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Patra G, Saha B, Mukhopadhyay S. Increased levels of pentraxins protein and cytokines bear good association in patients with severe dengue infection. Sci Rep 2021; 11:511. [PMID: 33436908 PMCID: PMC7804429 DOI: 10.1038/s41598-020-80144-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/14/2020] [Indexed: 01/08/2023] Open
Abstract
Dengue is an arboviral infection with high rates of morbidity and mortality throughout the tropics and sub-tropics. This work studied the status of pentraxin (CRP/SAP) protein, ferritin, TNF-α and IL-1β levels in Dengue patients of different pathophysiological manifestations. Accordingly, clinically confirmed Dengue cases (n = 97) were enrolled and subsequently blood parameters were studied by Haematology cell counter and Biochemistry Autoanalyser. CRP, SAP, ferritin, TNF-α and IL-1β ELISA were done in all the samples by using standard ELISA kits. Statistical Analysis was done in all the experiments. The levels of CRP (p < 0.0001), SAP (p < 0.0001), ferritin (p < 0.0001), TNF-α (p < 0.0001) and IL-1β (p < 0.0001) were high in patients with Severe Dengue as compared to Dengue without warning signs. High levels of SGOT, SGPT and decreased platelet counts were found in severe patients as compared to Healthy donor. CRP/SAP as well as TNF-α/IL-1β were independently associated with both dengue severity and overall disease manifestation. Statistically significant increased CRP, SAP, ferritin, TNF-α and IL-1β titres were correlated in patients with severe clinical manifestations as compared to mild disease forms of dengue. Elevated levels of pentraxin, TNF-α/IL-1β in blood during dengue infection could act as an early predictor in Severe Dengue infection.
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Affiliation(s)
- Goutam Patra
- Department of Laboratory Medicine, Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
| | - Bibhuti Saha
- Department of Tropical Medicine, Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
| | - Sumi Mukhopadhyay
- Department of Laboratory Medicine, Calcutta School of Tropical Medicine, Kolkata, West Bengal, India.
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Rabaan AA, Al-Ahmed SH, Sah R, Al-Tawfiq JA, Haque S, Harapan H, Arteaga-Livias K, Aldana DKB, Kumar P, Dhama K, Rodriguez-Morales AJ. Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19. CURRENT TROPICAL MEDICINE REPORTS 2020; 7:113-119. [PMID: 32989413 PMCID: PMC7513458 DOI: 10.1007/s40475-020-00212-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2020] [Indexed: 01/22/2023]
Abstract
Purpose of the Review The SARS-CoV-2 genome has been sequenced and the data is made available in the public domain. Molecular epidemiological investigators have utilized this information to elucidate the origin, mode of transmission, and contact tracing of SARS-CoV-2. The present review aims to highlight the recent advancements in the molecular epidemiological studies along with updating recent advancements in the molecular (nucleic acid based) diagnostics for COVID-19, the disease caused by SARS-CoV-2. Recent Findings Epidemiological studies with the integration of molecular genetics principles and tools are now mainly focused on the elucidation of molecular pathology of COVID-19. Molecular epidemiological studies have discovered the mutability of SARS-CoV-2 which is of utmost importance for the development of therapeutics and vaccines for COVID-19. The whole world is now participating in the race for development of better and rapid diagnostics and therapeutics for COVID-19. Several molecular diagnostic techniques have been developed for accurate and precise diagnosis of COVID-19. Summary Novel genomic techniques have helped in the understanding of the disease pathology, origin, and spread of COVID-19. The whole genome sequence established in the initial days of the outbreak has enabled to identify the virus taxonomy. Several rapid, accurate, and sensitive diagnostic methods have been developed; those are based on the principle of detecting SARS-CoV-2 nucleic acids in clinical samples. Most of these molecular diagnostics are based on RT-PCR principle.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia.,Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.,Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia
| | - Kovy Arteaga-Livias
