, Kovach AI, Kinnison MT. Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems. Evol Appl 2021; 14:2189-2205. [PMID: 34603492 PMCID: PMC8477602 DOI: 10.1111/eva.13264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/17/2023] Open
Abstract
Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.
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Affiliation(s)
- Zachary T. Wood
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| | - Andrew K. Wiegardt
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Kayla L. Barton
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Jonathan D. Clark
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Brian J. Olsen
- Maine Center for Genetics in the EnvironmentOronoMEUSA
- Department of Wildlife, Fisheries, and Conservation BiologyUniversity of MaineOronoMEUSA
| | - Benjamin L. King
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Michael T. Kinnison
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
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145
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Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes. mSystems 2021; 6:e0034621. [PMID: 34427505 PMCID: PMC8407197 DOI: 10.1128/msystems.00346-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is an important cause of bacterial infections worldwide, with multidrug-resistant strains incurring substantial costs on human lives. Besides therapeutic concentrations of antimicrobials in health care settings, the presence of subinhibitory antimicrobial residues in the environment and in clinics selects for antimicrobial resistance (AMR), but the underlying genetic repertoire is less well understood. Here, we used machine learning to predict the population doubling time and cell growth yield of 1,407 genetically diverse E. coli strains expanding under exposure to three subinhibitory concentrations of six classes of antimicrobials from single-nucleotide genetic variants, accessory gene variation, and the presence of known AMR genes. We predicted cell growth yields in the held-out test data with an average correlation (Spearman's ρ) of 0.63 (0.36 to 0.81 across concentrations) and cell doubling times with an average correlation of 0.59 (0.32 to 0.92 across concentrations), with moderate increases in sample size unlikely to improve predictions further. This finding points to the remaining missing heritability of growth under antimicrobial exposure being explained by effects that are too rare or weak to be captured unless sample size is dramatically increased, or by effects other than those conferred by the presence of individual single-nucleotide polymorphisms (SNPs) and genes. Predictions based on whole-genome information were generally superior to those based only on known AMR genes and were accurate for AMR resistance at therapeutic concentrations. We pinpointed genes and SNPs determining the predicted growth and thereby recapitulated many known AMR determinants. Finally, we estimated the effect sizes of resistance genes across the entire collection of strains, disclosing the growth effects for known resistance genes in each individual strain. Our results underscore the potential of predictive modeling of growth patterns from genomic data under subinhibitory concentrations of antimicrobials, although the remaining missing heritability poses a challenge for achieving the accuracy and precision required for clinical use. IMPORTANCE Predicting bacterial growth from genome sequences is important for a rapid characterization of strains in clinical diagnostics and to disclose candidate novel targets for anti-infective drugs. Previous studies have dissected the relationship between bacterial growth and genotype in mutant libraries for laboratory strains, yet no study so far has examined the predictive power of genome sequence in natural strains. In this study, we used a high-throughput phenotypic assay to measure the growth of a systematic collection of natural Escherichia coli strains and then employed machine learning models to predict bacterial growth from genomic data under nontherapeutic subinhibitory concentrations of antimicrobials that are common in nonclinical settings. We found a moderate to strong correlation between predicted and actual values for the different collected data sets. Moreover, we observed that the known resistance genes are still effective at sublethal concentrations, pointing to clinical implications of these concentrations.
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146
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Carmichael J, Hicks AJ, Spitz G, Gould KR, Ponsford J. Moderators of gene-outcome associations following traumatic brain injury. Neurosci Biobehav Rev 2021; 130:107-124. [PMID: 34411558 DOI: 10.1016/j.neubiorev.2021.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/04/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022]
Abstract
The field of genomics is the principal avenue in the ongoing development of precision/personalised medicine for a variety of health conditions. However, relating genes to outcomes is notoriously complex, especially when considering that other variables can change, or moderate, gene-outcome associations. Here, we comprehensively discuss moderation of gene-outcome associations in the context of traumatic brain injury (TBI), a common, chronically debilitating, and costly neurological condition that is under complex polygenic influence. We focus our narrative review on single nucleotide polymorphisms (SNPs) of three of the most studied genes (apolipoprotein E, brain-derived neurotrophic factor, and catechol-O-methyltransferase) and on three demographic variables believed to moderate associations between these SNPs and TBI outcomes (age, biological sex, and ethnicity). We speculate on the mechanisms which may underlie these moderating effects, drawing widely from biomolecular and behavioural research (n = 175 scientific reports) within the TBI population (n = 72) and other neurological, healthy, ageing, and psychiatric populations (n = 103). We conclude with methodological recommendations for improved exploration of moderators in future genetics research in TBI and other populations.
