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Engoren M, Jewell ES, Douville N, Moser S, Maile MD, Bauer ME. Genetic variants associated with sepsis. PLoS One 2022; 17:e0265052. [PMID: 35275946 PMCID: PMC8916629 DOI: 10.1371/journal.pone.0265052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The variable presentations and different phenotypes of sepsis suggest that risk of sepsis comes from many genes each having a small effect. The cumulative effect can be used to create individual risk profile. The purpose of this study was to create a polygenic risk score and determine the genetic variants associated with sepsis. METHODS We sequenced ~14 million single nucleotide polymorphisms with a minimac imputation quality R2>0.3 and minor allele frequency >10-6 in patients with Sepsis-2 or Sepsis-3. Genome-wide association was performed using Firth bias-corrected logistic regression. Semi-parsimonious logistic regression was used to create polygenic risk scores and reduced regression to determine the genetic variants independently associated with sepsis. FINDINGS 2261 patients had sepsis and 13,068 control patients did not. The polygenic risk scores had good discrimination: c-statistic = 0.752 ± 0.005 for Sepsis-2 and 0.752 ± 0.007 for Sepsis-3. We found 772 genetic variants associated with Sepsis-2 and 442 with Sepsis-3, p<0.01. After multivariate adjustment, 100 variants on 85 genes were associated with Sepsis-2 and 69 variants in 54 genes with Sepsis-3. Twenty-five variants were present in both the Sepsis-2 and Sepsis-3 groups out of 32 genes that were present in both groups. The other 7 genes had different variants present. Most variants had small effect sizes. CONCLUSIONS Sepsis-2 and Sepsis-3 have both separate and shared genetic variants. Most genetic variants have small effects sizes, but cumulatively, the polygenic risk scores have good discrimination.
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Affiliation(s)
- Milo Engoren
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Elizabeth S. Jewell
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Nicholas Douville
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Stephanie Moser
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Michael D. Maile
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Melissa E. Bauer
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Anesthesiology, Duke University, Durham, NC, United States of America
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2
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Keane C, Coalter M, Martin-Loeches I. Immune System Disequilibrium-Neutrophils, Their Extracellular Traps, and COVID-19-Induced Sepsis. Front Med (Lausanne) 2021; 8:711397. [PMID: 34485339 PMCID: PMC8416266 DOI: 10.3389/fmed.2021.711397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Equilibrium within the immune system can often determine the fate of its host. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the coronavirus disease 2019 (COVID-19) pandemic. Immune dysregulation remains one of the main pathophysiological components of SARS-CoV-2-associated organ injury, with over-activation of the innate immune system, and induced apoptosis of adaptive immune cells. Here, we provide an overview of the innate immune system, both in general and relating to COVID-19. We specifically discuss "NETosis," the process of neutrophil release of their extracellular traps, which may be a more recently described form of cell death that is different from apoptosis, and how this may propagate organ dysfunction in COVID-19. We complete this review by discussing Stem Cell Therapies in COVID-19 and emerging COVID-19 phenotypes, which may allow for more targeted therapy in the future. Finally, we consider the array of potential therapeutic targets in COVID-19, and associated therapeutics.
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Affiliation(s)
- Colm Keane
- Department of Anaesthesia and Intensive Care, St. James's Hospital, Dublin, Ireland
- Multidisciplinary Intensive Care Research Organization (MICRO), Trinity College Dublin, Dublin, Ireland
| | - Matthew Coalter
- Department of Anaesthesia and Intensive Care, St. James's Hospital, Dublin, Ireland
| | - Ignacio Martin-Loeches
- Department of Anaesthesia and Intensive Care, St. James's Hospital, Dublin, Ireland
- Multidisciplinary Intensive Care Research Organization (MICRO), Trinity College Dublin, Dublin, Ireland
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3
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Puskarich MA, Jennaro TS, Gillies CE, Evans CR, Karnovsky A, McHugh CE, Flott TL, Jones AE, Stringer KA. Pharmacometabolomics identifies candidate predictor metabolites of an L-carnitine treatment mortality benefit in septic shock. Clin Transl Sci 2021; 14:2288-2299. [PMID: 34216108 PMCID: PMC8604225 DOI: 10.1111/cts.13088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/22/2021] [Accepted: 05/12/2021] [Indexed: 01/08/2023] Open
Abstract
Sepsis‐induced metabolic dysfunction contributes to organ failure and death. L‐carnitine has shown promise for septic shock, but a recent phase II study of patients with vasopressor‐dependent septic shock demonstrated a non‐significant reduction in mortality. We undertook a pharmacometabolomics study of these patients (n = 250) to identify metabolic profiles predictive of a 90‐day mortality benefit from L‐carnitine. The independent predictive value of each pretreatment metabolite concentration, adjusted for L‐carnitine dose, on 90‐day mortality was determined by logistic regression. A grid‐search analysis maximizing the Z‐statistic from a binomial proportion test identified specific metabolite threshold levels that discriminated L‐carnitine responsive patients. Threshold concentrations were further assessed by hazard ratio and Kaplan‐Meier estimate. Accounting for L‐carnitine treatment and dose, 11 1H‐NMR metabolites and 12 acylcarnitines were independent predictors of 90‐day mortality. Based on the grid‐search analysis numerous acylcarnitines and valine were identified as candidate metabolites of drug response. Acetylcarnitine emerged as highly viable for the prediction of an L‐carnitine mortality benefit due to its abundance and biological relevance. Using its most statistically significant threshold concentration, patients with pretreatment acetylcarnitine greater than or equal to 35 µM were less likely to die at 90 days if treated with L‐carnitine (18 g) versus placebo (p = 0.01 by log rank test). Metabolomics also identified independent predictors of 90‐day sepsis mortality. Our proof‐of‐concept approach shows how pharmacometabolomics could be useful for tackling the heterogeneity of sepsis and informing clinical trial design. In addition, metabolomics can help understand mechanisms of sepsis heterogeneity and variable drug response, because sepsis induces alterations in numerous metabolite concentrations.
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Affiliation(s)
- Michael A Puskarich
- Department of Emergency Medicine, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
| | - Theodore S Jennaro
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher E Gillies
- Department of Emergency Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Integrative Research in Critical Care (MCIRCC), University of Michigan, Ann Arbor, Michigan, USA.,Michigan Institute for Data Science, Office of Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles R Evans
- Michigan Regional Comprehensive Metabolomics Resource Core (MRC2, ), University of Michigan, Ann Arbor, Michigan, USA.,Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Alla Karnovsky
- Michigan Regional Comprehensive Metabolomics Resource Core (MRC2, ), University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Cora E McHugh
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas L Flott
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Alan E Jones
- Department of Emergency Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Kathleen A Stringer
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Integrative Research in Critical Care (MCIRCC), University of Michigan, Ann Arbor, Michigan, USA.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
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4
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Rosier F, Brisebarre A, Dupuis C, Baaklini S, Puthier D, Brun C, Pradel LC, Rihet P, Payen D. Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer. Int J Mol Sci 2021; 22:ijms22115852. [PMID: 34072601 PMCID: PMC8198806 DOI: 10.3390/ijms22115852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
The high mortality rate in septic shock patients is likely due to environmental and genetic factors, which influence the host response to infection. Two genome-wide association studies (GWAS) on 832 septic shock patients were performed. We used integrative bioinformatic approaches to annotate and prioritize the sepsis-associated single nucleotide polymorphisms (SNPs). An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation. Among the 139 SNPs associated with death and the 1311 SNPs in strong linkage disequilibrium with them, we investigated 1439 SNPs within non-coding regions to identify regulatory variants. The highest integrative weighted score (IW-score) was obtained for rs143356980, indicating that this SNP is a robust regulatory candidate. The rs143356980 region is located in a non-coding region close to the CISH gene. A CRISPR-Cas9-mediated deletion of this region and specific luciferase assays in K562 cells showed that rs143356980 modulates the enhancer activity in K562 cells. These analyses allowed us to identify several genes associated with death in patients with septic shock. They suggest that genetic variations in key genes, such as CISH, perturb relevant pathways, increasing the risk of death in sepsis patients.
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Affiliation(s)
- Florian Rosier
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Audrey Brisebarre
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Claire Dupuis
- Medical Intensive Care Unit, Clermont-Ferrand University Hospital, 58 rue Montalembert, 63003 Clermont-Ferrand, France;
| | - Sabrina Baaklini
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Denis Puthier
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Christine Brun
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
- CNRS, 13288 Marseille, France
| | - Lydie C. Pradel
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
- Correspondence: (L.C.P.); (P.R.); (D.P.); Tel.: +33-491828745 (L.C.P.); +33-491828723 (P.R.); +33-687506599 (D.P.)
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
- Correspondence: (L.C.P.); (P.R.); (D.P.); Tel.: +33-491828745 (L.C.P.); +33-491828723 (P.R.); +33-687506599 (D.P.)
| | - Didier Payen
- UMR INSERM 1160: Alloimmunité, Autoimmunité, Transplantation, University of Paris 7 Denis Diderot, 2 rue Ambroise-Paré, CEDEX 10, 75475 Paris, France
- Correspondence: (L.C.P.); (P.R.); (D.P.); Tel.: +33-491828745 (L.C.P.); +33-491828723 (P.R.); +33-687506599 (D.P.)
