101
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Block I, Burton M, Sørensen KP, Andersen L, Larsen MJ, Bak M, Cold S, Thomassen M, Tan Q, Kruse TA. Association of miR-548c-5p, miR-7-5p, miR-210-3p, miR-128-3p with recurrence in systemically untreated breast cancer. Oncotarget 2018; 9:9030-9042. [PMID: 29507672 PMCID: PMC5823652 DOI: 10.18632/oncotarget.24088] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/02/2018] [Indexed: 01/10/2023] Open
Abstract
Current prognostic markers allocate the majority of lymph node (LN) negative and estrogen receptor (ER) positive breast cancer patients into the high-risk group. Accordingly, most patients receive systemic treatments although approximately 40% of these patients may have been cured by surgery and radiotherapy alone. Two studies identified seven prognostic microRNAs in systemically untreated, LN negative and ER positive breast cancer patients which may allow more precise patient classification. However, six of the seven microRNAs were analyzed in both studies but only found to be prognostic in one study. To validate their prognostic potential, we analyzed microRNA expression in an independent cohort (n = 110) using a pair-matched study design minimizing dependence of classical markers. The expression of hsa-miR-548c-5p was significantly associated with abridged disease-free survival (hazard ratio [HR]:1.96, p = 0.027). Contradicting published results, high hsa-miR-516-3p expression was associated with favorable outcome (HR:0.29, p = 0.0068). The association is probably time-dependent indicating later relapse. Additionally, re-analysis of previously published expression data of two matching cohorts (n = 100, n = 255) supports an association of hsa-miR-128-3p with shortened disease-free survival (HR:2.48, p = 0.0033) and an upregulation of miR-7-5p (p = 0.0038; p = 0.039) and miR-210-3p (p = 0.031) in primary tumors of patients who experienced metastases. Further analysis may verify the prognostic potential of these microRNAs.
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Affiliation(s)
- Ines Block
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Mark Burton
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kristina P Sørensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lars Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin Bak
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Søren Cold
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Epidemiology, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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102
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Debrabant B, Soerensen M, Christiansen L, Tan Q, McGue M, Christensen K, Hjelmborg J. DNA methylation age and perceived age in elderly Danish twins. Mech Ageing Dev 2018; 169:40-44. [PMID: 28965790 PMCID: PMC6190692 DOI: 10.1016/j.mad.2017.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/18/2017] [Accepted: 09/20/2017] [Indexed: 11/27/2022]
Abstract
Perceived age is an easily accessible biomarker of aging. Here, we studied its relation to DNA methylation age (DNAm age) as introduced in (Horvath, 2013) in 180 elderly Danish twins. We found perceived age and DNAm age to be associated with chronological age (P=0.04 resp. P=2.2e-10) when correcting for gender, but did not see an association between perceived age and DNAm age (P=0.44). Intrapair-analysis showed that the proportion of pairs where the twin with the highest perceived age also had the highest DNAm age was not different from 0.5 (P=1), and we did not see a trend when dividing pairs according to their difference in perceived age (P=0.36). Hence, intrapair analysis did not reveal links between perceived age and DNAm age. Moreover, none of the 353 CpGs underlying DNAm age was individually associated with perceived age after correction for multiple-testing (P>6e-4, FDR>0.21). Finally, when constructing an epigenetic signature based on these CpGs to predict perceived age, we only found a correlation of 0.18 (95%CI: -0.06 to 0.40) and a mean square error of 13.6 years2 between observed and predicted values in the test dataset, indicating poor predictive strength. Altogether, our results suggest that perceived age and DNAm age capture different aging aspects.
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Affiliation(s)
- Birgit Debrabant
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA; Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
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103
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Wang W, Zhang D, Xu C, Wu Y, Duan H, Li S, Tan Q. Heritability and Genome-Wide Association Analyses of Serum Uric Acid in Middle and Old-Aged Chinese Twins. Front Endocrinol (Lausanne) 2018; 9:75. [PMID: 29559957 PMCID: PMC5845532 DOI: 10.3389/fendo.2018.00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/19/2018] [Indexed: 12/13/2022] Open
Abstract
Serum uric acid (SUA), as the end product of purine metabolism, has proven emerging roles in human disorders. Here based on a sample of 379 middle and old-aged Chinese twin pairs, we aimed to explore the magnitude of genetic impact on SUA variation by performing sex-limitation twin modeling analyses and further detect specific genetic variants related to SUA by conducting a genome-wide association study. Monozygotic (MZ) twin correlation for SUA level (rMZ = 0.56) was larger than for dizygotic (DZ) twin correlation (rDZ = 0.39). The common effects sex-limitation model provided the best fit with additive genetic parameter (A) accounting for 46.3%, common or shared environmental parameter (C) accounting for 26.3% and unique/nonshared environmental parameter (E) accounting for 27.5% for females and 29.9, 33.1, and 37.0% for males, respectively. Although no SUA-related genetic variants reached genome-wide significance level, 25 SNPs were suggestive of association (P < 1 × 10-5). Most of the SNPs were located in an intronic region and detected to have regulatory effects on gene transcription. The cell-type specific enhancer of skeletal muscle was detected which has been reported to implicate SUA. Two promising genetic regions on chromosome 17 around rs2253277 and chromosome 14 around rs11621523 were found. Gene-based analysis found 167 genes nominally associated with SUA level (P < 0.05), including PTGR2, ENTPD5, well-known SLC2A9, etc. Enrichment analysis identified one pathway of transmembrane transport of small molecules and 20 GO gene sets involving in ion transport, transmembrane transporter activity, hydrolase activity acting on acid anhydrides, etc. In conclusion, SUA shows moderate heritability in women and low heritability in men in the Chinese population and genetic variations are significantly involved in functional genes and regulatory domains that mediate SUA level. Our findings provide clues to further elucidate molecular physiology of SUA homeostasis and identify new diagnostic biomarkers and therapeutic targets for hyperuricemia and gout.
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Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
- *Correspondence: Dongfeng Zhang,
| | - Chunsheng Xu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
- Qingdao Institute of Preventive Medicine, Qingdao, China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Haiping Duan
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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104
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Bolund ACS, Starnawska A, Miller MR, Schlünssen V, Backer V, Børglum AD, Christensen K, Tan Q, Christiansen L, Sigsgaard T. Lung function discordance in monozygotic twins and associated differences in blood DNA methylation. Clin Epigenetics 2017; 9:132. [PMID: 29299071 PMCID: PMC5740718 DOI: 10.1186/s13148-017-0427-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 01/16/2023] Open
Abstract
Background Lung function is an important predictor of morbidity and mortality, with accelerated lung function decline reported to have immense consequences for the world's healthcare systems. The lung function decline across individual's lifetime is a consequence of age-related changes in lung anatomical structure and combination of various environmental factors; however, the exact molecular mechanisms contributing to this decline are not fully understood. DNA methylation is an epigenetic modification that changes across individual's lifetime, as well as allows for interplay between environmental and genetic factors. DNA methylation plays a crucial role in regulation of gene expression, with increasing evidence linking aberrant DNA methylation levels with a number of common human diseases. In this study, we investigated possible associations between genome-wide DNA methylation levels and lung function in 169 pairs of middle-aged monozygotic twins (86 male pairs: mean age (min-max) = 66 years (57-79); 83 female pairs: mean age (min-max) = 66 years (56-78)). The twins were collected from the Danish Twin Registry and were examined at baseline (1998-1999) and follow-up (2008-2011) visits. Using the twin design, we correlated intra-pair differences in cross-sectional and longitudinal lung function with intra-pair blood DNA methylation differences at follow-up by linear regression analyses adjusted for sex, age, BMI, smoking, and blood cell composition measured for each individual with the use of flow cytometry. Results We identified several differentially methylated CpG sites associated with forced expiratory volume the first second (FEV1) and forced vital capacity (FVC). Three probes identified for level of FVC were located in GLIPR1L2 gene (lowest p value = 7.14 × 10-8), involved in innate immunity and tumour-suppressor/pro-oncogenic mechanisms. Change in FEV1 during the 11-year follow-up period was associated with blood DNA methylation level in TRIM27 gene (p value = 1.55 × 10-6), a negative regulator of CD4 T cells, and also involved in cancer development. Several enriched pathways were identified, especially for FEV1, with one being "TGFBR" (Benjamini-Hochbergadjp value = 0.045), the receptor for TGFβ, a growth factor involved in normal lung tissue repair through pro-fibrotic effects. Conclusions Our findings suggest that epigenetic regulation of immunological- and cancer-related genes, as well as TGF-β-receptor-related genes, may be involved in the cross-sectional level and longitudinal change in lung function in middle-aged monozygotic twins.
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Affiliation(s)
- Anneli C. S. Bolund
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Martin R. Miller
- Institute of Occupational and Environmental Medicine, University of Birmingham, Birmingham, UK
| | - Vivi Schlünssen
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Vibeke Backer
- Department of Respiratory Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Kaare Christensen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, University Hospital, Odense, Denmark
| | - Qihua Tan
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lene Christiansen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben Sigsgaard
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
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105
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Starnawska A, Tan Q, McGue M, Mors O, Børglum AD, Christensen K, Nyegaard M, Christiansen L. Epigenome-Wide Association Study of Cognitive Functioning in Middle-Aged Monozygotic Twins. Front Aging Neurosci 2017; 9:413. [PMID: 29311901 PMCID: PMC5733014 DOI: 10.3389/fnagi.2017.00413] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/28/2017] [Indexed: 12/22/2022] Open
Abstract
As the world's population ages, the age-related cognitive decline presents a great challenge to world's healthcare systems. One of the molecular mechanisms implicated in cognitive ageing is DNA methylation, an epigenetic modification known to be a key player in memory formation, maintenance, and synaptic plasticity. Using the twin design we performed an epigenome-wide association study (EWAS) in a population of 486 middle-aged monozygotic twins (mean age at follow-up 65.9, SD = 6.1) and correlated their blood DNA methylation to their level (cross-sectional analysis) and change in cognitive abilities over 10 years (longitudinal analysis). We identified several CpG sites where cross-sectional cognitive functioning was associated with DNA methylation levels. The top identified loci were located in ZBTB46 (p = 5.84 × 10-7), and TAF12 (p = 4.91 × 10-7). KEGG's enrichment analyses of the most associated findings identified "Neuroactive ligand-receptor interaction" as the most enriched pathway (p = 0.0098). Change in cognitive functioning over 10 years was associated with DNA methylation levels in AGBL4 (p = 9.01 × 10-7) and SORBS1 (p = 5.28 × 10-6), with the first gene playing an important role in neuronal survival and the latter gene implicated before in Alzheimer's disease and ischemic stroke. Our findings point to an association between changes in DNA methylation of genes related to neuronal survival and change of cognitive functioning in aging individuals.
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Affiliation(s)
- Anna Starnawska
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Qihua Tan
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Matt McGue
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Psychology, University of Minnesota, Minneapolis, MN, United States
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Kaare Christensen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- The Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Mette Nyegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Lene Christiansen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
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106
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Wang W, Jiang W, Hou L, Duan H, Wu Y, Xu C, Tan Q, Li S, Zhang D. Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI. BMC Genomics 2017; 18:872. [PMID: 29132311 PMCID: PMC5683603 DOI: 10.1186/s12864-017-4257-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/01/2017] [Indexed: 02/08/2023] Open
Abstract
Background The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. Results In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed. Conclusion We identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired. Electronic supplementary material The online version of this article (10.1186/s12864-017-4257-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Wenjie Jiang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Lin Hou
- Department of Biochemistry, Medical College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Haiping Duan
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.,Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.,Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China
| | - Qihua Tan
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Shuxia Li
- Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.
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107
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Wang W, Xu C, Tan Q, Song Z, Zhuang W, Chen Y, Xiong L, Chen G, Fang M, Lv T, Song Y. P3.02-065 Lung Adenocarcinoma Patient with EGFR Kinase Domain Duplication (KDD) and Its Response to Icotinib: A Case Report. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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108
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Almeida D, Skov I, Silva A, Vandin F, Tan Q, Röttger R, Baumbach J. Efficient detection of differentially methylated regions using DiMmeR. Bioinformatics 2017; 33:549-551. [PMID: 27794558 DOI: 10.1093/bioinformatics/btw657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/13/2016] [Indexed: 12/31/2022] Open
Abstract
Motivation Epigenome-wide association studies (EWAS) generate big epidemiological datasets. They aim for detecting differentially methylated DNA regions that are likely to influence transcriptional gene activity and, thus, the regulation of metabolic processes. The by far most widely used technology is the Illumina Methylation BeadChip, which measures the methylation levels of 450 (850) thousand cytosines, in the CpG dinucleotide context in a set of patients compared to a control group. Many bioinformatics tools exist for raw data analysis. However, most of them require some knowledge in the programming language R, have no user interface, and do not offer all necessary steps to guide users from raw data all the way down to statistically significant differentially methylated regions (DMRs) and the associated genes. Results Here, we present DiMmeR (Discovery of Multiple Differentially Methylated Regions), the first free standalone software that interactively guides with a user-friendly graphical user interface (GUI) scientists the whole way through EWAS data analysis. It offers parallelized statistical methods for efficiently identifying DMRs in both Illumina 450K and 850K EPIC chip data. DiMmeR computes empirical P -values through randomization tests, even for big datasets of hundreds of patients and thousands of permutations within a few minutes on a standard desktop PC. It is independent of any third-party libraries, computes regression coefficients, P -values and empirical P -values, and it corrects for multiple testing. Availability and Implementation DiMmeR is publicly available at http://dimmer.compbio.sdu.dk . Contact diogoma@bmb.sdu.dk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Diogo Almeida
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,Laboratory for Genomics and Bioinformatics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ida Skov
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | - Artur Silva
- Laboratory for Genomics and Bioinformatics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Fabio Vandin
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.,Department of Information Engineering, University of Padova, Padova I-35131, Italy
| | - Qihua Tan
- Clinical Institute (CI), University of Southern Denmark, 5000 Odense, Denmark
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.,Max Planck Institute for Informatics, Saarbruecken, Germany
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109
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Abstract
Among the major issues in gene expression profile classification, feature selection is an important and necessary step in achieving and creating good classification rules given the high dimensionality of microarray data. Although different feature selection methods have been reported, there has been no method specifically proposed for paired microarray experiments. In this paper, we introduce a simple procedure based on a modified t-statistic for feature selection to microarray experiments using the popular matched case-control design and apply to our recent study on tumor metastasis in a low-malignant group of breast cancer patients for selecting genes that best predict metastases. Gene or feature selection is optimized by thresholding in a leaving one-pair out cross-validation. Model comparison through empirical application has shown that our method manifests improved efficiency with high sensitivity and specificity.