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Affiliation(s)
- Jai Carmichael
- Monash-Epworth Rehabilitation Research Centre, Epworth HealthCare, Melbourne, Australia; Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia.
| | - Amelia J Hicks
- Monash-Epworth Rehabilitation Research Centre, Epworth HealthCare, Melbourne, Australia; Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia
| | - Gershon Spitz
- Monash-Epworth Rehabilitation Research Centre, Epworth HealthCare, Melbourne, Australia; Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia
| | - Kate Rachel Gould
- Monash-Epworth Rehabilitation Research Centre, Epworth HealthCare, Melbourne, Australia; Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia
| | - Jennie Ponsford
- Monash-Epworth Rehabilitation Research Centre, Epworth HealthCare, Melbourne, Australia; Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, Australia
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147
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Liu Y, Gao Y, Fang R, Cao H, Sa J, Wang J, Liu H, Wang T, Cui Y. Identifying complex gene-gene interactions: a mixed kernel omnibus testing approach. Brief Bioinform 2021; 22:6346804. [PMID: 34373892 DOI: 10.1093/bib/bbab305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/01/2021] [Accepted: 07/17/2021] [Indexed: 11/12/2022] Open
Abstract
Genes do not function independently; rather, they interact with each other to fulfill their joint tasks. Identification of gene-gene interactions has been critically important in elucidating the molecular mechanisms responsible for the variation of a phenotype. Regression models are commonly used to model the interaction between two genes with a linear product term. The interaction effect of two genes can be linear or nonlinear, depending on the true nature of the data. When nonlinear interactions exist, the linear interaction model may not be able to detect such interactions; hence, it suffers from substantial power loss. While the true interaction mechanism (linear or nonlinear) is generally unknown in practice, it is critical to develop statistical methods that can be flexible to capture the underlying interaction mechanism without assuming a specific model assumption. In this study, we develop a mixed kernel function which combines both linear and Gaussian kernels with different weights to capture the linear or nonlinear interaction of two genes. Instead of optimizing the weight function, we propose a grid search strategy and use a Cauchy transformation of the P-values obtained under different weights to aggregate the P-values. We further extend the two-gene interaction model to a high-dimensional setup using a de-biased LASSO algorithm. Extensive simulation studies are conducted to verify the performance of the proposed method. Application to two case studies further demonstrates the utility of the model. Our method provides a flexible and computationally efficient tool for disentangling complex gene-gene interactions associated with complex traits.
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Affiliation(s)
- Yan Liu
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Yuzhao Gao
- School of Statistics, Shanxi University of Finance and Economics, Taiyuan, PR China
| | - Ruiling Fang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Hongyan Cao
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Jian Sa
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Hongqi Liu
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Tong Wang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
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148
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Liu D, Ban HJ, El Sergani AM, Lee MK, Hecht JT, Wehby GL, Moreno LM, Feingold E, Marazita ML, Cha S, Szabo-Rogers HL, Weinberg SM, Shaffer JR. PRICKLE1 × FOCAD Interaction Revealed by Genome-Wide vQTL Analysis of Human Facial Traits. Front Genet 2021; 12:674642. [PMID: 34434215 PMCID: PMC8381734 DOI: 10.3389/fgene.2021.674642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The human face is a highly complex and variable structure resulting from the intricate coordination of numerous genetic and non-genetic factors. Hundreds of genomic loci impacting quantitative facial features have been identified. While these associations have been shown to influence morphology by altering the mean size and shape of facial measures, their effect on trait variance remains unclear. We conducted a genome-wide association analysis for the variance of 20 quantitative facial measurements in 2,447 European individuals and identified several suggestive variance quantitative trait loci (vQTLs). These vQTLs guided us to conduct an efficient search for gene-by-gene (G × G) interactions, which uncovered an interaction between PRICKLE1 and FOCAD affecting cranial base width. We replicated this G × G interaction signal at the locus level in an additional 5,128 Korean individuals. We used the hypomorphic Prickle1 Beetlejuice (Prickle1 Bj ) mouse line to directly test the function of Prickle1 on the cranial base and observed wider cranial bases in Prickle1 Bj/Bj . Importantly, we observed that the Prickle1 and Focadhesin proteins co-localize in murine cranial base chondrocytes, and this co-localization is abnormal in the Prickle1 Bj/Bj mutants. Taken together, our findings uncovered a novel G × G interaction effect in humans with strong support from both epidemiological and molecular studies. These results highlight the potential of studying measures of phenotypic variability in gene mapping studies of facial morphology.
