101
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Dong Y, Wang J, Zhu S, Zheng H, Wang C, Zhao P. Clinical profiles and diagnostic challenges in 1158 children with rare hepatobiliary disorders. Pediatr Res 2021; 89:238-245. [PMID: 32289814 DOI: 10.1038/s41390-020-0888-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND Diagnosis of rare diseases possesses a great challenge in pediatric hepatology because expert knowledge in the field is extremely insufficient. The study aims to explore new findings and collect diagnostic experience from pediatric rare liver diseases. METHODS The large-sample case analysis study included pediatric patients who had liver-involved rare diseases. All cases underwent liver biopsy and/or gene sequencing. RESULTS A total of 1158 pediatric patients were identified. Liver-based genetic diseases were most frequent (737 cases), followed by liver damages involved in extrahepatic or systemic disorders (151 cases) and cryptogenic hepatobilliary abnormalities (123 cases). Of note, diagnoses of 16 patients were re-evaluated according to genetic results combined with clinical pointers. In addition, 101 patients who underwent gene sequencing remained undiagnosed. Of them, 55 had negative genetic findings, 30 harbored mutations that failed to meet their typically pathogenic condition, and 16 had detected variants that were inconsistent with clinical pointers. CONCLUSIONS As a study involving known largest number of children with rare hepatobiliary disorders, it allows us to accumulate information (especially new findings) on the etiology and diagnosis of these disorders. The results can help to improve the diagnostic quality in the population. IMPACT Liver-based genetic diseases were most frequent in clinical profiles of pediatric rare liver diseases. Some novel variants in cases with genetic diseases (for example, two variants of c.3638G>T and c.1435G>C in a patient with progressive familial intrahepatic cholestasis type 2) were identified. As a study involving known largest number of pediatric cases with rare hepatobiliary disorders, it allows us to accumulate information on the etiology and diagnosis of these disorders. The study can help to optimize the diagnostic process and significantly improve the diagnostic quality in the field of pediatric hepatology. Given that clinical variability often exists within rare genetic disease entities and not all rare disorders are genetic, clinicians should not over-depend on the genetic results in the diagnosis.
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Affiliation(s)
- Yi Dong
- The Fifth Medical Center (formerly Beijing 302 Hospital), Chinese PLA General Hospital, 100039, Beijing, China
| | - Jian Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Shishu Zhu
- The Fifth Medical Center (formerly Beijing 302 Hospital), Chinese PLA General Hospital, 100039, Beijing, China
| | - Huanwei Zheng
- The Fifth Hospital of Shijiazhuang, 050021, Shijiazhuang, Hebei Province, China
| | - Chunya Wang
- Beijing Anzhen Hospital, Capital Medical University, 100029, Beijing, China
| | - Pan Zhao
- The Fifth Medical Center (formerly Beijing 302 Hospital), Chinese PLA General Hospital, 100039, Beijing, China.
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102
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Jäger S, Cuadrat R, Wittenbecher C, Floegel A, Hoffmann P, Prehn C, Adamski J, Pischon T, Schulze MB. Mendelian Randomization Study on Amino Acid Metabolism Suggests Tyrosine as Causal Trait for Type 2 Diabetes. Nutrients 2020; 12:E3890. [PMID: 33352682 PMCID: PMC7766372 DOI: 10.3390/nu12123890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Circulating levels of branched-chain amino acids, glycine, or aromatic amino acids have been associated with risk of type 2 diabetes. However, whether those associations reflect causal relationships or are rather driven by early processes of disease development is unclear. We selected diabetes-related amino acid ratios based on metabolic network structures and investigated causal effects of these ratios and single amino acids on the risk of type 2 diabetes in two-sample Mendelian randomization studies. Selection of genetic instruments for amino acid traits relied on genome-wide association studies in a representative sub-cohort (up to 2265 participants) of the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam Study and public data from genome-wide association studies on single amino acids. For the selected instruments, outcome associations were drawn from the DIAGRAM (DIAbetes Genetics Replication And Meta-analysis, 74,124 cases and 824,006 controls) consortium. Mendelian randomization results indicate an inverse association for a per standard deviation increase in ln-transformed tyrosine/methionine ratio with type 2 diabetes (OR = 0.87 (0.81-0.93)). Multivariable Mendelian randomization revealed inverse association for higher log10-transformed tyrosine levels with type 2 diabetes (OR = 0.19 (0.04-0.88)), independent of other amino acids. Tyrosine might be a causal trait for type 2 diabetes independent of other diabetes-associated amino acids.