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Affiliation(s)
- Qihua Tan
- Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark
- Department of epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Mads Thomassen
- Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark
| | - Torben A. Kruse
- Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark
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110
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Li S, Zhu D, Duan H, Ren A, Glintborg D, Andersen M, Skov V, Thomassen M, Kruse T, Tan Q. Differential DNA methylation patterns of polycystic ovarian syndrome in whole blood of Chinese women. Oncotarget 2017; 8:20656-20666. [PMID: 27192117 PMCID: PMC5400534 DOI: 10.18632/oncotarget.9327] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/26/2016] [Indexed: 01/01/2023] Open
Abstract
As a universally common endocrinopathy in women of reproductive age, the polycystic ovarian syndrome is characterized by composite clinical phenotypes reflecting the contributions of reproductive impact of ovarian dysfunction and metabolic abnormalities with widely varying symptoms resulting from interference of the genome with the environment through integrative biological mechanisms including epigenetics. We have performed a genome-wide DNA methylation analysis on polycystic ovarian syndrome and identified a substantial number of genomic sites differentially methylated in the whole blood of PCOS patients and healthy controls (52 sites, false discovery rate < 0.05 and corresponding p value < 5.68e–06), highly consistently replicating biological pathways extensively implicated in immunity and immunity-related inflammatory disorders (false discovery rate < 0.05) that were reportedly regulated in the DNA methylome from ovarian tissue under PCOS condition. Most importantly, our genome-wide profiling focusing on PCOS patients revealed a large number of DNA methylation sites and their enriched functional pathways significantly associated with diverse clinical features (levels of prolactin, estradiol, progesterone and menstrual cycle) that could serve as novel molecular basis of the clinical heterogeneity observed in PCOS women.
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Affiliation(s)
- Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Dongyi Zhu
- Center of Reproductive Medicine, Linyi People's Hospital, Linyi, China.,Department of Obstetrics and Gynecology, Shandong Medical College, Linyi, China
| | - Hongmei Duan
- Department of Medicine, Kolding Hospital, Kolding, Denmark
| | - Anran Ren
- Center of Reproductive Medicine, Linyi People's Hospital, Linyi, China.,Department of Obstetrics and Gynecology, Shandong Medical College, Linyi, China
| | - Dorte Glintborg
- Department of Endocrinology, Odense University Hospital, Odense, Denmark
| | - Marianne Andersen
- Department of Endocrinology, Odense University Hospital, Odense, Denmark
| | - Vibe Skov
- Department of Hematology, Roskilde Hospital, Roskilde, Denmark
| | - Mads Thomassen
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Epidemiology, Biostatistics, and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
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111
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Bolund AC, Starnawska A, Miller MR, Schlünssen V, Sigsgaard T, Backer V, Børglum AD, Christensen K, Tan Q, Christiansen L. Lung function discordance in monozygotic twins and associated differences in blood DNA methylation. Genes Environ 2017. [DOI: 10.1183/1393003.congress-2017.oa2943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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112
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Xu C, Tian X, Sun J, Wu Y, Zhang D, Pang Z, Li S, Petersen I, Mengel-From J, Christiansen L, Christensen K, Tan Q. Genetic and environmental influences on cardiovascular risk factors and cognitive function: A Chinese twin aging study. Geriatr Gerontol Int 2017; 18:352-359. [PMID: 28857473 DOI: 10.1111/ggi.13161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 05/09/2017] [Accepted: 07/05/2017] [Indexed: 11/30/2022]
Abstract
AIM To explore the genetic and environmental influences on cardiovascular risk factors (CVRF) and cognitive function in the world's largest and rapidly aging Chinese population. METHODS Cognitive function and CVRF, including body mass index, systolic blood pressure, diastolic blood pressure, pulse pressure, glucose, total cholesterol, triglyceride, high-density lipoprotein cholesterol (HDLC) and low-density lipoprotein cholesterol were measured in 379 complete twin pairs. Univariate and bivariate twin models were fitted to estimate the genetic and environmental components in the variance and covariance of CVRF and cognition. RESULTS Mild-to-high heritability was estimated for CVRF and cognition (0.27-0.74). Unique environmental factors showed low-to-moderate contributions (0.23-0.56). Only HDLC presented significant common environmental contribution (0.50). Bivariate analysis showed significantly negative genetic correlations (rG ) between cognition and systolic blood pressure (rG = -0.56), diastolic blood pressure (rG = -0.42), pulse pressure (rG = -0.45), and positive genetic correlations between cognition and total cholesterol (rG = 0.33), triglyceride (rG = 0.23) and HDLC (rG = 0.41). HDLC and cognition presented a unique environmental correlation (rE = -0.13), but in the opposite direction. CONCLUSIONS Cognitive function was genetically related to systolic blood pressure, diastolic blood pressure, pulse pressure, total cholesterol, triglyceride and HDLC with a negative or positive direction. Cognition and HDLC might share part of a similar unique environmental factor. Geriatr Gerontol Int 2018; 18: 352-359.
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Affiliation(s)
- Chunsheng Xu
- Department of Epidemiology and Health Statistics, Qingdao University Medical College, Qingdao, Shandong, China.,Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Jianping Sun
- Department of Epidemiology and Health Statistics, Qingdao University Medical College, Qingdao, Shandong, China.,Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Qingdao University Medical College, Qingdao, Shandong, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Qingdao University Medical College, Qingdao, Shandong, China
| | - Zengchang Pang
- Department of Epidemiology and Health Statistics, Qingdao University Medical College, Qingdao, Shandong, China.,Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Inge Petersen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
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113
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Xu C, Zhang D, Wu Y, Tian X, Pang Z, Li S, Tan Q. A genome-wide association study of cognitive function in Chinese adult twins. Biogerontology 2017; 18:811-819. [PMID: 28808816 DOI: 10.1007/s10522-017-9725-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/09/2017] [Indexed: 01/16/2023]
Abstract
Multiple loci or genes have been identified using genome-wide association studies mainly in western countries but with inconsistent results. No similar studies have been conducted in the world's largest and rapidly aging Chinese population. The paper aimed to identify the specific genetic variants associated with cognitive function in middle and old-aged Chinese dizygotic twins (DZ). Cognitive function was measured on 139 pairs of DZ by Montreal Cognitive Assessment. The subjects were genotyped at 1048575 SNP positions. Regression-based mixed-effect kinship model of GWAS was conducted to test the SNPs. Gene-based analysis was performed on VEGAS2. The statistically significant genes were then subject to gene set enrichment analysis to further identify the specific biological pathways associated with cognitive function. No SNPs reached genome-wide significance although there were 13 SNPs of suggestive significance (P < 10-5). Gene-based analysis found 823 significant genes topped by TNRC18P1 (P = 1.00 × 10-6), FGFR1OP2 (P = 6.00 × 10-6), and AKR1D1 (P = 2.30 × 10-5). Enrichment analysis identified 46 biological pathways, mainly involving in signaling transmission, metabolic process and Alzheimer's disease. Analysis of SNPs involved in the regulatory motif detected cell-type specific enhancers involving aorta and colon smooth muscle both have been reported to implicate in cognition. We conclude that genetic variations are significantly involved in functional genes, biological pathways and the regulatory domain that mediate cognitive performances.
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Affiliation(s)
- Chunsheng Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China.,Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China.
| | - Yili Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Zengchang Pang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China.,Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
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114
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Häsler R, Venkatesh G, Tan Q, Flachsbart F, Sinha A, Rosenstiel P, Lieb W, Schreiber S, Christensen K, Christiansen L, Nebel A. Genetic interplay between human longevity and metabolic pathways - a large-scale eQTL study. Aging Cell 2017; 16:716-725. [PMID: 28421666 PMCID: PMC5506416 DOI: 10.1111/acel.12598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2017] [Indexed: 11/30/2022] Open
Abstract
Human longevity is a complex phenotype influenced by genetic and environmental components. Unraveling the contribution of genetic vs. nongenetic factors to longevity is a challenging task. Here, we conducted a large‐scale RNA‐sequencing‐based expression quantitative trait loci study (eQTL) with subsequent heritability analysis. The investigation was performed on blood samples from 244 individuals from Germany and Denmark, representing various age groups including long‐lived subjects up to the age of 104 years. Our eQTL‐based approach revealed for the first time that human longevity is associated with a depletion of metabolic pathways in a genotype‐dependent and independent manner. Further analyses indicated that 20% of the differentially expressed genes are influenced by genetic variants in cis. The subsequent study of twins showed that the transcriptional activity of a third of the differentially regulated genes is heritable. These findings suggest that longevity‐associated biological processes such as altered metabolism are, to a certain extent, also the driving force of longevity rather than just a consequence of old age.
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Affiliation(s)
- Robert Häsler
- Institute of Clinical Molecular Biology; Kiel University; 24105 Kiel Germany
| | - Geetha Venkatesh
- Institute of Clinical Molecular Biology; Kiel University; 24105 Kiel Germany
| | - Qihua Tan
- The Danish Twin Registry; Unit of Epidemiology, Biostatistics and Biodemography; University of Southern Denmark; 5000 Odense Denmark
- Department of Clinical Genetics; Odense University Hospital; 5000 Odense Denmark
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology; Kiel University; 24105 Kiel Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology; Kiel University; 24105 Kiel Germany
| | - Wolfgang Lieb
- Institute of Epidemiology; Kiel University; 24105 Kiel Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology; Kiel University; 24105 Kiel Germany
| | - Kaare Christensen
- The Danish Twin Registry; Unit of Epidemiology, Biostatistics and Biodemography; University of Southern Denmark; 5000 Odense Denmark
- Department of Clinical Genetics; Odense University Hospital; 5000 Odense Denmark
- Department of Clinical Biochemistry and Pharmacology; Odense University Hospital; 5000 Odense Denmark
| | - Lene Christiansen
- The Danish Twin Registry; Unit of Epidemiology, Biostatistics and Biodemography; University of Southern Denmark; 5000 Odense Denmark
| | - Almut Nebel
- Institute of Clinical Molecular Biology; Kiel University; 24105 Kiel Germany
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115
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Graff RE, Möller S, Passarelli MN, Witte JS, Skytthe A, Christensen K, Tan Q, Adami HO, Czene K, Harris JR, Pukkala E, Kaprio J, Giovannucci E, Mucci LA, Hjelmborg JB. Familial Risk and Heritability of Colorectal Cancer in the Nordic Twin Study of Cancer. Clin Gastroenterol Hepatol 2017; 15:1256-1264. [PMID: 28130150 PMCID: PMC5522647 DOI: 10.1016/j.cgh.2016.12.041] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 12/05/2016] [Accepted: 12/29/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS We analyzed data from twins to determine how much the familial risk of colorectal cancer can be attributed to genetic factors vs environment. We also examined whether heritability is distinct for colon vs rectal cancer, given evidence of distinct etiologies. METHODS Our data set included 39,990 monozygotic and 61,443 same-sex dizygotic twins from the Nordic Twin Study of Cancer. We compared each cancer's risk in twins of affected co-twins relative to the cohort risk (familial risk ratio [FRR]). We then estimated the proportion of variation in risk that could be attributed to genetic factors (heritability). RESULTS From earliest registration in 1943 through 2010, there were 1861 individuals diagnosed with colon cancer and 1268 diagnosed with rectal cancer. Monozygotic twins of affected co-twins had an FRR for colorectal cancer of 3.1 (95% confidence interval [CI], 2.4-3.8) relative to the cohort risk. Dizygotic twins of affected co-twins had an FRR for colorectal cancer of 2.2 (95% CI, 1.7-2.7). We estimated that 40% (95% CI, 33%-48%) of the variation in colorectal cancer risk could be attributed to genetic factors; unique environment only accounted for the remaining liability. For colon cancer, the FRR was 3.3 (95% CI, 2.1-4.5) for monozygotic twins and 2.6 (95% CI, 1.7-3.5) for dizygotic twins. For rectal cancer, comparable estimates were 3.3 (95% CI, 1.5-5.1) for monozygotic twins and 2.6 (95% CI, 1.2-4.0) for dizygotic twins. Heritability estimates for colon and rectal cancer were 16% (95% CI, 0-46%) and 15% (95% CI, 0-50%), common environment estimates were 15% (95% CI, 0-38%) and 11% (95% CI, 0-38%), and unique environment estimates were 68% (95% CI, 57%-79%) and 75% (95% CI, 61%-88%), respectively. CONCLUSIONS Interindividual genetic differences could account for 40% of the variation in susceptibility to colorectal cancer; risk for colon and rectal cancers might have less of a genetic component than risk for colorectal cancer. Siblings, and particularly monozygotic co-twins, of individuals with colon or rectal cancer should consider personalized screening.
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Affiliation(s)
- Rebecca E. Graff
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sören Möller
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark,The Danish Twin Registry, University of Southern Denmark, Denmark
| | - Michael N. Passarelli
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - John S. Witte
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA,Department of Urology, University of California San Francisco, San Francisco, CA, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Axel Skytthe
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark,The Danish Twin Registry, University of Southern Denmark, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark,The Danish Twin Registry, University of Southern Denmark, Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark,The Danish Twin Registry, University of Southern Denmark, Denmark
| | - Hans-Olov Adami
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Jaakko Kaprio
- University of Helsinki, Department of Public Health, Helsinki, Finland,National Institute for Health and Welfare, Department of Health, Helsinki, Finland,University of Helsinki, Institute for Molecular Medicine (FIMM), Helsinki, Finland
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Nutrition, Harvard School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Centre for Public Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Jacob B. Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark,The Danish Twin Registry, University of Southern Denmark, Denmark
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116
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Silventoinen K, Jelenkovic A, Sund R, Yokoyama Y, Hur YM, Cozen W, Hwang AE, Mack TM, Honda C, Inui F, Iwatani Y, Watanabe M, Tomizawa R, Pietiläinen KH, Rissanen A, Siribaddana SH, Hotopf M, Sumathipala A, Rijsdijk F, Tan Q, Zhang D, Pang Z, Piirtola M, Aaltonen S, Öncel SY, Aliev F, Rebato E, Hjelmborg JB, Christensen K, Skytthe A, Kyvik KO, Silberg JL, Eaves LJ, Cutler TL, Ordoñana JR, Sánchez-Romera JF, Colodro-Conde L, Song YM, Yang S, Lee K, Franz CE, Kremen WS, Lyons MJ, Busjahn A, Nelson TL, Whitfield KE, Kandler C, Jang KL, Gatz M, Butler DA, Stazi MA, Fagnani C, D’Ippolito C, Duncan GE, Buchwald D, Martin NG, Medland SE, Montgomery GW, Jeong HU, Swan GE, Krasnow R, Magnusson PKE, Pedersen NL, Dahl Aslan AK, McAdams TA, Eley TC, Gregory AM, Tynelius P, Baker LA, Tuvblad C, Bayasgalan G, Narandalai D, Spector TD, Mangino M, Lachance G, Burt SA, Klump KL, Harris JR, Brandt I, Nilsen TS, Krueger RF, McGue M, Pahlen S, Corley RP, Huibregtse BM, Bartels M, van Beijsterveldt CEM, Willemsen G, Goldberg JH, Rasmussen F, Tarnoki AD, Tarnoki DL, Derom CA, Vlietinck RF, Loos RJF, Hopper JL, Sung J, Maes HH, Turkheimer E, Boomsma DI, Sørensen TIA, Kaprio J. Differences in genetic and environmental variation in adult BMI by sex, age, time period, and region: an individual-based pooled analysis of 40 twin cohorts. Am J Clin Nutr 2017; 106:457-466. [PMID: 28679550 PMCID: PMC5525120 DOI: 10.3945/ajcn.117.153643] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022] Open
Abstract
Background: Genes and the environment contribute to variation in adult body mass index [BMI (in kg/m2)], but factors modifying these variance components are poorly understood.Objective: We analyzed genetic and environmental variation in BMI between men and women from young adulthood to old age from the 1940s to the 2000s and between cultural-geographic regions representing high (North America and Australia), moderate (Europe), and low (East Asia) prevalence of obesity.Design: We used genetic structural equation modeling to analyze BMI in twins ≥20 y of age from 40 cohorts representing 20 countries (140,379 complete twin pairs).Results: The heritability of BMI decreased from 0.77 (95% CI: 0.77, 0.78) and 0.75 (95% CI: 0.74, 0.75) in men and women 20-29 y of age to 0.57 (95% CI: 0.54, 0.60) and 0.59 (95% CI: 0.53, 0.65) in men 70-79 y of age and women 80 y of age, respectively. The relative influence of unique environmental factors correspondingly increased. Differences in the sets of genes affecting BMI in men and women increased from 20-29 to 60-69 y of age. Mean BMI and variances in BMI increased from the 1940s to the 2000s and were greatest in North America and Australia, followed by Europe and East Asia. However, heritability estimates were largely similar over measurement years and between regions. There was no evidence of environmental factors shared by co-twins affecting BMI.Conclusions: The heritability of BMI decreased and differences in the sets of genes affecting BMI in men and women increased from young adulthood to old age. The heritability of BMI was largely similar between cultural-geographic regions and measurement years, despite large differences in mean BMI and variances in BMI. Our results show a strong influence of genetic factors on BMI, especially in early adulthood, regardless of the obesity level in the population.