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco, Peru.,Universidad Científica del Sur, Lima, Peru
| | - D Katterine Bonilla Aldana
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.,Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia
| | - Pawan Kumar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India
| | - Alfonso J Rodriguez-Morales
- Universidad Científica del Sur, Lima, Peru.,Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.,Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia.,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda Colombia
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Rigal J, Léglise A, Barnetche T, Cogniet A, Aunoble S, Le Huec JC. Meta-analysis of the effects of genetic polymorphisms on intervertebral disc degeneration. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2017; 26:2045-2052. [PMID: 28551829 DOI: 10.1007/s00586-017-5146-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 04/24/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Chronic low back pain is a significant public health issue. Both its direct and indirect cost represents tens of billions of US dollars. Although chronic low back pain can be the result of many factors, the predominant cause is disc degeneration. Recent studies have shown genetic involvement in up to 74% of cases. This study aimed to evaluate genetic risk factors of disc degeneration by performing a systematic analysis of association studies. The objective is to provide a guide for practice by assessing the clinical relevance of current information. METHODS AND MATERIALS We performed a meta-analysis of 3122 items collected from 6 databases. 74 articles were selected according to our inclusion criteria. 18 (24%) could be grouped into 16 meta-analyses of 16 mutations in 12 genes. The statistics of the meta-analysis were conducted through Revman 5.1 software. RESULTS The items included are 10,250 cases and 14,136 controls. The GOLD range from 3.42 to 0.38. Two alleles were significantly associated with disc degeneration: IL-6 rs1800797 and MMP-9 rs17576 and one proved to be protective: IL-6 rs1800795. 13 meta-analyses did not yield significant results and methodological heterogeneity. DISCUSSION The results highlight the lack of methodological rigor in most of the studies. The absence of international clinical and radiological classification of early disc degeneration, limits the homogeneity of studies. Understanding which populations are predisposed to this significant public health problem may change our approach to diagnostic and therapeutic methods. This work opens up enormous opportunities to provide a genetic solution and consider new diagnostic and therapeutic means to this public health problem.
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Affiliation(s)
- J Rigal
- Spine Unit 2, Orthopaedic Department, University of Bordeaux, Bordeaux, France
| | - A Léglise
- Spine Unit 2, Orthopaedic Department, University of Bordeaux, Bordeaux, France
| | - T Barnetche
- Spine Unit 2, Orthopaedic Department, University of Bordeaux, Bordeaux, France
| | - A Cogniet
- Spine Unit 2, Orthopaedic Department, University of Bordeaux, Bordeaux, France
| | - S Aunoble
- Spine Unit 2, Orthopaedic Department, University of Bordeaux, Bordeaux, France
| | - J C Le Huec
- Spine Unit 2, Orthopaedic Department, University of Bordeaux, Bordeaux, France.
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Dias MM, Sorich MJ, Rowland A, Wiese MD, McKinnon RA. The Routine Clinical use of Pharmacogenetic Tests: What it Will Require? Pharm Res 2017; 34:1544-1550. [PMID: 28236061 DOI: 10.1007/s11095-017-2128-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/16/2017] [Indexed: 01/04/2023]
Abstract
Pharmacogenetic testing aims to personalize drug therapy with a view to optimising drug efficacy and minimise toxicity. However, despite the potential benefits, pharmacogenetic testing is mostly confined to specialised medical areas, laboratories and centres. Widespread integration into routine clinical practice has been limited by a complex set of issues including regulatory and reimbursement frameworks, evidence of clinical utility and clinician perspectives, practices and education. Here we assess the current barriers to widespread clinical uptake and identify the key issue necessary to address to accelerate routine testing.
