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Hemani G, Bowden J, Davey Smith G. Evaluating the potential role of pleiotropy in Mendelian randomization studies. Hum Mol Genet 2018; 27:R195-R208. [PMID: 29771313 PMCID: PMC6061876 DOI: 10.1093/hmg/ddy163] [Citation(s) in RCA: 653] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 02/06/2023] Open
Abstract
Pleiotropy, the phenomenon of a single genetic variant influencing multiple traits, is likely widespread in the human genome. If pleiotropy arises because the single nucleotide polymorphism (SNP) influences one trait, which in turn influences another ('vertical pleiotropy'), then Mendelian randomization (MR) can be used to estimate the causal influence between the traits. Of prime focus among the many limitations to MR is the unprovable assumption that apparent pleiotropic associations are mediated by the exposure (i.e. reflect vertical pleiotropy), and do not arise due to SNPs influencing the two traits through independent pathways ('horizontal pleiotropy'). The burgeoning treasure trove of genetic associations yielded through genome wide association studies makes for a tantalizing prospect of phenome-wide causal inference. Recent years have seen substantial attention devoted to the problem of horizontal pleiotropy, and in this review we outline how newly developed methods can be used together to improve the reliability of MR.
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Affiliation(s)
- Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
| | - Jack Bowden
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
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de Vries PS, Yu B, Feofanova EV, Metcalf GA, Brown MR, Zeighami AL, Liu X, Muzny DM, Gibbs RA, Boerwinkle E, Morrison AC. Whole-genome sequencing study of serum peptide levels: the Atherosclerosis Risk in Communities study. Hum Mol Genet 2018; 26:3442-3450. [PMID: 28854705 DOI: 10.1093/hmg/ddx266] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/04/2017] [Indexed: 01/27/2023] Open
Abstract
Oligopeptides are important markers of protein metabolism, as they are cleaved from larger polypeptides and proteins. Genetic association studies may help elucidate their origin and function. In 1,552 European Americans and 1,872 African Americans of the Atherosclerosis Risk in Communities study, we performed whole-genome and whole-exome sequencing and measured serum levels of 25 peptides. Common variants (minor allele frequency > 5%) were analysed individually. We grouped low-frequency variants (minor allele frequency ≤ 5%) by a genome-wide sliding window using region-based aggregate tests. Furthermore, low-frequency regulatory variants were grouped by gene, as were functional coding variants. All analyses were performed separately in each ancestry group and then meta-analysed. We identified 22 common variant associations with peptide levels (P-value < 4.2 × 10-10), including 16 novel gene-peptide pairs. Notably, variants in kinin-kallikrein genes KNG1, F12, KLKB1, and ACE were associated with several different peptides. Variants in KLKB1 and ACE were associated with a fragment of complement component 3f. Both common variants and low-frequency coding variants in CPN1 were associated with a fibrinogen cleavage peptide. Four sliding windows were significantly associated with peptide levels (P-value < 4.2 × 10-10). Our results highlight the importance of the kinin-kallikrein system in the regulation of serum peptide levels, strengthen the evidence for a broad link between the kinin-kallikrein and complement systems, and suggest a role of CPN1 in the conversion of fibrinogen to fibrin.
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Affiliation(s)
- Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Elena V Feofanova
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030 TX, USA
| | - Michael R Brown
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Atefeh L Zeighami
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Xiaoming Liu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030 TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030 TX, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030 TX, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
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Abstract
Despite thousands of genetic loci identified to date, a large proportion of genetic variation predisposing to complex disease and traits remains unaccounted for. Advances in sequencing technology enable focused explorations on the contribution of low-frequency and rare variants to human traits. Here we review experimental approaches and current knowledge on the contribution of these genetic variants in complex disease and discuss challenges and opportunities for personalised medicine.
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Affiliation(s)
- Lorenzo Bomba
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Klaudia Walter
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Hills Rd, Cambridge, CB2 0AH, UK. .,The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.
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Pollard HB, Shivakumar C, Starr J, Eidelman O, Jacobowitz DM, Dalgard CL, Srivastava M, Wilkerson MD, Stein MB, Ursano RJ. "Soldier's Heart": A Genetic Basis for Elevated Cardiovascular Disease Risk Associated with Post-traumatic Stress Disorder. Front Mol Neurosci 2016; 9:87. [PMID: 27721742 PMCID: PMC5033971 DOI: 10.3389/fnmol.2016.00087] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/05/2016] [Indexed: 11/13/2022] Open
Abstract
"Soldier's Heart," is an American Civil War term linking post-traumatic stress disorder (PTSD) with increased propensity for cardiovascular disease (CVD). We have hypothesized that there might be a quantifiable genetic basis for this linkage. To test this hypothesis we identified a comprehensive set of candidate risk genes for PTSD, and tested whether any were also independent risk genes for CVD. A functional analysis algorithm was used to identify associated signaling networks. We identified 106 PTSD studies that report one or more polymorphic variants in 87 candidate genes in 83,463 subjects and controls. The top upstream drivers for these PTSD risk genes are predicted to be the glucocorticoid receptor (NR3C1) and Tumor Necrosis Factor alpha (TNFA). We find that 37 of the PTSD candidate risk genes are also candidate independent risk genes for CVD. The association between PTSD and CVD is significant by Fisher's Exact Test (P = 3 × 10-54). We also find 15 PTSD risk genes that are independently associated with Type 2 Diabetes Mellitus (T2DM; also significant by Fisher's Exact Test (P = 1.8 × 10-16). Our findings offer quantitative evidence for a genetic link between post-traumatic stress and cardiovascular disease, Computationally, the common mechanism for this linkage between PTSD and CVD is innate immunity and NFκB-mediated inflammation.
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Affiliation(s)
- Harvey B. Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Chittari Shivakumar
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Joshua Starr
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - David M. Jacobowitz
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Meera Srivastava
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Matthew D. Wilkerson
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health SciencesBethesda, MD, USA
| | - Murray B. Stein
- Department of Psychiatry, University of California, San DiegoSan Diego, CA, USA
| | - Robert J. Ursano
- Department of Psychiatry Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA
- Center for the Study of Traumatic stress, Uniformed Services University of the Health SciencesBethesda, MD, USA
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Matsumoto T, Shimizu T, Takai A, Marusawa H. Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis. Cancers (Basel) 2015; 7:1037-51. [PMID: 26083936 PMCID: PMC4491698 DOI: 10.3390/cancers7020823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/08/2015] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome research consortia, have increased over recent years. In addition to detecting somatic mutations in tumor cells, NGS technologies enable us to approach the subject of carcinogenic mechanisms from new perspectives. Deep sequencing, a method of optimizing the high throughput capacity of NGS technologies, allows for the detection of genetic aberrations in small subsets of premalignant and/or tumor cells in noncancerous chronically inflamed tissues. Genome-wide NGS data also make it possible to clarify the mutational signatures of each cancer tissue by identifying the precise pattern of nucleotide alterations in the cancer genome, providing new information regarding the mechanisms of tumorigenesis. In this review, we highlight these new methods taking advantage of NGS technologies, and discuss our current understanding of carcinogenic mechanisms elucidated from such approaches.
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Affiliation(s)
- Tomonori Matsumoto
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Hiroyuki Marusawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
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