101
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Yu J, Hu M, Li C. Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. BMC Genet 2019; 20:43. [PMID: 31039743 PMCID: PMC6492392 DOI: 10.1186/s12863-019-0744-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background Gene regulation is important for cells and tissues to function. It has been studied from two aspects at the genomic level, the identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. It is important to understand their relationship, such as whether eQTLs regulate their target genes through physical chromatin interaction. Although chromatin interactions have been widely believed to be one of the main mechanisms underlying eQTLs, most evidence came from studies of cell lines and yet no direct evidence exists for tissues. Results We performed various joint analyses of eQTL and high-throughput chromatin conformation capture (Hi-C) data from 11 human primary tissue types and 2 human cell lines. We found that chromatin interaction frequency is positively associated with the number of genes that have eQTLs and that eQTLs and their target genes tend to fall into the same topologically associating domain (TAD). These results are consistent across all tissues and cell lines we evaluated. Moreover, in 6 out of 11 tissues (aorta, dorsolateral prefrontal cortex, hippocampus, pancreas, small bowel, and spleen), tissue-specific eQTLs are significantly enriched in tissue-specific frequently interacting regions (FIREs). Conclusions Our data have demonstrated the close spatial proximity between eQTLs and their target genes among multiple human primary tissues. Electronic supplementary material The online version of this article (10.1186/s12863-019-0744-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingting Yu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Chun Li
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA. .,Cleveland Institute for Computational Biology, Cleveland, OH, USA.
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102
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Vornholt E, Luo D, Qiu W, McMichael GO, Liu Y, Gillespie N, Ma C, Vladimirov VI. Postmortem brain tissue as an underutilized resource to study the molecular pathology of neuropsychiatric disorders across different ethnic populations. Neurosci Biobehav Rev 2019; 102:195-207. [PMID: 31028758 DOI: 10.1016/j.neubiorev.2019.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/27/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022]
Abstract
In recent years, large scale meta-analysis of genome-wide association studies (GWAS) have reliably identified genetic polymorphisms associated with neuropsychiatric disorders such as schizophrenia (SCZ), bipolar disorder (BPD) and major depressive disorder (MDD). However, the majority of disease-associated single nucleotide polymorphisms (SNPs) appear within functionally ambiguous non-coding genomic regions. Recently, increased emphasis has been placed on identifying the functional relevance of disease-associated variants via correlating risk polymorphisms with gene expression levels in etiologically relevant tissues. For neuropsychiatric disorders, the etiologically relevant tissue is brain, which requires robust postmortem sample sizes from varying genetic backgrounds. While small sample sizes are of decreasing concern, postmortem brain databases are composed almost exclusively of Caucasian samples, which significantly limits study design and result interpretation. In this review, we highlight the importance of gene expression and expression quantitative loci (eQTL) studies in clinically relevant postmortem tissue while addressing the current limitations of existing postmortem brain databases. Finally, we introduce future collaborations to develop postmortem brain databases for neuropsychiatric disorders from Chinese and Asian subpopulations.
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Affiliation(s)
- Eric Vornholt
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 E. Leigh St., Biotech One, Suite 100, Richmond, VA 23219, USA.
| | - Dan Luo
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Wenying Qiu
- Institute of Basic Medical Sciences, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 100005, China
| | - Gowon O McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 E. Leigh St., Biotech One, Suite 100, Richmond, VA 23219, USA
| | - Yangyang Liu
- School of Education, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Nathan Gillespie
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 E. Leigh St., Biotech One, Suite 100, Richmond, VA 23219, USA; Department Psychiatry, Virginia Commonwealth University, 1200 East Broad Street, Richmond, VA 23298, USA
| | - Chao Ma
- Institute of Basic Medical Sciences, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 100005, China; Joint Laboratory of Anesthesia and Pain, Peking Union Medical College. Beijing, 100730, China.
| | - Vladimir I Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 E. Leigh St., Biotech One, Suite 100, Richmond, VA 23219, USA; Department Psychiatry, Virginia Commonwealth University, 1200 East Broad Street, Richmond, VA 23298, USA; Center for Biomarker Research, Virginia Commonwealth University, Richmond, 410 North 12th Street, Richmond, VA 23298, USA; Department of Physiology & Biophysics, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA 23298, USA; Lieber Institute for Brain Development, Johns Hopkins University, 855 North Wolfe Street, Suite 300, 3rd Floor, Baltimore, MD 21205, USA.
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103
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Huckins LM, Dobbyn A, Ruderfer DM, Hoffman G, Wang W, Pardiñas AF, Rajagopal VM, Als TD, T Nguyen H, Girdhar K, Boocock J, Roussos P, Fromer M, Kramer R, Domenici E, Gamazon ER, Purcell S, Demontis D, Børglum AD, Walters JTR, O'Donovan MC, Sullivan P, Owen MJ, Devlin B, Sieberts SK, Cox NJ, Im HK, Sklar P, Stahl EA. Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. Nat Genet 2019; 51:659-674. [PMID: 30911161 PMCID: PMC7034316 DOI: 10.1038/s41588-019-0364-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/30/2019] [Indexed: 01/23/2023]
Abstract
Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.
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Affiliation(s)
- Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Amanda Dobbyn
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Gabriel Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weiqing Wang
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Veera M Rajagopal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Hoang T Nguyen
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kiran Girdhar
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Menachem Fromer
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robin Kramer
- Human Brain Collection Core, National Institute of Mental Health, Bethesda, MD, USA
| | - Enrico Domenici
- Laboratory of Neurogenomic Biomarkers, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Eric R Gamazon
- Vanderbilt University Medical Center, Nashville, TN, USA
- Clare Hall, University of Cambridge, Cambridge, UK
| | - Shaun Purcell
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Patrick Sullivan
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Karolinska Institutet, Stockholm, Sweden
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Nancy J Cox
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Pamela Sklar
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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104
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Lee C. Bayesian Inference for Mixed Model-Based Genome-Wide Analysis of Expression Quantitative Trait Loci by Gibbs Sampling. Front Genet 2019; 10:199. [PMID: 30967893 PMCID: PMC6438854 DOI: 10.3389/fgene.2019.00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/25/2019] [Indexed: 11/13/2022] Open
Abstract
The importance of expression quantitative trait locus (eQTL) has been emphasized in understanding the genetic basis of cellular activities and complex phenotypes. Mixed models can be employed to effectively identify eQTLs by explaining polygenic effects. In these mixed models, the polygenic effects are considered as random variables, and their variability is explained by the polygenic variance component. The polygenic and residual variance components are first estimated, and then eQTL effects are estimated depending on the variance component estimates within the frequentist mixed model framework. The Bayesian approach to the mixed model-based genome-wide eQTL analysis can also be applied to estimate the parameters that exhibit various benefits. Bayesian inferences on unknown parameters are based on their marginal posterior distributions, and the marginalization of the joint posterior distribution is a challenging task. This problem can be solved by employing a numerical algorithm of integrals called Gibbs sampling as a Markov chain Monte Carlo. This article reviews the mixed model-based Bayesian eQTL analysis by Gibbs sampling. Theoretical and practical issues of Bayesian inference are discussed using a concise description of Bayesian modeling and the corresponding Gibbs sampling. The strengths of Bayesian inference are also discussed. Posterior probability distribution in the Bayesian inference reflects uncertainty in unknown parameters. This factor is useful in the context of eQTL analysis where a sample size is too small to apply the frequentist approach. Bayesian inference based on the posterior that reflects prior knowledge, will be increasingly preferred with the accumulation of eQTL data. Extensive use of the mixed model-based Bayesian eQTL analysis will accelerate understanding of eQTLs exhibiting various regulatory functions.
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Affiliation(s)
- Chaeyoung Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
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105
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Chen X, Liu X, Zhu S, Tang S, Mei S, Chen J, Li S, Liu M, Gu Y, Dai Q, Liu T. Transcriptome-referenced association study of clove shape traits in garlic. DNA Res 2019; 25:587-596. [PMID: 30084885 PMCID: PMC6289775 DOI: 10.1093/dnares/dsy027] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 07/25/2018] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.
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Affiliation(s)
- Xiaojun Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xia Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shiyong Mei
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jing Chen
- Novogene Bioinformatics Institute, Beijing, China
| | - Shan Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Mengdi Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuejiao Gu
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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106
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Sieber KB, Batorsky A, Siebenthall K, Hudkins KL, Vierstra JD, Sullivan S, Sur A, McNulty M, Sandstrom R, Reynolds A, Bates D, Diegel M, Dunn D, Nelson J, Buckley M, Kaul R, Sampson MG, Himmelfarb J, Alpers CE, Waterworth D, Akilesh S. Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci. J Am Soc Nephrol 2019; 30:421-441. [PMID: 30760496 PMCID: PMC6405142 DOI: 10.1681/asn.2018030309] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 12/26/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Linking genetic risk loci identified by genome-wide association studies (GWAS) to their causal genes remains a major challenge. Disease-associated genetic variants are concentrated in regions containing regulatory DNA elements, such as promoters and enhancers. Although researchers have previously published DNA maps of these regulatory regions for kidney tubule cells and glomerular endothelial cells, maps for podocytes and mesangial cells have not been available. METHODS We generated regulatory DNA maps (DNase-seq) and paired gene expression profiles (RNA-seq) from primary outgrowth cultures of human glomeruli that were composed mainly of podocytes and mesangial cells. We generated similar datasets from renal cortex cultures, to compare with those of the glomerular cultures. Because regulatory DNA elements can act on target genes across large genomic distances, we also generated a chromatin conformation map from freshly isolated human glomeruli. RESULTS We identified thousands of unique regulatory DNA elements, many located close to transcription factor genes, which the glomerular and cortex samples expressed at different levels. We found that genetic variants associated with kidney diseases (GWAS) and kidney expression quantitative trait loci were enriched in regulatory DNA regions. By combining GWAS, epigenomic, and chromatin conformation data, we functionally annotated 46 kidney disease genes. CONCLUSIONS We demonstrate a powerful approach to functionally connect kidney disease-/trait-associated loci to their target genes by leveraging unique regulatory DNA maps and integrated epigenomic and genetic analysis. This process can be applied to other kidney cell types and will enhance our understanding of genome regulation and its effects on gene expression in kidney disease.