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Affiliation(s)
- Mafalda M Dias
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia.,Department of Clinical Pharmacology, School of Medicine, Flinders University, Bedford Park, Australia
| | - Michael J Sorich
- Department of Clinical Pharmacology, School of Medicine, Flinders University, Bedford Park, Australia.,Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
| | - Andrew Rowland
- Department of Clinical Pharmacology, School of Medicine, Flinders University, Bedford Park, Australia.,Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
| | - Michael D Wiese
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Ross A McKinnon
- Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
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Rigal J, Thelen T, Byrne F, Cogniet A, Boissière L, Aunoble S, Le Huec JC. Prospective study using anterior approach did not show association between Modic 1 changes and low grade infection in lumbar spine. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2016; 25:1000-5. [PMID: 26818032 DOI: 10.1007/s00586-016-4396-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/30/2022]
Abstract
INTRODUCTION The modern literature is producing a rapidly growing number of articles which highlight the relationship between infection and lumbar disc degeneration. However, the means by which samples are collected is questionable. Posterior approach surgery is not free from skin contamination. The possibility of intraoperative contamination of disc biopsies cannot be excluded. OBJECTIVE The objective of this study was to determine if an association existed between lumbar disc degeneration and chronic infection of the intervertebral disc. MATERIALS AND METHODS 313 patients (186/127, F/M) with chronic low back pain secondary to degenerative disc disease which was resistant to medical treatment were included in a single-centre prospective study. All underwent a lumbar anterior video-assisted minimally invasive fusion or disc prosthesis in L4-L5 and/or L5-S1 via an anterior retroperitoneal approach. The patients MRI scans demonstrated in Pfirrmann's classification grade IV or V disc degeneration; 385 disc drives were taken. In terms of Modic changes, 303 Modic 1, 58 Modic II and 24 absence of Modic change, respectively. All underwent intraoperative biopsy, performed according to a strict aseptic protocol. The biopsies were then cultured for 4 weeks with specialised enrichment cultures and subjected to histopathological analysis. RESULTS The mean age was 47 ± 8.6 years sterile cultures were obtained in 379 samples (98.4%) and 6 were positive (1.6%). The cultured bacteria were: Propionibacterium acnes (n:2), Staphylococcus epidermidis (n:2), Citrobacter freundii (n:1), and Saccharopolyspora hirsuta (n:1). Histopathological analysis did not demonstrate any evidence of a neutrophilia. There were no delayed or secondary infections. DISCUSSION AND CONCLUSION Unlike the posterior approach where contamination is common, the anterior video-assisted approach allows a biopsy without skin contact. This approach to the spine is the most effective way to eliminate the risk of contamination. Our results confirm the absence of any relationship between infection and disc degeneration. We suggest that the 6 positive samples in our study may be related to contamination. The absence of infection at 1-year followup is an additional argument in favour of our results. In conclusion, our study shows no association between infection and disc degeneration. The pathophysiology of disc degeneration is complex, but the current literature opens new perspectives.
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Affiliation(s)
- Julien Rigal
- Orthorachis 2, Orthopaedic Department, University of Bordeaux, Talence, France
| | - Thomas Thelen
- Orthorachis 2, Orthopaedic Department, University of Bordeaux, Talence, France
| | - Fergus Byrne
- Orthorachis 2, Orthopaedic Department, University of Bordeaux, Talence, France
| | - Arnaud Cogniet
- Orthorachis 2, Orthopaedic Department, University of Bordeaux, Talence, France
| | - Louis Boissière
- Orthorachis 2, Orthopaedic Department, University of Bordeaux, Talence, France
| | - Stephane Aunoble
- Orthorachis 2, Orthopaedic Department, University of Bordeaux, Talence, France
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Meta-analysis of the association between COL9A2 genetic polymorphisms and lumbar disc disease susceptibility. Spine (Phila Pa 1976) 2014; 39:1699-706. [PMID: 24983932 DOI: 10.1097/brs.0000000000000497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN Meta-analysis to collect all the relevant studies to date to further investigate whether or not the COL9A2 gene rs12077871, rs12722877, and rs7533552 polymorphism are associated with susceptibility to lumbar disc disease (LDD). OBJECTIVE The aim of this study was to assess the association between the COL9A2 gene rs12077871, rs12722877, and rs7533552 and LDD. SUMMARY OF BACKGROUND DATA LDD is a common musculoskeletal disease with strong genetic determinants. COL9A2 encodes the α2 (IX) chain of type IX collagen, which is the major collagen component of the hyaline cartilage. Growing numbers of studies have revealed the association between COL9A2 polymorphisms and susceptibility to LDD. However, those studies have yielded contradictory results. METHODS Data were collected from the following electronic databases: PubMed, Web of Knowledge, and China National Knowledge Infrastructure, with the last report up to November 30, 2013. The odds ratio (OR) and 95% confidence interval (CI) were used to assess the strength of association under the allelic genetic model. We summarized the data on the association between COL9A2 rs12077871, rs12722877, and rs7533552 polymorphism and LDD in the overall studies. RESULTS Nine case-control studies, including 1522 LDD cases and 1646 controls, were identified. The results indicated that the rs12077871, rs12722877, and rs7533552 variants in COL9A2 were not associated with LDD (rs12077871: C vs. T, OR = 0.541, 95% CI = 0.256-1.147, P = 0.109; rs12722877: C vs. G, OR = 1.199, 95% CI = 0.992-1.448, P = 0.06; rs7533552: A vs. G, OR = 0.993, 95% CI = 0.815-1.069, P = 0.320). Furthermore, the Egger test and the Begg funnel plot did not show any evidence of publication bias. CONCLUSION Our results suggest that the COL9A2 rs12077871, rs12722877, and rs7533552 polymorphisms may not be associated with LDD. More studies based on larger sample sizes and homogeneous samples of patients with LDD are needed to confirm these findings. LEVEL OF EVIDENCE 2.