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Affiliation(s)
- Dongjing Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Hyo-Jeong Ban
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Ahmed M. El Sergani
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical Center, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - George L. Wehby
- Department of Health Management and Policy, The University of Iowa, Iowa City, IA, United States
| | - Lina M. Moreno
- Department of Orthodontics, The University of Iowa, Iowa City, IA, United States
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Psychiatry, Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seongwon Cha
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Heather L. Szabo-Rogers
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Regenerative Medicine at the McGowan Institute, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Craniofacial Regeneration, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
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149
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Clarke TK, Adams MJ, Howard DM, Xia C, Davies G, Hayward C, Campbell A, Padmanabhan S, Smith BH, Murray A, Porteous D, Deary IJ, McIntosh AM. Genetic and shared couple environmental contributions to smoking and alcohol use in the UK population. Mol Psychiatry 2021; 26:4344-4354. [PMID: 31767999 PMCID: PMC8550945 DOI: 10.1038/s41380-019-0607-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 11/22/2022]
Abstract
Alcohol use and smoking are leading causes of death and disability worldwide. Both genetic and environmental factors have been shown to influence individual differences in the use of these substances. In the present study we tested whether genetic factors, modelled alongside common family environment, explained phenotypic variance in alcohol use and smoking behaviour in the Generation Scotland (GS) family sample of up to 19,377 individuals. SNP and pedigree-associated effects combined explained between 18 and 41% of the variance in substance use. Shared couple effects explained a significant amount of variance across all substance use traits, particularly alcohol intake, for which 38% of the phenotypic variance was explained. We tested whether the within-couple substance use associations were due to assortative mating by testing the association between partner polygenic risk scores in 34,987 couple pairs from the UK Biobank (UKB). No significant association between partner polygenic risk scores were observed. Associations between an individual's alcohol PRS (b = 0.05, S.E. = 0.006, p < 2 × 10-16) and smoking status PRS (b = 0.05, S.E. = 0.005, p < 2 × 10-16) were found with their partner's phenotype. In support of this, G carriers of a functional ADH1B polymorphism (rs1229984), known to be associated with greater alcohol intake, were found to consume less alcohol if they had a partner who carried an A allele at this SNP. Together these results show that the shared couple environment contributes significantly to patterns of substance use. It is unclear whether this is due to shared environmental factors, assortative mating, or indirect genetic effects. Future studies would benefit from longitudinal data and larger sample sizes to assess this further.
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Affiliation(s)
- Toni-Kim Clarke
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK.
| | - Mark J Adams
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - David M Howard
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Charley Xia
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Blair H Smith
- Division of Population and Health Genomics, University of Dundee, Dundee, UK
| | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
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150
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Maglione A, Zuccalà M, Tosi M, Clerico M, Rolla S. Host Genetics and Gut Microbiome: Perspectives for Multiple Sclerosis. Genes (Basel) 2021; 12:1181. [PMID: 34440354 PMCID: PMC8394267 DOI: 10.3390/genes12081181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
As a complex disease, Multiple Sclerosis (MS)'s etiology is determined by both genetic and environmental factors. In the last decade, the gut microbiome has emerged as an important environmental factor, but its interaction with host genetics is still unknown. In this review, we focus on these dual aspects of MS pathogenesis: we describe the current knowledge on genetic factors related to MS, based on genome-wide association studies, and then illustrate the interactions between the immune system, gut microbiome and central nervous system in MS, summarizing the evidence available from Experimental Autoimmune Encephalomyelitis mouse models and studies in patients. Finally, as the understanding of influence of host genetics on the gut microbiome composition in MS is in its infancy, we explore this issue based on the evidence currently available from other autoimmune diseases that share with MS the interplay of genetic with environmental factors (Inflammatory Bowel Disease, Rheumatoid Arthritis and Systemic Lupus Erythematosus), and discuss avenues for future research.
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Affiliation(s)
- Alessandro Maglione
- Department of Clinical and Biological Sciences, University of Torino, 10100 Torino, Italy; (A.M.); (M.C.)
| | - Miriam Zuccalà
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy; (M.Z.); (M.T.)
| | - Martina Tosi
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy; (M.Z.); (M.T.)
| | - Marinella Clerico
- Department of Clinical and Biological Sciences, University of Torino, 10100 Torino, Italy; (A.M.); (M.C.)
| | - Simona Rolla
- Department of Clinical and Biological Sciences, University of Torino, 10100 Torino, Italy; (A.M.); (M.C.)
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