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Affiliation(s)
| | - Anna Batorsky
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | | | | | - Jeff D Vierstra
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | | | - Aakash Sur
- Phase Genomics Inc., Seattle, Washington
- Department of Biomedical and Health Informatics, and
| | - Michelle McNulty
- Division of Pediatric Nephrology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | | | - Alex Reynolds
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Douglass Dunn
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Matthew G Sampson
- Division of Pediatric Nephrology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
- Kidney Research Institute, Seattle, Washington
| | - Charles E Alpers
- Department of Anatomic Pathology
- Kidney Research Institute, Seattle, Washington
| | | | - Shreeram Akilesh
- Department of Anatomic Pathology,
- Kidney Research Institute, Seattle, Washington
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107
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Angelin-Bonnet O, Biggs PJ, Vignes M. Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling. Methods Mol Biol 2019; 1883:347-383. [PMID: 30547408 DOI: 10.1007/978-1-4939-8882-2_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Modelling gene regulatory networks requires not only a thorough understanding of the biological system depicted, but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to familiarize the reader with the biological processes and molecular factors at play in the process of gene expression regulation. We first describe the different interactions controlling each step of the expression process, from transcription to mRNA and protein decay. In the second section, we provide statistical tools to accurately represent this biological complexity in the form of mathematical models. Among other considerations, we discuss the topological properties of biological networks, the application of deterministic and stochastic frameworks, and the quantitative modelling of regulation. We particularly focus on the use of such models for the simulation of expression data that can serve as a benchmark for the testing of network inference algorithms.
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Affiliation(s)
- Olivia Angelin-Bonnet
- Institute of Fundamental Sciences, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- Institute of Fundamental Sciences, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Matthieu Vignes
- Institute of Fundamental Sciences, Palmerston North, New Zealand.
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
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108
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Norris ET, Wang L, Conley AB, Rishishwar L, Mariño-Ramírez L, Valderrama-Aguirre A, Jordan IK. Genetic ancestry, admixture and health determinants in Latin America. BMC Genomics 2018; 19:861. [PMID: 30537949 PMCID: PMC6288849 DOI: 10.1186/s12864-018-5195-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. RESULTS We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population's genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. CONCLUSIONS Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.
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Affiliation(s)
- Emily T Norris
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA
| | - Lu Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Biomedical Research Institute, Faculty of Health, Universidad Libre-Seccional Cali, Cali, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,IHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL), Atlanta, GA, USA.
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109
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Weeks KL, McMullen JR. Divergent Effects of PKC (Protein Kinase C) α in the Human and Animal Heart? Therapeutic Implications for PKC Inhibitors in Cardiac Patients. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2018. [PMID: 29540469 DOI: 10.1161/circgen.118.002104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kate L Weeks
- From the Department of Cardiac Hypertrophy, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (K.L.W., J.R.M.); Departments of Physiology and Medicine, Alfred Hospital, Melbourne, Victoria, Australia (J.R.M.); Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia (J.R.M); and Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, Victoria, Australia (J.R.M.)
| | - Julie R McMullen
- From the Department of Cardiac Hypertrophy, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (K.L.W., J.R.M.); Departments of Physiology and Medicine, Alfred Hospital, Melbourne, Victoria, Australia (J.R.M.); Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia (J.R.M); and Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, Victoria, Australia (J.R.M.).
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Reilly JP, Wang F, Jones TK, Palakshappa JA, Anderson BJ, Shashaty MGS, Dunn TG, Johansson ED, Riley TR, Lim B, Abbott J, Ittner CAG, Cantu E, Lin X, Mikacenic C, Wurfel MM, Christiani DC, Calfee CS, Matthay MA, Christie JD, Feng R, Meyer NJ. Plasma angiopoietin-2 as a potential causal marker in sepsis-associated ARDS development: evidence from Mendelian randomization and mediation analysis. Intensive Care Med 2018; 44:1849-1858. [PMID: 30343317 PMCID: PMC6697901 DOI: 10.1007/s00134-018-5328-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/18/2018] [Indexed: 12/16/2022]
Abstract
PURPOSE A causal biomarker for acute respiratory distress syndrome (ARDS) could fuel precision therapy options. Plasma angiopoietin-2 (ANG2), a vascular permeability marker, is a strong candidate on the basis of experimental and observational evidence. We used genetic causal inference methods-Mendelian randomization and mediation-to infer potential effects of plasma ANG2. METHODS We genotyped 703 septic subjects, measured ICU admission plasma ANG2, and performed a quantitative trait loci (QTL) analysis to determine variants in the ANGPT2 gene associated with plasma ANG2 (p < 0.005). We then used linear regression and post-estimation analysis to genetically predict plasma ANG2 and tested genetically predicted ANG2 for ARDS association using logistic regression. We estimated the proportion of the genetic effect explained by plasma ANG2 using mediation analysis. RESULTS Plasma ANG2 was strongly associated with ARDS (OR 1.59 (95% CI 1.35, 1.88) per log). Five ANGPT2 variants were associated with ANG2 in European ancestry subjects (n = 404). Rs2442608C, the most extreme cis QTL (coefficient 0.22, 95% CI 0.09-0.36, p = 0.001), was associated with higher ARDS risk: adjusted OR 1.38 (95% CI 1.01, 1.87), p = 0.042. No significant QTL were identified in African ancestry subjects. Genetically predicted plasma ANG2 was associated with ARDS risk: adjusted OR 2.25 (95% CI 1.06-4.78), p = 0.035. Plasma ANG2 mediated 34% of the rs2442608C-related ARDS risk. CONCLUSIONS In septic European ancestry subjects, the strongest ANG2-determining ANGPT2 genetic variant is associated with higher ARDS risk. Plasma ANG2 may be a causal factor in ARDS development. Strategies to reduce plasma ANG2 warrant testing to prevent or treat sepsis-associated ARDS.
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Affiliation(s)
- John P Reilly
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Fan Wang
- Department of Molecular Cardiology, Cleveland Clinic Lerner Research Institute, Cleveland, USA
| | - Tiffanie K Jones
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Jessica A Palakshappa
- Pulmonary, Critical Care, Allergy, and Immunologic Medicine, Wake Forest School of Medicine, Winston-Salem, USA
| | - Brian J Anderson
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Michael G S Shashaty
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Thomas G Dunn
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Erik D Johansson
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Thomas R Riley
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Brian Lim
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Jason Abbott
- Departments of Medicine and Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, USA
| | - Caroline A G Ittner
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
| | - Edward Cantu
- Divison of Cardiothoracic Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Xihong Lin
- Harvard University T.H. Chan School of Public Health, Boston, USA
| | - Carmen Mikacenic
- Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, USA
| | - Mark M Wurfel
- Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, USA
| | - David C Christiani
- Harvard University T.H. Chan School of Public Health, Boston, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, USA
| | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, USA
| | - Michael A Matthay
- Departments of Medicine and Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, USA
| | - Jason D Christie
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, USA
| | - Rui Feng
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, USA
| | - Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Medicine Division, University of Pennsylvania Perelman School of Medicine, 3600 Spruce Street 5039 Gates Building, Philadelphia, PA, 19104, USA.
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Moreno V, Alonso MH, Closa A, Vallés X, Diez-Villanueva A, Valle L, Castellví-Bel S, Sanz-Pamplona R, Lopez-Doriga A, Cordero D, Solé X. Colon-specific eQTL analysis to inform on functional SNPs. Br J Cancer 2018; 119:971-977. [PMID: 30283144 PMCID: PMC6203735 DOI: 10.1038/s41416-018-0018-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/17/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Background Genome-wide association studies on colorectal cancer have identified more than 60 susceptibility loci, but for most of them there is no clear knowledge of functionality or the underlying gene responsible for the risk modification. Expression quantitative trail loci (eQTL) may provide functional information for such single nucleotide polymorphisms (SNPs). Methods We have performed detailed eQTL analysis specific for colon tissue on a series of 97 colon tumours, their paired adjacent normal mucosa and 47 colon mucosa samples donated by healthy individuals. R package MatrixEQTL was used to search for genome-wide cis-eQTL and trans-eQTL fitting linear models adjusted for age, gender and tissue type to rank transformed expression data. Results The cis-eQTL analyses has revealed 29,073 SNP-gene associations with permutation-adjusted P-values < 0.01. These correspond to 363 unique genes. The trans-eQTL analysis identified 10,665 significant SNP-gene associations, most of them in the same chromosome, further than 1 Mb of the gene. We provide a web tool to search for specific SNPs or genes. The tool calculates Pearson or Spearman correlation, and allows to select tissue type for analysis. Data and plots can be exported. Conclusions This resource should be useful to prioritise SNPs for further functional studies and to identify relevant genes behind identified loci.