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Eskola PJ, Lemmelä S, Kjaer P, Solovieva S, Männikkö M, Tommerup N, Lind-Thomsen A, Husgafvel-Pursiainen K, Cheung KMC, Chan D, Samartzis D, Karppinen J. Genetic association studies in lumbar disc degeneration: a systematic review. PLoS One 2012. [PMID: 23185509 PMCID: PMC3503778 DOI: 10.1371/journal.pone.0049995] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Objective Low back pain is associated with lumbar disc degeneration, which is mainly due to genetic predisposition. The objective of this study was to perform a systematic review to evaluate genetic association studies in lumbar disc degeneration as defined on magnetic resonance imaging (MRI) in humans. Methods A systematic literature search was conducted in MEDLINE, MEDLINE In-Process, SCOPUS, ISI Web of Science, The Genetic Association Database and The Human Genome Epidemiology Network for information published between 1990–2011 addressing genes and lumbar disc degeneration. Two investigators independently identified studies to determine inclusion, after which they performed data extraction and analysis. The level of cumulative genetic association evidence was analyzed according to The HuGENet Working Group guidelines. Results Fifty-two studies were included for review. Forty-eight studies reported at least one positive association between a genetic marker and lumbar disc degeneration. The phenotype definition of lumbar disc degeneration was highly variable between the studies and replications were inconsistent. Most of the associations presented with a weak level of evidence. The level of evidence was moderate for ASPN (D-repeat), COL11A1 (rs1676486), GDF5 (rs143383), SKT (rs16924573), THBS2 (rs9406328) and MMP9 (rs17576). Conclusions Based on this first extensive systematic review on the topic, the credibility of reported genetic associations is mostly weak. Clear definition of lumbar disc degeneration phenotypes and large population-based cohorts are needed. An international consortium is needed to standardize genetic association studies in relation to disc degeneration.
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Affiliation(s)
- Pasi J Eskola
- Oulu Center for Cell - Matrix Research, Biocenter and Department of Medical Biochemistry and Molecular Biology, University of Oulu, Oulu, Finland
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Jennings RG, Van Horn JD. Publication bias in neuroimaging research: implications for meta-analyses. Neuroinformatics 2012; 10:67-80. [PMID: 21643733 DOI: 10.1007/s12021-011-9125-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Neuroimaging and the neurosciences have made notable advances in sharing activation results through detailed databases, making meta-analysis of the published research faster and easier. However, the effect of publication bias in these fields has not been previously addressed or accounted for in the developed meta-analytic methods. In this article, we examine publication bias in functional magnetic resonance imaging (fMRI) for tasks involving working memory in the frontal lobes (Brodmann Areas 4, 6, 8, 9, 10, 37, 45, 46, and 47). Seventy-four studies were selected from the literature and the effect of publication bias was examined using a number of regression-based techniques. Pearson's r correlation coefficient and Cohen's d effect size estimates were computed for the activation in each study and compared to the study sample size using Egger's regression, Macaskill's regression, and the 'Trim and Fill' method. Evidence for publication bias was identified in this body of literature (p < 0.01 for each test), generally, though was neither task- nor sub-region-dependent. While we focused our analysis on this subgroup of brain mapping studies, we believe our findings generalize to the brain imaging literature as a whole and databases seeking to curate their collective results. While neuroimaging databases of summary effects are of enormous value to the community, the potential publication bias should be considered when performing meta-analyses based on database contents.