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Affiliation(s)
- Karri Silventoinen
- Departments of Social Research and .,Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Aline Jelenkovic
- Departments of Social Research and,Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Reijo Sund
- Departments of Social Research and,Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Yoshie Yokoyama
- Department of Public Health Nursing, Osaka City University, Osaka, Japan
| | - Yoon-Mi Hur
- Department of Education, Mokpo National University, Jeonnam, South Korea
| | - Wendy Cozen
- Department of Preventive Medicine, Keck School of Medicine,,Norris Comprehensive Cancer Center, and
| | - Amie E Hwang
- Department of Preventive Medicine, Keck School of Medicine
| | - Thomas M Mack
- Department of Preventive Medicine, Keck School of Medicine,,Norris Comprehensive Cancer Center, and
| | - Chika Honda
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Fujio Inui
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan;,Faculty of Health Science, Kio University, Nara, Japan
| | - Yoshinori Iwatani
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mikio Watanabe
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Rie Tomizawa
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland;,Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Aila Rissanen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland;,Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Sisira H Siribaddana
- Institute of Research and Development, Battaramulla, Sri Lanka;,Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Matthew Hotopf
- National Institute for Health Research Mental Health Biomedical Research Centre, South London and Maudsley National Health Service Foundation Trust, Institute of Psychiatry Psychology and Neuroscience
| | - Athula Sumathipala
- Institute of Research and Development, Battaramulla, Sri Lanka;,Research Institute for Primary Care and Health Sciences, School for Primary Care Research, Faculty of Health, Keele University, Staffordshire, United Kingdom
| | - Fruhling Rijsdijk
- Medical Research Council Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, and
| | - Qihua Tan
- Unit of Epidemiology, Biostatistics, and Biodemography, Departments of Public Health and
| | - Dongfeng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China
| | - Zengchang Pang
- Department of Noncommunicable Diseases Prevention, Qingdao Centers for Disease Control and Prevention, Qingdao, China
| | - Maarit Piirtola
- Departments of Social Research and,Institute for Molecular Medicine, Helsinki, Finland
| | - Sari Aaltonen
- Departments of Social Research and,Public Health, and
| | - Sevgi Y Öncel
- Department of Statistics, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, Turkey
| | - Fazil Aliev
- Faculty of Business, Karabuk University, Karabuk, Turkey;,Departments of Psychology and,African American Studies
| | - Esther Rebato
- Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Leioa, Spain
| | | | - Kaare Christensen
- The Danish Twin Registry,,Departments of Clinical Biochemistry and Pharmacology and Clinical Genetics, and
| | | | - Kirsten O Kyvik
- Clinical Research, University of Southern Denmark, Odense, Denmark;,Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Judy L Silberg
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, and
| | - Lindon J Eaves
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, and
| | - Tessa L Cutler
- The Australian Twin Registry, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Juan R Ordoñana
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain;,Biomedical Research Institute of Murcia (IMIB)-Arrixaca, Murcia, Spain
| | - Juan F Sánchez-Romera
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain;,Biomedical Research Institute of Murcia (IMIB)-Arrixaca, Murcia, Spain
| | - Lucia Colodro-Conde
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain;,Quantitative Genetics Laboratory and
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sarah Yang
- Department of Epidemiology, School of Public Health, and,Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Kayoung Lee
- Department of Family Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, CA
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, CA;,US Department of Veterans Affairs San Diego Center of Excellence for Stress and Mental Health, La Jolla, CA
| | | | | | - Tracy L Nelson
- Department of Health and Exercise Sciences, Colorado School of Public Health, Colorado State University, Aurora, CO
| | | | | | - Kerry L Jang
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada; Departments of
| | - Margaret Gatz
- Department of Psychology, University of Southern California, Los Angeles, CA;,Medical Epidemiology and Biostatistics and
| | - David A Butler
- Health and Medicine Division, National Academies of Sciences, Engineering, and Medicine, Washington, DC
| | - Maria A Stazi
- Italian National Institute of Health National Center for Epidemiology, Surveillance, and Health Promotion, Rome, Italy
| | - Corrado Fagnani
- Italian National Institute of Health National Center for Epidemiology, Surveillance, and Health Promotion, Rome, Italy
| | - Cristina D’Ippolito
- Italian National Institute of Health National Center for Epidemiology, Surveillance, and Health Promotion, Rome, Italy
| | - Glen E Duncan
- Washington State Twin Registry, Health Sciences, Washington State University, Spokane, WA
| | - Dedra Buchwald
- Washington State Twin Registry, Health Sciences, Washington State University, Spokane, WA
| | - Nicholas G Martin
- Genetic Epidemiology Department, Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Australia
| | - Sarah E Medland
- Genetic Epidemiology Department, Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Australia
| | - Grant W Montgomery
- Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Hoe-Uk Jeong
- Department of Education, Mokpo National University, Jeonnam, South Korea
| | - Gary E Swan
- Department of Medicine, Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA
| | - Ruth Krasnow
- Center for Health Sciences, SRI International, Menlo Park, CA
| | | | | | - Anna K Dahl Aslan
- Medical Epidemiology and Biostatistics and,Institute of Gerontology and Aging Research Network, School of Health and Welfare, Jönköping University, Jönköping, Sweden
| | - Tom A McAdams
- Medical Research Council Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, and
| | - Thalia C Eley
- Medical Research Council Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, and
| | - Alice M Gregory
- Department of Psychology, Goldsmiths, University of London, London, United Kingdom
| | - Per Tynelius
- Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Laura A Baker
- Department of Psychology, University of Southern California, Los Angeles, CA
| | - Catherine Tuvblad
- Department of Psychology, University of Southern California, Los Angeles, CA;,School of Law, Psychology, and Social Work, Örebro University, Örebro, Sweden
| | | | - Danshiitsoodol Narandalai
- Healthy Twin Association of Mongolia, Ulaanbaatar, Mongolia;,Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom;,National Institute for Health Research Biomedical Research Centre at Guy’s and St. Thomas’ Foundation Trust, London, United Kingdom
| | - Genevieve Lachance
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | | | | | | | | | | | - Robert F Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN
| | - Shandell Pahlen
- Department of Psychology, University of Minnesota, Minneapolis, MN
| | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado
| | - Brooke M Huibregtse
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado
| | - Meike Bartels
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | | | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Jack H Goldberg
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Finn Rasmussen
- Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Adam D Tarnoki
- Department of Radiology, Semmelweis University, Budapest, Hungary;,Hungarian Twin Registry, Budapest, Hungary
| | - David L Tarnoki
- Department of Radiology, Semmelweis University, Budapest, Hungary;,Hungarian Twin Registry, Budapest, Hungary
| | - Catherine A Derom
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium;,Department of Obstetrics and Gynaecology, Ghent University Hospitals, Ghent, Belgium
| | | | - Ruth JF Loos
- Charles Bronfman Institute for Personalized Medicine, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John L Hopper
- Department of Epidemiology, School of Public Health, and,The Australian Twin Registry, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Joohon Sung
- Department of Epidemiology, School of Public Health, and,Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Hermine H Maes
- Departments of Human and Molecular Genetics and Psychiatry, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
| | - Eric Turkheimer
- Department of Psychology, University of Virginia, Charlottesville, VA
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Thorkild IA Sørensen
- Section on Metabolic Genetics, Novo Nordisk Foundation Centre for Basic Metabolic Research, Copenhagen, Denmark;,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; and,Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospitals, Copenhagen, Denmark
| | - Jaakko Kaprio
- Public Health, and,Institute for Molecular Medicine, Helsinki, Finland
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Mose KF, Burton M, Thomassen M, Andersen F, Kruse TA, Tan Q, Skov L, Røpke MA, Litman T, Clemmensen O, Kristensen BW, Friedmann PS, Andersen KE. The gene expression and immunohistochemical time-course of diphenylcyclopropenone-induced contact allergy in healthy humans following repeated epicutaneous challenges. Exp Dermatol 2017; 26:926-933. [DOI: 10.1111/exd.13345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Kristian F. Mose
- Department of Dermatology and Allergy Centre; Odense University Hospital; University of Southern Denmark; Odense C Denmark
- Dermatological Investigations Scandinavia; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Mark Burton
- Department of Clinical Genetics; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Mads Thomassen
- Department of Clinical Genetics; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Flemming Andersen
- Department of Dermatology and Allergy Centre; Odense University Hospital; University of Southern Denmark; Odense C Denmark
- Dermatological Investigations Scandinavia; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Torben A. Kruse
- Department of Clinical Genetics; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Qihua Tan
- Department of Clinical Genetics; Odense University Hospital; University of Southern Denmark; Odense C Denmark
- Epidemiology, Biostatistics and Biodemography; Department of Public Health; University of Southern Denmark; Odense C Denmark
| | - Lone Skov
- Department of Dermato-Allergology; Herlev and Gentofte Hospital; University of Copenhagen; Hellerup Denmark
| | - Mads A. Røpke
- Departments of Clinical Pharmacology and Molecular Biomedicine; LEO Pharma A/S; Ballerup Denmark
| | - Thomas Litman
- Departments of Clinical Pharmacology and Molecular Biomedicine; LEO Pharma A/S; Ballerup Denmark
- Department of Immunology and Microbiology; University of Copenhagen; Copenhagen N Denmark
| | - Ole Clemmensen
- Department of Clinical Pathology; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Bjarne W. Kristensen
- Department of Clinical Pathology; Odense University Hospital; University of Southern Denmark; Odense C Denmark
| | - Peter S. Friedmann
- Division of Infection, Inflammation & Immunity; Sir Henry Wellcome Laboratories; Southampton University Hospitals NHS Trust; Southampton UK
| | - Klaus E. Andersen
- Department of Dermatology and Allergy Centre; Odense University Hospital; University of Southern Denmark; Odense C Denmark
- Dermatological Investigations Scandinavia; Odense University Hospital; University of Southern Denmark; Odense C Denmark
- Centre for Innovative Medical Technology; Institute of Clinical Research; University of Southern Denmark; Odense C Denmark
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118
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Tang CQ, Li JQ, Shou BM, Pan BH, Chen TS, Xiao YQ, Zheng XP, Xiao SC, Tan Q, Xia ZF. Epidemiology and outcomes of bloodstream infections in 177 severe burn patients from an industrial disaster: a multicentre retrospective study. Clin Microbiol Infect 2017. [PMID: 28642142 DOI: 10.1016/j.cmi.2017.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To determine the characteristics of bloodstream infections (BSIs) and to evaluate the impact of BSIs on mortality in severe burn patients. METHODS A retrospective observational study was conducted in 20 tertiary hospitals. A total of 185 patients who experienced a massive dust explosion in eastern China were included. RESULTS After exclusion, 177 patients were analysed. The median total body surface area (TBSA) burned was 95% (interquartile range 85%-98%). Inhalation injuries occurred in 97.2%. The overall 90-day mortality was 35% (62/177). During the study period, 120 (67.8%) patients developed 253 episodes of BSI with 323 unique causative pathogens. Sixty-six episodes were polymicrobial infections. Catheter-related BSIs (CRBSIs) accounted for 41.5% of the episodes. Acinetobacter baumannii (19.5%), Klebsiella pneumoniae (13.9%) and Candida (12.7%) were the most common organisms. Antimicrobial resistance was found in 63.5% of the isolates, particularly in Gram-negative bacteria. Patients who developed BSIs had a greater illness severity at admission to the intensive care unit, and worse outcomes. After adjusting for demographics, severity of illness and treatment characteristics in a multivariate logistic model, there was a trend toward BSI increasing the risk of 90-day mortality (adjusted OR 3.4; 95% CI 0.9-12.9; p=0.069). In subgroup analyses, CRBSIs (adjusted OR 5.7; 95% CI 1.3-24.9; p=0.021 versus no BSI) and polymicrobial BSIs (adjusted OR 6.1; 95% CI 1.3-28.1; p=0.020 versus no BSI) had greater risk of 90-day mortality. CONCLUSIONS A strikingly high rate of BSIs was observed in severe burn patients. Gram-negative organisms and fungi were the leading causes. CRBSIs and polymicrobial BSIs were associated with high mortality.
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Affiliation(s)
- C Q Tang
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - J Q Li
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - B M Shou
- Department of Burns and Plastic Surgery, The Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu, China
| | - B H Pan
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - T S Chen
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Y Q Xiao
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - X P Zheng
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - S C Xiao
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China.
| | - Q Tan
- Department of Burns and Plastic Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China.
| | - Z F Xia
- Department of Burn Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China.
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119
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Tan Q, Thomassen M, Burton M, Mose KF, Andersen KE, Hjelmborg J, Kruse T. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data. J Integr Bioinform 2017; 14:/j/jib.2017.14.issue-2/jib-2017-0011/jib-2017-0011.xml. [PMID: 28753536 PMCID: PMC6042830 DOI: 10.1515/jib-2017-0011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/04/2017] [Indexed: 11/15/2022] Open
Abstract
Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.
