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Xing H, Wu Y, Zhang MQ, Chen Y. Deciphering hierarchical organization of topologically associated domains through change-point testing. BMC Bioinformatics 2021; 22:183. [PMID: 33838653 PMCID: PMC8037919 DOI: 10.1186/s12859-021-04113-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Background The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them. Results We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p values calculated by the GLR test. Large-scale validations of simulation data show that HiCKey has good precision in recalling known TADs and is robust against random collisions of chromatin interactions. By applying HiCKey to Hi-C data of seven human cell lines, we identified multiple layers of TAD organization among them, but the vast majority had no more than four layers. In particular, we found that TAD boundaries are significantly enriched in active chromosomal regions compared to repressed regions. Conclusions HiCKey is optimized for processing large matrices constructed from high-resolution Hi-C experiments. The method and theoretical result of the GLR test provide a general framework for significance testing of similar experimental chromatin interaction data that may not fully follow negative binomial distributions but rather more general mixture distributions. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04113-8.
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Affiliation(s)
- Haipeng Xing
- Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, 100 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Yingru Wu
- Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, 100 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Michael Q Zhang
- Center for System Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Yong Chen
- Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ, 08028, USA.
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Fiatal S, Ádány R. Application of Single-Nucleotide Polymorphism-Related Risk Estimates in Identification of Increased Genetic Susceptibility to Cardiovascular Diseases: A Literature Review. Front Public Health 2018; 5:358. [PMID: 29445720 PMCID: PMC5797796 DOI: 10.3389/fpubh.2017.00358] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/15/2017] [Indexed: 12/17/2022] Open
Abstract
Background Although largely preventable, cardiovascular diseases (CVDs) are the biggest cause of death worldwide. Common complex cardiovascular disorders (e.g., coronary heart disease, hypertonia, or thrombophilia) result from a combination of genetic alterations and environmental factors. Recent advances in the genomics of CVDs have fostered huge expectations about future use of susceptibility variants for prevention, diagnosis, and treatment. Our aim was to summarize the latest developments in the field from a public health perspective focusing on the applicability of data on single-nucleotide polymorphisms (SNPs), through a systematic review of studies from the last decade on genetic risk estimating for common CVDs. Methods Several keywords were used for searching the PubMed, Embase, CINAHL, and Web of Science databases. Recent advances were summarized and structured according to the main public health domains (prevention, early detection, and treatment) using a framework suggested recently for translational research. This framework includes four recommended phases: “T1. From gene discovery to candidate health applications; T2. From health application to evidence-based practice guidelines; T3. From evidence-based practice guidelines to health practice; and T4. From practice to population health impacts.” Results The majority of translation research belongs to the T1 phase “translation of basic genetic/genomic research into health application”; there are only a few population-based impacts estimated. The studies suggest that an SNP is a poor estimator of individual risk, whereas an individual’s genetic profile combined with non-genetic risk factors may better predict CVD risk among certain patient subgroups. Further research is needed to validate whether these genomic profiles can prospectively identify individuals at risk to develop CVDs. Several research gaps were identified: little information is available on studies suggesting “Health application to evidence-based practice guidelines”; no study is available on “Guidelines to health practice.” It was not possible to identify studies that incorporate environmental or lifestyle factors in the risk estimation. Conclusion Currently, identifying populations having a larger risk of developing common CVDs may result in personalized prevention programs by reducing people’s risk of onset or disease progression. However, limited evidence is available on the application of genomic results in health and public health practice.