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Affiliation(s)
- Susanne Jäger
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.C.); (C.W.); (M.B.S.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
| | - Rafael Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.C.); (C.W.); (M.B.S.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
| | - Clemens Wittenbecher
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.C.); (C.W.); (M.B.S.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Anna Floegel
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany;
| | - Per Hoffmann
- Human Genomics Research Group, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland;
- Institute of Human Genetics, Division of Genomics, Life & Brain Research Centre, University Hospital of Bonn, 53105 Bonn, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
- Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany;
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health (BIH), 10117 Berlin, Germany
- MDC/BIH Biobank, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC) and Berlin Institute of Health (BIH), 13125 Berlin, Germany
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.C.); (C.W.); (M.B.S.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany
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103
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Host genetics and infectious disease: new tools, insights and translational opportunities. Nat Rev Genet 2020; 22:137-153. [PMID: 33277640 PMCID: PMC7716795 DOI: 10.1038/s41576-020-00297-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Understanding how human genetics influence infectious disease susceptibility offers the opportunity for new insights into pathogenesis, potential drug targets, risk stratification, response to therapy and vaccination. As new infectious diseases continue to emerge, together with growing levels of antimicrobial resistance and an increasing awareness of substantial differences between populations in genetic associations, the need for such work is expanding. In this Review, we illustrate how our understanding of the host–pathogen relationship is advancing through holistic approaches, describing current strategies to investigate the role of host genetic variation in established and emerging infections, including COVID-19, the need for wider application to diverse global populations mirroring the burden of disease, the impact of pathogen and vector genetic diversity and a broad array of immune and inflammation phenotypes that can be mapped as traits in health and disease. Insights from study of inborn errors of immunity and multi-omics profiling together with developments in analytical methods are further advancing our knowledge of this important area. Infectious diseases are an ever-present global threat. In this Review, Kwok, Mentzer and Knight discuss our latest understanding of how human genetics influence susceptibility to disease. Furthermore, they discuss emerging progress in the interplay between host and pathogen genetics, molecular responses to infection and vaccination, and opportunities to bring these aspects together for rapid responses to emerging diseases such as COVID-19.
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104
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Associations of the serum metabolite profile with a healthy Nordic diet and risk of coronary artery disease. Clin Nutr 2020; 40:3250-3262. [PMID: 33190988 DOI: 10.1016/j.clnu.2020.10.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIM A healthy Nordic diet (HND) rich in wholegrain cereals, berries, vegetables, and fish, has been associated with a lower risk of cardiovascular disease, but the molecular links remain unclear. Here, we present the application of nontargeted metabolic profiling based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) to identify metabolites that would potentially reflect the adherence to HND and their relationship with the risk of coronary artery disease (CAD). METHODS From a Finnish population-based prospective cohort (Kuopio Ischaemic Heart Disease Risk Factor Study; KIHD), we collected 364 baseline serum samples in 4 groups: 1) 94 participants with high adherence to HND who developed CAD during the follow-up of 20.4 ± 7.6 years (cases), 2) 88 participants with high adherence who did not develop CAD during follow-up (controls), 3) 93 CAD cases with low adherence, and 4) 89 controls with low adherence. RESULTS Indolepropionic acid, proline betaine, vitamin E derivatives, and medium-chain acylcarnitines were associated with adherence to HND after adjustments for age, waist-to-hip ratio (WHR), physical activity, and total cholesterol. These metabolites also correlated negatively with blood lipid profiles, BMI, insulin, inflammation marker high-sensitivity C reactive protein (hsCRP), smoking, and alcohol consumption, as well as positively with physical activity. Predictors of CAD risk included several lipid molecules, which also indicated lower adherence to HND. But, only the associations with the plasmalogens PC(O-16:0/18:2) and PC(O-16:1/18:2) remained significant after adjusting for age, smoking, systolic blood pressure, LDL cholesterol, and WHR. These plasmalogens did not correlate with any investigated risk factors of CAD at baseline, which may highlight their potential as novel predictors of CAD risk. Interestingly, the metabolic profile predicting CAD risk differed based on the adherence to HND. Also, HND adherence was more distinct within CAD cases than controls, which may emphasize the interaction between HND adherence and CAD risk. CONCLUSIONS The association between higher adherence to HND and a lower risk of CAD likely involves a complex interaction of various endogenous, plant-, and microbial-derived metabolites.