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Affiliation(s)
- Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
- Epidemiology, Biostatistics, and Biodemography, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Mads Thomassen
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Mark Burton
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Kristian Fredløv Mose
- Department of Dermatology and Allergy Centre, Odense University Hospital, University of Southern Denmark, 5000 Odense C, Denmark
| | - Klaus Ejner Andersen
- Department of Dermatology and Allergy Centre, Odense University Hospital, University of Southern Denmark, 5000 Odense C, Denmark
- Dermatological Investigations Scandinavia, J.B. Winsløwsvej 9, 5000 Odense C, Denmark
- Centre for Innovative Medical Technology, Institute of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics, and Biodemography, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9B, DK-5000, Odense C, Denmark
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
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Bogl LH, Jelenkovic A, Vuoksimaa E, Ahrenfeldt L, Pietiläinen KH, Stazi MA, Fagnani C, D'Ippolito C, Hur YM, Jeong HU, Silberg JL, Eaves LJ, Maes HH, Bayasgalan G, Narandalai D, Cutler TL, Kandler C, Jang KL, Christensen K, Skytthe A, Kyvik KO, Cozen W, Hwang AE, Mack TM, Derom CA, Vlietinck RF, Nelson TL, Whitfield KE, Corley RP, Huibregtse BM, McAdams TA, Eley TC, Gregory AM, Krueger RF, McGue M, Pahlen S, Willemsen G, Bartels M, van Beijsterveldt TCEM, Pang Z, Tan Q, Zhang D, Martin NG, Medland SE, Montgomery GW, Hjelmborg JVB, Rebato E, Swan GE, Krasnow R, Busjahn A, Lichtenstein P, Öncel SY, Aliev F, Baker LA, Tuvblad C, Siribaddana SH, Hotopf M, Sumathipala A, Rijsdijk F, Magnusson PKE, Pedersen NL, Aslan AKD, Ordoñana JR, Sánchez-Romera JF, Colodro-Conde L, Duncan GE, Buchwald D, Tarnoki AD, Tarnoki DL, Yokoyama Y, Hopper JL, Loos RJF, Boomsma DI, Sørensen TIA, Silventoinen K, Kaprio J. Does the sex of one's co-twin affect height and BMI in adulthood? A study of dizygotic adult twins from 31 cohorts. Biol Sex Differ 2017; 8:14. [PMID: 28465822 PMCID: PMC5408365 DOI: 10.1186/s13293-017-0134-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Background The comparison of traits in twins from opposite-sex (OS) and same-sex (SS) dizygotic twin pairs is considered a proxy measure of prenatal hormone exposure. To examine possible prenatal hormonal influences on anthropometric traits, we compared mean height, body mass index (BMI), and the prevalence of being overweight or obese between men and women from OS and SS dizygotic twin pairs. Methods The data were derived from the COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) database, and included 68,494 SS and 53,808 OS dizygotic twin individuals above the age of 20 years from 31 twin cohorts representing 19 countries. Zygosity was determined by questionnaires or DNA genotyping depending on the study. Multiple regression and logistic regression models adjusted for cohort, age, and birth year with the twin type as a predictor were carried out to compare height and BMI in twins from OS pairs with those from SS pairs and to calculate the adjusted odds ratios and 95% confidence intervals for being overweight or obese. Results OS females were, on average, 0.31 cm (95% confidence interval (CI) 0.20, 0.41) taller than SS females. OS males were also, on average, taller than SS males, but this difference was only 0.14 cm (95% CI 0.02, 0.27). Mean BMI and the prevalence of overweight or obesity did not differ between males and females from SS and OS twin pairs. The statistically significant differences between OS and SS twins for height were small and appeared to reflect our large sample size rather than meaningful differences of public health relevance. Conclusions We found no evidence to support the hypothesis that prenatal hormonal exposure or postnatal socialization (i.e., having grown up with a twin of the opposite sex) has a major impact on height and BMI in adulthood. Electronic supplementary material The online version of this article (doi:10.1186/s13293-017-0134-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonie H Bogl
- Institute for Molecular Medicine FIMM, University of Helsinki, P.O. Box 20, FI-00014 Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aline Jelenkovic
- Department of Social Research, University of Helsinki, Helsinki, Finland.,Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Eero Vuoksimaa
- Institute for Molecular Medicine FIMM, University of Helsinki, P.O. Box 20, FI-00014 Helsinki, Finland
| | - Linda Ahrenfeldt
- Department of Public Health, Epidemiology, Biostatistics & Biodemography, The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Maria A Stazi
- Istituto Superiore di Sanità-National Center for Epidemiology, Surveillance and Health Promotion, Rome, Italy
| | - Corrado Fagnani
- Istituto Superiore di Sanità-National Center for Epidemiology, Surveillance and Health Promotion, Rome, Italy
| | - Cristina D'Ippolito
- Istituto Superiore di Sanità-National Center for Epidemiology, Surveillance and Health Promotion, Rome, Italy
| | - Yoon-Mi Hur
- Department of Education, Mokpo National University, Jeonnam, South Korea
| | - Hoe-Uk Jeong
- Department of Education, Mokpo National University, Jeonnam, South Korea
| | - Judy L Silberg
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA USA
| | - Lindon J Eaves
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA USA
| | - Hermine H Maes
- Department of Human and Molecular Genetics, Psychiatry & Massey Cancer Center, Virginia Commonwealth University, Richmond, VA USA
| | | | - Danshiitsoodol Narandalai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Healthy Twin Association of Mongolia, Ulaanbaatar, Mongolia
| | - Tessa L Cutler
- The Australian Twin Registry, Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC Australia
| | | | - Kerry L Jang
- Department of Psychiatry, University of British Columbia, Vancouver, BC Canada
| | - Kaare Christensen
- Department of Public Health, Epidemiology, Biostatistics & Biodemography, The Danish Twin Registry, University of Southern Denmark, Odense, Denmark.,Department of Clinical Biochemistry and Pharmacology and Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Axel Skytthe
- Department of Public Health, Epidemiology, Biostatistics & Biodemography, The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | - Kirsten O Kyvik
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Odense Patient data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Wendy Cozen
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA USA.,USC Norris Comprehensive Cancer Center, Los Angeles, CA USA
| | - Amie E Hwang
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA USA
| | - Thomas M Mack
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA USA.,USC Norris Comprehensive Cancer Center, Los Angeles, CA USA
| | - Catherine A Derom
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium.,Department of Obstetrics and Gynaecology, Ghent University Hospitals, Ghent, Belgium
| | | | - Tracy L Nelson
- Department of Health and Exercise Sciences and Colorado School of Public Health, Colorado State University, Fort Collins, USA
| | | | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO USA
| | | | - Tom A McAdams
- Institute of Psychiatry, Psychology & Neuroscience, MRC Social, Genetic & Developmental Psychiatry Centre, King's College London, London, UK
| | - Thalia C Eley
- Institute of Psychiatry, Psychology & Neuroscience, MRC Social, Genetic & Developmental Psychiatry Centre, King's College London, London, UK
| | - Alice M Gregory
- Department of Psychology, Goldsmiths, University of London, London, UK
| | - Robert F Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN USA
| | - Shandell Pahlen
- Department of Psychology, University of Minnesota, Minneapolis, MN USA
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Meike Bartels
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | | | - Zengchang Pang
- Department of Noncommunicable Diseases Prevention, Qingdao Centers for Disease Control and Prevention, Qingdao, China
| | - Qihua Tan
- Institute of Public Health, Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Dongfeng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China
| | - Nicholas G Martin
- Genetic Epidemiology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sarah E Medland
- Genetic Epidemiology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Grant W Montgomery
- Molecular Epidemiology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jacob V B Hjelmborg
- Department of Public Health, Epidemiology, Biostatistics & Biodemography, The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | - Esther Rebato
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Gary E Swan
- Department of Medicine, Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA USA
| | - Ruth Krasnow
- Center for Health Sciences, SRI International, Menlo Park, CA USA
| | | | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sevgi Y Öncel
- Department of Statistics, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, Turkey
| | - Fazil Aliev
- Psychology and African American Studies, Virginia Commonwealth University, Richmond, USA.,Faculty of Business, Karabuk University, Karabuk, Turkey
| | - Laura A Baker
- Department of Psychology, University of Southern California, Los Angeles, CA USA
| | - Catherine Tuvblad
- Department of Psychology, University of Southern California, Los Angeles, CA USA.,School of Law, Psychology and Social Work, Örebro University, Örebro, Sweden
| | - Sisira H Siribaddana
- Institute of Research & Development, Battaramulla, Sri Lanka.,Faculty of Medicine & Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Matthew Hotopf
- Institute of Psychiatry Psychology and Neuroscience, NIHR Mental Health Biomedical Research Centre, South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Athula Sumathipala
- Institute of Research & Development, Battaramulla, Sri Lanka.,Research Institute for Primary Care and Health Sciences, School for Primary Care Research (SPCR), Faculty of Health, Keele University, Staffordshire, UK
| | - Fruhling Rijsdijk
- Institute of Psychiatry, Psychology & Neuroscience, MRC Social, Genetic & Developmental Psychiatry Centre, King's College London, London, UK
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anna K Dahl Aslan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Institute of Gerontology and Aging Research Network-Jönköping (ARN-J), School of Health and Welfare, Jönköping University, Jönköping, Sweden
| | - Juan R Ordoñana
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain.,IMIB-Arrixaca, Murcia, Spain
| | - Juan F Sánchez-Romera
- Department of Developmental and Educational Psychology, University of Murcia, Murcia, Spain.,IMIB-Arrixaca, Murcia, Spain
| | - Lucia Colodro-Conde
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Glen E Duncan
- Washington State Twin Registry, Washington State University-Health Sciences Spokane, Spokane, WA USA
| | - Dedra Buchwald
- Washington State Twin Registry, Washington State University-Health Sciences Spokane, Spokane, WA USA
| | - Adam D Tarnoki
- Department of Radiology, Semmelweis University, Budapest, Hungary.,Hungarian Twin Registry, Budapest, Hungary
| | - David L Tarnoki
- Department of Radiology, Semmelweis University, Budapest, Hungary.,Hungarian Twin Registry, Budapest, Hungary
| | - Yoshie Yokoyama
- Department of Public Health Nursing, Osaka City University, Osaka, Japan
| | - John L Hopper
- The Australian Twin Registry, Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC Australia.,Department of Epidemiology, School of Public Health, Seoul National University, Seoul, South Korea
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Centre for Basic Metabolic Research (Section on Metabolic Genetics), and Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, Copenhagen, The Capital Region Denmark
| | - Karri Silventoinen
- Department of Social Research, University of Helsinki, Helsinki, Finland.,Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM, University of Helsinki, P.O. Box 20, FI-00014 Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
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Liu N, Liu YF, Sui J, Zhang YQ, Ma SM, Wu WJ, Liang G, Tan Q. [Polymorphism analysis of MTHFR,BMPR1B and TYMS in microtia]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2017; 31:409-414. [PMID: 29871275 DOI: 10.13201/j.issn.1001-1781.2017.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Indexed: 11/12/2022]
Abstract
Objective:To explore the relationship between MTHFR,BMPR1B and TYMS polymorphism and congenitial microtia in Chinese Han population.Method:A total of 180 microtia patients and 141 healthy participants were enrolled in this study.The genotyping of MTHFR rs4846049, BMPR1B rs1434536 and TYMS rs2790 of the participants were examined with multiple PCR. Frequencies and allele distribution of MTHFR rs4846049,BMPR1B rs1434536 and TYMS rs2790 between cases and control were analyzed with Chi-square test. Result:The genotype frequency distribution of TYMS rs27901 polymorphism was significantly different between two groups(P<0.05).Furthermore, gender stratified analysis showed that TYMS rs2790 polymorphism mainly increase the risks of congenitial microtia in male(P<0.05).Compared with AA genotype,the mircotia risks of subjects with AG GG AG+GG raised to 1.93, 3.23 and 2.10 times,respectively(95%CI:1.07-3.48、1.12-9.33 and 1.20-3.68).However,there was no relationship between MTHFR rs4846049, BMPR1B rs1434536 and microtia. Conclusion:The TYMS rs2790 polymorphism may be a risk factor of microtia in male.
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Affiliation(s)
- N Liu
- Department of Plastic Surgery, Hospital of Traditional Chinese Medicine,Nanjing,210029,China
| | - Y F Liu
- Department of Plastic Surgery, Hospital of Traditional Chinese Medicine,Nanjing,210029,China
| | - J Sui
- Key Laboratory of Enviromental Medicine Engineering,Ministry of Education,School of Public Health,Southeast University
| | - Y Q Zhang
- Key Laboratory of Enviromental Medicine Engineering,Ministry of Education,School of Public Health,Southeast University
| | - S M Ma
- Key Laboratory of Enviromental Medicine Engineering,Ministry of Education,School of Public Health,Southeast University
| | - W J Wu
- Key Laboratory of Enviromental Medicine Engineering,Ministry of Education,School of Public Health,Southeast University
| | - G Liang
- Key Laboratory of Enviromental Medicine Engineering,Ministry of Education,School of Public Health,Southeast University
| | - Q Tan
- Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine,Nanjing University of Chinese Medicine
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Abstract
Genome-wide association studies with moderate sample sizes are underpowered, especially when testing SNP alleles with low allele counts, a situation that may lead to high frequency of false-positive results and lack of replication in independent studies. Related individuals, such as twin pairs concordant for a disease, should confer increased power in genetic association analysis because of their genetic relatedness. We conducted a computer simulation study to explore the power advantage of the disease-concordant twin design, which uses singletons from disease-concordant twin pairs as cases and ordinary healthy samples as controls. We examined the power gain of the twin-based design for various scenarios (i.e., cases from monozygotic and dizygotic twin pairs concordant for a disease) and compared the power with the ordinary case-control design with cases collected from the unrelated patient population. Simulation was done by assigning various allele frequencies and allelic relative risks for different mode of genetic inheritance. In general, for achieving a power estimate of 80%, the sample sizes needed for dizygotic and monozygotic twin cases were one half and one fourth of the sample size of an ordinary case-control design, with variations depending on genetic mode. Importantly, the enriched power for dizygotic twins also applies to disease-concordant sibling pairs, which largely extends the application of the concordant twin design. Overall, our simulation revealed a high value of disease-concordant twins in genetic association studies and encourages the use of genetically related individuals for highly efficiently identifying both common and rare genetic variants underlying human complex diseases without increasing laboratory cost.