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5
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Stoppe C, Wendt S, Mehta NM, Compher C, Preiser JC, Heyland DK, Kristof AS. Biomarkers in critical care nutrition. Crit Care 2020; 24:499. [PMID: 32787899 PMCID: PMC7425162 DOI: 10.1186/s13054-020-03208-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
The goal of nutrition support is to provide the substrates required to match the bioenergetic needs of the patient and promote the net synthesis of macromolecules required for the preservation of lean mass, organ function, and immunity. Contemporary observational studies have exposed the pervasive undernutrition of critically ill patients and its association with adverse clinical outcomes. The intuitive hypothesis is that optimization of nutrition delivery should improve ICU clinical outcomes. It is therefore surprising that multiple large randomized controlled trials have failed to demonstrate the clinical benefit of restoring or maximizing nutrient intake. This may be in part due to the absence of biological markers that identify patients who are most likely to benefit from nutrition interventions and that monitor the effects of nutrition support. Here, we discuss the need for practical risk stratification tools in critical care nutrition, a proposed rationale for targeted biomarker development, and potential approaches that can be adopted for biomarker identification and validation in the field.
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Affiliation(s)
- Christian Stoppe
- 3CARE—Cardiovascular Critical Care & Anesthesia Evaluation and Research, Aachen, Germany
- Department of Anesthesiology, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Sebastian Wendt
- 3CARE—Cardiovascular Critical Care & Anesthesia Evaluation and Research, Aachen, Germany
| | - Nilesh M. Mehta
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Charlene Compher
- Department of Biobehavioral Health Science, University of Pennsylvania and Clinical Nutrition Support Service, Hospital of the University of Pennsylvania, Philadelphia, PA USA
| | - Jean-Charles Preiser
- Erasme University Hospital, Université Libre de Bruxelles, 808 route de Lennik, B-1070 Brussels, Belgium
| | - Daren K. Heyland
- Department of Critical Care Medicine, Queen’s University, Angada 4, Kingston, ON K7L 2V7 Canada
- Clinical Evaluation Research Unit, Kingston General Hospital, Angada 4, Kingston, ON K7L 2V7 Canada
| | - Arnold S. Kristof
- Meakins-Christie Laboratories and Translational Research in Respiratory Diseases Program, Faculty of Medicine, Departments of Medicine and Critical Care, Research Institute of the McGill University Health Centre, 1001 Décarie Blvd., EM3.2219, Montreal, QC H4A 3J1 Canada
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6
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Gomez JL, Himes BE, Kaminski N. Precision Medicine in Critical Illness: Sepsis and Acute Respiratory Distress Syndrome. PRECISION IN PULMONARY, CRITICAL CARE, AND SLEEP MEDICINE 2019. [PMCID: PMC7120471 DOI: 10.1007/978-3-030-31507-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Sepsis and the acute respiratory distress syndrome (ARDS) each cause substantial morbidity and mortality. In contrast to other lung diseases, the entire course of disease in these syndromes is measured in days to weeks rather than months to years, which raises unique challenges in achieving precision medicine. We review advances in sepsis and ARDS resulting from omics studies, including those involving genome-wide association, gene expression, targeted proteomics, and metabolomics approaches. We focus on promising evidence of biological subtypes in both sepsis and ARDS that consistently display high risk for death. In sepsis, a gene expression signature with dysregulated adaptive immune signaling has evidence for a differential response to systemic steroid therapy, whereas in ARDS, a hyperinflammatory pattern identified in plasma using targeted proteomics responded more favorably to randomized interventions including high positive end-expiratory pressure, volume conservative fluid therapy, and simvastatin therapy. These early examples suggest heterogeneous biology that may be challenging to detect by clinical factors alone and speak to the promise of a precision approach that targets the right treatment at the right time to the right patient.
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Affiliation(s)
- Jose L. Gomez
- Assistant Professor Pulmonary, Critical Care and Sleep Medicine Section, Department of Medicine, Yale University School of Medicine, New Haven, CT USA
| | - Blanca E. Himes
- Assistant Professor of Informatics, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Naftali Kaminski
- Boehringer-Ingelheim Endowed, Professor of Internal Medicine, Chief of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT USA
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7
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CTLA-4 Genetic Variants Predict Survival in Patients with Sepsis. J Clin Med 2019; 8:jcm8010070. [PMID: 30634576 PMCID: PMC6352177 DOI: 10.3390/jcm8010070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/26/2018] [Accepted: 01/07/2019] [Indexed: 01/28/2023] Open
Abstract
Cytotoxic T lymphocyte-associated protein 4 (CTLA-4) is a coinhibitory checkpoint protein expressed on the surface of T cells. A recent study by our working group revealed that the rs231775 single nucleotide polymorphism (SNP) in the CTLA-4 gene was associated with the survival of patients with sepsis and served as an independent prognostic variable. To further investigate the impact of CTLA-4 genetic variants on sepsis survival, we examined the effect of two functional SNPs, CTLA-4 rs733618 and CTLA-4 rs3087243, and inferred haplotypes, on the survival of 644 prospectively enrolled septic patients. Kaplan⁻Meier survival analysis revealed significantly lower 90-day mortality for rs3087243 G allele carriers (n = 502) than for AA-homozygous (n = 142) patients (27.3% vs. 40.8%, p = 0.0024). Likewise, lower 90-day mortality was observed for TAA haplotype-negative patients (n = 197; compound rs733618 T/rs231775 A/rs3087243 A) than for patients carrying the TAA haplotype (n = 447; 24.4% vs. 32.9%, p = 0.0265). Carrying the rs3087243 G allele hazard ratio (HR): 0.667; 95% confidence interval (CI): 0.489⁻0.909; p = 0.0103) or not carrying the TAA haplotype (HR: 0.685; 95% CI: 0.491⁻0.956; p = 0.0262) remained significant covariates for 90-day survival in the multivariate Cox regression analysis and thus served as independent prognostic variables. In conclusion, our findings underscore the significance of CTLA-4 genetic variants as predictors of survival of patients with sepsis.
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8
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Průcha M, Zazula R, Russwurm S. Sepsis Diagnostics in the Era of "Omics" Technologies. Prague Med Rep 2018; 119:9-29. [PMID: 29665344 DOI: 10.14712/23362936.2018.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Sepsis is a multifactorial clinical syndrome with an extremely dynamic clinical course and with high diverse clinical phenotype. Early diagnosis is crucial for the final clinical outcome. Previous studies have not identified a biomarker for the diagnosis of sepsis which would have sufficient sensitivity and specificity. Identification of the infectious agents or the use of molecular biology, next gene sequencing, has not brought significant benefit for the patient in terms of early diagnosis. Therefore, we are currently searching for biomarkers, through "omics" technologies with sufficient diagnostic specificity and sensitivity, able to predict the clinical course of the disease and the patient response to therapy. Current progress in the use of systems biology technologies brings us hope that by using big data from clinical trials such biomarkers will be found.
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Affiliation(s)
- Miroslav Průcha
- Department of Clinical Biochemistry, Haematology and Immunology, Na Homolce Hospital, Prague, Czech Republic.
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Stefan Russwurm
- Department of Anesthesiology and Intensive Care, University Hospital Jena, Jena, Germany
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9
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Abstract
PURPOSE OF REVIEW Disruption of metabolic homeostasis is universal in the critically ill. Macronutrients and micronutrients are major environmental regulators of metabolite production through their gene regulation effects. The study of large numbers of circulating metabolites is beginning to emerge through the comprehensive profiling of the critically ill. In the critically ill, metabolomic studies consistently show that changes in fatty acids, lipids and tryptophan metabolite pathways are common and are associated with disease state and outcomes. RECENT FINDINGS Metabolomics is now being applied in research studies to determine the critical illness response to nutrient deficiency and delivery. Nutritional metabolomics approaches in nutrient deficiency, malnutrition and nutrient delivery have included single time point studies and dynamic studies of critically ill patients over time. Integration of metabolomics and clinical outcome data may create a more complete understanding of the control of metabolism in critical illness. SUMMARY The integration of metabolomic profiling with transcription and genomic data may allow for a unique window into the mechanism of how nutrient deficiency and delivery alters cellular homeostasis during critical illness and modulates the regain of cellular homeostasis during recovery. The progress and the challenges of the study of nutritional metabolomics are reviewed here.