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105
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Loftfield E, Herzig KH, Caporaso JG, Derkach A, Wan Y, Byrd DA, Vogtmann E, Männikkö M, Karhunen V, Knight R, Gunter MJ, Järvelin MR, Sinha R. Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort. Cancer Epidemiol Biomarkers Prev 2020; 29:2289-2299. [PMID: 32855266 PMCID: PMC7642019 DOI: 10.1158/1055-9965.epi-20-0824] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/27/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Obesity is an established risk factor for multiple cancer types. Lower microbial richness has been linked to obesity, but human studies are inconsistent, and associations of early-life body mass index (BMI) with the fecal microbiome and metabolome are unknown. METHODS We characterized the fecal microbiome (n = 563) and metabolome (n = 340) in the Northern Finland Birth Cohort 1966 using 16S rRNA gene sequencing and untargeted metabolomics. We estimated associations of adult BMI and BMI history with microbial features and metabolites using linear regression and Spearman correlations (rs ) and computed correlations between bacterial sequence variants and metabolites overall and by BMI category. RESULTS Microbial richness, including the number of sequence variants (rs = -0.21, P < 0.0001), decreased with increasing adult BMI but was not independently associated with BMI history. Adult BMI was associated with 56 metabolites but no bacterial genera. Significant correlations were observed between microbes in 5 bacterial phyla, including 18 bacterial genera, and metabolites in 49 of the 62 metabolic pathways evaluated. The genera with the strongest correlations with relative metabolite levels (positively and negatively) were Blautia, Oscillospira, and Ruminococcus in the Firmicutes phylum, but associations varied by adult BMI category. CONCLUSIONS BMI is strongly related to fecal metabolite levels, and numerous associations between fecal microbial features and metabolite levels underscore the dynamic role of the gut microbiota in metabolism. IMPACT Characterizing the associations between the fecal microbiome, the fecal metabolome, and BMI, both recent and early-life exposures, provides critical background information for future research on cancer prevention and etiology.
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Affiliation(s)
- Erikka Loftfield
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.
| | - Karl-Heinz Herzig
- Research Unit of Biomedicine, Medical Research Center (MRC), University of Oulu, University Hospital, Oulu, Finland and Department of Gastroenterology and Metabolism, Poznan University of Medical Sciences, Poznan, Poland
| | - J Gregory Caporaso
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Andriy Derkach
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Yunhu Wan
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Doratha A Byrd
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Minna Männikkö
- Northern Finland Birth Cohorts, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California
- Department of Bioengineering, and Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer-WHO, Lyon, France
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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106
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Barbeira AN, Melia OJ, Liang Y, Bonazzola R, Wang G, Wheeler HE, Aguet F, Ardlie KG, Wen X, Im HK. Fine-mapping and QTL tissue-sharing information improves the reliability of causal gene identification. Genet Epidemiol 2020; 44:854-867. [PMID: 32964524 PMCID: PMC7693040 DOI: 10.1002/gepi.22346] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 01/01/2023]
Abstract
The integration of transcriptomic studies and genome-wide association studies (GWAS) via imputed expression has seen extensive application in recent years, enabling the functional characterization and causal gene prioritization of GWAS loci. However, the techniques for imputing transcriptomic traits from DNA variation remain underdeveloped. Furthermore, associations found when linking eQTL studies to complex traits through methods like PrediXcan can lead to false positives due to linkage disequilibrium between distinct causal variants. Therefore, the best prediction performance models may not necessarily lead to more reliable causal gene discovery. With the goal of improving discoveries without increasing false positives, we develop and compare multiple transcriptomic imputation approaches using the most recent GTEx release of expression and splicing data on 17,382 RNA-sequencing samples from 948 post-mortem donors in 54 tissues. We find that informing prediction models with posterior causal probability from fine-mapping (dap-g) and borrowing information across tissues (mashr) can lead to better performance in terms of number and proportion of significant associations that are colocalized and the proportion of silver standard genes identified as indicated by precision-recall and receiver operating characteristic curves. All prediction models are made publicly available at predictdb.org.