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Affiliation(s)
- Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark
| | - Weilong Li
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark
| | - Fabio Vandin
- Department of Mathematics and Computer Science, University of Southern Denmark, Denmark.,Department of Information Engineering, University of Padova, Italy
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Jelenkovic A, Hur YM, Sund R, Yokoyama Y, Siribaddana SH, Hotopf M, Sumathipala A, Rijsdijk F, Tan Q, Zhang D, Pang Z, Aaltonen S, Heikkilä K, Öncel SY, Aliev F, Rebato E, Tarnoki AD, Tarnoki DL, Christensen K, Skytthe A, Kyvik KO, Silberg JL, Eaves LJ, Maes HH, Cutler TL, Hopper JL, Ordoñana JR, Sánchez-Romera JF, Colodro-Conde L, Cozen W, Hwang AE, Mack TM, Sung J, Song YM, Yang S, Lee K, Franz CE, Kremen WS, Lyons MJ, Busjahn A, Nelson TL, Whitfield KE, Kandler C, Jang KL, Gatz M, Butler DA, Stazi MA, Fagnani C, D'Ippolito C, Duncan GE, Buchwald D, Derom CA, Vlietinck RF, Loos RJ, Martin NG, Medland SE, Montgomery GW, Jeong HU, Swan GE, Krasnow R, Magnusson PK, Pedersen NL, Dahl-Aslan AK, McAdams TA, Eley TC, Gregory AM, Tynelius P, Baker LA, Tuvblad C, Bayasgalan G, Narandalai D, Lichtenstein P, Spector TD, Mangino M, Lachance G, Bartels M, van Beijsterveldt TC, Willemsen G, Burt SA, Klump KL, Harris JR, Brandt I, Nilsen TS, Krueger RF, McGue M, Pahlen S, Corley RP, Hjelmborg JVB, Goldberg JH, Iwatani Y, Watanabe M, Honda C, Inui F, Rasmussen F, Huibregtse BM, Boomsma DI, Sørensen TIA, Kaprio J, Silventoinen K. Genetic and environmental influences on adult human height across birth cohorts from 1886 to 1994. eLife 2016; 5. [PMID: 27964777 PMCID: PMC5156525 DOI: 10.7554/elife.20320] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/21/2016] [Indexed: 12/23/2022] Open
Abstract
Human height variation is determined by genetic and environmental factors, but it remains unclear whether their influences differ across birth-year cohorts. We conducted an individual-based pooled analysis of 40 twin cohorts including 143,390 complete twin pairs born 1886–1994. Although genetic variance showed a generally increasing trend across the birth-year cohorts, heritability estimates (0.69-0.84 in men and 0.53-0.78 in women) did not present any clear pattern of secular changes. Comparing geographic-cultural regions (Europe, North America and Australia, and East Asia), total height variance was greatest in North America and Australia and lowest in East Asia, but no clear pattern in the heritability estimates across the birth-year cohorts emerged. Our findings do not support the hypothesis that heritability of height is lower in populations with low living standards than in affluent populations, nor that heritability of height will increase within a population as living standards improve. DOI:http://dx.doi.org/10.7554/eLife.20320.001
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Affiliation(s)
- Aline Jelenkovic
- Department of Social Research, University of Helsinki, Helsinki, Finland.,Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Yoon-Mi Hur
- Department of Education, Mokpo National University, Jeonnam, South Korea
| | - Reijo Sund
- Department of Social Research, University of Helsinki, Helsinki, Finland
| | - Yoshie Yokoyama
- Department of Public Health Nursing, Osaka City University, Osaka, Japan
| | - Sisira H Siribaddana
- Institute of Research & Development, Battaramulla, Sri Lanka.,Faculty of Medicine & Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Matthew Hotopf
- NIHR Mental Health Biomedical Research Centre, South London and Maudsley NHS Foundation Trust and, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Athula Sumathipala
- Institute of Research & Development, Battaramulla, Sri Lanka.,Research Institute for Primary Care and Health Sciences, School for Primary Care Research, Faculty of Health, Keele University, Staffordshire, United Kingdom
| | - Fruhling Rijsdijk
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Dongfeng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China
| | - Zengchang Pang
- Department of Noncommunicable Diseases Prevention, Qingdao Centers for Disease Control and Prevention, Qingdao, China
| | - Sari Aaltonen
- Department of Social Research, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Kauko Heikkilä
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Sevgi Y Öncel
- Department of Statistics, Faculty of Arts and Sciences, Kirikkale University, Kirikkale, Turkey
| | - Fazil Aliev
- Faculty of Business, Karabuk University, Karabuk, Turkey.,Department of Psychology, Virginia Commonwealth University, Richmond, United States.,Department of African American Studies, Virginia Commonwealth University, Richmond, United States
| | - Esther Rebato
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Adam D Tarnoki
- Department of Radiology and Oncotherapy, Semmelweis University, Budapest, Hungary.,Hungarian Twin Registry, Budapest, Hungary
| | - David L Tarnoki
- Department of Radiology and Oncotherapy, Semmelweis University, Budapest, Hungary.,Hungarian Twin Registry, Budapest, Hungary
| | - Kaare Christensen
- The Danish Twin Registry, University of Southern Denmark, Odense, Denmark.,Department of Public Health, Epidemiology, Biostatistics & Biodemography, University of Southern Denmark, Odense, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Axel Skytthe
- The Danish Twin Registry, University of Southern Denmark, Odense, Denmark.,Department of Public Health, Epidemiology, Biostatistics & Biodemography, University of Southern Denmark, Odense, Denmark
| | - Kirsten O Kyvik
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Odense Patient data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Judy L Silberg
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States
| | - Lindon J Eaves
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States
| | - Hermine H Maes
- Department of Human and Molecular Genetics, Psychiatry & Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States
| | - Tessa L Cutler
- The Australian Twin Registry, Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Australia
| | - John L Hopper
- The Australian Twin Registry, Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Australia.,Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea
| | - Juan R Ordoñana
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain.,IMIB-Arrixaca, Murcia, Spain
| | - Juan F Sánchez-Romera
- IMIB-Arrixaca, Murcia, Spain.,Department of Developmental and Educational Psychology, University of Murcia, Murcia, Spain
| | - Lucia Colodro-Conde
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Wendy Cozen
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, United States.,USC Norris Comprehensive Cancer Center, Los Angeles, United States
| | - Amie E Hwang
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, United States
| | - Thomas M Mack
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, United States.,USC Norris Comprehensive Cancer Center, Los Angeles, United States
| | - Joohon Sung
- Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, South-Korea
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South-Korea
| | - Sarah Yang
- Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, South-Korea
| | - Kayoung Lee
- Department of Family Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, San Diego, United States
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, San Diego, United States.,VA San Diego Center of Excellence for Stress and Mental Health, La Jolla, CA, United States
| | - Michael J Lyons
- Department of Psychology, Boston University, Boston, United States
| | | | - Tracy L Nelson
- Department of Health and Exercise Sciences and Colorado School of Public Health, Colorado State University, Colorado, United States
| | | | | | - Kerry L Jang
- Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Margaret Gatz
- Department of Psychology, University of Southern California, Los Angeles, United States.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - David A Butler
- Health and Medicine Division, The National Academies of Sciences, Engineering, and Medicine, Washington, United States
| | - Maria A Stazi
- Istituto Superiore di Sanità - National Center for Epidemiology, Surveillance and Health Promotion, Rome, Italy
| | - Corrado Fagnani
- Istituto Superiore di Sanità - National Center for Epidemiology, Surveillance and Health Promotion, Rome, Italy
| | - Cristina D'Ippolito
- Istituto Superiore di Sanità - National Center for Epidemiology, Surveillance and Health Promotion, Rome, Italy
| | - Glen E Duncan
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, United States
| | - Dedra Buchwald
- Washington State Twin Registry, Washington State University, Seattle, United States
| | - Catherine A Derom
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium.,Department of Obstetrics and Gynaecology, Ghent University Hospitals, Ghent, Belgium
| | | | - Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nicholas G Martin
- Genetic Epidemiology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sarah E Medland
- Genetic Epidemiology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Grant W Montgomery
- Molecular Epidemiology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Hoe-Uk Jeong
- Department of Education, Mokpo National University, Jeonnam, South Korea
| | - Gary E Swan
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Ruth Krasnow
- Center for Health Sciences, SRI International, Menlo Park, United States
| | - Patrik Ke Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anna K Dahl-Aslan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Institute of Gerontology and Aging Research Network - Jönköping (ARN-J), School of Health and Welfare, Jönköping University, Jönköping, Sweden
| | - Tom A McAdams
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Thalia C Eley
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Alice M Gregory
- Department of Psychology, Goldsmiths, University of London, London, United Kingdom
| | - Per Tynelius
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Laura A Baker
- Department of Psychology, University of Southern California, Los Angeles, United States
| | - Catherine Tuvblad
- Department of Psychology, University of Southern California, Los Angeles, United States.,School of Law, Psychology and Social Work, Örebro University, Örebro, Sweden
| | | | - Danshiitsoodol Narandalai
- Healthy Twin Association of Mongolia, Ulaanbaatar, Mongolia.,Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College, London, United Kingdom
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College, London, United Kingdom
| | - Genevieve Lachance
- Department of Twin Research and Genetic Epidemiology, King's College, London, United Kingdom
| | - Meike Bartels
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | | | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - S Alexandra Burt
- Michigan State University, East Lansing, Michigan, United States
| | - Kelly L Klump
- Michigan State University, East Lansing, Michigan, United States
| | | | | | | | - Robert F Krueger
- Department of Psychology, University of Minnesota, Minneapolis, United States
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, United States
| | - Shandell Pahlen
- Department of Psychology, University of Minnesota, Minneapolis, United States
| | - Robin P Corley
- Institute for Behavioral Genetics, University of Colorado, Boulder, United States
| | - Jacob V B Hjelmborg
- The Danish Twin Registry, University of Southern Denmark, Odense, Denmark.,Department of Public Health, Epidemiology, Biostatistics & Biodemography, University of Southern Denmark, Odense, Denmark
| | - Jack H Goldberg
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, United States
| | - Yoshinori Iwatani
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mikio Watanabe
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Chika Honda
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Fujio Inui
- Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan.,Faculty of Health Science, Kio University, Nara, Japan
| | - Finn Rasmussen
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Brooke M Huibregtse
- Institute for Behavioral Genetics, University of Colorado, Boulder, United States
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Centre for Basic Metabolic Research (Section on Metabolic Genetics), University of Copenhagen, Copenhagen, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, Copenhagen, Denmark
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine FIMM, Helsinki, Finland
| | - Karri Silventoinen
- Department of Social Research, University of Helsinki, Helsinki, Finland.,Osaka University Graduate School of Medicine, Osaka University, Osaka, Japan
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Abstract
Polycystic ovarian syndrome (PCOS) is a complex condition of ovarian dysfunction and metabolic abnormalities with widely varying clinical manifestations resulting from interference of the genome and the environment through integrative biological mechanisms with the emerging field of epigenetics offering an appealing tool for studying the nature and nurture of the disease. We review the current literature of epigenetic studies on PCOS from disease development to the association analysis of the DNA methylome and to exploratory studies on the molecular mechanisms of disease heterogeneity and comorbidity. Recent data based on profiling of the DNA methylome of PCOS in different tissues provided consistent molecular evidence in support of epidemiological findings on disease comorbidity suggesting a possible autoimmune basis in the pathogenesis of the disease. We show that the field of epigenetics and epigenomics could serve to link molecular regulatory mechanisms with disease development and disease manifestation which could contribute to PCOS prevention and treatment and eventually promote reproductive health in fertile age women. We summarize the up-to-date findings and discuss the implications of various studies and point to new avenues of research on PCOS in the rapidly developing field of epigenetics and epigenomics.
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Affiliation(s)
- Shuxia Li
- a Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark , Odense , Denmark
| | - Dongyi Zhu
- b Center of Reproductive Medicine, Linyi People's Hospital , Linyi , China
- c Department of Obstetrics and Gynecology , Shandong Medical College , Linyi , China
| | - Hongmei Duan
- d Department of Medicine , Kolding Hospital , Kolding , Denmark , and
| | - Qihua Tan
- a Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark , Odense , Denmark
- e Epidemiology, Biostatistics, and Biodemography, Department of Public Health, University of Southern Denmark , Odense , Denmark
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125
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Yang ML, Li YH, Tan Q, Li JT, Que LL. [Effect of hydrocinnamoyl-L-valyl pyrrolidine on healing quality of deep partial-thickness scald wound in mice]. Zhonghua Shao Shang Za Zhi 2016; 32:658-666. [PMID: 27894387 DOI: 10.3760/cma.j.issn.1009-2587.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To observe the effect of Toll interleukin-1 recptor homology/BB-loop mimetic hydrocinnamoyl-L-valyl pyrrolidine (AS-1) on the healing quality of deep partial-thickness scald wound in mice. Methods: Forty-two adult C57BL/6 mice were divided into sham injury group (SI), scald group (S), early AS-1 treatment group (EAT), early dimethyl sulfoxide (DMSO) control group (EDC), late AS-1 treatment group (LAT), late DMSO control group (LDC) according to the random number table, with 7 mice in each group. Mice in group SI were sham injured without other treatment. Deep partial-thickness scald model with 10% total body surface area was reproduced on the back of the other mice, and the wound was treated by daily wound cleaning with saline and dressing changing with vaseline gauze after injury. Mice in group EAT and those in group LAT were intraperitoneally injected with 20 mg/mL AS-1 50 mg/kg each day respectively from post scald hour (PSH) 8 and post scald day (PSD) 15 on. Mice in group EDC and those in group LDC were intraperitoneally injected with 20 mg/mL DMSO 50 mg/kg each day respectively from PSH 8 and PSD 15 on. On PSD 21, the gross condition of wound healing of mice with scald was observed, and the wound healing rate was calculated. Tissue samples of healed wound were collected and stained with HE and Masson respectively to observe the histomorphological change and fibrosis of collagen, and the percentage of fibrosis of collagen was calculated. The mRNA expressions of interleukin-1β (IL-1β), tumor necrosis factor α (TNF-α), transforming growth factor β1 (TGF-β1), matrix metalloproteinase-1 (MMP-1), tissue inhibitors of metalloproteinase 1 (TIMP-1), connective tissue growth factor (CTGF), type Ⅰ collagen and type Ⅲ collagen in healed wound tissue were detected by real time fluorescent quantitive reverse transcription polymerase chain reaction. The protein expressions of type Ⅰ collagen and type Ⅲ collagen in healed wound tissue were detected by Western blotting. Skin tissue of mice in group SI at the same area as that observed and collected in mice with scald was performed with the same observation and detection as mentioned above at the same time. Data were processed with one-way analysis of variance and Tukey test. Results: On PSD 21, no abnormal appearance was found in skin tissue of mice in group SI. Wounds of mice in group EAT were healed completely without scar formation, while those in the other four groups were not completely healed with scars formed in different degree. The wound healing rate of mice in group EAT was (97±4)%, close to that of group SI (100%, q=1.753, P>0.05), and both of them were obviously higher than those of groups S, EDC, LAT, and LDC [respectively (83±8)%, (87±6)%, (85±9)%, and (85±7)%, with q values from 4.819 to 6.803, P<0.05 or P<0.01]. On PSD 21, no abnormal appearance was found in morphology of skin tissue of mice in group SI. The morphology of healed wound tissue of mice in group EAT was close to that in group SI, with little epidermis hyalinosis and few newly formed collagen fibers arranged orderly. Epidermis hyalinosis in band- or flake-shape and obvious proliferation of collagen fibers arranged disorderly were observed in healed wound tissue of mice in the other four groups. Much infiltration of inflammatory cells was found in group S. The percentage of fibrosis of collagen in healed wound tissue of mice in group EAT was (30±3)%, close to that of group SI [(30±4)%, q=0.159, P>0.05], and both of them were obviously lower than those of groups S, EDC, LAT, and LDC [respectively (86±9)%, (74±5)%, (82±4)%, and (82±7)%, with q values from 12.080 to 15.530, P values below 0.01]. On PSD 21, compared with those of group SI, the mRNA expressions of IL-1β, TNF-α, TGF-β1, MMP-1, and CTGF in healed wound tissue of mice in group S, the mRNA expressions of TGF-β1 in healed wound tissue of mice in groups EDC and LDC, and the mRNA expression of MMP-1 in healed wound tissue of mice in group LAT were significantly increased (with q values from 4.039 to 5.232, P values below 0.05), while the mRNA expression of TIMP-1 in healed wound tissue of mice in group S was significantly decreased (q=4.921, P<0.05). Compared with those of group S, the mRNA expressions of IL-1β, TNF-α, TGF-β1, MMP-1, and CTGF in healed wound tissue of mice in group EAT and the mRNA expressions of IL-1β and CTGF in healed wound tissue of mice in group LAT were significantly decreased (with q values from 4.418 to 6.402, P<0.05 or P<0.01), while the mRNA expressions of TIMP-1 in healed wound tissue of mice in groups EAT and LAT were significantly increased (with q values respectively 3.929 and 8.299, P<0.05 or P<0.01). Compared with those of group SI, the mRNA and protein expressions of type Ⅲ collagen in healed wound tissue of mice in the other groups and the mRNA and protein expressions of type Ⅰ collagen in healed wound tissue of mice in groups S, EDC, LAT, and LDC were significantly increased (with q values from 7.054 to 11.650, P values below 0.01). Compared with those of group EAT, the mRNA and protein expressions of type Ⅰ collagen in healed wound tissue of mice in groups S, EDC, LAT, and LDC were significantly increased (with q values from 5.156 to 7.451, P<0.05 or P<0.01). Conclusions: AS-1 can effectively promote wound healing and reduce fibrosis degree in the early stage of inflammation response after deep partial-thickness scald in mice, which may be related to its effect in decreasing the expression of inflammation related factors IL-1β and TNF-α and fibrosis related factors TGF-β1, MMP-1, CTGF, and type Ⅰ collagen.