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Affiliation(s)
- Kenneth B Christopher
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, Massachusetts, USA
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10
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Annane D, Mira JP, Ware LB, Gordon AC, Hinds CJ, Christiani DC, Sevransky J, Barnes K, Buchman TG, Heagerty PJ, Balshaw R, Lesnikova N, de Nobrega K, Wellman HF, Neira M, Mancini ADJ, Walley KR, Russell JA. Pharmacogenomic biomarkers do not predict response to drotrecogin alfa in patients with severe sepsis. Ann Intensive Care 2018; 8:16. [PMID: 29388048 PMCID: PMC5792380 DOI: 10.1186/s13613-018-0353-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/01/2018] [Indexed: 12/12/2022] Open
Abstract
Purpose
To explore potential design for pharmacogenomics trials in sepsis, we investigate the interaction between pharmacogenomic biomarkers and response to drotrecogin alfa (activated) (DrotAA). This trial was designed to validate whether previously identified improved response polymorphisms (IRPs A and B) were associated with an improved response to DrotAA in severe sepsis. Methods Patients with severe sepsis at high risk of death, who received DrotAA or not, with DNA available were included and matched to controls adjusting for age, APACHE II or SAPS II, organ dysfunction, ventilation, medical/surgical status, infection site, and propensity score (probability that a patient would have received DrotAA given their baseline characteristics). Independent genotyping and two-phase data transfer mitigated bias. The primary analysis compared the effect of DrotAA in IRP+ and IRP− groups on in-hospital 28-day mortality. Secondary endpoints included time to death in hospital; intensive care unit (ICU)-, hospital-, and ventilator-free days; and overall DrotAA treatment effect on mortality.
Results Six hundred and ninety-two patients treated with DrotAA were successfully matched to 1935 patients not treated with DrotAA. Genotyping was successful for 639 (DrotAA) and 1684 (nonDrotAA) matched patients. The primary hypothesis of a genotype-by-treatment interaction (assessed by conditional logistic regression analysis) was not significant (P = 0.30 IRP A; P = 0.78 IRP B), and there was no significant genotype by treatment interaction for any secondary endpoint. Conclusions
Neither IRP A nor IRP B predicted differential response to DrotAA on in-hospital 28-day mortality. ClinicalTrials.gov registration NCT01486524 Electronic supplementary material The online version of this article (10.1186/s13613-018-0353-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Djillali Annane
- Service de Reanimation Medicale, Hopital R. Poincare, 104 Bd Raymond Poincare, 92380, Garches, France
| | - Jean-Paul Mira
- Sorbonne Paris Cité, Cochin Hotel-Dieu University Hospital Medical Intensive Care Unit, AP-HP, Université Paris Descartes, 75014, Paris, France
| | - Lorraine B Ware
- Departments of Medicine and Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, 1161 21st Avenue South T1218 MCN, Nashville, TN, 37232-2650, USA
| | - Anthony C Gordon
- Section of Anaesthetics, Pain Medicine, and Intensive Care, Charing Cross Hospital, Imperial College London, Fulham Palace Road, London, W6 8RF, UK
| | - Charles J Hinds
- Barts and The London School of Medicine, Queen Mary University of London, London, UK
| | - David C Christiani
- Harvard Medical School and School of Public Health, 665 Huntington Avenue, Building I Room 1401, Boston, MA, 02115, USA
| | - Jonathan Sevransky
- Emory Center for Critical Care, Woodruff Health Sciences Center, Emory University, Atlanta, GA, USA
| | - Kathleen Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Timothy G Buchman
- Emory Center for Critical Care, Woodruff Health Sciences Center, Emory University, Atlanta, GA, USA
| | - Patrick J Heagerty
- Department of Biostatistics, University of Washington, F-600, Health Sciences Building, Office: H-665D HSB, Box 357232, Seattle, WA, 98195-7232, USA
| | | | | | | | - Hugh F Wellman
- Formerly with Sirius Genomics Inc, Vancouver, BC, Canada
| | - Mauricio Neira
- Formerly with Sirius Genomics Inc, Vancouver, BC, Canada
| | | | - Keith R Walley
- Critical Care Research Laboratories, Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Burrard Building, Rm 166 - 1081 Burrard St, Vancouver, BC, V6Z 1Y6, Canada
| | - James A Russell
- Critical Care Research Laboratories, Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Burrard Building, Rm 166 - 1081 Burrard St, Vancouver, BC, V6Z 1Y6, Canada.
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11
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Vincent JL. The coming era of precision medicine for intensive care. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2017; 21:314. [PMID: 29297399 PMCID: PMC5751549 DOI: 10.1186/s13054-017-1910-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent advances in technology and better understanding of mechanisms underlying disease are beginning to enable us to better characterize critically ill patients. Instead of using nonspecific syndromic groupings, such as sepsis or acute respiratory distress syndrome, we can now classify individual patients according to various specific characteristics, such as immune status. This "personalized" medicine approach will enable us to distinguish patients who have similar clinical presentations but different cellular and molecular responses that will influence their need for and responses (both negative and positive) to specific treatments. Treatments will be able to be chosen more accurately for each patient, resulting in more rapid institution of appropriate, effective therapy. We will also increasingly be able to conduct trials in groups of patients specifically selected as being most likely to respond to the intervention in question. This has already begun with, for example, some new interventions being tested only in patients with coagulopathy or immunosuppressive patterns. Ultimately, as we embrace this era of precision medicine, we may be able to offer precision therapies specifically designed to target the molecular set-up of an individual patient, as has begun to be done in cancer therapeutics.
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Affiliation(s)
- Jean-Louis Vincent
- Department of Intensive Care, Erasme University Hospital, Université libre de Bruxelles, route de Lennik 808, 1070, Bruxelles, Belgium.
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12
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Abstract
Abstract
Sepsis is a life-threatening syndrome resulting in shock and organ dysfunction stemming from a microbial infection. Sepsis has a mortality of 40% and is implicated in half of all in-hospital deaths. The host immune response to microbial infection is critical, with early-phase sepsis characterized by a hyperinflammatory immune response, whereas the later phase of sepsis is often complicated by suppression. Sepsis has no treatment, and management remains supportive.
Stem cells constitute exciting potential therapeutic agents for sepsis. In this review, we examine the rationale for stem cells in sepsis, focusing on mesenchymal stem/stromal cells, which currently demonstrate the greatest therapeutic promise. We examine the preclinical evidence base and evaluate potential mechanisms of action of these cells that are important in the setting of sepsis. We discuss early-phase clinical trials and critically appraise translational barriers to the use of mesenchymal stem/stromal cells in patients with sepsis.
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Srinivasan L, Page G, Kirpalani H, Murray JC, Das A, Higgins RD, Carlo WA, Bell EF, Goldberg RN, Schibler K, Sood BG, Stevenson DK, Stoll BJ, Van Meurs KP, Johnson KJ, Levy J, McDonald SA, Zaterka-Baxter KM, Kennedy KA, Sánchez PJ, Duara S, Walsh MC, Shankaran S, Wynn JL, Cotten CM. Genome-wide association study of sepsis in extremely premature infants. Arch Dis Child Fetal Neonatal Ed 2017; 102:F439-F445. [PMID: 28283553 PMCID: PMC5563277 DOI: 10.1136/archdischild-2016-311545] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To identify genetic variants associated with sepsis (early-onset and late-onset) using a genome-wide association (GWA) analysis in a cohort of extremely premature infants. STUDY DESIGN Previously generated GWA data from the Neonatal Research Network's anonymised genomic database biorepository of extremely premature infants were used for this study. Sepsis was defined as culture-positive early-onset or late-onset sepsis or culture-proven meningitis. Genomic and whole-genome-amplified DNA was genotyped for 1.2 million single-nucleotide polymorphisms (SNPs); 91% of SNPs were successfully genotyped. We imputed 7.2 million additional SNPs. p Values and false discovery rates (FDRs) were calculated from multivariate logistic regression analysis adjusting for gender, gestational age and ancestry. Target statistical value was p<10-5. Secondary analyses assessed associations of SNPs with pathogen type. Pathway analyses were also run on primary and secondary end points. RESULTS Data from 757 extremely premature infants were included: 351 infants with sepsis and 406 infants without sepsis. No SNPs reached genome-wide significance levels (5×10-8); two SNPs in proximity to FOXC2 and FOXL1 genes achieved target levels of significance. In secondary analyses, SNPs for ELMO1, IRAK2 (Gram-positive sepsis), RALA, IMMP2L (Gram-negative sepsis) and PIEZO2 (fungal sepsis) met target significance levels. Pathways associated with sepsis and Gram-negative sepsis included gap junctions, fibroblast growth factor receptors, regulators of cell division and interleukin-1-associated receptor kinase 2 (p values<0.001 and FDR<20%). CONCLUSIONS No SNPs met genome-wide significance in this cohort of extremely low birthweight infants; however, areas of potential association and pathways meriting further study were identified.