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Affiliation(s)
- Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain. .,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain. .,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain. .,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, 08907, Spain.
| | - M Henar Alonso
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Adrià Closa
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Xavier Vallés
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain
| | - Anna Diez-Villanueva
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain
| | - Laura Valle
- Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Oncologia (CIBERONC), Madrid, 28029, Spain
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic de Barcelona, Barcelona, 08036, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, 28029, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - David Cordero
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Xavier Solé
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain.,Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Barcelona, 08908, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, 28029, Spain
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Santos DJA, Cole JB, Null DJ, Byrem TM, Ma L. Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle. J Dairy Sci 2018; 101:9987-10000. [PMID: 30219417 DOI: 10.3168/jds.2018-14682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/23/2018] [Indexed: 01/12/2023]
Abstract
Pregnancy-associated glycoproteins (PAG) are secreted by the trophoblast and are detectable in maternal circulation around the time of attachment of the fetal placenta, as well as in blood and milk throughout gestation. The understanding of the genetic mechanisms controlling PAG levels can confer advantages for livestock breeding programs given the precocity and the ease of obtaining this phenotype from routine pregnancy diagnosis. The aim of this study was to characterize PAG levels by estimating genetic parameters and correlations with other dairy traits, and to identify genomic regions and candidate genes associated with PAG levels in milk. The PAG data consisted of pregnancy diagnoses using commercial assays from 2012 to 2017, and genotype data consisted of 54,123 SNP markers for 2,352 individuals (embryos and dams). The model included contemporary group (herd, year, and season) and embryo age as fixed effects, and random embryonic (direct) and maternal (indirect) genetic effects. Using genomic data, the estimated heritability for direct and maternal genetic effects (± standard deviations) were 0.23 ± 0.05 and 0.11 ± 0.05, respectively. The genetic correlation between these effects was almost zero (0.001 ± 0.06). A preliminary analysis revealed low correlations between milk PAG levels and other dairy traits. The genome-wide association analysis was performed using 2 approaches: single-marker and single-step using all markers. Four genomic regions with direct genetic effects were detected on Bos taurus autosome (BTA) 6, BTA7, BTA19, and BTA29 of the embryonic genome. The BTA29 locus was within the bovine PAG gene cluster, suggesting a cis-regulatory quantitative trait locus on the PAG expression. However, other associations, without an obvious link to PAG expression, could be related to the transportation of PAG and their concentration in milk. Only 1 region from the maternal genome, on BTA4, had a significant indirect effect, where WNT2 is a candidate gene related to placenta vascularization and gestation health. Collectively, our results suggest a moderate genetic control of milk PAG levels from both maternal and fetal genomes, but larger studies are needed to fully evaluate the usefulness of milk PAG in the genetic evaluation of fetal growth and cow fertility.
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Affiliation(s)
- D J A Santos
- Department of Animal and Avian Sciences, University of Maryland, College Park 20742; Departamento de Zootecinia, Universidade Estadual Paulista, Jaboticabal, 14884-900, Brazil
| | - J B Cole
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - D J Null
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - T M Byrem
- Antel BioSystems Inc., Lansing, MI 48910
| | - L Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park 20742.
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113
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Cai Z, Guldbrandtsen B, Lund MS, Sahana G. Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle. BMC Genomics 2018; 19:656. [PMID: 30189836 PMCID: PMC6127918 DOI: 10.1186/s12864-018-5050-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Background Improving resistance to mastitis, one of the costliest diseases in dairy production, has become an important objective in dairy cattle breeding. However, mastitis resistance is influenced by many genes involved in multiple processes, including the response to infection, inflammation, and post-infection healing. Low genetic heritability, environmental variations, and farm management differences further complicate the identification of links between genetic variants and mastitis resistance. Consequently, studies of the genetics of variation in mastitis resistance in dairy cattle lack agreement about the responsible genes. Results We associated 15,552,968 imputed whole-genome sequencing markers for 5147 Nordic Holstein cattle with mastitis resistance in a genome-wide association study (GWAS). Next, we augmented P-values for markers in genes in the associated regions using Gene Ontology terms, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and mammalian phenotype database. To confirm results of gene-based analyses, we used gene expression data from E. coli-challenged cow udders. We identified 22 independent quantitative trait loci (QTL) that collectively explained 14% of the variance in breeding values for resistance to clinical mastitis (CM). Using association test statistics with multiple pieces of independent information on gene function and differential expression during bacterial infection, we suggested putative causal genes with biological relevance for 12 QTL affecting resistance to CM in dairy cattle. Conclusion Combining information on the nearest positional genes, gene-based analyses, and differential gene expression data from RNA-seq, we identified putative causal genes (candidate genes with biological evidence) in QTL for mastitis resistance in Nordic Holstein cattle. The same strategy can be applied for other traits. Electronic supplementary material The online version of this article (10.1186/s12864-018-5050-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
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Ferrão LFV, Benevenuto J, Oliveira IDB, Cellon C, Olmstead J, Kirst M, Resende MFR, Munoz P. Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00107] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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115
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Wang M, Tai C, E W, Wei L. DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants. Nucleic Acids Res 2018; 46:e69. [PMID: 29617928 PMCID: PMC6009584 DOI: 10.1093/nar/gky215] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 01/19/2023] Open
Abstract
The complex system of gene expression is regulated by the cell type-specific binding of transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding and lead to human diseases remains a great challenge. To address this, we implement sequence-based deep learning models that accurately predict the TF binding intensities to given DNA sequences. In addition to accurately classifying TF-DNA binding or unbinding, our models are capable of accurately predicting real-valued TF binding intensities by leveraging large-scale TF ChIP-seq data. The changes in the TF binding intensities between the altered sequence and the reference sequence reflect the degree of functional impact for the variant. This enables us to develop the tool DeFine (Deep learning based Functional impact of non-coding variants evaluator, http://define.cbi.pku.edu.cn) with improved performance for assessing the functional impact of non-coding variants including SNPs and indels. DeFine accurately identifies the causal functional non-coding variants from disease-associated variants in GWAS. DeFine is an effective and easy-to-use tool that facilities systematic prioritization of functional non-coding variants.
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Affiliation(s)
- Meng Wang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Cheng Tai
- Center for Data Science, Peking University, Beijing, 100871, P.R. China
- Beijing Institute of Big Data Research, Beijing, 100871, P.R. China
| | - Weinan E
- Center for Data Science, Peking University, Beijing, 100871, P.R. China
- Beijing Institute of Big Data Research, Beijing, 100871, P.R. China
- Department of Mathematics and PACM, Princeton University, Princeton, NJ, 08544, USA
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, P.R. China
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Dobbyn A, Huckins LM, Boocock J, Sloofman LG, Glicksberg BS, Giambartolomei C, Hoffman GE, Perumal TM, Girdhar K, Jiang Y, Raj T, Ruderfer DM, Kramer RS, Pinto D, Akbarian S, Roussos P, Domenici E, Devlin B, Sklar P, Stahl EA, Sieberts SK. Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS. Am J Hum Genet 2018; 102:1169-1184. [PMID: 29805045 PMCID: PMC5993513 DOI: 10.1016/j.ajhg.2018.04.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/24/2018] [Indexed: 12/12/2022] Open
Abstract
Causal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which variants underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissect this signal into multiple conditionally independent signals for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (n = 467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context-specific (e.g., tissue-, cell type-, or developmental time point-specific) regulation of gene expression. Integrating the 2014 Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC primary and conditional eQTL data reveals 40 loci with strong evidence for co-localization (posterior probability > 0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes, identify novel genes associated with schizophrenia risk, and provide specific hypotheses for their functional follow-up.
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Affiliation(s)
- Amanda Dobbyn
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura M Huckins
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Laura G Sloofman
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Next Generation Healthcare, Mount Sinai Health System, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gabriel E Hoffman
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Kiran Girdhar
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Jiang
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, Psychiatry and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Robin S Kramer
- Human Brain Collection Core, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Dalila Pinto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Enrico Domenici
- Laboratory of Neurogenomic Biomarkers, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy; The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Palowitch J, Shabalin A, Zhou YH, Nobel AB, Wright FA. Estimation of cis-eQTL effect sizes using a log of linear model. Biometrics 2018; 74:616-625. [PMID: 29073327 PMCID: PMC5920774 DOI: 10.1111/biom.12810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/01/2017] [Accepted: 09/01/2017] [Indexed: 11/29/2022]
Abstract
The study of expression Quantitative Trait Loci (eQTL) is an important problem in genomics and biomedicine. While detection (testing) of eQTL associations has been widely studied, less work has been devoted to the estimation of eQTL effect size. To reduce false positives, detection methods frequently rely on linear modeling of rank-based normalized or log-transformed gene expression data. Unfortunately, these approaches do not correspond to the simplest model of eQTL action, and thus yield estimates of eQTL association that can be uninterpretable and inaccurate. In this article, we propose a new, log-of-linear model for eQTL action, termed ACME, that captures allelic contributions to cis-acting eQTLs in an additive fashion, yielding effect size estimates that correspond to a biologically coherent model of cis-eQTLs. We describe a non-linear least-squares algorithm to fit the model by maximum likelihood, and obtain corresponding p-values. We perform careful investigation of the model using a combination of simulated data and data from the Genotype Tissue Expression (GTEx) project. Our results reveal little evidence for dominance effects, a parsimonious result that accords with a simple biological model for allele-specific expression and supports use of the ACME model. We show that Type-I error is well-controlled under our approach in a realistic setting, so that rank-based normalizations are unnecessary. Furthermore, we show that such normalizations can be detrimental to power and estimation accuracy under the proposed model. We then show, through effect size analyses of whole-genome cis-eQTLs in the GTEx data, that using standard normalizations instead of ACME noticeably affects the ranking and sign of estimates.