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Affiliation(s)
- M L Yang
- Gulou Clinical Medical College of Nanjing Medical University, Nanjing 210008, China
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Svendsen AJ, Gervin K, Lyle R, Christiansen L, Kyvik K, Junker P, Nielsen C, Houen G, Tan Q. Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis: An Epigenome-Wide Study. Front Immunol 2016; 7:510. [PMID: 27909437 PMCID: PMC5112246 DOI: 10.3389/fimmu.2016.00510] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/02/2016] [Indexed: 12/29/2022] Open
Abstract
Objectives In an explorative epigenome-wide association study (EWAS) to search for gene independent, differentially methylated DNA positions and regions (DMRs) associated with rheumatoid arthritis (RA) by studying monozygotic (MZ) twin pairs discordant for RA. Methods Genomic DNA was isolated from whole blood samples from 28 MZ twin pairs discordant for RA. DNA methylation was measured using the HumanMethylation450 BeadChips. Smoking, anti-cyclic citrullinated peptide antibodies, and immunosuppressive treatment were included as covariates. Pathway analysis was performed using GREAT. Results Smoking was significantly associated with hypomethylation of a DMR overlapping the promoter region of the RNF5 and the AGPAT1, which are implicated in inflammation and autoimmunity, whereas DMARD treatment induced hypermethylation of the same region. Additionally, the promotor region of both S100A6 and EFCAB4B were hypomethylated, and both genes have previously been associated with RA. We replicated several candidate genes identified in a previous EWAS in treatment-naïve RA singletons. Gene-set analysis indicated the involvement of immunologic signatures and cancer-related pathways in RA. Conclusion We identified several differentially methylated regions associated with RA, which may represent environmental effects or consequences of the disease and plausible biological pathways pertinent to the pathogenesis of RA.
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Affiliation(s)
- Anders J Svendsen
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark , Odense , Denmark
| | - Kristina Gervin
- Department of Medical Genetics, Oslo University Hospital, University of Oslo , Oslo , Norway
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, University of Oslo , Oslo , Norway
| | - Lene Christiansen
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark , Odense , Denmark
| | - Kirsten Kyvik
- Denmark and Odense Patient data Explorative Network (OPEN), Institute of Clinical Research, Odense University Hospital, University of Southern Denmark , Odense , Denmark
| | - Peter Junker
- Department of Rheumatology, Odense University Hospital, University of Southern Denmark , Odense , Denmark
| | - Christian Nielsen
- Department of Clinical Immunology, Odense University Hospital , Odense , Denmark
| | - Gunnar Houen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institute , Copenhagen , Denmark
| | - Qihua Tan
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Starnawska A, Tan Q, Lenart A, McGue M, Mors O, Børglum AD, Christensen K, Nyegaard M, Christiansen L. Blood DNA methylation age is not associated with cognitive functioning in middle-aged monozygotic twins. Neurobiol Aging 2016; 50:60-63. [PMID: 27889677 DOI: 10.1016/j.neurobiolaging.2016.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/23/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
Abstract
The epigenetic clock, also known as DNA methylation age (DNAmAge), represents age-related changes of DNA methylation at multiple sites of the genome and is suggested to be a biomarker for biological age. Elevated blood DNAmAge is associated with all-cause mortality, with the strongest effects reported in a recent intrapair twin study where epigenetically older twins had increased mortality risk in comparison to their co-twins. In the study presented here, we hypothesize that DNAmAge in blood is associated with cross-sectional and longitudinal cognitive abilities in middle-aged individuals. In 486 monozygotic twins, we investigated the association of DNAmAge, difference between DNAmAge and chronological age and age acceleration with cognition. Despite using a powerful paired twin design, we found no evidence for association of blood DNAmAge with cognitive abilities. This observation was confirmed in unpaired analyses, where DNAmAge initially correlated with cognitive abilities, until adjusting for chronological age. Overall, our study shows that for middle-aged individuals DNAmAge calculated in blood does not correlate with cognitive abilities.
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Affiliation(s)
- A Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.
| | - Q Tan
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - A Lenart
- Max Planck Odense Center on the Biodemography of Aging, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - M McGue
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - O Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - A D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - K Christensen
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - M Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - L Christiansen
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
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List M, Elnegaard MP, Schmidt S, Christiansen H, Tan Q, Mollenhauer J, Baumbach J. Efficient Management of High-Throughput Screening Libraries with SAVANAH. SLAS Discov 2016; 22:196-202. [PMID: 27729504 DOI: 10.1177/1087057116673607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-throughput screening (HTS) has become an indispensable tool for the pharmaceutical industry and for biomedical research. A high degree of automation allows for experiments in the range of a few hundred up to several hundred thousand to be performed in close succession. The basis for such screens are molecular libraries, that is, microtiter plates with solubilized reagents such as siRNAs, shRNAs, miRNA inhibitors or mimics, and sgRNAs, or small compounds, that is, drugs. These reagents are typically condensed to provide enough material for covering several screens. Library plates thus need to be serially diluted before they can be used as assay plates. This process, however, leads to an explosion in the number of plates and samples to be tracked. Here, we present SAVANAH, the first tool to effectively manage molecular screening libraries across dilution series. It conveniently links (connects) sample information from the library to experimental results from the assay plates. All results can be exported to the R statistical environment or piped into HiTSeekR ( http://hitseekr.compbio.sdu.dk ) for comprehensive follow-up analyses. In summary, SAVANAH supports the HTS community in managing and analyzing HTS experiments with an emphasis on serially diluted molecular libraries.
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Affiliation(s)
- Markus List
- 1 NanoCAN Center of Excellence, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,3 Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Marlene Pedersen Elnegaard
- 1 NanoCAN Center of Excellence, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Steffen Schmidt
- 1 NanoCAN Center of Excellence, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Helle Christiansen
- 1 NanoCAN Center of Excellence, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- 2 Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.,4 Department of Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jan Mollenhauer
- 1 NanoCAN Center of Excellence, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Joint last author
| | - Jan Baumbach
- 3 Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,5 Institute of Computer Science and Mathematics, University of Southern Denmark, Odense, Denmark.,Joint last author
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Almeida D, Skov I, Lund J, Mohammadnejad A, Silva A, Vandin F, Tan Q, Baumbach J, Röttger R. Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing. J Integr Bioinform 2016. [DOI: 10.1515/jib-2016-294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Summary
Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html
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Hansen A, Tannock I, Templeton A, Prawira A, Knox J, Vera-Badillo F, Chen E, Zavitz M, Wang L, Evans A, Tan Q, Wouters B, Sridhar S, Joshua A. Pantoprazole affecting docetaxel resistance pathways via autophagy (PANDORA): A phase II trial in men with metastatic castrate resistant prostate cancer (mCRPC). Ann Oncol 2016. [DOI: 10.1093/annonc/mdw372.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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131
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Li S, Kyvik KO, Duan H, Zhang D, Pang Z, Hjelmborg J, Tan Q, Kruse T, Dalgård C. Longitudinal Investigation into Genetics in the Conservation of Metabolic Phenotypes in Danish and Chinese Twins. PLoS One 2016; 11:e0162805. [PMID: 27618179 PMCID: PMC5019416 DOI: 10.1371/journal.pone.0162805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/29/2016] [Indexed: 12/02/2022] Open
Abstract
Longitudinal twin studies on long term conservation of individual metabolic phenotypes can help to explore the genetic and environmental basis in maintaining metabolic homeostasis and metabolic health. We performed a longitudinal twin study on 12 metabolic phenotypes from Danish twins followed up for 12 years and Chinese twins traced for 7 years. The study covered a relatively large sample of 502 pairs of Danish adult twins with a mean age at intake of 38 years and a total of 181 Chinese adult twin pairs with a mean baseline age of 39.5 years. Bivariate twin models were fitted to the longitudinal measurements taken at two time points (at baseline and follow-up) to estimate the genetic and environmental contributions to phenotype variation and correlation at and between the two time points. High genetic components in the regulation of intra-individual phenotype correlation or stability over time were estimated in both Danish (h2>0.75 except fasting blood glucose) and Chinese (h2>0.72 except blood pressure) twins; moderate to high genetic contribution to phenotype variation at the two time points were also estimated except for the low genetic regulation on glucose in Danish and on blood pressure in Chinese twins. Meanwhile the bivariate twin models estimated shared environmental contributions to the variance and covariance in fasting blood glucose in Danish twins, and in systolic and diastolic blood pressure, low and high density lipoprotein cholesterol in Chinese twins. Overall, our longitudinal twin study on long-term stability of metabolic phenotypes in Danish and Chinese twins identified a common pattern of high genetic control over phenotype conservation, and at the same time revealed population-specific patterns of genetic and common environmental regulation on the variance as well as covariance of glucose and blood pressure.
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Affiliation(s)
- Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- * E-mail:
| | - Kirsten Ohm Kyvik
- Department of Clinical Research, University of Southern Denmark, and Odense Patient data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Haiping Duan
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Dongfeng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Christine Dalgård
- Environmental Medicine, Department of Public Health, University of Southern Denmark, Odense, Denmark
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Tan Q, Yan X. [To improve the effect of reconstruction of scar contracture deformity on face and neck]. Zhonghua Shao Shang Za Zhi 2016; 32:456-7. [PMID: 27562153 DOI: 10.3760/cma.j.issn.1009-2587.2016.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This article briefly summarizes the methods for repair of scar contracture deformity on face and neck in recent years, including new technologies in this field. We can choose non-surgical treatment or surgical treatment to achieve the purpose of repair and reconstruction of scar contracture deformity on face and neck after considering the factors of function and appearance.
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Affiliation(s)
- Q Tan
- Department of Plastic Surgery and Burns, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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133
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Zhang WF, Tang SH, Tan Q, Liu YM. [An investigation of ionizing radiation dose in a manufacturing enterprise of ion-absorbing type rare earth ore]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2016; 34:620-622. [PMID: 27682674 DOI: 10.3760/cma.j.issn.1001-9391.2016.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Objective: To investigate radioactive source term dose monitoring and estimation results in a manufacturing enterprise of ion-absorbing type rare earth ore and the possible ionizing radiation dose received by its workers. Methods: Ionizing radiation monitoring data of the posts in the control area and supervised area of workplace were collected, and the annual average effective dose directly estimated or estimated using formulas was evaluated and analyzed. Results: In the control area and supervised area of the workplace for this rare earth ore, α surface contamination activity had a maximum value of 0.35 Bq/cm2 and a minimum value of 0.01 Bq/cm2; β radioactive surface contamination activity had a maximum value of 18.8 Bq/cm2 and a minimum value of 0.22 Bq/cm2. In 14 monitoring points in the workplace, the maximum value of the annual average effective dose of occupational exposure was 1.641 mSv/a, which did not exceed the authorized limit for workers (5 mSv/a) , but exceeded the authorized limit for general personnel (0.25 mSv/a) . The radionuclide specific activity of ionic mixed rare earth oxides was determined to be 0.9. Conclusion: The annual average effective dose of occupational exposure in this enterprise does not exceed the authorized limit for workers, but it exceeds the authorized limit for general personnel. We should pay attention to the focus of the radiation process, especially for public works radiation.
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Affiliation(s)
- W F Zhang
- The Hospital of Prevention and Treatment for Occupational Diseases in Guangzhou, Guangzhou 510620, China
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134
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Xu P, Wang SQ, Yan X, Lin Y, Ge HH, Tan Q. [Reconstruction of postburn facial scar contracture deformity with expanded flap containing cervical cutaneous branch of transverse cervical artery]. Zhonghua Shao Shang Za Zhi 2016; 32:458-62. [PMID: 27562154 DOI: 10.3760/cma.j.issn.1009-2587.2016.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To observe the effect of expanded flap containing cervical cutaneous branch of transverse cervical artery (TCA) on reconstruction of postburn facial scar contracture deformity. METHODS Six patients with postburn facial scar contracture deformity, hospitalized from September 2011 to January 2016, with the scar area ranging from 12 cm×10 cm to 20 cm×15 cm, were reconstructed with expanded flap containing cervical cutaneous branch of TCA. One expander of 300 mL or 350 mL implanted in anterior pectoral area was injected for excessive expanding; one patient was conducted with expansion in both sides of the anterior pectoral area. The volume of expansion varied from 1 260 to 2 010 mL after 6 to 15 months. Two flaps were delayed for their poor blood supply. After expansion, the flaps with the area ranging from 20 cm×7 cm to 25 cm×9 cm were transferred with no tension to cover the wounds after scar excision. The donor site was closed directly. Three to four weeks later, the vascular pedicle was dissected combined with local reconstruct surgery. RESULTS All the flaps survived, with two wounds suffered delayed healing. During the follow-up for 4 to 15 months, the flaps were thin and soft with good sensation and color close to the facial skin. CONCLUSIONS Expanded flap containing cervical cutaneous branch of TCA is a good choice for reconstruction of postburn facial scar contracture deformity because of its good texture and color, thin thickness, as well as it can provide large avaliable area while causing less injury to the donor site.
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Affiliation(s)
- P Xu
- Department of Plastic Surgery and Burns, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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135
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Tan Q, Heijmans BT, Hjelmborg JVB, Soerensen M, Christensen K, Christiansen L. Epigenetic drift in the aging genome: a ten-year follow-up in an elderly twin cohort. Int J Epidemiol 2016; 45:1146-1158. [PMID: 27498152 DOI: 10.1093/ije/dyw132] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Current epigenetic studies on aging are dominated by the cross-sectional design that correlates subjects' ages or age groups with their measured epigenetic profiles. Such studies have been more aimed at age prediction or building up the epigenetic clock of age rather than focusing on the dynamic patterns in epigenetic changes during the aging process. METHODS We performed an epigenome-wide association study of intra-individual longitudinal changes in DNA methylation at CpG (cytosine-phosphate-guanine) sites measured in whole-blood samples of a cohort of 43 elderly twin pairs followed for 10 years (age at intake 73-82 years). Biological pathway analysis and survival analysis were also conducted on CpGs showing longitudinal change in their DNA-methylation levels. Classical twin models were fitted to each CpG site to estimate the genetic and environmental effects on DNA-methylation. RESULTS Our analysis identified 2284 CpG sites whose DNA-methylation levels changed longitudinally over the follow-up. Twin modelling revealed that the longitudinal change for 90% of these CpG sites was explained solely by individual unique environmental factors and only for 10% of these sites was it influenced by familial factors (genetic or shared environment). Over 60% of the identified CpG sites were replicated (same direction and replication P < 0.05) in an independent cross-sectional sample of 300 twins aged from 30 to 74 years. The replication rate went up to 91% for the top 53 CpGs with P < 1 × 10-07. Pathway analysis of genes linked to these CpGs identified biologically meaningful gene-sets involved in cellular-signalling events and in transmission across chemical synapses, which are important molecular underpinnings of aging-related degenerative disorders. CONCLUSION Our epigenome-wide association studies on a cohort of old twins followed up for 10 years identified highly replicable epigenetic biomarkers predominantly implicated in signalling pathways of degenerative disorders and survival in the elderly.
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Affiliation(s)
- Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark, .,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark and Odense University Hospital, Odense C, Denmark and
| | - Bastiaan T Heijmans
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacob V B Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark and Odense University Hospital, Odense C, Denmark and
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark and Odense University Hospital, Odense C, Denmark and
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
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Tan Q, Qiu HB, Sun BW, Shen YM, Nie LJ, Zhang HW. [Model and enlightenment from rescue of August 2nd Kunshan explosion casualty]. Zhonghua Shao Shang Za Zhi 2016; 32:26-30. [PMID: 27426066 DOI: 10.3760/cma.j.issn.1009-2587.2016.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
On August 2nd, 2014, a massive dust explosion occurred in a factory of Kunshan, resulting in a mass casualty involving 185 burn patients. They were transported to 20 medical institutions in Jiangsu province and Shanghai. More than one thousand of medical personnel of our country participated in this emergency rescue, and satisfactory results were achieved. In this paper, the characteristics of this accident were analyzed, the positive effects of interdisciplinary cooperation were affirmed, and the contingency plan, rescue process and pattern, and reserve, organization and management of talents during this rescue process were reviewed retrospectively.