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Affiliation(s)
- Szilvia Fiatal
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary.,WHO Collaborating Centre on Vulnerability and Health, Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary.,WHO Collaborating Centre on Vulnerability and Health, Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary.,MTA-DE Public Health Research Group of the Hungarian Academy of Sciences, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
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3
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Zhao J, Zhu X, Shrubsole MJ, Ness RM, Hibler EA, Cai Q, Long J, Chen Z, Jiang M, Kabagambe EK, Zhang B, Hou L, Smalley WE, Edwards TL, Giovannucci EL, Zheng W, Dai Q. Interactions between calcium intake and polymorphisms in genes essential for calcium reabsorption and risk of colorectal neoplasia in a two-phase study. Mol Carcinog 2017; 56:2258-2266. [PMID: 28544176 DOI: 10.1002/mc.22678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/09/2017] [Accepted: 05/19/2017] [Indexed: 12/31/2022]
Abstract
The SLC8A1 (solute carrier family 8, member 1) gene, encoding Na+ /Ca2+ exchanger, is essential in regulating calcium reabsorption and homeostasis. Calcium homeostasis plays a key role in cell proliferation and apoptosis. We hypothesized that polymorphisms in five calcium-regulating genes (SLC8A1, ATP2B1, CALB1, CALB2, and CABP1) interact with calcium intake in relation to the risk of colorectal neoplasia. A two-phase (discovery and replication) study was conducted within the Tennessee Colorectal Polyp Study, including a total of 1275 cases and 2811 controls. In Phase I, we identified six out of 135 SNPs that significantly interacted with calcium intake in relation to adenoma risk. In Phase II, the calcium intake by rs4952490 (SLC8A1) interaction was replicated (Pinteraction = 0.048). We found an inverse association between calcium intake (1000-2000 mg/day) and colorectal adenomas, particularly for multiple/advanced adenomas, among the G-allele carriers but not among homozygous carriers of the common variant (A) in rs4952490. In the joint analysis of SLC8A1, KCNJ1, and SLC12A1 SNPs, carriers of variant alleles in at least two genes and with calcium intake above the DRI (1000 mg/day) were approximately 30-57% less likely to have adenomas than those whose calcium intake was below the DRI. The association was stronger for multiple/advanced adenomas. No association was found among those who did not carry any variant alleles in these genes when calcium intake was below 2500 mg/day. These findings, if confirmed, may provide a new avenue for the personalized prevention of colorectal adenoma and cancer.
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Affiliation(s)
- Jing Zhao
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee
| | - Xiangzhu Zhu
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee.,Department of Medicine, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Reid M Ness
- Department of Medicine, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.,Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elizabeth A Hibler
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Zhi Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ming Jiang
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Laboratory of Nuclear Receptors and Cancer Research, Center for Basic Medical Research, School of Medicine, Nantong University, Jiangsu, China
| | - Edmond K Kabagambe
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bing Zhang
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Walter E Smalley
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee.,Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee
| | - Edward L Giovannucci
- Department of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee.,Department of Medicine, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qi Dai
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Geriatric, Research, Education and Clinical Center (GRECC), Nashville, Tennessee.,Department of Medicine, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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Reardon HT, Zhang J, Kothapalli KSD, Kim AJ, Park WJ, Brenna JT. Insertion-deletions in a FADS2 intron 1 conserved regulatory locus control expression of fatty acid desaturases 1 and 2 and modulate response to simvastatin. Prostaglandins Leukot Essent Fatty Acids 2012; 87:25-33. [PMID: 22748975 DOI: 10.1016/j.plefa.2012.04.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 12/19/2022]
Abstract
The fatty acid desaturase genes (FADS1 and FADS2) code for enzymes required for synthesis of omega-3 and omega-6 long-chain polyunsaturated fatty acids (LCPUFA) important in the central nervous system, inflammatory response, and cardiovascular health. SNPs in these genes are associated with numerous health outcomes, but it is unclear how genetic variation affects enzyme function. Here, lymphoblasts obtained from Japanese participants in the International HapMap Project were evaluated for association of expression microarray results with SNPs in the FADS gene cluster. Six SNPs in the first intron of the FADS2 gene were associated with FADS1 expression. A 10-SNP haplotype in FADS2 (rs2727270 to rs2851682) present in 24% of the population was associated with lower expression of FADS1. A highly conserved region coinciding with the most significant SNPs contained predicted binding sites for SREBP and PPARγ. Lymphoblasts homozygous for either the major or minor haplotype were treated with agonists for these transcription factors and expression of FADS1 and FADS2 determined. Simvastatin and the LXR agonist GW3965 both upregulated expression of FADS1 and FADS2; no response was found for PPARγ agonist rosiglitazone. The minor haplotype homozygotes had 20-40% higher induction of FADS1 and FADS2 after simvastatin or GW3965 treatment. A 22 bp polymorphic insertion-deletion (INDEL) was found 137 bp downstream from the putative sterol response element, as well as a 3 or 1 bp INDEL 81-83 bp downstream. All carriers of the minor haplotype had deletions while all carriers of the major haplotype had insertions. Individuals carrying the minor haplotype may be vulnerable to alterations in diet that reduce LCPUFA intake, and especially responsive to statin or marine oil therapy.