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Affiliation(s)
- John Palowitch
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, U.S.A
| | - Andrey Shabalin
- Department of Psychiatry, University of Utah, Salt Lake City, Utah 84108, U.S.A
| | - Yi-Hui Zhou
- Bioinformatics Research Center and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, U.S.A
| | - Andrew B Nobel
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, U.S.A
| | - Fred A Wright
- Bioinformatics Research Center and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, U.S.A
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, U.S.A
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118
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Abstract
PURPOSE OF REVIEW Following a life-threatening traumatic exposure, about 10% of those exposed are at considerable risk for developing posttraumatic stress disorder (PTSD), a severe and disabling syndrome characterized by uncontrollable intrusive memories, nightmares, avoidance behaviors, and hyperarousal in addition to impaired cognition and negative emotion symptoms. This review will explore recent genetic and epigenetic approaches to PTSD that explain some of the differential risk following trauma exposure. RECENT FINDINGS A substantial portion of the variance explaining differential risk responses to trauma exposure may be explained by differential inherited and acquired genetic and epigenetic risk. This biological risk is complemented by alterations in the functional regulation of genes via environmentally induced epigenetic changes, including prior childhood and adult trauma exposure. This review will cover recent findings from large-scale genome-wide association studies as well as newer epigenome-wide studies. We will also discuss future "phenome-wide" studies utilizing electronic medical records as well as targeted genetic studies focusing on mechanistic ways in which specific genetic or epigenetic alterations regulate the biological risk for PTSD.
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119
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Revilla M, Puig-Oliveras A, Crespo-Piazuelo D, Criado-Mesas L, Castelló A, Fernández AI, Ballester M, Folch JM. Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions. Sci Rep 2018; 8:2045. [PMID: 29391556 PMCID: PMC5794915 DOI: 10.1038/s41598-018-20473-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/16/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. A total of 193 expression-associated SNPs located in 19 chromosomal regions were associated with expression levels of ACSM5, ELOVL6, FABP4, FADS2, and SLC27A4 genes. Three expression quantitative trail loci (eQTLs) corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs have trans-regulatory effects. Remarkably, a SNP in the ACSM5 promoter region and a SNP in the 3′UTR region of FABP4 were the most associated polymorphisms with the ACSM5 and FABP4 expression levels, respectively. Moreover, relevant lipid-related genes mapped in the trans-eQTLs regions associated with the ACSM5, FABP4, FADS2, and SLC27A4 genes. Interestingly, a trans-eQTL hotspot on SSC13 regulating the gene expression of ELOVL6, ELOLV5, and SCD, three important genes implicated in the elongation and desaturation of fatty acids, was identified. These findings provide new data to further understand the functional regulatory mechanisms implicated in the variation of fatty acid composition in pigs.
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Affiliation(s)
- Manuel Revilla
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
| | - Anna Puig-Oliveras
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Daniel Crespo-Piazuelo
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Lourdes Criado-Mesas
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Anna Castelló
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Ana I Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Josep M Folch
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
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120
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Zhao J, Cheng F, Jia P, Cox N, Denny JC, Zhao Z. An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies. Genome Med 2018; 10:7. [PMID: 29378629 PMCID: PMC5789733 DOI: 10.1186/s13073-018-0513-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genome-phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genome-wide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases. METHODS In this study, we developed an integrative functional genomics framework that maps 215,107 significant single nucleotide polymorphism (SNP) traits generated from the PheWAS Catalog and 28,870 genome-wide significant SNP traits collected from the GWAS Catalog into a global human genome regulatory map via incorporating various functional annotation data, including transcription factor (TF)-based motifs, promoters, enhancers, and expression quantitative trait loci (eQTLs) generated from four major functional genomics databases: FANTOM5, ENCODE, NIH Roadmap, and Genotype-Tissue Expression (GTEx). In addition, we performed a tissue-specific regulatory circuit analysis through the integration of the identified regulatory variants and tissue-specific gene expression profiles in 7051 samples across 32 tissues from GTEx. RESULTS We found that the disease-associated loci in both the PheWAS and GWAS Catalogs were significantly enriched with functional SNPs. The integration of functional annotations significantly improved the power of detecting novel associations in PheWAS, through which we found a number of functional associations with strong regulatory evidence in the PheWAS Catalog. Finally, we constructed tissue-specific regulatory circuits for several complex traits: mental diseases, autoimmune diseases, and cancer, via exploring tissue-specific TF-promoter/enhancer-target gene interaction networks. We uncovered several promising tissue-specific regulatory TFs or genes for Alzheimer's disease (e.g. ZIC1 and STX1B) and asthma (e.g. CSF3 and IL1RL1). CONCLUSIONS This study offers powerful tools for exploring the functional consequences of variants generated from genome-phenome association studies in terms of their mechanisms on affecting multiple complex diseases and traits.
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Affiliation(s)
- Junfei Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Feixiong Cheng
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Center for Complex Networks Research, Northeastern University, Boston, MA, 02215, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Nancy Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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121
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Dahlin A, Qiu W, Litonjua AA, Lima JJ, Tamari M, Kubo M, Irvin CG, Peters SP, Wu AC, Weiss ST, Tantisira KG. The phosphatidylinositide 3-kinase (PI3K) signaling pathway is a determinant of zileuton response in adults with asthma. THE PHARMACOGENOMICS JOURNAL 2018; 18:665-677. [PMID: 29298996 PMCID: PMC6150906 DOI: 10.1038/s41397-017-0006-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/18/2017] [Indexed: 12/31/2022]
Abstract
Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control). We identified 1060 QTLs jointly associated with zileuton-related differential LTB4 production in LCLs and lung function change in patients taking zileuton, of which eight QTLs were also significantly associated with persistent LTB4 production in LCLs following zileuton treatment (i.e., ‘poor’ responders). Four nominally significant trans-eQTLs were predicted to regulate three candidate genes (SELL, MTF2, and GAL), the expression of which was significantly reduced in LCLs following zileuton treatment. Gene and pathway enrichment analyses of QTL associations identified multiple genes and pathways, predominantly related to phosphatidyl inositol signaling via PI3K. We validated the PI3K pathway activation status in a subset of LCLs demonstrating variable zileuton-related LTB4 production, and show that in contrast to LCLs that responded to zileuton, the PI3K pathway was activated in poor responder LCLs. Collectively, these findings demonstrate a role for the PIK3 pathway and its targets as important determinants of differential responsiveness to zileuton.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Stephen P Peters
- Wake Forest University Health Science Center, Winston-Salem, NC, USA
| | - Ann C Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Partners Center for Personalized Genetic Medicine, Partners Health Care, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,University of Vermont, Burlington, VT, USA
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122
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Murthy MN, Ramachandra NB. Prioritization of differentially expressed genes in Substantia nigra transcriptomes of Parkinson's disease reveals key protein interactions and pathways. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.07.005] [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] Open
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123
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Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. Nat Genet 2017; 49:1714-1721. [PMID: 29083405 PMCID: PMC5714271 DOI: 10.1038/ng.3959] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022]
Abstract
By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.
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Affiliation(s)
- Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ivette Zelaya
- Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles CA, USA
| | - Susan K. Service
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston TX, USA
| | - Rita M. Cantor
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA,USA
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Joseph DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA,USA
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lynn A. Fairbanks
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Scott Fears
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Allison E. Furterer
- Interdepartmental Graduate Program in Neuroscience, University of California Los Angeles, Los Angeles CA, USA
| | - Yu S. Huang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Christopher A. Schmitt
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Jay R. Kaplan
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Bronwen L. Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emily S. Wong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John Blangero
- South Texas Diabetes and Obesity Institute, UTHSCSA/UTRGV, Brownsville, TX, USA
| | - Thomas D. Dyer
- South Texas Diabetes and Obesity Institute, UTHSCSA/UTRGV, Brownsville, TX, USA
| | - Marina Bogomolov
- Faculty of Industrial Engineering and Management, Technion, Haifa, Israel
| | - Yoav Benjamini
- Department of Statistics and Operation Research, Tel Aviv University, Tel Aviv, Israel
| | | | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Statistics, Stanford University, Stanford, California, USA
| | - Richard K. Wilson
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - J. David Jentsch
- Department of Psychology, University of California, Los Angeles, Los Angeles, California, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wesley Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles CA, USA
| | - Roger P. Woods
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles CA, USA
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA,USA
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Tan JY, Smith AAT, Ferreira da Silva M, Matthey-Doret C, Rueedi R, Sönmez R, Ding D, Kutalik Z, Bergmann S, Marques AC. cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. Cell Rep 2017; 18:2280-2288. [PMID: 28249171 DOI: 10.1016/j.celrep.2017.02.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/16/2016] [Accepted: 01/30/2017] [Indexed: 11/26/2022] Open
Abstract
Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD) boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits.