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Affiliation(s)
- Alvaro N. Barbeira
- Section of Genetic Medicine, Department of MedicineThe University of ChicagoChicagoIllinois
| | - Owen J. Melia
- Section of Genetic Medicine, Department of MedicineThe University of ChicagoChicagoIllinois
| | - Yanyu Liang
- Section of Genetic Medicine, Department of MedicineThe University of ChicagoChicagoIllinois
| | - Rodrigo Bonazzola
- Section of Genetic Medicine, Department of MedicineThe University of ChicagoChicagoIllinois
| | - Gao Wang
- Department of Human GeneticsThe University of ChicagoChicagoIllinois
| | - Heather E. Wheeler
- Department of BiologyLoyola University ChicagoChicagoIllinois
- Department of Computer ScienceLoyola University ChicagoChicagoIllinois
- Department of Public Health Sciences, Stritch School of MedicineLoyola University ChicagoMaywoodIllinois
| | - François Aguet
- The Broad Institute of MIT and HarvardCambridgeMassachusetts
| | | | - Xiaoquan Wen
- Department of BiostatisticsUniversity of MichiganAnn ArborMichigan
| | - Hae K. Im
- Section of Genetic Medicine, Department of MedicineThe University of ChicagoChicagoIllinois
- Department of Human GeneticsThe University of ChicagoChicagoIllinois
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Bandesh K, Bharadwaj D. Genetic variants entail type 2 diabetes as an innate immune disorder. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140458. [DOI: 10.1016/j.bbapap.2020.140458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/28/2020] [Accepted: 05/21/2020] [Indexed: 02/09/2023]
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108
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Kim HI, Ye B, Gosalia N, Köroğlu Ç, Hanson RL, Hsueh WC, Knowler WC, Baier LJ, Bogardus C, Shuldiner AR, Van Hout CV, Van Hout CV. Characterization of Exome Variants and Their Metabolic Impact in 6,716 American Indians from the Southwest US. Am J Hum Genet 2020; 107:251-264. [PMID: 32640185 DOI: 10.1016/j.ajhg.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/10/2020] [Indexed: 12/21/2022] Open
Abstract
Applying exome sequencing to populations with unique genetic architecture has the potential to reveal novel genes and variants associated with traits and diseases. We sequenced and analyzed the exomes of 6,716 individuals from a Southwestern American Indian (SWAI) population with well-characterized metabolic traits. We found that the SWAI population has distinct allelic architecture compared to populations of European and East Asian ancestry, and there were many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private in the SWAI population. We used pLOF and nonsynonymous variants in the SWAI population to evaluate gene-burden associations of candidate genes from European genome-wide association studies (GWASs) for type 2 diabetes, body mass index, and four major plasma lipids. We found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. Interestingly, these associations were mainly driven by pLOF and nonsynonymous variants that are unique or highly enriched in the SWAI population. Particularly, we found four pLOF or nonsynonymous variants in APOB, APOE, PCSK9, and TM6SF2 that are private or enriched in the SWAI population and associated with low-density lipoprotein (LDL) cholesterol levels. Their large estimated effects on LDL cholesterol levels suggest strong impacts on protein function and potential clinical implications of these variants in cardiovascular health. In summary, our study illustrates the utility and potential of exome sequencing in genetically unique populations, such as the SWAI population, to prioritize candidate effector genes within GWAS loci and to find additional variants in known disease genes with potential clinical impact.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Cristopher V Van Hout
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
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Chen M, Sidore C, Akiyama M, Ishigaki K, Kamatani Y, Schlessinger D, Cucca F, Okada Y, Chiang CWK. Evidence of Polygenic Adaptation in Sardinia at Height-Associated Loci Ascertained from the Biobank Japan. Am J Hum Genet 2020; 107:60-71. [PMID: 32533944 PMCID: PMC7332648 DOI: 10.1016/j.ajhg.2020.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/19/2020] [Indexed: 01/31/2023] Open
Abstract