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Affiliation(s)
- Q Tan
- Department of Plastic Surgery and Burns, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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137
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Abstract
Identifying functional modules or novel active pathways, recently termed de novo pathway enrichment, is a computational systems biology challenge that has gained much attention during the last decade. Given a large biological interaction network, KeyPathwayMiner extracts connected subnetworks that are enriched for differentially active entities from a series of molecular profiles encoded as binary indicator matrices. Since interaction networks constantly evolve, an important question is how robust the extracted results are when the network is modified. We enable users to study this effect through several network perturbation techniques and over a range of perturbation degrees. In addition, users may now provide a gold-standard set to determine how enriched extracted pathways are with relevant genes compared to randomized versions of the original network.
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Affiliation(s)
- Nicolas Alcaraz
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Markus List
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark; Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark; Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark; Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
| | - Martin Dissing-Hansen
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | - Marc Rehmsmeier
- Integrated Research Institute (IRI) for the Life Sciences and Department of Biology, Humboldt-Universitat zu Berlin, 10099 Berlin, Germany
| | - Qihua Tan
- Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark; Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, 5000 Odense, Denmark
| | - Jan Mollenhauer
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark; Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark; Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark; Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
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List M, Schmidt S, Christiansen H, Rehmsmeier M, Tan Q, Mollenhauer J, Baumbach J. Comprehensive analysis of high-throughput screens with HiTSeekR. Nucleic Acids Res 2016; 44:6639-48. [PMID: 27330136 PMCID: PMC5001608 DOI: 10.1093/nar/gkw554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022] Open
Abstract
High-throughput screening (HTS) is an indispensable tool for drug (target) discovery that currently lacks user-friendly software tools for the robust identification of putative hits from HTS experiments and for the interpretation of these findings in the context of systems biology. We developed HiTSeekR as a one-stop solution for chemical compound screens, siRNA knock-down and CRISPR/Cas9 knock-out screens, as well as microRNA inhibitor and -mimics screens. We chose three use cases that demonstrate the potential of HiTSeekR to fully exploit HTS screening data in quite heterogeneous contexts to generate novel hypotheses for follow-up experiments: (i) a genome-wide RNAi screen to uncover modulators of TNFα, (ii) a combined siRNA and miRNA mimics screen on vorinostat resistance and (iii) a small compound screen on KRAS synthetic lethality. HiTSeekR is publicly available at http://hitseekr.compbio.sdu.dk It is the first approach to close the gap between raw data processing, network enrichment and wet lab target generation for various HTS screen types.
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Affiliation(s)
- Markus List
- Lundbeckfonden Center of Excellence in Nanomedicine (NanoCAN), University of Southern Denmark, 5000 Odense, Denmark Molecular Oncology, Institute of Molecular Medicin (IMM), University of Southern Denmark, 5000 Odense, Denmark Clinical Institute (CI), University of Southern Denmark, 5000 Odense, Denmark
| | - Steffen Schmidt
- Lundbeckfonden Center of Excellence in Nanomedicine (NanoCAN), University of Southern Denmark, 5000 Odense, Denmark Molecular Oncology, Institute of Molecular Medicin (IMM), University of Southern Denmark, 5000 Odense, Denmark
| | - Helle Christiansen
- Lundbeckfonden Center of Excellence in Nanomedicine (NanoCAN), University of Southern Denmark, 5000 Odense, Denmark Molecular Oncology, Institute of Molecular Medicin (IMM), University of Southern Denmark, 5000 Odense, Denmark
| | - Marc Rehmsmeier
- Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Qihua Tan
- Clinical Institute (CI), University of Southern Denmark, 5000 Odense, Denmark Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, 5000 Odense, Denmark
| | - Jan Mollenhauer
- Lundbeckfonden Center of Excellence in Nanomedicine (NanoCAN), University of Southern Denmark, 5000 Odense, Denmark Molecular Oncology, Institute of Molecular Medicin (IMM), University of Southern Denmark, 5000 Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science (IMADA), University of Southern Denmark, 5230 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
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Munk H, Fakih D, Sorensen G, Tan Q, Christiansen L, Christensen A, Ejstrup L, Loft A, Kyvik K, Jounblat R, Holmskov U, Junker P. SAT0028 Circulating Surfactant Protein-D (SP-D) Molecular Size Profile Differs between Patients with Untreated Axial Spondyloarthritis and Healthy Control Subjects. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.1936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Sorensen GL, Bladbjerg EM, Steffensen R, Tan Q, Madsen J, Drivsholm T, Holmskov U. Association between the surfactant protein D (SFTPD) gene and subclinical carotid artery atherosclerosis. Atherosclerosis 2016; 246:7-12. [DOI: 10.1016/j.atherosclerosis.2015.12.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/07/2015] [Accepted: 12/23/2015] [Indexed: 12/14/2022]
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Li S, Kyvik KO, Pang Z, Zhang D, Duan H, Tan Q, Hjelmborg J, Kruse T, Dalgård C. Genetic and Environmental Regulation on Longitudinal Change of Metabolic Phenotypes in Danish and Chinese Adult Twins. PLoS One 2016; 11:e0148396. [PMID: 26862898 PMCID: PMC4749287 DOI: 10.1371/journal.pone.0148396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/18/2016] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The rate of change in metabolic phenotypes can be highly indicative of metabolic disorders and disorder-related modifications. We analyzed data from longitudinal twin studies on multiple metabolic phenotypes in Danish and Chinese twins representing two populations of distinct ethnic, cultural, social-economic backgrounds and geographical environments. MATERIALS AND METHODS The study covered a relatively large sample of 502 pairs of Danish adult twins followed up for a long period of 12 years with a mean age at intake of 38 years (range: 18-65) and a total of 181 Chinese adult twin pairs traced for about 7 years with a mean baseline age of 39.5 years (range: 23-64). The classical twin models were fitted to the longitudinal change in each phenotype (Δphenotype) to estimate the genetic and environmental contributions to the variation in Δphenotype. RESULTS Moderate to high contributions by the unique environment were estimated for all phenotypes in both Danish (from 0.51 for low density lipoprotein cholesterol up to 0.72 for triglycerides) and Chinese (from 0.41 for triglycerides up to 0.73 for diastolic blood pressure) twins; low to moderate genetic components were estimated for long-term change in most of the phenotypes in Danish twins except for triglycerides and hip circumference. Compared with Danish twins, the Chinese twins tended to have higher genetic control over the longitudinal changes in lipids (except high density lipoprotein cholesterol) and glucose, higher unique environmental contribution to blood pressure but no genetic contribution to longitudinal change in body mass traits. CONCLUSION Our results emphasize the major contribution of unique environment to the observed intra-individual variation in all metabolic phenotypes in both samples, and meanwhile reveal differential patterns of genetic and common environmental regulation on changes over time in metabolic phenotypes across the two samples.
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Affiliation(s)
- Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- * E-mail:
| | - Kirsten Ohm Kyvik
- Department of Clinical Research, University of Southern Denmark, and Odense Patient data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Dongfeng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China
| | - Haiping Duan
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Qihua Tan
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Christine Dalgård
- Environmental Medicine, Department of Public Health, University of Southern Denmark, Odense, Denmark
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142
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Zeng Y, Chen H, Ni T, Ruan R, Nie C, Liu X, Feng L, Zhang F, Lu J, Li J, Li Y, Tao W, Gregory SG, Gottschalk W, Lutz MW, Land KC, Yashin A, Tan Q, Yang Z, Bolund L, Ming Q, Yang H, Min J, Willcox DC, Willcox BJ, Gu J, Hauser E, Tian XL, Vaupel JW. Interaction Between the FOXO1A-209 Genotype and Tea Drinking Is Significantly Associated with Reduced Mortality at Advanced Ages. Rejuvenation Res 2016; 19:195-203. [PMID: 26414954 DOI: 10.1089/rej.2015.1737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
On the basis of the genotypic/phenotypic data from Chinese Longitudinal Healthy Longevity Survey (CLHLS) and Cox proportional hazard model, the present study demonstrates that interactions between carrying FOXO1A-209 genotypes and tea drinking are significantly associated with lower risk of mortality at advanced ages. Such a significant association is replicated in two independent Han Chinese CLHLS cohorts (p = 0.028-0.048 in the discovery and replication cohorts, and p = 0.003-0.016 in the combined dataset). We found the associations between tea drinking and reduced mortality are much stronger among carriers of the FOXO1A-209 genotype compared to non-carriers, and drinking tea is associated with a reversal of the negative effects of carrying FOXO1A-209 minor alleles, that is, from a substantially increased mortality risk to substantially reduced mortality risk at advanced ages. The impacts are considerably stronger among those who carry two copies of the FOXO1A minor allele than those who carry one copy. On the basis of previously reported experiments on human cell models concerning FOXO1A-by-tea-compounds interactions, we speculate that results in the present study indicate that tea drinking may inhibit FOXO1A-209 gene expression and its biological functions, which reduces the negative impacts of FOXO1A-209 gene on longevity (as reported in the literature) and offers protection against mortality risk at oldest-old ages. Our empirical findings imply that the health outcomes of particular nutritional interventions, including tea drinking, may, in part, depend upon individual genetic profiles, and the research on the effects of nutrigenomics interactions could potentially be useful for rejuvenation therapies in the clinic or associated healthy aging intervention programs.
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Affiliation(s)
- Yi Zeng
- 1 Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University , Durham, North Carolina.,2 Center for Healthy Aging and Development Studies, National School of Development, Peking University , Beijing, China
| | - Huashuai Chen
- 1 Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University , Durham, North Carolina.,3 Department of Management, Business School of Xiangtan University , Xiangtan, China
| | - Ting Ni
- 4 State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai, China
| | - Rongping Ruan
- 5 Department of Agriculture Economics. Renmin University of China , Beijing, China
| | - Chao Nie
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China
| | - Xiaomin Liu
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China
| | - Lei Feng
- 7 Department of Psychological Medicine, National University of Singapore , Singapore
| | - Fengyu Zhang
- 8 Lieber Institute for Brain Development, Johns Hopkins University , Baltimore, Maryland
| | - Jiehua Lu
- 9 Department of Sociology, Peking University , Beijing, China
| | - Jianxin Li
- 9 Department of Sociology, Peking University , Beijing, China
| | - Yang Li
- 10 Department of Human Population Genetics, Institute of Molecular Medicine, Peking University , Beijing, China
| | - Wei Tao
- 11 School of Life Sciences, Peking University , Beijing, China
| | - Simon G Gregory
- 12 Duke Molecular Physiology Institute, Duke University , Durham, North Carolina
| | - William Gottschalk
- 13 Department of Neurology, Medical Center, Duke University , Durham, North Carolina
| | - Michael W Lutz
- 13 Department of Neurology, Medical Center, Duke University , Durham, North Carolina
| | - Kenneth C Land
- 14 Population Research Institute, Duke University , Durham, North Carolina
| | - Anatoli Yashin
- 14 Population Research Institute, Duke University , Durham, North Carolina
| | - Qihua Tan
- 15 Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark , Odense, Denmark
| | - Ze Yang
- 16 National Institute of Geriatrics, Beijing Hospital , Ministry of Health of China, Beijing, China
| | - Lars Bolund
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China .,17 Department of Biomedicine, Aarhus University , Aarhus, Denmark
| | - Qi Ming
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China .,18 Center for Genetic & Genomic Medicine, Zhejiang University School of Medicine , Hangzhou, China
| | - Huanming Yang
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China .,19 James D. Watson Institute of Genome Sciences , Hangzhou, China .,20 Princess Al-Jawhara Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Junxia Min
- 21 School of Medicine, Zhejiang University , Hangzhou, China
| | - D Craig Willcox
- 22 Department of Human Welfare, Okinawa International University , Ginowan, Japan .,23 Department of Research, Kuakini Medical Center and Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii , Hawaii
| | - Bradley J Willcox
- 23 Department of Research, Kuakini Medical Center and Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii , Hawaii
| | - Jun Gu
- 11 School of Life Sciences, Peking University , Beijing, China
| | - Elizabeth Hauser
- 12 Duke Molecular Physiology Institute, Duke University , Durham, North Carolina
| | - Xiao-Li Tian
- 10 Department of Human Population Genetics, Institute of Molecular Medicine, Peking University , Beijing, China
| | - James W Vaupel
- 24 Max Planck Institute for Demographic Research , Rostock, Germany
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Nygaard M, Debrabant B, Tan Q, Deelen J, Andersen‐Ranberg K, Craen AJ, Beekman M, Jeune B, Slagboom PE, Christensen K, Christiansen L. Copy number variation associates with mortality in long-lived individuals: a genome-wide assessment. Aging Cell 2016; 15:49-55. [PMID: 26446717 PMCID: PMC4717275 DOI: 10.1111/acel.12407] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/30/2022] Open
Abstract
Copy number variants (CNVs) represent a significant source of genetic variation in the human genome and have been implicated in numerous diseases and complex traits. To date, only a few studies have investigated the role of CNVs in human lifespan. To investigate the impact of CNVs on prospective mortality at the extreme end of life, where the genetic component of lifespan appears most profound, we analyzed genomewide CNV data in 603 Danish nonagenarians and centenarians (mean age 96.9 years, range 90.0–102.5 years). Replication was performed in 500 long‐lived individuals from the Leiden Longevity Study (mean age 93.2 years, range 88.9–103.4 years). First, we assessed the association between the CNV burden of each individual (the number of CNVs, the average CNV length, and the total CNV length) and mortality and found a significant increase in mortality per 10 kb increase in the average CNV length, both for all CNVs (hazard ratio (HR) = 1.024, P = 0.002) and for duplications (HR = 1.011, P = 0.005), as well as per 100 kb increase in the total length of deletions (HR = 1.009, P = 0.0005). Next, we assessed the relation between specific deletions and duplications and mortality. Although no genome–wide significant associations were discovered, we identified six deletions and one duplication that showed consistent association with mortality in both or either of the sexes across both study populations. These results indicate that the genome–wide CNV burden, specifically the average CNV length and the total CNV length, associates with higher mortality in long‐lived individuals.