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Affiliation(s)
- Jennifer Yihong Tan
- Department of Physiology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Adam Alexander Thil Smith
- Department of Physiology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maria Ferreira da Silva
- Department of Physiology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cyril Matthey-Doret
- Department of Physiology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Reyhan Sönmez
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Ding
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Institute of Social and Preventive Medicine, University Hospital Lausanne (CHUV), 1011 Lausanne, Switzerland
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ana Claudia Marques
- Department of Physiology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.
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125
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Rose NH, Bay RA, Morikawa MK, Palumbi SR. Polygenic evolution drives species divergence and climate adaptation in corals. Evolution 2017; 72:82-94. [DOI: 10.1111/evo.13385] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Noah H. Rose
- Hopkins Marine Station, Department of Biology; Stanford University; Pacific Grove California 93950
- Current Address: Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey
| | - Rachael A. Bay
- Institute of the Environment and Sustainability; University of California; Los Angeles California 90095
| | - Megan K. Morikawa
- Hopkins Marine Station, Department of Biology; Stanford University; Pacific Grove California 93950
| | - Stephen R. Palumbi
- Hopkins Marine Station, Department of Biology; Stanford University; Pacific Grove California 93950
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126
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Zeng P, Wang T, Huang S. Cis-SNPs Set Testing and PrediXcan Analysis for Gene Expression Data using Linear Mixed Models. Sci Rep 2017; 7:15237. [PMID: 29127305 PMCID: PMC5681585 DOI: 10.1038/s41598-017-15055-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022] Open
Abstract
Understanding the functional mechanism of SNPs identified in GWAS on complex diseases is currently a challenging task. The studies of expression quantitative trait loci (eQTL) have shown that regulatory variants play a crucial role in the function of associated SNPs. Detecting significant genes (called eGenes) in eQTL studies and analyzing the effect sizes of cis-SNPs can offer important implications on the genetic architecture of associated SNPs and interpretations of the molecular basis of diseases. We applied linear mixed models (LMM) to the gene expression level and constructed likelihood ratio tests (LRT) to test for eGene in the Geuvadis data. We identified about 11% genes as eGenes in the Geuvadis data and found some eGenes were enriched in approximately independent linkage disequilibrium (LD) blocks (e.g. MHC). We further performed PrediXcan analysis for seven diseases in the WTCCC data with weights estimated using LMM and identified 64, 5, 21 and 1 significant genes (p < 0.05 after Bonferroni correction) associated with T1D, CD, RA and T2D. We found most of the significant genes of T1D and RA were also located within the MHC region. Our results provide strong evidence that gene expression plays an intermediate role for the associated variants in GWAS.
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Affiliation(s)
- Ping Zeng
- Xuzhou Medical University, Department of Epidemiology and Biostatistics, Xuzhou, 221004, China.
- University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48104, USA.
| | - Ting Wang
- Xuzhou Medical University, Department of Epidemiology and Biostatistics, Xuzhou, 221004, China
| | - Shuiping Huang
- Xuzhou Medical University, Department of Epidemiology and Biostatistics, Xuzhou, 221004, China.
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127
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Environmental and genetic determinants of transcriptional plasticity in Chinook salmon. Heredity (Edinb) 2017; 120:38-50. [PMID: 29234168 DOI: 10.1038/s41437-017-0009-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/30/2017] [Accepted: 09/13/2017] [Indexed: 11/08/2022] Open
Abstract
Variation in gene transcription is widely believed to be the mechanistic basis of phenotypically plastic traits; however, comparatively little is known about the inheritance patterns of transcriptional variation that would allow us to predict its response to selection. In addition, acclimation to different environmental conditions influences acute transcriptional responses to stress and it is unclear if these effects are heritable. To address these gaps in knowledge, we assayed levels of messenger RNA for 14 candidate genes at rest and in response to a 24-h confinement stress for 72 half-sib families of Chinook salmon reared in two different environments (hatchery and semi-natural stream channel). We observed extensive plasticity for mRNA levels of metabolic and stress response genes and demonstrated that mRNA level plasticity due to rearing environment affects mRNA level plasticity in response to stress. These effects have important implications for natural populations experiencing multiple stressors. We identified genotype-by-environment interactions for mRNA levels that were dominated by maternal effects; however, mRNA level response to challenge also exhibited a non-additive genetic basis. Our results indicate that while plasticity for mRNA levels can evolve, predicting the outcome of selection will be difficult. The inconsistency in genetic architecture among treatment groups suggests there is considerable cryptic genetic variation for gene expression.
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128
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Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen. G3-GENES GENOMES GENETICS 2017; 7:3317-3329. [PMID: 28790145 PMCID: PMC5633382 DOI: 10.1534/g3.117.300125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Powdery mildew pathogens colonize over 9500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh. Two highly significant regions possessing trans eQTL were identified near the telomeric ends of chromosomes (Chr) 2HL and 1HS. Within these regions reside diverse resistance loci derived from barley landrace H. laevigatum (MlLa) and H. vulgare cv. Algerian (Mla1), which associate with the altered expression of 961 and 3296 genes during fungal penetration of the host and haustorial development, respectively. Regulatory control of transcript levels for 299 of the 961 genes is reprioritized from MlLa on 2HL to Mla1 on 1HS as infection progresses, with 292 of the 299 alternating the allele responsible for higher expression, including Adaptin Protein-2 subunit μ AP2M and Vesicle Associated Membrane Protein VAMP72 subfamily members VAMP721/722. AP2M mediates effector-triggered immunity (ETI) via endocytosis of plasma membrane receptor components. VAMP721/722 and SNAP33 form a Soluble N-ethylmaleimide-sensitive factor Attachment Protein REceptor (SNARE) complex with SYP121 (PEN1), which is engaged in pathogen associated molecular pattern (PAMP)-triggered immunity via exocytosis. We postulate that genes regulated by alternate chromosomal positions are repurposed as part of a conserved immune complex to respond to different pathogen attack scenarios.
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129
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Lu Y, Biancotto A, Cheung F, Remmers E, Shah N, McCoy JP, Tsang JS. Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations. Immunity 2017; 45:1162-1175. [PMID: 27851916 DOI: 10.1016/j.immuni.2016.10.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 12/21/2022]
Abstract
Cell-to-cell expression variation (CEV) is a prevalent feature of even well-defined cell populations, but its functions, particularly at the organismal level, are not well understood. Using single-cell data obtained via high-dimensional flow cytometry of T cells as a model, we introduce an analysis framework for quantifying CEV in primary cell populations and studying its functional associations in human cohorts. Analyses of 840 CEV phenotypes spanning multiple baseline measurements of 14 proteins in 28 T cell subpopulations suggest that the quantitative extent of CEV can exhibit substantial subject-to-subject differences and yet remain stable within healthy individuals over months. We linked CEV to age and disease-associated genetic polymorphisms, thus implicating CEV as a biomarker of aging and disease susceptibility and suggesting that it might play an important role in health and disease. Our dataset, interactive figures, and software for computing CEV with flow cytometry data provide a resource for exploring CEV functions.
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Affiliation(s)
- Yong Lu
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Angelique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA
| | - Elaine Remmers
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Naisha Shah
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - J Philip McCoy
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA; Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA.
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130
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He P, Xia W, Wang L, Wu J, Guo YF, Zeng KQ, Wang MJ, Bing PF, Xie FF, Lu X, Zhang YH, Lei SF, Deng FY. Identification of expression quantitative trait loci (eQTLs) in human peripheral blood mononuclear cells (PBMCs) and shared with liver and brain. J Cell Biochem 2017; 119:1659-1669. [PMID: 28792098 DOI: 10.1002/jcb.26325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022]
Abstract
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified. We identified 443 cis- and 2386 trans-eSNPs (FDR <0.05), which regulated 128 and 635 target genes, respectively. A transcriptome-wide expression regulation network was constructed, highlighting the importance of 28 pleiotropic eSNPs and 18 dually (cis- and trans-) regulated genes. Three genes, that is, TIPRL, HSPB8, and EGLN3, were commonly regulated by hundreds of eSNPs and constituted a very complex interaction network. Strikingly, the missense SNP rs371513 trans- regulated 25 target genes, which were functionally related to poly(A) RNA binding. Among 8904 eQTLs (P < 0.001) identified herein in PBMCs, a minority (163) was overlapped with lymphoblastoid, monocytes, liver, and/or brain. Besides, two cis-eSNPs in PBMC were confirmed by AEI. The present results demonstrated a comprehensive expression regulation network for human PBMCs and may provide novel insights into the pathogenesis of immunological diseases related to PBMCs.
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Affiliation(s)
- Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Wei Xia
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Lan Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Jian Wu
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yu-Fan Guo
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ke-Qin Zeng
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ming-Jun Wang
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Peng-Fei Bing
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fang-Fei Xie
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
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131
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Wang L, Zhu J, Deng FY, Wu LF, Mo XB, Zhu XW, Xia W, Xie FF, He P, Bing PF, Qiu YH, Lin X, Lu X, Zhang L, Yi NJ, Zhang YH, Lei SF. Correlation analyses revealed global microRNA-mRNA expression associations in human peripheral blood mononuclear cells. Mol Genet Genomics 2017; 293:95-105. [PMID: 28879530 DOI: 10.1007/s00438-017-1367-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/01/2017] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study. We predicted and achieved 861 miRNA-mRNA pairs (65 miRNAs, 412 mRNAs) using multiple bioinformatics programs, and found global negative miRNA-mRNA correlations in PBMC from all 46 study subjects. Among the 861 pairs of correlations, 19.5% were significant (P < 0.05) and ~70% were negative. The correlation network was complex and highlighted key miRNAs/genes in PBMC. Some miRNAs, such as hsa-miR-29a, hsa-miR-148a, regulate a cluster of target genes. Some genes, e.g., TNRC6A, are regulated by multiple miRNAs. The identified genes tend to be enriched in molecular functions of DNA and RNA binding, and biological processes such as protein transport, regulation of translation and chromatin modification. The results provided a global view of the miRNA-mRNA expression correlation profile in human PBMCs, which would facilitate in-depth investigation of biological functions of key miRNAs/mRNAs and better understanding of the pathogenesis underlying PBMC-related diseases.