Adult height is one of the earliest putative examples of polygenic adaptation in humans. However, this conclusion was recently challenged because residual uncorrected stratification from large-scale consortium studies was considered responsible for the previously noted genetic difference. It thus remains an open question whether height loci exhibit signals of polygenic adaptation in any human population. We re-examined this question, focusing on one of the shortest European populations, the Sardinians, in addition to mainland European populations. We utilized height-associated loci from the Biobank Japan (BBJ) dataset to further alleviate concerns of biased ascertainment of GWAS loci and showed that the Sardinians remain significantly shorter than expected under neutrality (∼0.22 standard deviation shorter than Utah residents with ancestry from northern and western Europe [CEU] on the basis of polygenic height scores, p = 3.89 × 10-4). We also found the trajectory of polygenic height scores between the Sardinian and the British populations diverged over at least the last 10,000 years (p = 0.0082), consistent with a signature of polygenic adaptation driven primarily by the Sardinian population. Although the polygenic score-based analysis showed a much subtler signature in mainland European populations, we found a clear and robust adaptive signature in the UK population by using a haplotype-based statistic, the trait singleton density score (tSDS), driven by the height-increasing alleles (p = 9.1 × 10-4). In summary, by ascertaining height loci in a distant East Asian population, we further supported the evidence of polygenic adaptation at height-associated loci among the Sardinians. In mainland Europeans, the adaptive signature was detected in haplotype-based analysis but not in polygenic score-based analysis.
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Affiliation(s)
- Minhui Chen
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato 09042, Cagliari, Italy
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, US National Institutes of Health, Baltimore, MD 21224, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato 09042, Cagliari, Italy
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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110
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Maukonen M, Havulinna AS, Männistö S, Kanerva N, Salomaa V, Partonen T. Genetic Associations of Chronotype in the Finnish General Population. J Biol Rhythms 2020; 35:501-511. [PMID: 32579418 PMCID: PMC7534025 DOI: 10.1177/0748730420935328] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Individuals with a later chronotype (evening types) tend to have unhealthier behaviors and increased morbidity and mortality as compared with those with an earlier chronotype (morning types). However, the role of genetics in explaining evening types' adverse health and health behavior is unclear. Our aim was to study genetic associations of chronotype among 8433 Finns from the cross-sectional National FINRISK 2007 and 2012 studies. First, we studied associations between chronotype and 20 key clock genes with a candidate-gene approach and then performed a full genome-wide association study (GWAS) of chronotype. We also developed a genetic risk score (GRS) for chronotype based on 313 single nucleotide polymorphisms (SNPs) that have previously been associated with chronotype. Chronotype was assessed with a shortened version of Horne and Östberg's Morningness-Eveningness Questionnaire (sMEQ), and for comparison, we also used the single self-evaluation question on chronotype from the questionnaire. Linear and logistic regression was used for statistical analysis assuming additive effects. The clock gene analysis revealed 1 independent association signal within NR1D2 (lead SNP rs4131403) that was associated with chronotype (p < 0.05; as based on both chronotype assessment methods). The GWAS analysis did not yield any genome-wide significant associations (p > 5 × 10-8). However, higher GRS was associated with evening chronotype (p < 0.001; as based on both chronotype assessment methods). In conclusion, our findings indicated novel genetic associations between chronotype and the NR1D2 clock gene, which has previously been associated with carbohydrate and lipid metabolism. Furthermore, the GRS was able to capture the genetic aspect of chronotype in our study population. These findings expand our knowledge of the genetic basis of chronotype.