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Affiliation(s)
- Marianne Nygaard
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
- Department of Clinical Genetics Odense University Hospital Sdr. Boulevard 29, 5000, Odense C Denmark
| | - Birgit Debrabant
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
| | - Qihua Tan
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
- Department of Clinical Genetics Odense University Hospital Sdr. Boulevard 29, 5000, Odense C Denmark
| | - Joris Deelen
- Department of Molecular Epidemiology Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Karen Andersen‐Ranberg
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
| | - Anton J.M. Craen
- Department of Gerontology and Geriatrics Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Marian Beekman
- Department of Molecular Epidemiology Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Bernard Jeune
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
| | - Pieternella E. Slagboom
- Department of Molecular Epidemiology Leiden University Medical Center P.O. Box 9600, 2300 RC Leiden The Netherlands
| | - Kaare Christensen
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
- Department of Clinical Genetics Odense University Hospital Sdr. Boulevard 29, 5000, Odense C Denmark
- Department of Clinical Biochemistry and Pharmacology Odense University Hospital Sdr. Boulevard 29, 5000 Odense C Denmark
| | - Lene Christiansen
- The Danish Aging Research Center Epidemiology, Biostatistics and Biodemography Department of Public Health University of Southern Denmark J.B. Winsloews Vej 9B, 5000, Odense C Denmark
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144
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Christiansen L, Lenart A, Tan Q, Vaupel JW, Aviv A, McGue M, Christensen K. DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell 2016; 15:149-54. [PMID: 26594032 PMCID: PMC4717264 DOI: 10.1111/acel.12421] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2015] [Indexed: 12/15/2022] Open
Abstract
An epigenetic profile defining the DNA methylation age (DNAm age) of an individual has been suggested to be a biomarker of aging, and thus possibly providing a tool for assessment of health and mortality. In this study, we estimated the DNAm age of 378 Danish twins, age 30–82 years, and furthermore included a 10‐year longitudinal study of the 86 oldest‐old twins (mean age of 86.1 at follow‐up), which subsequently were followed for mortality for 8 years. We found that the DNAm age is highly correlated with chronological age across all age groups (r = 0.97), but that the rate of change of DNAm age decreases with age. The results may in part be explained by selective mortality of those with a high DNAm age. This hypothesis was supported by a classical survival analysis showing a 35% (4–77%) increased mortality risk for each 5‐year increase in the DNAm age vs. chronological age. Furthermore, the intrapair twin analysis revealed a more‐than‐double mortality risk for the DNAm oldest twin compared to the co‐twin and a ‘dose–response pattern’ with the odds of dying first increasing 3.2 (1.05–10.1) times per 5‐year DNAm age difference within twin pairs, thus showing a stronger association of DNAm age with mortality in the oldest‐old when controlling for familial factors. In conclusion, our results support that DNAm age qualifies as a biomarker of aging.
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Affiliation(s)
- Lene Christiansen
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
| | - Adam Lenart
- Max Planck Odense Center on the Biodemography of Aging Institute of Public Health University of Southern Denmark Odense Denmark
| | - Qihua Tan
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
- Department of Clinical Genetics Odense University Hospital Odense Denmark
| | - James W. Vaupel
- Max Planck Odense Center on the Biodemography of Aging Institute of Public Health University of Southern Denmark Odense Denmark
- Max Planck Institute for Demographic Research Rostock Germany
| | - Abraham Aviv
- The Center for Human Development and Aging New Jersey Medical School University of Medicine and Dentistry of New Jersey Newark NJ USA
| | - Matt McGue
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
- Department of Psychology University of Minnesota Minneapolis MN USA
| | - Kaare Christensen
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
- Department of Clinical Genetics Odense University Hospital Odense Denmark
- Department of Clinical Biochemistry and Pharmacology Odense University Hospital Odense Denmark
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145
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Chen M, Baumbach J, Vandin F, Röttger R, Barbosa E, Dong M, Frost M, Christiansen L, Tan Q. Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs. Ann Hum Genet 2016; 80:81-7. [DOI: 10.1111/ahg.12146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Mubo Chen
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
- Department of Electrical and Computer Engineering, Faculty of Science and Technology; University of Macau; Macau China
| | - Jan Baumbach
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Fabio Vandin
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
- Department of Information Engineering; University of Padova; Padova Italy
| | - Richard Röttger
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Eudes Barbosa
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Mingchui Dong
- Department of Electrical and Computer Engineering, Faculty of Science and Technology; University of Macau; Macau China
| | - Morten Frost
- Department of Endocrinology; Odense University Hospital; Odense Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health; University of Southern Denmark; Odense Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health; University of Southern Denmark; Odense Denmark
- Unit of Human Genetics, Department of Clinical Research; University of Southern Denmark; Odense Denmark
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146
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Tepel M, Beck HC, Tan Q, Borst C, Rasmussen LM. The 82-plex plasma protein signature that predicts increasing inflammation. Sci Rep 2015; 5:14882. [PMID: 26445912 PMCID: PMC4597208 DOI: 10.1038/srep14882] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/10/2015] [Indexed: 12/22/2022] Open
Abstract
The objective of the study was to define the specific plasma protein signature that predicts the increase of the inflammation marker C-reactive protein from index day to next-day using proteome analysis and novel bioinformatics tools. We performed a prospective study of 91 incident kidney transplant recipients and quantified 359 plasma proteins simultaneously using nano-Liquid-Chromatography-Tandem Mass-Spectrometry in individual samples and plasma C-reactive protein on the index day and the next day. Next-day C-reactive protein increased in 59 patients whereas it decreased in 32 patients. The prediction model selected and validated 82 plasma proteins which determined increased next-day C-reactive protein (area under receiver-operator-characteristics curve, 0.772; 95% confidence interval, 0.669 to 0.876; P < 0.0001). Multivariable logistic regression showed that 82-plex protein signature (P < 0.001) was associated with observed increased next-day C-reactive protein. The 82-plex protein signature outperformed routine clinical procedures. The category-free net reclassification index improved with 82-plex plasma protein signature (total net reclassification index, 88.3%). Using the 82-plex plasma protein signature increased net reclassification index with a clinical meaningful 10% increase of risk mainly by the improvement of reclassification of subjects in the event group. An 82-plex plasma protein signature predicts an increase of the inflammatory marker C-reactive protein.
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Affiliation(s)
- Martin Tepel
- Department of Nephrology, Odense University Hospital, and University of Southern Denmark, Institute of Molecular Medicine, Cardiovascular and Renal Research, Institute of Clinical Research
| | - Hans C Beck
- Department of Clinical Biochemistry and Pharmacology, Centre for Individualized Medicine in Arterial Diseases (Odense University Hospital), and Centre for Clinical Proteomics (Odense University Hospital/University of Southern Denmark)
| | - Qihua Tan
- Department of Epidemiology, Biostatistics and Biodemography, Institute of Public Health; Unit of Human Genetics, Institute of Clinical Research, University of Southern Denmark
| | - Christoffer Borst
- Department of Nephrology, Odense University Hospital, and University of Southern Denmark, Institute of Molecular Medicine, Cardiovascular and Renal Research, Institute of Clinical Research
| | - Lars M Rasmussen
- Department of Clinical Biochemistry and Pharmacology, Centre for Individualized Medicine in Arterial Diseases (Odense University Hospital), and Centre for Clinical Proteomics (Odense University Hospital/University of Southern Denmark)
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147
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Abstract
Since the final decades of the last century, twin studies have made a remarkable contribution to the genetics of human complex traits and diseases. With the recent rapid development in modern biotechnology of high-throughput genetic and genomic analyses, twin modelling is expanding from analysis of diseases to molecular phenotypes in functional genomics especially in epigenetics, a thriving field of research that concerns the environmental regulation of gene expression through DNA methylation, histone modification, microRNA and long non-coding RNA expression, etc. The application of the twin method to molecular phenotypes offers new opportunities to study the genetic (nature) and environmental (nurture) contributions to epigenetic regulation of gene activity during developmental, ageing and disease processes. Besides the classical twin model, the case co-twin design using identical twins discordant for a trait or disease is becoming a popular and powerful design for epigenome-wide association study in linking environmental exposure to differential epigenetic regulation and to disease status while controlling for individual genetic make-up. It can be expected that novel uses of twin methods in epigenetic studies are going to help with efficiently unravelling the genetic and environmental basis of epigenomics in human complex diseases.
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Affiliation(s)
- Qihua Tan
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Jacob von Bornemann Hjelmborg
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
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148
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List M, Franz M, Tan Q, Mollenhauer J, Baumbach J. OpenLabNotes – An Electronic Laboratory Notebook Extension for OpenLabFramework. J Integr Bioinform 2015. [DOI: 10.1515/jib-2015-274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Summary Electronic laboratory notebooks (ELNs) are more accessible and reliable than their paper based alternatives and thus find widespread adoption. While a large number of commercial products is available, small- to mid-sized laboratories can often not afford the costs or are concerned about the longevity of the providers. Turning towards free alternatives, however, raises questions about data protection, which are not sufficiently addressed by available solutions. To serve as legal documents, ELNs must prevent scientific fraud through technical means such as digital signatures. It would also be advantageous if an ELN was integrated with a laboratory information management system to allow for a comprehensive documentation of experimental work including the location of samples that were used in a particular experiment. Here, we present OpenLabNotes, which adds state-of-the-art ELN capabilities to OpenLabFramework, a powerful and flexible laboratory information management system. In contrast to comparable solutions, it allows to protect the intellectual property of its users by offering data protection with digital signatures. OpenLabNotes effectively closes the gap between research documentation and sample management, thus making Open- LabFramework more attractive for laboratories that seek to increase productivity through electronic data management.
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Affiliation(s)
- Markus List
- 1Lundbeckfonden Center of Excellence in Nanomedicine (NanoCAN), University of Southern Denmark, 5000 Odense, Denmark
- 2Institute of Molecular Medicine, University of Southern Denmark, 5000Odense, Denmark
- 3Clinical Institute, University of Southern Denmark, 5000Odense, Denmark
| | - Michael Franz
- 4Computational Biology group, Department of Mathematics and Computer Science, University of Southern Denmark, 5230Odense, Denmark
| | - Qihua Tan
- 5Clinical Institute, University of Southern Denmark, 5000Odense, Denmark
- 6Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, 5000Odense, Denmark
| | - Jan Mollenhauer
- 1Lundbeckfonden Center of Excellence in Nanomedicine (NanoCAN), University of Southern Denmark, 5000 Odense, Denmark
- 7Institute of Molecular Medicine, University of Southern Denmark, 5000Odense, Denmark
| | - Jan Baumbach
- 8Computational Biology group, Department of Mathematics and Computer Science, University of Southern Denmark, 5230Odense, Denmark
- 9Max Planck Institute for Informatics, 66123Saarbrücken, Germany
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149
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Xu C, Sun J, Duan H, Ji F, Tian X, Zhai Y, Wang S, Pang Z, Zhang D, Zhao Z, Li S, Gue MM, Hjelmborg JVB, Christensen K, Tan Q. Gene, environment and cognitive function: a Chinese twin ageing study. Age Ageing 2015; 44:452-7. [PMID: 25833745 DOI: 10.1093/ageing/afv015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 11/25/2014] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND the genetic and environmental contributions to cognitive function in the old people have been well addressed for the Western populations using twin modelling showing moderate to high heritability. No similar study has been conducted in the world largest and rapidly ageing Chinese population living under distinct environmental condition as the Western populations. OBJECTIVE this study aims to explore the genetic and environmental impact on normal cognitive ageing in the Chinese twins. DESIGN/SETTING cognitive function was measured on 384 complete twin pairs with median age of 50 years for seven cognitive measurements including visuospatial, linguistic skills, naming, memory, attention, abstraction and orientation abilities. Data were analysed by fitting univariate and bivariate twin models to estimate the genetic and environmental components in the variance and co-variance of the cognitive assessments. RESULTS intra-pair correlation on cognitive measurements was low to moderate in monozygotic twins (0.23-0.41, overall 0.42) and low in dizygotic twins (0.05-0.30, overall 0.31) with the former higher than the latter for each item. Estimate for heritability was moderate for overall cognitive function (0.44, 95% CI: 0.34-0.53) and low to moderate for visuospatial, naming, attention and orientation abilities ranging from 0.28 to 0.38. No genetic contribution was estimated to linguistic skill, abstraction and memory which instead were under low to moderate control by shared environmental factors accounting for 23-33% of the total variances. In contrast, all cognitive performances showed moderate to high influences by the unique environmental factors. CONCLUSIONS genetic factor and common family environment have a limited contribution to cognitive function in the Chinese adults. Individual unique environment is likely to play a major role in determining the levels of cognitive performance.
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Affiliation(s)
- Chunsheng Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong, China Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Jianping Sun
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Haiping Duan
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Fuling Ji
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Xiaocao Tian
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Yaoming Zhai
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Shaojie Wang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Zengchang Pang
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong, China Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Dongfeng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China
| | - Zhongtang Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong, China
| | - Shuxia Li
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Matt Mc Gue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Jacob V B Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark The Danish Twin Registry and The Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark The Danish Twin Registry and The Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark The Danish Twin Registry and The Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
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150
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Ji GJ, Zhang Z, Xu Q, Wang Z, Wang J, Jiao Q, Yang F, Tan Q, Chen G, Zang YF, Liao W, Lu G. Identifying Corticothalamic Network Epicenters in Patients with Idiopathic Generalized Epilepsy. AJNR Am J Neuroradiol 2015; 36:1494-500. [PMID: 25907518 DOI: 10.3174/ajnr.a4308] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/17/2015] [Indexed: 01/25/2023]
Abstract
BACKGROUND AND PURPOSE Corticothalamic networks are considered core pathologic substrates for idiopathic generalized epilepsy; however, the predominant epileptogenic epicenters within these networks are still largely unknown. The current study aims to identify these epicenters by resting-state functional connectivity. MATERIALS AND METHODS To identify epicenters within the corticothalamic networks in idiopathic generalized epilepsy, we retrospectively studied a large cohort of patients with this condition (n = 97) along with healthy controls (n = 123) by resting-state functional MR imaging. The thalamus was functionally divided into subregions corresponding to distinct cortical lobes for 5 parallel corticothalamic networks. The functional connectivity between each voxel in the cortical lobe and the corresponding thalamic subregion was calculated, and functional connectivity strength was used to evaluate the interconnectivity of voxels in the cortex and thalamus. RESULTS The projection of 5 cortical lobes to the thalamus is consistent with previous histologic findings in humans. Compared with controls, patients with idiopathic generalized epilepsy showed increased functional connectivity strength in 4 corticothalamic networks: 1) the supplementary motor area, pulvinar, and ventral anterior nucleus in the prefrontal-thalamic network; 2) the premotor cortex and ventrolateral nucleus in motor/premotor-thalamic networks; 3) the visual cortex, posterior default mode regions, and pulvinar in parietal/occipital-thalamic networks; and 4) the middle temporal gyrus in the temporal-thalamic network. CONCLUSIONS Several key nodes were distinguished in 4 corticothalamic networks. The identification of these epicenters refines the corticothalamic network theory and provides insight into the pathophysiology of idiopathic generalized epilepsy.
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Affiliation(s)
- G-J Ji
- From the Center for Cognition and Brain Disorders and the Affiliated Hospital (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou Normal University, Hangzhou, China Zhejiang Key Laboratory for Research in Assessment of Cognitive Impairments (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou, China
| | - Z Zhang
- Departments of Medical Imaging (Z.Z., Q.X., W.L., G.L.)
| | - Q Xu
- Departments of Medical Imaging (Z.Z., Q.X., W.L., G.L.)
| | - Z Wang
- Department of Medical Imaging (Z.W.), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - J Wang
- From the Center for Cognition and Brain Disorders and the Affiliated Hospital (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou Normal University, Hangzhou, China Zhejiang Key Laboratory for Research in Assessment of Cognitive Impairments (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou, China
| | - Q Jiao
- Department of Radiology (Q.J.), Taishan Medical University, Tai'an, China
| | | | - Q Tan
- Neurosurgery (Q.T.), Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | | | - Y-F Zang
- From the Center for Cognition and Brain Disorders and the Affiliated Hospital (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou Normal University, Hangzhou, China Zhejiang Key Laboratory for Research in Assessment of Cognitive Impairments (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou, China
| | - W Liao
- From the Center for Cognition and Brain Disorders and the Affiliated Hospital (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou Normal University, Hangzhou, China Zhejiang Key Laboratory for Research in Assessment of Cognitive Impairments (G.-J.J., J.W., Y.-F.Z., W.L.), Hangzhou, China Departments of Medical Imaging (Z.Z., Q.X., W.L., G.L.)
| | - G Lu
- Departments of Medical Imaging (Z.Z., Q.X., W.L., G.L.)
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