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Affiliation(s)
- Lan Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Center for Disease Prevention and Control, Yichun, 336000, Jiangxi, People's Republic of China
| | - Jiang Zhu
- The Second Affiliated Hospital of Soochow University, Suzhou, 215008, Jiangsu, People's Republic of China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Long-Fei Wu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xiao-Wei Zhu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Wei Xia
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Fang-Fei Xie
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Peng-Fei Bing
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Ying-Hua Qiu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xiang Lin
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Neng-Jun Yi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China. .,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
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132
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Highfill CA, Tran JH, Nguyen SKT, Moldenhauer TR, Wang X, Macdonald SJ. Naturally Segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster. Genetics 2017; 207:311-325. [PMID: 28743761 PMCID: PMC5586381 DOI: 10.1534/genetics.117.300058] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/24/2017] [Indexed: 12/16/2022] Open
Abstract
Identifying the sequence polymorphisms underlying complex trait variation is a key goal of genetics research, since knowing the precise causative molecular events allows insight into the pathways governing trait variation. Genetic analysis of complex traits in model systems regularly starts by constructing QTL maps, but generally fails to identify causative sequence polymorphisms. Previously we mapped a series of QTL contributing to resistance to nicotine in a Drosophila melanogaster multiparental mapping resource and here use a battery of functional tests to resolve QTL to the molecular level. One large-effect QTL resided over a cluster of UDP-glucuronosyltransferases, and quantitative complementation tests using deficiencies eliminating subsets of these detoxification genes revealed allelic variation impacting resistance. RNAseq showed that Ugt86Dd had significantly higher expression in genotypes that are more resistant to nicotine, and anterior midgut-specific RNA interference (RNAi) of this gene reduced resistance. We discovered a segregating 22-bp frameshift deletion in Ugt86Dd, and accounting for the InDel during mapping largely eliminates the QTL, implying the event explains the bulk of the effect of the mapped locus. CRISPR/Cas9 editing of a relatively resistant genotype to generate lesions in Ugt86Dd that recapitulate the naturally occurring putative loss-of-function allele, leads to a large reduction in resistance. Despite this major effect of the deletion, the allele appears to be very rare in wild-caught populations and likely explains only a small fraction of the natural variation for the trait. Nonetheless, this putatively causative coding InDel can be a launchpad for future mechanistic exploration of xenobiotic detoxification.
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Affiliation(s)
- Chad A Highfill
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Jonathan H Tran
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Samantha K T Nguyen
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Taylor R Moldenhauer
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Xiaofei Wang
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
- Center for Computational Biology, University of Kansas, Lawrence, Kansas 66047
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133
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Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
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134
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Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome. Nat Biotechnol 2017; 35:732-746. [DOI: 10.1038/nbt.3863] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
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135
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Abstract
MOTIVATION It remains a challenge to detect associations between genotypes and phenotypes because of insufficient sample sizes and complex underlying mechanisms involved in associations. Fortunately, it is becoming more feasible to obtain gene expression data in addition to genotypes and phenotypes, giving us new opportunities to detect true genotype-phenotype associations while unveiling their association mechanisms. RESULTS In this article, we propose a novel method, NETAM, that accurately detects associations between SNPs and phenotypes, as well as gene traits involved in such associations. We take a network-driven approach: NETAM first constructs an association network, where nodes represent SNPs, gene traits or phenotypes, and edges represent the strength of association between two nodes. NETAM assigns a score to each path from an SNP to a phenotype, and then identifies significant paths based on the scores. In our simulation study, we show that NETAM finds significantly more phenotype-associated SNPs than traditional genotype-phenotype association analysis under false positive control, taking advantage of gene expression data. Furthermore, we applied NETAM on late-onset Alzheimer's disease data and identified 477 significant path associations, among which we analyzed paths related to beta-amyloid, estrogen, and nicotine pathways. We also provide hypothetical biological pathways to explain our findings. AVAILABILITY AND IMPLEMENTATION Software is available at http://www.sailing.cs.cmu.edu/ CONTACT : epxing@cs.cmu.edu.
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Affiliation(s)
- Seunghak Lee
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Soonho Kong
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Eric P Xing
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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136
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Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E. Using genomic annotations increases statistical power to detect eGenes. Bioinformatics 2017; 32:i156-i163. [PMID: 27307612 PMCID: PMC4908356 DOI: 10.1093/bioinformatics/btw272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Motivation: Expression quantitative trait loci (eQTLs) are genetic variants that affect gene expression. In eQTL studies, one important task is to find eGenes or genes whose expressions are associated with at least one eQTL. The standard statistical method to determine whether a gene is an eGene requires association testing at all nearby variants and the permutation test to correct for multiple testing. The standard method however does not consider genomic annotation of the variants. In practice, variants near gene transcription start sites (TSSs) or certain histone modifications are likely to regulate gene expression. In this article, we introduce a novel eGene detection method that considers this empirical evidence and thereby increases the statistical power. Results: We applied our method to the liver Genotype-Tissue Expression (GTEx) data using distance from TSSs, DNase hypersensitivity sites, and six histone modifications as the genomic annotations for the variants. Each of these annotations helped us detected more candidate eGenes. Distance from TSS appears to be the most important annotation; specifically, using this annotation, our method discovered 50% more candidate eGenes than the standard permutation method. Contact:buhm.han@amc.seoul.kr or eeskin@cs.ucla.edu
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Affiliation(s)
| | | | | | - Jae Hoon Sul
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason Ernst
- Department of Computer Science Department of Biological Chemistry
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Eleazar Eskin
- Department of Computer Science Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
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137
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Kel I, Chang Z, Galluccio N, Romeo M, Beretta S, Diomede L, Mezzelani A, Milanesi L, Dieterich C, Merelli I. SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans. MOLECULAR BIOSYSTEMS 2017; 12:3447-3458. [PMID: 27722582 DOI: 10.1039/c6mb00453a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles. In particular, tools are needed for the analysis of next-generation sequencing (NGS) data on a genome-wide scale, which is essential to identify eQTLs able to control a large number of genes (hotspots). Here we present SPIRE (Software for Polymorphism Identification Regulating Expression), a generic, modular and functionally highly flexible pipeline for eQTL processing. SPIRE integrates different univariate and multivariate approaches for eQTL analysis, paying particular attention to the scalability of the procedure in order to support cis- as well as trans-mapping, thus allowing the identification of hotspots in NGS data. In particular, we demonstrated how SPIRE can handle big association study datasets, reproducing published results and improving the identification of trans-eQTLs. Furthermore, we employed the pipeline to analyse novel data concerning the genotypes of two different C. elegans strains (N2 and Hawaii) and related miRNA expression data, obtained using RNA-Seq. A miRNA regulatory hotspot was identified in chromosome 1, overlapping the transcription factor grh-1, known to be involved in the early phases of embryonic development of C. elegans. In a follow-up qPCR experiment we were able to verify most of the predicted eQTLs, as well as to show, for a novel miRNA, a significant difference in the sequences of the two analysed strains of C. elegans. SPIRE is publicly available as open source software at , together with some example data, a readme file, supplementary material and a short tutorial.
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Affiliation(s)
- Ivan Kel
- Instituto di Tecnologie Biomediche - Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, 20090, Segrate, Milano, Italy.
| | - Zisong Chang
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
| | - Nadia Galluccio
- Instituto di Tecnologie Biomediche - Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, 20090, Segrate, Milano, Italy.
| | - Margherita Romeo
- Dipartimento di Biochimica e Farmacologia Molecolare, IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri", Via Giuseppe La Masa 19, Milan, Italy.
| | - Stefano Beretta
- Dipartimento di Informatica Sistemistica e Comunicazione, Università degli studi di Milano-Biccoca, Viale Sarca 336, 20125 Milano, Italy.
| | - Luisa Diomede
- Dipartimento di Biochimica e Farmacologia Molecolare, IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri", Via Giuseppe La Masa 19, Milan, Italy.
| | - Alessandra Mezzelani
- Instituto di Tecnologie Biomediche - Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, 20090, Segrate, Milano, Italy.
| | - Luciano Milanesi
- Instituto di Tecnologie Biomediche - Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, 20090, Segrate, Milano, Italy.
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University of Heidelberg, Grabengasse 1, 69117 Heidelberg, Germany.
| | - Ivan Merelli
- Instituto di Tecnologie Biomediche - Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, 20090, Segrate, Milano, Italy.