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Affiliation(s)
- Mirkka Maukonen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S Havulinna
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM/HiLIFE), Helsinki, Finland
| | - Satu Männistö
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Veikko Salomaa
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Timo Partonen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
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111
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Yang S, Zhou X. Accurate and Scalable Construction of Polygenic Scores in Large Biobank Data Sets. Am J Hum Genet 2020; 106:679-693. [PMID: 32330416 PMCID: PMC7212266 DOI: 10.1016/j.ajhg.2020.03.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/30/2020] [Indexed: 01/24/2023] Open
Abstract
Accurate construction of polygenic scores (PGS) can enable early diagnosis of diseases and facilitate the development of personalized medicine. Accurate PGS construction requires prediction models that are both adaptive to different genetic architectures and scalable to biobank scale datasets with millions of individuals and tens of millions of genetic variants. Here, we develop such a method called Deterministic Bayesian Sparse Linear Mixed Model (DBSLMM). DBSLMM relies on a flexible modeling assumption on the effect size distribution to achieve robust and accurate prediction performance across a range of genetic architectures. DBSLMM also relies on a simple deterministic search algorithm to yield an approximate analytic estimation solution using summary statistics only. The deterministic search algorithm, when paired with further algebraic innovations, results in substantial computational savings. With simulations, we show that DBSLMM achieves scalable and accurate prediction performance across a range of realistic genetic architectures. We then apply DBSLMM to analyze 25 traits in UK Biobank. For these traits, compared to existing approaches, DBSLMM achieves an average of 2.03%-101.09% accuracy gain in internal cross-validations. In external validations on two separate datasets, including one from BioBank Japan, DBSLMM achieves an average of 14.74%-522.74% accuracy gain. In these real data applications, DBSLMM is 1.03-28.11 times faster and uses only 7.4%-24.8% of physical memory as compared to other multiple regression-based PGS methods. Overall, DBSLMM represents an accurate and scalable method for constructing PGS in biobank scale datasets.
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Affiliation(s)
- Sheng Yang
- Department of Biostatistics, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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112
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Ritari J, Hyvärinen K, Clancy J, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort. NAR Genom Bioinform 2020; 2:lqaa030. [PMID: 33575586 PMCID: PMC7671345 DOI: 10.1093/nargab/lqaa030] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 01/02/2023] Open
Abstract
The HLA genes, the most polymorphic genes in the human genome, constitute the strongest single genetic susceptibility factor for autoimmune diseases, transplantation alloimmunity and infections. HLA imputation via statistical inference of alleles based on single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with alleles is a powerful first-step screening tool. Due to different LD structures between populations, the accuracy of HLA imputation may benefit from matching the imputation reference with the study population. To evaluate the potential advantage of using population-specific reference in HLA imputation, we constructed an HLA reference panel consisting of 1150 Finns with 5365 major histocompatibility complex region SNPs consistent between genome builds. We evaluated the accuracy of the panel against a European panel in an independent test set of 213 Finnish subjects. We show that the Finnish panel yields a lower imputation error rate (1.24% versus 1.79%). More than 30% of imputation errors occurred in haplotypes enriched in Finland. The frequencies of imputed HLA alleles were highly correlated with clinical-grade HLA allele frequencies and allowed accurate replication of established HLA–disease associations in ∼102 000 biobank participants. The results show that a population-specific reference increases imputation accuracy in a relatively isolated population within Europe and can be successfully applied to biobank-scale genome data collections.
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Affiliation(s)
- Jarmo Ritari
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Kati Hyvärinen
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Jonna Clancy
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | | | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
| | - Satu Koskela
- Research and Development, Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
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113
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Li R, Chen Y, Ritchie MD, Moore JH. Electronic health records and polygenic risk scores for predicting disease risk. Nat Rev Genet 2020; 21:493-502. [PMID: 32235907 DOI: 10.1038/s41576-020-0224-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 01/03/2023]
Abstract
Accurate prediction of disease risk based on the genetic make-up of an individual is essential for effective prevention and personalized treatment. Nevertheless, to date, individual genetic variants from genome-wide association studies have achieved only moderate prediction of disease risk. The aggregation of genetic variants under a polygenic model shows promising improvements in prediction accuracies. Increasingly, electronic health records (EHRs) are being linked to patient genetic data in biobanks, which provides new opportunities for developing and applying polygenic risk scores in the clinic, to systematically examine and evaluate patient susceptibilities to disease. However, the heterogeneous nature of EHR data brings forth many practical challenges along every step of designing and implementing risk prediction strategies. In this Review, we present the unique considerations for using genotype and phenotype data from biobank-linked EHRs for polygenic risk prediction.