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Affiliation(s)
- Lakshmi Srinivasan
- Department of Pediatrics, The Children’s Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA
| | - Grier Page
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, NC
| | - Haresh Kirpalani
- Department of Pediatrics, The Children’s Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA
| | | | - Abhik Das
- Social, Statistical and Environmental Sciences Unit, RTI International, Rockville, MD
| | - Rosemary D. Higgins
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Waldemar A. Carlo
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Edward F. Bell
- University of Iowa, Department of Pediatrics, Iowa City, IA
| | | | - Kurt Schibler
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Beena G. Sood
- Department of Pediatrics, Wayne State University, Detroit, MI
| | - David K. Stevenson
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine and Lucile Packard Children’s Hospital, Palo Alto, CA
| | - Barbara J. Stoll
- Emory University School of Medicine, Department of Pediatrics, Children’s Healthcare of Atlanta, Atlanta, GA
| | - Krisa P. Van Meurs
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine and Lucile Packard Children’s Hospital, Palo Alto, CA
| | | | - Joshua Levy
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, NC
| | - Scott A. McDonald
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, NC
| | | | - Kathleen A. Kennedy
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX
| | - Pablo J. Sánchez
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Shahnaz Duara
- University of Miami Miller School of Medicine, Miami, FL
| | - Michele C. Walsh
- Department of Pediatrics, Rainbow Babies & Children’s Hospital, Case Western Reserve University, Cleveland, OH
| | | | - James L. Wynn
- Department of Pediatrics, University of Florida, Gainesville, FL
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Prescott HC, Calfee CS, Thompson BT, Angus DC, Liu VX. Toward Smarter Lumping and Smarter Splitting: Rethinking Strategies for Sepsis and Acute Respiratory Distress Syndrome Clinical Trial Design. Am J Respir Crit Care Med 2017; 194:147-55. [PMID: 27244481 DOI: 10.1164/rccm.201512-2544cp] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Both quality improvement and clinical research efforts over the past few decades have focused on consensus definition of sepsis and acute respiratory distress syndrome (ARDS). Although clinical definitions based on readily available clinical data have advanced recognition and timely use of broad supportive treatments, they likely hinder the identification of more targeted therapies that manipulate select biological mechanisms underlying critical illness. Sepsis and ARDS are by definition heterogeneous, and patients vary in both their underlying biology and their severity of illness. We have long been able to identify subtypes of sepsis and ARDS that confer different prognoses. The key is that we are now on the verge of identifying subtypes that may confer different response to therapy. In this perspective, inspired by a 2015 American Thoracic Society International Conference Symposium entitled "Lumpers and Splitters: Phenotyping in Critical Illness," we highlight promising approaches to uncovering patient subtypes that may predict treatment responsiveness and not just differences in prognosis. We then discuss how this information can be leveraged to improve the success and translatability of clinical trials by using predictive enrichment and other design strategies. Last, we discuss the challenges and limitations to identifying biomarkers and endotypes and incorporating them into routine clinical practice.
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Affiliation(s)
- Hallie C Prescott
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, Michigan.,2 Veterans Affairs Center for Clinical Management Research, Ann Arbor, Michigan
| | - Carolyn S Calfee
- 3 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and.,4 Department of Anesthesia, University of California, San Francisco, San Francisco, California
| | - B Taylor Thompson
- 5 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts
| | - Derek C Angus
- 6 Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
| | - Vincent X Liu
- 7 Division of Research, Kaiser Permanente, Oakland, California
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Maslove DM, Lamontagne F, Marshall JC, Heyland DK. A path to precision in the ICU. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2017; 21:79. [PMID: 28366166 PMCID: PMC5376689 DOI: 10.1186/s13054-017-1653-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Precision medicine is increasingly touted as a groundbreaking new paradigm in biomedicine. In the ICU, the complexity and ambiguity of critical illness syndromes have been identified as fundamental justifications for the adoption of a precision approach to research and practice. Inherently protean diseases states such as sepsis and acute respiratory distress syndrome have manifestations that are physiologically and anatomically diffuse, and that fluctuate over short periods of time. This leads to considerable heterogeneity among patients, and conditions in which a “one size fits all” approach to therapy can lead to widely divergent results. Current ICU therapy can thus be seen as imprecise, with the potential to realize substantial gains from the adoption of precision medicine approaches. A number of challenges still face the development and adoption of precision critical care, a transition that may occur incrementally rather than wholesale. This article describes a few concrete approaches to addressing these challenges. First, novel clinical trial designs, including registry randomized controlled trials and platform trials, suggest ways in which conventional trials can be adapted to better accommodate the physiologic heterogeneity of critical illness. Second, beyond the “omics” technologies already synonymous with precision medicine, the data-rich environment of the ICU can generate complex physiologic signatures that could fuel precision-minded research and practice. Third, the role of computing infrastructure and modern informatics methods will be central to the pursuit of precision medicine in the ICU, necessitating close collaboration with data scientists. As work toward precision critical care continues, small proof-of-concept studies may prove useful in highlighting the potential of this approach.
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Affiliation(s)
- David M Maslove
- Department of Critical Care Medicine, Queen's University, Kingston, ON, Canada. .,Department of Medicine, Queen's University, Kingston, ON, Canada. .,Department of Critical Care Medicine, Kingston General Hospital, Davies 2, 76 Stuart St., Kingston, Ontario, K7L 2V7, Canada.
| | - Francois Lamontagne
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada.,Centre de Recherche du CHU de Sherbrooke, Sherbrooke, QC, Canada.,Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - John C Marshall
- Department of Surgery, University of Toronto, Toronto, ON, Canada.,Interdepartmental Division of Critical Care, University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada
| | - Daren K Heyland
- Department of Critical Care Medicine, Queen's University, Kingston, ON, Canada.,Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, ON, Canada
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Goh C, Knight JC. Enhanced understanding of the host-pathogen interaction in sepsis: new opportunities for omic approaches. THE LANCET. RESPIRATORY MEDICINE 2017; 5:212-223. [PMID: 28266329 DOI: 10.1016/s2213-2600(17)30045-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/14/2016] [Accepted: 01/20/2017] [Indexed: 12/12/2022]
Abstract
Progress in sepsis research has been severely hampered by a heterogeneous disease phenotype, limiting the interpretation of clinical trials and the development of effective therapeutic interventions. Application of omics-based methodologies is advancing understanding of the dysregulated host immune response to infection in sepsis. However, the frequently elusive nature of the infecting organism in sepsis has limited efforts to understand the effect of disease heterogeneity involving the pathogen. Recent advances in nucleic acid sequencing-based pathogen analysis provide the opportunity for more accurate and comprehensive microbiological diagnosis. In this Review, we explore how better understanding of the host-pathogen interaction can substantially enhance, and in turn benefit from, current and future application of omics-based approaches to understand the host response in sepsis. We illustrate this using recent work accounting for heterogeneity involving the pathogen. We propose that there is a timely opportunity to further resolve sepsis heterogeneity by considering host-pathogen interactions, enabling progress towards a precision medicine approach.
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Affiliation(s)
- Cyndi Goh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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Masica DL, Dal Molin M, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Irene Canto M, Pittman M, Eshleman JR, Ali SZ, Fishman EK, Kamel IR, Raman SP, Zaheer A, Ahuja N, Makary MA, Weiss MJ, Hirose K, Cameron JL, Rezaee N, He J, Joon Ahn Y, Wu W, Wang Y, Springer S, Diaz LL, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Lennon AM. A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts. J Am Med Inform Assoc 2017; 24:145-152. [PMID: 27330075 PMCID: PMC5201184 DOI: 10.1093/jamia/ocw069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/02/2016] [Accepted: 04/07/2016] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Our objective was to develop an approach for selecting combinatorial markers of pathology from diverse clinical data types. We demonstrate this approach on the problem of pancreatic cyst classification. MATERIALS AND METHODS We analyzed 1026 patients with surgically resected pancreatic cysts, comprising 584 intraductal papillary mucinous neoplasms, 332 serous cystadenomas, 78 mucinous cystic neoplasms, and 42 solid-pseudopapillary neoplasms. To derive optimal markers for cyst classification from the preoperative clinical and radiological data, we developed a statistical approach for combining any number of categorical, dichotomous, or continuous-valued clinical parameters into individual predictors of pathology. The approach is unbiased and statistically rigorous. Millions of feature combinations were tested using 10-fold cross-validation, and the most informative features were validated in an independent cohort of 130 patients with surgically resected pancreatic cysts. RESULTS We identified combinatorial clinical markers that classified serous cystadenomas with 95% sensitivity and 83% specificity; solid-pseudopapillary neoplasms with 89% sensitivity and 86% specificity; mucinous cystic neoplasms with 91% sensitivity and 83% specificity; and intraductal papillary mucinous neoplasms with 94% sensitivity and 90% specificity. No individual features were as accurate as the combination markers. We further validated these combinatorial markers on an independent cohort of 130 pancreatic cysts, and achieved high and well-balanced accuracies. Overall sensitivity and specificity for identifying patients requiring surgical resection was 84% and 81%, respectively. CONCLUSIONS Our approach identified combinatorial markers for pancreatic cyst classification that had improved performance relative to the individual features they comprise. In principle, this approach can be applied to any clinical dataset comprising dichotomous, categorical, and continuous-valued parameters.