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138
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Genetic Dissection of Nutrition-Induced Plasticity in Insulin/Insulin-Like Growth Factor Signaling and Median Life Span in a Drosophila Multiparent Population. Genetics 2017; 206:587-602. [PMID: 28592498 DOI: 10.1534/genetics.116.197780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/13/2017] [Indexed: 11/18/2022] Open
Abstract
The nutritional environments that organisms experience are inherently variable, requiring tight coordination of how resources are allocated to different functions relative to the total amount of resources available. A growing body of evidence supports the hypothesis that key endocrine pathways play a fundamental role in this coordination. In particular, the insulin/insulin-like growth factor signaling (IIS) and target of rapamycin (TOR) pathways have been implicated in nutrition-dependent changes in metabolism and nutrient allocation. However, little is known about the genetic basis of standing variation in IIS/TOR or how diet-dependent changes in expression in this pathway influence phenotypes related to resource allocation. To characterize natural genetic variation in the IIS/TOR pathway, we used >250 recombinant inbred lines (RILs) derived from a multiparental mapping population, the Drosophila Synthetic Population Resource, to map transcript-level QTL of genes encoding 52 core IIS/TOR components in three different nutritional environments [dietary restriction (DR), control (C), and high sugar (HS)]. Nearly all genes, 87%, were significantly differentially expressed between diets, though not always in ways predicted by loss-of-function mutants. We identified cis (i.e., local) expression QTL (eQTL) for six genes, all of which are significant in multiple nutrient environments. Further, we identified trans (i.e., distant) eQTL for two genes, specific to a single nutrient environment. Our results are consistent with many small changes in the IIS/TOR pathways. A discriminant function analysis for the C and DR treatments identified a pattern of gene expression associated with the diet treatment. Mapping the composite discriminant function scores revealed a significant global eQTL within the DR diet. A correlation between the discriminant function scores and the median life span (r = 0.46) provides evidence that gene expression changes in response to diet are associated with longevity in these RILs.
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139
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Benowitz KM, McKinney EC, Cunningham CB, Moore AJ. Relating quantitative variation within a behavior to variation in transcription. Evolution 2017; 71:1999-2009. [PMID: 28542920 DOI: 10.1111/evo.13273] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/27/2017] [Accepted: 04/21/2017] [Indexed: 12/14/2022]
Abstract
Many studies have shown that variation in transcription is associated with changes in behavioral state, or with variation within a state, but little has been done to address if the same genes are involved in both. Here, we investigate the transcriptional basis of variation in parental provisioning using two species of burying beetle, Nicrophorus orbicollis and Nicrophorus vespilloides. We used RNA-seq to compare transcription in parents that provided high amounts of provisioning behavior versus low amounts in males and females of each species. We found no overarching transcriptional patterns distinguishing high from low caring parents, and no informative transcripts that displayed particularly large expression differences in either sex. However, we did find subtler gene expression differences between high and low provisioning parents that are consistent across both sexes and species. Furthermore, we show that transcripts previously implicated in transitioning into parental care in N. vespilloides had high variance in the levels of transcription and were unusually likely to display differential expression between high and low provisioning parents. Thus, quantitative behavioral variation appears to reflect many transcriptional differences of small effect. Furthermore, the same transcripts required for the transition between behavioral states are also related to variation within a behavioral state.
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Affiliation(s)
- Kyle M Benowitz
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | | | - Christopher B Cunningham
- Department of Genetics, University of Georgia, Athens, Georgia, 30602.,Department of Biosciences, Swansea University, Swansea, SA2 8PP, UK
| | - Allen J Moore
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
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140
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Mossman JA, Tross JG, Jourjine NA, Li N, Wu Z, Rand DM. Mitonuclear Interactions Mediate Transcriptional Responses to Hypoxia in Drosophila. Mol Biol Evol 2017; 34:447-466. [PMID: 28110272 PMCID: PMC6095086 DOI: 10.1093/molbev/msw246] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Among the major challenges in quantitative genetics and personalized medicine is to understand how gene × gene interactions (G × G: epistasis) and gene × environment interactions (G × E) underlie phenotypic variation. Here, we use the intimate relationship between mitochondria and oxygen availability to dissect the roles of nuclear DNA (nDNA) variation, mitochondrial DNA (mtDNA) variation, hypoxia, and their interactions on gene expression in Drosophila melanogaster. Mitochondria provide an important evolutionary and medical context for understanding G × G and G × E given their central role in integrating cellular signals. We hypothesized that hypoxia would alter mitonuclear communication and gene expression patterns. We show that first order nDNA, mtDNA, and hypoxia effects vary between the sexes, along with mitonuclear epistasis and G × G × E effects. Females were generally more sensitive to genetic and environmental perturbation. While dozens to hundreds of genes are altered by hypoxia in individual genotypes, we found very little overlap among mitonuclear genotypes for genes that were significantly differentially expressed as a consequence of hypoxia; excluding the gene hairy. Oxidative phosphorylation genes were among the most influenced by hypoxia and mtDNA, and exposure to hypoxia increased the signature of mtDNA effects, suggesting retrograde signaling between mtDNA and nDNA. We identified nDNA-encoded genes in the electron transport chain (succinate dehydrogenase) that exhibit female-specific mtDNA effects. Our findings have important implications for personalized medicine, the sex-specific nature of mitonuclear communication, and gene × gene coevolution under variable or changing environments.
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Affiliation(s)
- Jim A Mossman
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI
| | - Jennifer G Tross
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA
| | - Nick A Jourjine
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI.,Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Nan Li
- Department of Biostatistics, Brown University, Providence, RI
| | - Zhijin Wu
- Department of Biostatistics, Brown University, Providence, RI
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI
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141
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Lawson LP, Petren K. The adaptive genomic landscape of beak morphology in Darwin's finches. Mol Ecol 2017; 26:4978-4989. [DOI: 10.1111/mec.14166] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Lucinda P. Lawson
- Department of Biological Sciences; University of Cincinnati; Cincinnati OH USA
| | - Kenneth Petren
- Department of Biological Sciences; University of Cincinnati; Cincinnati OH USA
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142
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Ju JH, Shenoy SA, Crystal RG, Mezey JG. An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci. PLoS Comput Biol 2017; 13:e1005537. [PMID: 28505156 PMCID: PMC5448815 DOI: 10.1371/journal.pcbi.1005537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/30/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In light of these results, we discuss the broad impact eQTL that have been previously reported from the analysis of human data and suggest that considerable caution should be exercised when making biological inferences based on these reported eQTL.
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Affiliation(s)
- Jin Hyun Ju
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Sushila A. Shenoy
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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143
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Zeng P, Zhou X, Huang S. Prediction of gene expression with cis-SNPs using mixed models and regularization methods. BMC Genomics 2017; 18:368. [PMID: 28490319 PMCID: PMC5425981 DOI: 10.1186/s12864-017-3759-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 05/03/2017] [Indexed: 12/25/2022] Open
Abstract
Background It has been shown that gene expression in human tissues is heritable, thus predicting gene expression using only SNPs becomes possible. The prediction of gene expression can offer important implications on the genetic architecture of individual functional associated SNPs and further interpretations of the molecular basis underlying human diseases. Methods We compared three types of methods for predicting gene expression using only cis-SNPs, including the polygenic model, i.e. linear mixed model (LMM), two sparse models, i.e. Lasso and elastic net (ENET), and the hybrid of LMM and sparse model, i.e. Bayesian sparse linear mixed model (BSLMM). The three kinds of prediction methods have very different assumptions of underlying genetic architectures. These methods were evaluated using simulations under various scenarios, and were applied to the Geuvadis gene expression data. Results The simulations showed that these four prediction methods (i.e. Lasso, ENET, LMM and BSLMM) behaved best when their respective modeling assumptions were satisfied, but BSLMM had a robust performance across a range of scenarios. According to R2 of these models in the Geuvadis data, the four methods performed quite similarly. We did not observe any clustering or enrichment of predictive genes (defined as genes with R2 ≥ 0.05) across the chromosomes, and also did not see there was any clear relationship between the proportion of the predictive genes and the proportion of genes in each chromosome. However, an interesting finding in the Geuvadis data was that highly predictive genes (e.g. R2 ≥ 0.30) may have sparse genetic architectures since Lasso, ENET and BSLMM outperformed LMM for these genes; and this observation was validated in another gene expression data. We further showed that the predictive genes were enriched in approximately independent LD blocks. Conclusions Gene expression can be predicted with only cis-SNPs using well-developed prediction models and these predictive genes were enriched in some approximately independent LD blocks. The prediction of gene expression can shed some light on the functional interpretation for identified SNPs in GWASs.
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Affiliation(s)
- Ping Zeng
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, 209 Tongshan Rd, Xuzhou, Jiangsu, 221004, China. .,Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48104, USA.
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48104, USA
| | - Shuiping Huang
- Department of Epidemiology and Biostatistics, Xuzhou Medical University, 209 Tongshan Rd, Xuzhou, Jiangsu, 221004, China.