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Affiliation(s)
- Ruowang Li
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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114
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Raj R, Seppä K, Luostarinen T, Malila N, Seppälä M, Pitkäniemi J, Korja M. Disparities in glioblastoma survival by case volume: a nationwide observational study. J Neurooncol 2020; 147:361-370. [PMID: 32060840 PMCID: PMC7136186 DOI: 10.1007/s11060-020-03428-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/08/2020] [Indexed: 12/11/2022]
Abstract
Introduction High hospital case volumes are associated with improved treatment outcomes for numerous diseases. We assessed the association between academic non-profit hospital case volume and survival of adult glioblastoma patients. Methods From the nationwide Finnish Cancer Registry, we identified all adult (≥ 18 years) patients with histopathological diagnoses of glioblastoma from 2000 to 2013. Five university hospitals (treating all glioblastoma patients in Finland) were classified as high-volume (one hospital), middle-volume (one hospital), and low-volume (three hospitals) based on their annual numbers of cases. We estimated one-year survival rates, estimated median overall survival times, and compared relative excess risk (RER) of death between high, middle, and low-volume hospitals. Results A total of 2,045 patients were included. The mean numbers of annually treated patients were 54, 40, and 17 in the high, middle, and low-volume hospitals, respectively. One-year survival rates and median survival times were higher and longer in the high-volume (39%, 9.3 months) and medium-volume (38%, 8.9 months) hospitals than in the low-volume (32%, 7.8 months) hospitals. RER of death was higher in the low-volume hospitals than in the high-volume hospital (RER = 1.19, 95% CI 1.07–1.32, p = 0.002). There was no difference in RER of death between the high-volume and medium-volume hospitals (p = 0.690). Conclusion Higher glioblastoma case volumes were associated with improved survival. Future studies should assess whether this association is due to differences in patient-specific factors or treatment quality. Electronic supplementary material The online version of this article (10.1007/s11060-020-03428-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rahul Raj
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Topeliuksenkatu 5, P.O. Box 266, 00029, Helsinki, Finland
| | - Karri Seppä
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, 00130, Helsinki, Finland
| | - Tapio Luostarinen
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, 00130, Helsinki, Finland
| | - Nea Malila
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, 00130, Helsinki, Finland
| | - Matti Seppälä
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Topeliuksenkatu 5, P.O. Box 266, 00029, Helsinki, Finland
| | - Janne Pitkäniemi
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, 00130, Helsinki, Finland.,School of Social Sciences, Tampere University, Tampere, Finland.,Department of Public Health, School of Medicine, University of Helsinki, Helsinki, Finland
| | - Miikka Korja
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Topeliuksenkatu 5, P.O. Box 266, 00029, Helsinki, Finland.
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115
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Li R, Wang J, Wang L, Lu Y, Wang C. Two novel mutations of COL1A1 in fetal genetic skeletal dysplasia of Chinese. Mol Genet Genomic Med 2020; 8:e1105. [PMID: 31898422 PMCID: PMC7057086 DOI: 10.1002/mgg3.1105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/23/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022] Open
Abstract
Background Skeletal disorders, which have great genotypic and phenotypic varieties, are a considerable challenge to differentiate these diseases and provide a definitive prenatal diagnosis or pre‐implantation. The present study aims to identify the causative mutation in two unrelated outbred Han–Chinese families. Method Two short‐limb fetuses were referred to our hospital. Genomic DNA was extracted from the amniotic fluid of the short‐limb fetuses and from peripheral blood of their parents. To identify the causative gene, next‐generation‐based target capture sequencing was performed on these two fetuses, followed by Sanger Sequencing in unrelated healthy controls. Segregation analysis of the candidate variant was performed in parents by using Sanger sequencing. The mutations were analyzed by SIFT, PolyPhen and Provean. Results We found that fetal genetic skeletal dysplasia was confirmed according to the correlations between genetic mutations and phenotypes in two Chinese families. Targeted next generation sequencing was performed to screen causative mutations in patients. Two novel heterozygous mutations COL1A1 c.1706 G > C (p. G569A) and c.3307 G > A (p. G1103S) were respectively identified. The results suggested that COL1A1 novel mutations were in highly conserved glycine residues present in the Gly‐X‐Y sequence repeats of the triple helical region of the collagen type I α chain, which was responsible for Osteogenesis Imperfecta. The presence of the missense mutation was also confirmed with the Sanger sequence. These two mutations were predicted to be pathogenic by SIFT, PolyPhen and Provean. Conclusion Our findings showed that the mutations of COL1A1 may play important roles in fetal genetic skeletal dysplasia in Chinese patients. Exome sequencing enhances the accurate diagnosis in utero then provides appropriate genetic counseling.