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Affiliation(s)
- David L Masica
- *Drs Masica and Dal Molin contributed equally as first authors
- Department of Biomedical Engineering and the Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
- Departments of the Sol Goldman Pancreatic Cancer Research Center
| | - Marco Dal Molin
- *Drs Masica and Dal Molin contributed equally as first authors
- Departments of Pathology
- Departments of the Sol Goldman Pancreatic Cancer Research Center
| | - Christopher L Wolfgang
- Departments of Surgery
- Departments of Oncology
- Departments of the Sol Goldman Pancreatic Cancer Research Center
| | - Tyler Tomita
- Department of Biomedical Engineering and the Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | | | | | | | | | | | - Michael Goggins
- Departments of Medicine
- Departments of Oncology
- Departments of the Sol Goldman Pancreatic Cancer Research Center
| | | | - Meredith Pittman
- Departments of Pathology
- Departments of the Sol Goldman Pancreatic Cancer Research Center
| | - James R Eshleman
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yuxuan Wang
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Simeon Springer
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Luis L Diaz
- Departments of Surgery
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ralph H Hruban
- Departments of Pathology
- Departments of Oncology
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Kenneth W Kinzler
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Bert Vogelstein
- Departments of the Sol Goldman Pancreatic Cancer Research Center
- Departments of the Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Rachel Karchin
- †Drs Lennon and Karchin contributed equally as senior authors
- Department of Biomedical Engineering and the Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
- Departments of Oncology
- Departments of the Sol Goldman Pancreatic Cancer Research Center
| | - Anne Marie Lennon
- †Drs Lennon and Karchin contributed equally as senior authors
- Departments of Surgery
- Departments of Medicine
- Departments of the Sol Goldman Pancreatic Cancer Research Center
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Reilly JP, Meyer NJ, Christie JD. Genetics in the Prevention and Treatment of Sepsis. SEPSIS 2017. [DOI: 10.1007/978-3-319-48470-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Genomic Insights Into Sepsis Course Using Whole Exome Sequencing. EBioMedicine 2016; 12:18-19. [PMID: 27688093 PMCID: PMC5078624 DOI: 10.1016/j.ebiom.2016.09.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
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Taudien S, Lausser L, Giamarellos-Bourboulis EJ, Sponholz C, Schöneweck F, Felder M, Schirra LR, Schmid F, Gogos C, Groth S, Petersen BS, Franke A, Lieb W, Huse K, Zipfel PF, Kurzai O, Moepps B, Gierschik P, Bauer M, Scherag A, Kestler HA, Platzer M. Genetic Factors of the Disease Course After Sepsis: Rare Deleterious Variants Are Predictive. EBioMedicine 2016; 12:227-238. [PMID: 27639823 PMCID: PMC5078585 DOI: 10.1016/j.ebiom.2016.08.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/20/2022] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. For its clinical course, host genetic factors are important and rare genomic variants are suspected to contribute. We sequenced the exomes of 59 Greek and 15 German patients with bacterial sepsis divided into two groups with extremely different disease courses. Variant analysis was focusing on rare deleterious single nucleotide variants (SNVs). We identified significant differences in the number of rare deleterious SNVs per patient between the ethnic groups. Classification experiments based on the data of the Greek patients allowed discrimination between the disease courses with estimated sensitivity and specificity > 75%. By application of the trained model to the German patients we observed comparable discriminatory properties despite lower population-specific rare SNV load. Furthermore, rare SNVs in genes of cell signaling and innate immunity related pathways were identified as classifiers discriminating between the sepsis courses. Sepsis patients with favorable disease course after sepsis, even in the case of unfavorable preconditions, seem to be affected more often by rare deleterious SNVs in cell signaling and innate immunity related pathways, suggesting a protective role of impairments in these processes against a poor disease course. Rare SNV load is higher in the Greek vs. German population. Subsets of rare deleterious SNVs are predictive for the disease course after sepsis. Patients with favorable disease course seem to carry protective deleterious variants in sepsis related pathways.
Sepsis is a life-threatening disease caused by improper response to infection. Only little is known about the role of genetic factors. From > 4000 patients we selected the most extreme cases showing either a favorable or adverse disease course. We determined rare (< 1/200) protein-damaging genetic variants, as they may have a large effect. Using a computational model that includes knowledge on genes we can predict the disease course with > 75% accuracy. Surprisingly, favorable courses can be expected if defense mechanisms are damaged and prevented from overshooting. This underlines the relevance of rare variants for better understanding of sepsis and may offer new treatment options.
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Affiliation(s)
- Stefan Taudien
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Ludwig Lausser
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany
| | - Evangelos J Giamarellos-Bourboulis
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Christoph Sponholz
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Florian Schmid
- Institute of Medical Systems Biology, Ulm University, Germany
| | - Charalambos Gogos
- Department of Internal Medicine, University of Patras, Medical School, Greece
| | - Susann Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Klaus Huse
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Peter F Zipfel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany; Friedrich Schiller University Jena, Jena, Germany
| | - Oliver Kurzai
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Septomics Research Center Jena, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Barbara Moepps
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Peter Gierschik
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - André Scherag
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Hans A Kestler
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany; Friedrich Schiller University Jena, Jena, Germany.
| | - Matthias Platzer
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.
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Genetic Factors of the Disease Course after Sepsis: A Genome-Wide Study for 28Day Mortality. EBioMedicine 2016; 12:239-246. [PMID: 27639821 PMCID: PMC5078589 DOI: 10.1016/j.ebiom.2016.08.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/30/2022] Open
Abstract
Sepsis is the dysregulated host response to an infection which leads to life-threatening organ dysfunction that varies by host genomic factors. We conducted a genome-wide association study (GWAS) in 740 adult septic patients and focused on 28 day mortality as outcome. Variants with suggestive evidence for an association (p ≤ 10− 5) were validated in two additional GWA studies (n = 3470) and gene coding regions related to the variants were assessed in an independent exome sequencing study (n = 74). In the discovery GWAS, we identified 243 autosomal variants which clustered in 14 loci (p ≤ 10− 5). The best association signal (rs117983287; p = 8.16 × 10− 8) was observed for a missense variant located at chromosome 9q21.2 in the VPS13A gene. VPS13A was further supported by additional GWAS (p = 0.03) and sequencing data (p = 0.04). Furthermore, CRISPLD2 (p = 5.99 × 10− 6) and a region on chromosome 13q21.33 (p = 3.34 × 10− 7) were supported by both our data and external biological evidence. We found 14 loci with suggestive evidence for an association with 28 day mortality and found supportive, converging evidence for three of them in independent data sets. Elucidating the underlying biological mechanisms of VPS13A, CRISPLD2, and the chromosome 13 locus should be a focus of future research activities. A low frequency missense variant in VPS13A on chromosome 9q21.2 was associated with 28 day mortality after sepsis A frequent intronic variant in CRISPLD2 was also supported and was reported to be associated with procalcitonin levels Similarly supported was an intergenic frequent variant on chromosome13q21.33 – a region related to chronic kidney disease
Sepsis is the dysregulated host response to an infection which leads to life-threatening organ dysfunction that is known to vary by host genomic factors. However, the detection of genetic variants related to sepsis outcomes has been challenging so far. We conducted a discovery genome-wide association study (GWAS) in 740 adult patients with sepsis looking for variants that vary with 28 day mortality. We followed-up our best findings by additional GWAS and exome sequencing data in 3544 adult patients and report three regions including the genes VPS13A and CRISPLD2 that were supported by our data and external biological evidence.
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Vincent JL. Individual gene expression and personalised medicine in sepsis. THE LANCET RESPIRATORY MEDICINE 2016; 4:242-3. [DOI: 10.1016/s2213-2600(16)00068-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/29/2022]
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Abstract
Sepsis is a major cause of neonatal morbidity and mortality, especially in vulnerable preterm populations. Immature immune defenses, and environmental and maternal factors contribute to this risk, with as many as a third of very preterm infants experiencing sepsis during their stay in the neonatal intensive care unit (NICU). Epidemiologic and twin studies have suggested that there is a genetic contribution to sepsis predilection. Several investigators have conducted candidate gene association studies on variants of specific interest and potential functional significance in neonatal sepsis. In this review, we describe details of studies that have evaluated genetic susceptibility in neonatal sepsis, and summarize findings from a review of candidate gene association studies.
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Affiliation(s)
- Lakshmi Srinivasan
- Department of Pediatrics, The Children's Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, PA.
| | - Haresh Kirpalani
- Department of Pediatrics, The Children's Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, PA
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Pharmacometabolomics of l-carnitine treatment response phenotypes in patients with septic shock. Ann Am Thorac Soc 2015; 12:46-56. [PMID: 25496487 DOI: 10.1513/annalsats.201409-415oc] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RATIONALE Sepsis therapeutics have a poor history of success in clinical trials, due in part to the heterogeneity of enrolled patients. Pharmacometabolomics could differentiate drug response phenotypes and permit a precision medicine approach to sepsis. OBJECTIVES To use existing serum samples from the phase 1 clinical trial of l-carnitine treatment for severe sepsis to metabolically phenotype l-carnitine responders and nonresponders. METHODS Serum samples collected before (T0) and after completion of the infusion (T24, T48) from patients randomized to either l-carnitine (12 g) or placebo for the treatment of vasopressor-dependent septic shock were assayed by untargeted (1)H-nuclear magnetic resonance metabolomics. The normalized, quantified metabolite data sets of l-carnitine- and placebo-treated patients at each time point were compared by analysis of variance with post-hoc testing for multiple comparisons. Pathway analysis was performed to statistically rank metabolic networks. MEASUREMENTS AND MAIN RESULTS Thirty-eight metabolites were identified in all samples. Concentrations of 3-hydroxybutyrate, acetoacetate, and 3-hydroxyisovalerate were different at T0 and over time in l-carnitine-treated survivors versus nonsurvivors. Pathway analysis of pretreatment metabolites revealed that synthesis and degradation of ketone bodies had the greatest impact in differentiating l-carnitine treatment response. Analysis of all patients based on pretreatment 3-hydroxybutyrate concentration yielded distinct phenotypes. Using the T0 median 3-hydroxybutyrate level (153 μM), patients were categorized as either high or low ketone. l-Carnitine-treated low-ketone patients had greater use of carnitine as evidenced by lower post-treatment l-carnitine levels. The l-carnitine responders also had faster resolution of vasopressor requirement and a trend toward a greater improvement in mortality at 1 year (P = 0.038) compared with patients with higher 3-hydroxybutyrate. CONCLUSIONS The results of this preliminary study, which were not readily apparent from the parent clinical trial, show a unique metabolite profile of l-carnitine responders and introduce pharmacometabolomics as a viable strategy for informing l-carnitine responsiveness. The approach taken in this study represents a concrete example for the application of precision medicine to sepsis therapeutics that warrants further study.