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144
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Mirza N, Appleton R, Burn S, du Plessis D, Duncan R, Farah JO, Feenstra B, Hviid A, Josan V, Mohanraj R, Shukralla A, Sills GJ, Marson AG, Pirmohamed M. Genetic regulation of gene expression in the epileptic human hippocampus. Hum Mol Genet 2017; 26:1759-1769. [PMID: 28334860 PMCID: PMC5411756 DOI: 10.1093/hmg/ddx061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/12/2016] [Accepted: 02/16/2017] [Indexed: 01/21/2023] Open
Abstract
Epilepsy is a serious and common neurological disorder. Expression quantitative loci (eQTL) analysis is a vital aid for the identification and interpretation of disease-risk loci. Many eQTLs operate in a tissue- and condition-specific manner. We have performed the first genome-wide cis-eQTL analysis of human hippocampal tissue to include not only normal (n = 22) but also epileptic (n = 22) samples. We demonstrate that disease-associated variants from an epilepsy GWAS meta-analysis and a febrile seizures (FS) GWAS are significantly more enriched with epilepsy-eQTLs than with normal hippocampal eQTLs from two larger independent published studies. In contrast, GWAS meta-analyses of two other brain diseases associated with hippocampal pathology (Alzheimer's disease and schizophrenia) are more enriched with normal hippocampal eQTLs than with epilepsy-eQTLs. These observations suggest that an eQTL analysis that includes disease-affected brain tissue is advantageous for detecting additional risk SNPs for the afflicting and closely related disorders, but not for distinct diseases affecting the same brain regions. We also show that epilepsy eQTLs are enriched within epilepsy-causing genes: an epilepsy cis-gene is significantly more likely to be a causal gene for a Mendelian epilepsy syndrome than to be a causal gene for another Mendelian disorder. Epilepsy cis-genes, compared to normal hippocampal cis-genes, are more enriched within epilepsy-causing genes. Hence, we utilize the epilepsy eQTL data for the functional interpretation of epilepsy disease-risk variants and, thereby, highlight novel potential causal genes for sporadic epilepsy. In conclusion, an epilepsy-eQTL analysis is superior to normal hippocampal tissue eQTL analyses for identifying the variants and genes underlying epilepsy.
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Affiliation(s)
- Nasir Mirza
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
| | - Richard Appleton
- The Roald Dahl EEG Unit, Paediatric Neurosciences Foundation, Alder Hey Children's NHS Foundation Trust, Liverpool L12 2AP, UK
| | - Sasha Burn
- Department of Neurosurgery, Alder Hey Children's NHS Foundation Trust, Liverpool L12 2AP, UK
| | - Daniel du Plessis
- Department of Cellular Pathology, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Roderick Duncan
- Department of Neurology, Christchurch Hospital, Christchurch 8140, New Zealand
| | - Jibril Osman Farah
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool L9 7LJ, UK
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Hviid
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Vivek Josan
- Department of Neurosurgery, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Rajiv Mohanraj
- Department of Neurology, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Arif Shukralla
- Department of Neurology, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Graeme J. Sills
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
| | - Anthony G. Marson
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
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145
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Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics 2017; 16:959-981. [PMID: 28456751 DOI: 10.1074/mcp.mr117.000024] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/20/2022] Open
Abstract
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.
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Affiliation(s)
- Kelly V Ruggles
- From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016
| | - Karsten Krug
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaojing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Karl R Clauser
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel H Payne
- **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - David Fenyö
- ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; .,§§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016
| | - Bing Zhang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; .,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - D R Mani
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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146
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Bogunia-Kubik K, Łacina P. From genetic single candidate gene studies to complex genomics of GvHD. Br J Haematol 2017; 178:661-675. [DOI: 10.1111/bjh.14704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
- Laboratory of Tissue Immunology; Medical Centre; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
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147
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Abstract
Gene expression changes, the driving forces for cellular diversity in multicellular organisms, are regulated by a diverse set of gene regulatory elements that direct transcription in specific cells. Mutations in these elements, ranging from chromosomal aberrations to single-nucleotide polymorphisms, are a major cause of human disease. However, we currently have a very limited understanding of how regulatory element genotypes lead to specific phenotypes. In this review, we discuss the various methods of regulatory element identification, the different types of mutations they harbor, and their impact on human disease. We highlight how these variations can affect transcription of multiple genes in gene regulatory networks. In addition, we describe how novel technologies, such as massively parallel reporter assays and CRISPR/Cas9 genome editing, are beginning to provide a better understanding of the functional roles that these elements have and how their alteration can lead to specific phenotypes.
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Affiliation(s)
- Sumantra Chatterjee
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, University of California, San Francisco, California 94158;
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148
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Brynedal B, Choi J, Raj T, Bjornson R, Stranger BE, Neale BM, Voight BF, Cotsapas C. Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation. Am J Hum Genet 2017; 100:581-591. [PMID: 28285767 DOI: 10.1016/j.ajhg.2017.02.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/09/2017] [Indexed: 12/15/2022] Open
Abstract
Efforts to decipher the causal relationships between differences in gene regulation and corresponding differences in phenotype have been stymied by several basic technical challenges. Although detecting local, cis-eQTLs is now routine, trans-eQTLs, which are distant from the genes of origin, are far more difficult to find because millions of SNPs must currently be compared to thousands of transcripts. Here, we demonstrate an alternative approach: we looked for SNPs associated with the expression of many genes simultaneously and found that hundreds of trans-eQTLs each affect hundreds of transcripts in lymphoblastoid cell lines across three African populations. These trans-eQTLs target the same genes across the three populations and show the same direction of effect. We discovered that target transcripts of a high-confidence set of trans-eQTLs encode proteins that interact more frequently than expected by chance, are bound by the same transcription factors, and are enriched for pathway annotations indicative of roles in basic cell homeostasis. We thus demonstrate that our approach can uncover trans-acting transcriptional control circuits that affect co-regulated groups of genes: a key to understanding how cellular pathways and processes are orchestrated.
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Affiliation(s)
- Boel Brynedal
- Department of Neurology, Yale University School of Medicine, New Haven, CT 06520, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - JinMyung Choi
- Department of Neurology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Towfique Raj
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Robert Bjornson
- Department of Computer Science, Yale University, New Haven, CT 06510, USA
| | - Barbara E Stranger
- Institute for Genomics and Systems Biology The University of Chicago, Chicago, IL 60637, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chris Cotsapas
- Department of Neurology, Yale University School of Medicine, New Haven, CT 06520, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
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149
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Mähler N, Wang J, Terebieniec BK, Ingvarsson PK, Street NR, Hvidsten TR. Gene co-expression network connectivity is an important determinant of selective constraint. PLoS Genet 2017; 13:e1006402. [PMID: 28406900 PMCID: PMC5407845 DOI: 10.1371/journal.pgen.1006402] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 04/27/2017] [Accepted: 03/31/2017] [Indexed: 12/12/2022] Open
Abstract
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure. Here we utilised RNA-Sequencing to assay gene expression in winter buds undergoing bud flush in a natural population of Populus tremula, an outbreeding forest tree species. We performed expression Quantitative Trait Locus (eQTL) mapping and identified 164,290 significant eQTLs associating 6,241 unique genes (eGenes) with 147,419 unique SNPs (eSNPs). We found approximately four times as many local as distant eQTLs, with local eQTLs having significantly higher effect sizes. eQTLs were primarily located in regulatory regions of genes (UTRs or flanking regions), regardless of whether they were local or distant. We used the gene expression data to infer a co-expression network and investigated the relationship between network topology, the genetic architecture of gene expression and signatures of selection. Within the co-expression network, eGenes were underrepresented in network module cores (hubs) and overrepresented in the periphery of the network, with a negative correlation between eQTL effect size and network connectivity. We additionally found that module core genes have experienced stronger selective constraint on coding and non-coding sequence, with connectivity associated with signatures of selection. Our integrated genetics and genomics results suggest that purifying selection is the primary mechanism underlying the genetic architecture of natural variation in gene expression assayed in flushing leaf buds of P. tremula and that connectivity within the co-expression network is linked to the strength of purifying selection.
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Affiliation(s)
- Niklas Mähler
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Jing Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Centre for Integrative Genetics, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Barbara K. Terebieniec
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Pär K. Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Torgeir R. Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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Fang X, Yin Z, Li X, Xia L, Quan X, Zhao Y, Zhou B. Multiple functional SNPs in differentially expressed genes modify risk and survival of non-small cell lung cancer in Chinese female non-smokers. Oncotarget 2017; 8:18924-18934. [PMID: 28148898 PMCID: PMC5386658 DOI: 10.18632/oncotarget.14836] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022] Open
Abstract
DNA genotype can affect gene expression, and gene expression can influence the onset and progression of diseases. Here we conducted a comprehensive study, we integrated analysis of gene expression profile and single nucleotide polymorphism (SNP) microarray data in order to scan out the critical genetic changes that participate in the onset and development of non-small cell lung cancer (NSCLC). Gene expression profile datasets were downloaded from the GEO database. Firstly, differentially expressed genes (DEGs) between NSCLC samples and adjacent normal samples were identified. Next, by STRING database, protein-protein interaction (PPI) network was constructed. At the same time, hub genes in PPI network were identified. Then, some functional SNPs in hub genes that may affect gene expression have been annotated. Finally, we carried a study to explore the relationship between functional SNPs and NSCLC risk and overall survival in Chinese female non-smokers. A total of 488 DEGs were identified in our study. There are 29 proteins with a higher degree of connectivity in the PPI network, including FOS, IL6 and MMP9. By using database annotation, we got 8 candidate functional SNPs that may affect the expression level of hub proteins. In the case-control study, we found that rs4754-T allele, rs959173-C allele and rs2239144-G allele were the protective allele of NSCLC risk. In dominant model, rs4754-CT+TT genotype were associated with a shorter survival time. In general, our study provides a novel research direction in the field of multi-omic data integration, and helps us find some critical genetic changes in disease.
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Affiliation(s)
- Xue Fang
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Lingzi Xia
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xiaowei Quan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Yuxia Zhao
- Department of Radiotherapy, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
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