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Affiliation(s)
- Ruibing Li
- Department of Obstetrics and Gynecology, the First Medical Center, Chinese PLA General Hospital, Beijing, China.,Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jianan Wang
- Department of Obstetrics and Gynecology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Longxia Wang
- Department of Ultrasonography, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yanping Lu
- Department of Obstetrics and Gynecology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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Ohukainen P, Kuusisto S, Kettunen J, Perola M, Järvelin MR, Mäkinen VP, Ala-Korpela M. Data-driven multivariate population subgrouping via lipoprotein phenotypes versus apolipoprotein B in the risk assessment of coronary heart disease. Atherosclerosis 2019; 294:10-15. [PMID: 31931463 DOI: 10.1016/j.atherosclerosis.2019.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/12/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND AND AIMS Population subgrouping has been suggested as means to improve coronary heart disease (CHD) risk assessment. We explored here how unsupervised data-driven metabolic subgrouping, based on comprehensive lipoprotein subclass data, would work in large-scale population cohorts. METHODS We applied a self-organizing map (SOM) artificial intelligence methodology to define subgroups based on detailed lipoprotein profiles in a population-based cohort (n = 5789) and utilised the trained SOM in an independent cohort (n = 7607). We identified four SOM-based subgroups of individuals with distinct lipoprotein profiles and CHD risk and compared those to univariate subgrouping by apolipoprotein B quartiles. RESULTS The SOM-based subgroup with highest concentrations for non-HDL measures had the highest, and the subgroup with lowest concentrations, the lowest risk for CHD. However, apolipoprotein B quartiles produced better resolution of risk than the SOM-based subgroups and also striking dose-response behaviour. CONCLUSIONS These results suggest that the majority of lipoprotein-mediated CHD risk is explained by apolipoprotein B-containing lipoprotein particles. Therefore, even advanced multivariate subgrouping, with comprehensive data on lipoprotein metabolism, may not advance CHD risk assessment.
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Affiliation(s)
- Pauli Ohukainen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sanna Kuusisto
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland; NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland; National Institute for Health and Welfare, Helsinki, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland; Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland; Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland; Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland; Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK; Department of Life Sciences, College of Health and Life Sciences, Brunel University London, UK
| | - Ville-Petteri Mäkinen
- Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Australia; Hopwood Centre for Neurobiology, Lifelong Health Theme, SAHMRI, Australia
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland; NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland.
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The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 2019; 576:106-111. [PMID: 31802016 PMCID: PMC7054211 DOI: 10.1038/s41586-019-1793-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 10/11/2019] [Indexed: 12/30/2022]
Abstract
The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide. Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide.
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Hernández-Beeftink T, Guillen-Guio B, Villar J, Flores C. Genomics and the Acute Respiratory Distress Syndrome: Current and Future Directions. Int J Mol Sci 2019; 20:E4004. [PMID: 31426444 PMCID: PMC6721149 DOI: 10.3390/ijms20164004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/05/2019] [Accepted: 08/11/2019] [Indexed: 12/19/2022] Open
Abstract
The excessive hospital mortality associated with acute respiratory distress syndrome (ARDS) in adults mandates an urgent need for developing new therapies and tools for the early risk assessment of these patients. ARDS is a heterogeneous syndrome with multiple different pathogenetic processes contributing differently in different patients depending on clinical as well as genetic factors. Identifying genetic-based biomarkers holds the promise for establishing effective predictive and prognostic stratification methods and for targeting new therapies to improve ARDS outcomes. Here we provide an updated review of the available evidence supporting the presence of genetic factors that are predictive of ARDS development and of fatal outcomes in adult critically ill patients and that have been identified by applying different genomic and genetic approaches. We also introduce other incipient genomics approximations, such as admixture mapping, metagenomics and genome sequencing, among others, that will allow to boost this knowledge and likely reveal new genetic predictors of ARDS susceptibility and prognosis among critically ill patients.
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Affiliation(s)
- Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria 35010, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife 38010, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife 38010, Spain
| | - Jesús Villar
- Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria 35010, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife 38010, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain.
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife 38600, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife 38200, Spain.
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