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Affiliation(s)
- Holly T Reardon
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
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Org E, Veldre G, Viigimaa M, Juhanson P, Putku M, Rosenberg M, Tomberg K, Uuetoa T, Laan M. HYPEST study: profile of hypertensive patients in Estonia. BMC Cardiovasc Disord 2011; 11:55. [PMID: 21880150 PMCID: PMC3179926 DOI: 10.1186/1471-2261-11-55] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 08/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND More than one third of adult population in Estonia has problems with elevated blood pressure (BP). The Hypertension in Estonia (HYPEST) study represents the country's first hypertension-targeted sample collection aiming to examine the epidemiological and genetic determinants for hypertension (HTN) and related cardiovascular diseases (CVD) in Estonian population. The HYPEST subjects (n = 1,966) were recruited across Estonia between 2004-2007 including clinically diagnosed HTN cases and population-based controls. The present report is focused on the clinical and epidemiological profile of HYPEST cases, and gender-specific effects on the pathophysiology of hypertension. METHODS Current analysis was performed on 1,007 clinically diagnosed HTN patients (617 women and 390 men) aged 18-85 years. The hypertensives were recruited to the study by BP specialists at the North Estonia Medical Center, Centre of Cardiology, Tallinn or at the Cardiology Clinic, Tartu University Hospital, Estonia. Longitudinal BP data was extracted retrospectively from clinical records. Current and retrospective data of patient's medical history, medication intake and lifestyle habits were derived from self-administrated questionnaire and each variable was examined separately for men and women. Eleven biochemical parameters were measured from fasting serum samples of 756 patients. RESULTS The distribution of recruited men and women was 39% and 61% respectively. Majority of Estonian HTN patients (85%) were overweight (BMI ≥ 25 kg/m2) and a total of 79% of patients had additional complications with cardiovascular system. In men, the hypertension started almost 5 years earlier than in women (40.5 ± 14.5 vs 46.1 ± 12.7 years), which led to earlier age of first myocardial infarction (MI) and overall higher incidence rate of MI among male patients (men 21.2%, women 8.9%, P < 0.0001). Heart arrhythmia, thyroid diseases, renal tubulo-intestinal diseases and hyperlipidemia were more prevalent in hypertensive women compared to men (P < 0.0001). An earlier age of HTN onset was significantly associated with smoking (P = 0.00007), obesity (BMI ≥ 30 kg/m2; P = 0.0003), increased stress (P = 0.0003) and alcohol consumption (P = 0.004). CONCLUSION Understanding the clinical profile of HTN patients contributes to CVD management. Estonian hypertension patients exhibited different disease and risk profiles of male and female patients. This well-characterized sample set provides a good resource for studying hypertension and other cardiovascular phenotypes.
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Affiliation(s)
- Elin Org
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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Bi XH, Lu CM, Liu Q, Zhang ZX, Zhao HL, Yu J, Zhang JW. A 14 bp indel variation in the NCX1 gene modulates the age at onset in late-onset Alzheimer's disease. J Neural Transm (Vienna) 2011; 119:383-6. [PMID: 21833492 DOI: 10.1007/s00702-011-0696-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 07/27/2011] [Indexed: 01/30/2023]
Abstract
Calcium homeostasis is critical to amyloid beta precursor protein (APP) processing. Na(+)/Ca(2+) exchanger (NCX) proteins play an important role in maintaining intracellular Na(+) and Ca(2+) homeostasis in the brain under physiological and pathological conditions. We sequenced a hyper-variable region in intron 2 of the Na(+)/Ca(2+) exchanger 1 gene (NCX1), and investigated whether insertion/deletion variations in this region are associated with the occurrence for Alzheimer's disease (AD). Examining 413 AD patients and 361 healthy controls, we identified 3 insertion/deletion polymorphisms. No significant differences of the allele and genotype frequencies were observed between the AD cases and the controls for any of the three polymorphisms. However, among the AD patients whose age at onset (AAO) was 65 years or older (n = 299), carriers of a 14 bp insertion showed a lower average AAO (ins/ins and ins/del vs. del/del, 72.49 ± 5.17 vs. 74.28 ± 5.79, p = 0.016). It suggested that this 14 bp insertion/deletion polymorphism might modulate AAO in late-onset AD patients.
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Affiliation(s)
- Xiu-Hua Bi
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
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