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Schlapbach LJ, Giannoni E, Wellmann S, Stocker M, Ammann RA, Graf R. Normal values for pancreatic stone protein in different age groups. BMC Anesthesiol 2015; 15:168. [PMID: 26588901 PMCID: PMC4654823 DOI: 10.1186/s12871-015-0149-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022] Open
Abstract
Background Pancreatic stone protein (PSP) has been identified as a promising sepsis marker in adults, children and neonates. However, data on population-based reference values are lacking. This study aimed to establish age-specific reference values for PSP. Methods PSP was determined using a specific ELISA. PSP serum concentrations were determined in 372 healthy subjects including 217 neonates, 94 infants and children up to 16 years, and 61 adults. The adjacent categories method was used to determine which age categories had significantly different PSP concentrations. Results PSP circulating levels were not gender-dependent and ranged from 1.0 to 99.4 ng/ml with a median of 9.2 ng/ml. PSP increased significantly between the age categories, from a median of 2.6 ng/ml in very preterm newborns, to 6.3 ng/ml in term newborns, to 16.1 ng/ml in older children (p < 0.001). PSP levels were higher on postnatal day three compared to levels measured immediately post delivery (p < 0.001). Paired umbilical artery and umbilical vein samples were strongly correlated (p < 0.001). Simultaneously obtained capillary heel-prick versus venous samples showed a good level of agreement for PSP (Rho 0.89, bias 19 %). Conclusions This study provides age-specific normal values that may be used to define cut-offs for future trials on PSP. We demonstrate an age-dependent increase of PSP from birth to childhood.
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Affiliation(s)
- Luregn J Schlapbach
- Mater Research Institute, Paediatric Critical Care Research Group, University of Queensland, Brisbane, Australia. .,Paediatric Intensive Care Unit, Lady Cilento Children's Hospital, Children's Health Queensland, South Brisbane, QLD, 4101, Australia. .,Department of Pediatrics, University of Bern, Bern, Switzerland.
| | - Eric Giannoni
- Service of Neonatology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland. .,Infectious Diseases Service, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland.
| | - Sven Wellmann
- Department of Neonatology, University Children's Hospital Basel, Basel, Switzerland.
| | - Martin Stocker
- Neonatal and Pediatric Intensive Care Unit, Children's Hospital Lucerne, Lucerne, Switzerland.
| | - Roland A Ammann
- Department of Pediatrics, University of Bern, Bern, Switzerland.
| | - Rolf Graf
- Department of Surgery, Swiss HPB Center, University Hospital Zurich, Zurich, Switzerland.
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Cardoso CP, de Oliveira AJDA, Botoni FA, Rezende ICP, Alves-Filho JC, Cunha FDQ, Estanislau JDASG, Magno LAV, Rios-Santos F. Interleukin-10 rs2227307 and CXCR2 rs1126579 polymorphisms modulate the predisposition to septic shock. Mem Inst Oswaldo Cruz 2015; 110:453-60. [PMID: 26038959 PMCID: PMC4501407 DOI: 10.1590/0074-02760150003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022] Open
Abstract
Despite major improvements in its treatment and diagnosis, sepsis is still a leading
cause of death and admittance to the intensive care unit (ICU). Failure to identify
patients at high risk of developing septic shock contributes to an increase in the
sepsis burden and rapid molecular tests are currently the most promising avenue to
aid in patient risk determination and therapeutic anticipation. The primary goal of
this study was to evaluate the genetic susceptibility that affects sepsis outcome in
72 sepsis patients admitted to the ICU. Seven polymorphisms were genotyped in key
inflammatory response genes in sepsis, including tumour necrosis
factor-α, interlelukin (IL)-1β, IL-10,
IL-8, Toll-like receptor 4,
CXCR1 and CXCR2. The primary finding showed that
patients who were homozygous for the major A allele in IL-10
rs1800896 had almost five times higher chance to develop septic shock compared to
heterozygotes. Similarly, selected clinical features and CXCR2
rs1126579 single nucleotide polymorphisms modulated septic shock susceptibility
without affecting survival. These data support the hypothesis that molecular testing
has clinical usefulness to improve sepsis prognostic models. Therefore, enrichment of
the ICU portfolio by including these biomarkers will aid in the early identification
of sepsis patients who may develop septic shock.
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Affiliation(s)
- Cristina Padre Cardoso
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brasil
| | | | | | - Isabela Cristina Porto Rezende
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Jose Carlos Alves-Filho
- Departamento de Farmacologia, Escola de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Fernando de Queiroz Cunha
- Departamento de Farmacologia, Escola de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | | | - Luiz Alexandre Viana Magno
- Instituto Nacional de Ciência e Tecnologia de Medicina Molecular, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Fabricio Rios-Santos
- Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brasil
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Mills TC, Chapman S, Hutton P, Gordon AC, Bion J, Chiche JD, Holloway PAH, Stüber F, Garrard CS, Hinds CJ, Hill AVS, Rautanen A. Variants in the Mannose-binding Lectin Gene MBL2 do not Associate With Sepsis Susceptibility or Survival in a Large European Cohort. Clin Infect Dis 2015; 61:695-703. [PMID: 25969530 PMCID: PMC4530723 DOI: 10.1093/cid/civ378] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/05/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Sepsis is an increasingly common condition, which continues to be associated with unacceptably high mortality. A large number of association studies have investigated susceptibility to, or mortality from, sepsis for variants in the functionally important immune-related gene MBL2. These studies have largely been underpowered and contradictory. METHODS We genotyped and analyzed 4 important MBL2 single nucleotide polymorphisms (SNPs; rs5030737, rs1800450, rs1800451, and rs7096206) in 1839 European community-acquired pneumonia (CAP) and peritonitis sepsis cases, and 477 controls from the United Kingdom. We analyzed the following predefined subgroups and outcomes: 28-day and 6 month mortality from sepsis due to CAP or peritonitis combined, 28-day mortality from CAP sepsis, peritonitis sepsis, pneumococcal sepsis or sepsis in younger patients, and susceptibility to CAP sepsis or pneumococcal sepsis in the United Kingdom. RESULTS There were no significant associations (all P-values were greater than .05 after correction for multiple testing) between MBL2 genotypes and any of our predefined analyses. CONCLUSIONS In this large, well-defined cohort of immune competent adult patients, no associations between MBL2 genotype and sepsis susceptibility or outcome were identified.
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Affiliation(s)
- Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Stephen Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford
| | | | - Anthony C Gordon
- Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London
| | - Julian Bion
- School of Clinical and Experimental Medicine, University of Birmingham, United Kingdom
| | | | - Paul A H Holloway
- Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London
| | - Frank Stüber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital and University of Bern, Switzerland
| | | | - Charles J Hinds
- Barts and The London School of Medicine Queen Mary University of London, United Kingdom
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford
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Finding a needle in the haystack: leveraging bioinformatics to identify a functional genetic risk factor for sepsis death. Crit Care Med 2015; 43:242-3. [PMID: 25514715 DOI: 10.1097/ccm.0000000000000664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Rautanen A, Mills TC, Gordon AC, Hutton P, Steffens M, Nuamah R, Chiche JD, Parks T, Chapman SJ, Davenport EE, Elliott KS, Bion J, Lichtner P, Meitinger T, Wienker TF, Caulfield MJ, Mein C, Bloos F, Bobek I, Cotogni P, Sramek V, Sarapuu S, Kobilay M, Ranieri VM, Rello J, Sirgo G, Weiss YG, Russwurm S, Schneider EM, Reinhart K, Holloway PAH, Knight JC, Garrard CS, Russell JA, Walley KR, Stüber F, Hill AVS, Hinds CJ. Genome-wide association study of survival from sepsis due to pneumonia: an observational cohort study. THE LANCET. RESPIRATORY MEDICINE 2015; 3:53-60. [PMID: 25533491 PMCID: PMC4314768 DOI: 10.1016/s2213-2600(14)70290-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sepsis continues to be a major cause of death, disability, and health-care expenditure worldwide. Despite evidence suggesting that host genetics can influence sepsis outcomes, no specific loci have yet been convincingly replicated. The aim of this study was to identify genetic variants that influence sepsis survival. METHODS We did a genome-wide association study in three independent cohorts of white adult patients admitted to intensive care units with sepsis, severe sepsis, or septic shock (as defined by the International Consensus Criteria) due to pneumonia or intra-abdominal infection (cohorts 1-3, n=2534 patients). The primary outcome was 28 day survival. Results for the cohort of patients with sepsis due to pneumonia were combined in a meta-analysis of 1553 patients from all three cohorts, of whom 359 died within 28 days of admission to the intensive-care unit. The most significantly associated single nucleotide polymorphisms (SNPs) were genotyped in a further 538 white patients with sepsis due to pneumonia (cohort 4), of whom 106 died. FINDINGS In the genome-wide meta-analysis of three independent pneumonia cohorts (cohorts 1-3), common variants in the FER gene were strongly associated with survival (p=9·7 × 10(-8)). Further genotyping of the top associated SNP (rs4957796) in the additional cohort (cohort 4) resulted in a combined p value of 5·6 × 10(-8) (odds ratio 0·56, 95% CI 0·45-0·69). In a time-to-event analysis, each allele reduced the mortality over 28 days by 44% (hazard ratio for death 0·56, 95% CI 0·45-0·69; likelihood ratio test p=3·4 × 10(-9), after adjustment for age and stratification by cohort). Mortality was 9·5% in patients carrying the CC genotype, 15·2% in those carrying the TC genotype, and 25·3% in those carrying the TT genotype. No significant genetic associations were identified when patients with sepsis due to pneumonia and intra-abdominal infection were combined. INTERPRETATION We have identified common variants in the FER gene that associate with a reduced risk of death from sepsis due to pneumonia. The FER gene and associated molecular pathways are potential novel targets for therapy or prevention and candidates for the development of biomarkers for risk stratification. FUNDING European Commission and the Wellcome Trust.
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Affiliation(s)
- Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Michael Steffens
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE) of the University of Bonn, Bonn, Germany
| | - Rosamond Nuamah
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | | | - Tom Parks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen J Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Julian Bion
- School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Technische Universität München, Institute of Human Genetics, Munich, Germany
| | - Thomas F Wienker
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE) of the University of Bonn, Bonn, Germany
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | - Charles Mein
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | - Frank Bloos
- Jena University Hospital and Center for Sepsis Control and Care, Jena, Germany
| | - Ilona Bobek
- National Health Service Centre, Budapest, Hungary
| | | | | | | | | | | | - Jordi Rello
- CIBERES, Vall d'Hebron Institute of Research, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Gonzalo Sirgo
- Joan XXIII University Hospital, Pere Virgili Health Institute, University Rovirai Virgili, Tarragona, Spain
| | | | | | - E Marion Schneider
- Section of Experimental Anesthesiology, University Hospital, Ulm, Germany
| | - Konrad Reinhart
- Jena University Hospital and Center for Sepsis Control and Care, Jena, Germany
| | | | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | - Frank Stüber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital, and University of Bern, Switzerland
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Charles J Hinds
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
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Meyer NJ, Ferguson JF, Feng R, Wang F, Patel PN, Li M, Xue C, Qu L, Liu Y, Boyd JH, Russell JA, Christie JD, Walley KR, Reilly MP. A functional synonymous coding variant in the IL1RN gene is associated with survival in septic shock. Am J Respir Crit Care Med 2014; 190:656-64. [PMID: 25089931 DOI: 10.1164/rccm.201403-0586oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RATIONALE Death from infection is a highly heritable trait, yet there are few genetic variants with known mechanism influencing survival during septic shock. OBJECTIVES We hypothesized that a synonymous coding variant in the IL-1 receptor antagonist gene (IL1RN), rs315952, previously associated with reduced risk for acute respiratory distress syndrome, would be functional and associate with improved survival in septic shock. METHODS We used a human endotoxin (LPS) model of evoked inflammatory stress to measure plasma IL-1 receptor antagonist (IL1RA) following low-dose Food and Drug Administration-grade LPS injection (1 ng/kg) in 294 human volunteers. RNA sequencing of adipose tissue pre- and post-LPS was used to test for allelic imbalance at rs315952. In the Vasopressin and Septic Shock Trial cohort, we performed a genetic association study for survival, mortality, and organ failure-free days. MEASUREMENTS AND MAIN RESULTS Adipose tissue displayed significant allelic imbalance favoring the rs315952C allele in subjects of European ancestry. Consistent with this, carriers of rs315952C had slightly higher plasma IL1RA at baseline (0.039) and higher evoked IL1RA post-LPS (0.011). In the Vasopressin and Septic Shock Trial cohort, rs315952C associated with improved survival (P = 0.028), decreased adjusted 90-day mortality (P = 0.044), and faster resolution of shock (P = 0.029). CONCLUSIONS In European ancestry subjects, the IL1RN variant rs315952C is preferentially transcribed and associated with increased evoked plasma IL1RA and with improved survival from septic shock. It may be that genetically determined IL1RA levels influence survival from septic shock.
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Affiliation(s)
- Nuala J Meyer
- 1 Center for Translational Lung Biology, Pulmonary, Allergy, and Critical Care Division
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State-of-the-Art Technologies to Interrogate Genetic/Genomic Components of Drug Response. CURRENT GENETIC MEDICINE REPORTS 2013. [DOI: 10.1007/s40142-013-0022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rietveld CA, Medland SE, Derringer J, Yang J, Esko T, Martin NW, Westra HJ, Shakhbazov K, Abdellaoui A, Agrawal A, Albrecht E, Alizadeh BZ, Amin N, Barnard J, Baumeister SE, Benke KS, Bielak LF, Boatman JA, Boyle PA, Davies G, de Leeuw C, Eklund N, Evans DS, Ferhmann R, Fischer K, Gieger C, Gjessing HK, Hägg S, Harris JR, Hayward C, Holzapfel C, Ibrahim-Verbaas CA, Ingelsson E, Jacobsson B, Joshi PK, Jugessur A, Kaakinen M, Kanoni S, Karjalainen J, Kolcic I, Kristiansson K, Kutalik Z, Lahti J, Lee SH, Lin P, Lind PA, Liu Y, Lohman K, Loitfelder M, McMahon G, Vidal PM, Meirelles O, Milani L, Myhre R, Nuotio ML, Oldmeadow CJ, Petrovic KE, Peyrot WJ, Polašek O, Quaye L, Reinmaa E, Rice JP, Rizzi TS, Schmidt H, Schmidt R, Smith AV, Smith JA, Tanaka T, Terracciano A, van der Loos MJ, Vitart V, Völzke H, Wellmann J, Yu L, Zhao W, Allik J, Attia JR, Bandinelli S, Bastardot F, Beauchamp J, Bennett DA, Berger K, Bierut LJ, Boomsma DI, Bültmann U, Campbell H, Chabris CF, Cherkas L, Chung MK, Cucca F, de Andrade M, De Jager PL, De Neve JE, Deary IJ, Dedoussis GV, Deloukas P, Dimitriou M, Eiriksdottir G, Elderson MF, Eriksson JG, Evans DM, Faul JD, Ferrucci L, Garcia ME, Grönberg H, Gudnason V, Hall P, Harris JM, Harris TB, Hastie ND, Heath AC, Hernandez DG, Hoffmann W, Hofman A, Holle R, Holliday EG, Hottenga JJ, Iacono WG, Illig T, Järvelin MR, Kähönen M, Kaprio J, Kirkpatrick RM, Kowgier M, Latvala A, Launer LJ, Lawlor DA, Lehtimäki T, Li J, Lichtenstein P, Lichtner P, Liewald DC, Madden PA, Magnusson PKE, Mäkinen TE, Masala M, McGue M, Metspalu A, Mielck A, Miller MB, Montgomery GW, Mukherjee S, Nyholt DR, Oostra BA, Palmer LJ, Palotie A, Penninx B, Perola M, Peyser PA, Preisig M, Räikkönen K, Raitakari OT, Realo A, Ring SM, Ripatti S, Rivadeneira F, Rudan I, Rustichini A, Salomaa V, Sarin AP, Schlessinger D, Scott RJ, Snieder H, Pourcain BS, Starr JM, Sul JH, Surakka I, Svento R, Teumer A, Tiemeier H, Rooij FJA, Van Wagoner DR, Vartiainen E, Viikari J, Vollenweider P, Vonk JM, Waeber G, Weir DR, Wichmann HE, Widen E, Willemsen G, Wilson JF, Wright AF, Conley D, Davey-Smith G, Franke L, Groenen PJF, Hofman A, Johannesson M, Kardia SL, Krueger RF, Laibson D, Martin NG, Meyer MN, Posthuma D, Thurik AR, Timpson NJ, Uitterlinden AG, van Duijn CM, Visscher PM, Benjamin DJ, Cesarini D, Koellinger PD. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science 2013; 340:1467-71. [PMID: 23722424 PMCID: PMC3751588 DOI: 10.1126/science.1235488] [Citation(s) in RCA: 484] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) ≈ 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ≈2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.
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Affiliation(s)
- Cornelius A. Rietveld
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Sarah E. Medland
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Jaime Derringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO 80309–0447, USA
| | - Jian Yang
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Nicolas W. Martin
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
- School of Psychology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Konstantin Shakhbazov
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - John Barnard
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Kelly S. Benke
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Jeffrey A. Boatman
- Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patricia A. Boyle
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Gail Davies
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Christiaan de Leeuw
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Niina Eklund
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA 94107–1728, USA
| | - Rudolf Ferhmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Håkon K. Gjessing
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Sara Hägg
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jennifer R. Harris
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Christina Holzapfel
- Else Kroener-Fresenius-Centre for Nutritional Medicine, Technische Universität München, 81675 Munich, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Carla A. Ibrahim-Verbaas
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Department of Neurology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Erik Ingelsson
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Bo Jacobsson
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
- Department of Obstetrics and Gynecology, Institute of Public Health, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, 413 45, Sweden
| | - Peter K. Joshi
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Astanand Jugessur
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Marika Kaakinen
- Institute of Health Sciences, University of Oulu, Oulu 90014, Finland
- Biocenter Oulu, University of Oulu, Oulu 90014, Finland
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Juha Karjalainen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Kati Kristiansson
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jari Lahti
- Institute of Behavioral Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Sang H. Lee
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Peng Lin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Penelope A. Lind
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157–1063, USA
| | - Kurt Lohman
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157–1063, USA
| | - Marisa Loitfelder
- Division for Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz 8036, Austria
| | - George McMahon
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Pedro Marques Vidal
- Institute of Social and Preventive Medicine, Lausanne University Hospital, 1005 Lausanne, Switzerland
| | - Osorio Meirelles
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Ronny Myhre
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Marja-Liisa Nuotio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Christopher J. Oldmeadow
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Katja E. Petrovic
- Division of General Neurology, Department of Neurology, General Hospital and Medical University of Graz, Graz 8036, Austria
| | - Wouter J. Peyrot
- Department of Psychiatry, VU University Medical Center, 1081 HL Amsterdam, The Netherlands
| | - Ozren Polašek
- Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Lydia Quaye
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - John P. Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thais S. Rizzi
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz 8036, Austria
| | - Reinhold Schmidt
- Division for Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz 8036, Austria
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur 201, Iceland
- Department of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Antonio Terracciano
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
- College of Medicine, Florida State University, Tallahassee, FL 32306–4300, USA
| | - Matthijs J.H.M. van der Loos
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Veronique Vitart
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Jürgen Wellmann
- Institute of Epidemiology and Social Medicine, University of Muenster, 48129 Muenster, Germany
| | - Lei Yu
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Jüri Allik
- Department of Psychology, University of Tartu, Tartu 50410, Estonia
| | - John R. Attia
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | | | - François Bastardot
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | | | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Muenster, 48129 Muenster, Germany
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Ute Bültmann
- Department of Health Sciences, Community & Occupational Medicine, University Medical Center Groningen, 9700 AD Groningen, The Netherlands
| | - Harry Campbell
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Lynn Cherkas
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Mina K. Chung
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 SS, Italy
| | - Mariza de Andrade
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Philip L. De Jager
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jan-Emmanuel De Neve
- School of Public Policy, University College London, London WC1H 9QU, UK
- Centre for Economic Performance, London School of Economics, London WC2A 2AE, UK
| | - Ian J. Deary
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
- Department of Psychology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - George V. Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Maria Dimitriou
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | | | - Martin F. Elderson
- LifeLines Cohort Study, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki 00014, Finland
- Unit of General Practice, Helsinki University Central Hospital, Helsinki 00280, Finland
- Folkhälsan Research Center, Helsinki 00250, Finland
- Vaasa Central Hospital, Vaasa 65130, Finland
| | - David M. Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Melissa E. Garcia
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur 201, Iceland
- Department of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Juliette M. Harris
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Nicholas D. Hastie
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew C. Heath
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63110–1093, USA
| | - Dena G. Hernandez
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Wolfgang Hoffmann
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Adriaan Hofman
- Faculty of Behavioral and Social Sciences, University of Groningen, 9747 AD Groningen, The Netherlands
| | - Rolf Holle
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Elizabeth G. Holliday
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - William G. Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Marjo-Riitta Järvelin
- Institute of Health Sciences, University of Oulu, Oulu 90014, Finland
- Biocenter Oulu, University of Oulu, Oulu 90014, Finland
- Department of Epidemiology and Biostatistics, MRC-HPA Centre for Environment and Health, Imperial College London, London W2 1PG, UK
- Unit of Primary Care, Oulu University Hospital, Oulu 90220, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu 90101, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere 33520, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
- Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | | | - Matthew Kowgier
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Antti Latvala
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
- Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | - Lenore J. Launer
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Debbie A. Lawlor
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere University Hospital, Tampere 33520, Finland
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David C. Liewald
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Pamela A. Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Tomi E. Mäkinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Andreas Mielck
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Michael B. Miller
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Grant W. Montgomery
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Sutapa Mukherjee
- Western Australia Sleep Disorders Research Institute, Sir Charles Gairdner Hospital, Perth, Western Australia 6009, Australia
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Women’s College Research Institute, University of Toronto, Toronto, Ontario M5G 1N8, Canada
| | - Dale R. Nyholt
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Ben A. Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Lyle J. Palmer
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Medical Genetics, University of Helsinki, 00014 Helsinki, Finland
| | - Brenda Penninx
- Department of Psychiatry, VU University Medical Center, 1081 HL Amsterdam, The Netherlands
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Martin Preisig
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - Katri Räikkönen
- Institute of Behavioral Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - Anu Realo
- Department of Psychology, University of Tartu, Tartu 50410, Estonia
| | - Susan M. Ring
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Aldo Rustichini
- Department of Economics, University of Minnesota, Minneapolis, MN 55455–0462, USA
| | - Veikko Salomaa
- Chronic Disease Epidemiology Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Rodney J. Scott
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Beate St Pourcain
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - John M. Starr
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Jae Hoon Sul
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Ida Surakka
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Rauli Svento
- Department of Economics, Oulu Business School, University of Oulu, Oulu 90014, Finland
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald 17487, Germany
| | | | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
| | - Frank JAan Rooij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - David R. Van Wagoner
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Erkki Vartiainen
- Division of Welfare and Health Promotion, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Jorma Viikari
- Department of Medicine, Turku University Hospital, Turku 20520, Finland
| | - Peter Vollenweider
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - Judith M. Vonk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Gérard Waeber
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - H.-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
- Klinikum Grosshadern, 81377 Munich, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - James F. Wilson
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Alan F. Wright
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Dalton Conley
- Department of Sociology, New York University, New York, NY 10012, USA
| | - George Davey-Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Patrick J. F. Groenen
- Econometric Institute, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam 3000 DR, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm 113 83, Sweden
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Robert F. Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - David Laibson
- Department of Economics, Harvard University, Cambridge, MA 02138, USA
| | - Nicholas G. Martin
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Michelle N. Meyer
- Petrie-Flom Center for Health Law Policy, Biotechnology, & Bioethics, Harvard Law School, Cambridge, MA 02138, USA
- Nelson A. Rockefeller Institute of Government, State University of New York, Albany, NY 12203–1003, USA
| | - Danielle Posthuma
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
- Department of Clinical Genetics, VU University Medical Centrer, 1081 BT Amsterdam, The Netherlands
| | - A. Roy Thurik
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Panteia, Zoetermeer 2701 AA, Netherlands
- GSCM-Montpellier Business School, Montpellier 34185, France
| | - Nicholas J. Timpson
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Centre for Medical Systems Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Peter M. Visscher
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - David Cesarini
- Center for Experimental Social Science, Department of Economics, New York University, New York, NY 10012, USA
- Division of Social Science, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, UAE
- Research Institute of Industrial Economics, Stockholm 102 15, Sweden
| | - Philipp D. Koellinger
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
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Harper AR, Topol EJ. Pharmacogenomics in clinical practice and drug development. Nat Biotechnol 2012; 30:1117-24. [PMID: 23138311 PMCID: PMC3819119 DOI: 10.1038/nbt.2424] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/17/2012] [Indexed: 12/30/2022]
Abstract
Genome-wide association studies (GWAS) of responses to drugs, including clopidogrel, pegylated-interferon and carbamazepine, have led to the identification of specific patient subgroups that benefit from therapy. However, the identification and replication of common sequence variants that are associated with either efficacy or safety for most prescription medications at odds ratios (ORs) >3.0 (equivalent to >300% increased efficacy or safety) has yet to be translated to clinical practice. Although some of the studies have been completed, the results have not been incorporated into therapy, and a large number of commonly used medications have not been subject to proper pharmacogenomic analysis. Adoption of GWAS, exome or whole genome sequencing by drug development and treatment programs is the most striking near-term opportunity for improving the drug candidate pipeline and boosting the efficacy of medications already in use.
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Affiliation(s)
- Andrew R Harper
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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