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Affiliation(s)
- Robin G Jennings
- Department of Biostatistics, University of California Los Angeles, 635 Charles Young Drive South, Suite 225, Los Angeles, CA, 90095, USA.
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Tong F, Yu W, Liu H. Efficient association analysis between colorectal cancer and allelic polymorphisms of HLA-DQB1 by comparison of age of onset. Oncol Lett 2011; 3:517-519. [PMID: 22740942 DOI: 10.3892/ol.2011.540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 12/19/2011] [Indexed: 11/05/2022] Open
Abstract
Common methods for identifying cancer-related genes are solely based on differences between gene frequencies in the disease and control groups, and do not take into account the age of onset in the gene carriers. In the present investigation, we developed a new study design based on the age of onset of cancer for the identification of colorectal cancer-related genes. The samples from patients with colorectal cancer were typed using an HLA-DQB1 polymerase chain reaction using a sequence-specific primers (PCR-SSP) typing kit. The mean age of subjects with and without the alleles was calculated. The mean age of subjects with the HLA-DQB1*02 allele was significantly less than that of subjects without this allele (p<0.05). We found that the HLA-DQB1*02 allele was associated with colorectal cancer susceptibility. This new method of analysis may therefore be an efficient and reliable approach for the identification of cancer-causing genes.
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Affiliation(s)
- Fengzhi Tong
- Dalian Fifth Hospital, Dalian Medical University, Dalian 116044, P.R. China
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Abstract
Much remains to be learned about the pathogenesis of the different manifestations of dengue virus (DENV) infections in humans. They may range from subclinical infection to dengue fever, dengue hemorrhagic fever (DHF), and eventually dengue shock syndrome (DSS). As both cell tropism and tissue tropism of DENV are considered major determinants in the pathogenesis of dengue, there is a critical need for adequate tropism assays, animal models, and human autopsy data. More than 50 years of research on dengue has resulted in a host of literature, which strongly suggests that the pathogenesis of DHF and DSS involves viral virulence factors and detrimental host responses, collectively resulting in abnormal hemostasis and increased vascular permeability. Differential targeting of specific vascular beds is likely to trigger the localized vascular hyperpermeability underlying DSS. A personalized approach to the study of pathogenesis will elucidate the basis of individual risk for development of DHF and DSS as well as identify the genetic and environmental bases for differences in risk for development of severe disease.
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Hui L, Liping G. Statistical estimation of diagnosis with genetic markers based on decision tree analysis of complex disease. Comput Biol Med 2009; 39:989-92. [PMID: 19712931 DOI: 10.1016/j.compbiomed.2009.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2006] [Revised: 07/19/2009] [Accepted: 07/27/2009] [Indexed: 10/20/2022]
Abstract
To explore combinations of genetic markers and to estimate their joint action, decision trees are built on the basis of marker frequencies in both disease and control groups. Youden's index (0.1-0.9 for a single marker) is calculated for genetic markers with different diagnostic capacities. When 23 single genetic markers with diagnostic power 0.10 are combined, the resulting diagnostic power is 0.5. Medium diagnostic power (Youden's index 0.7) can be obtained by combining four low effect diagnostic items. High diagnostic power (Youden's index 0.9) can be obtained by combining either eight low power items or four medium power ones. This implies that selection of about 100 genetic markers, differing in capacity to distinguish between the disease and control groups by (say) 10%, will meet the requirement for clinic diagnosis. Thus, diagnosis of complex diseases by genetic markers is possible through the discovery and characterization of markers throughout the human genome and the development of genotyping technology.
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Affiliation(s)
- Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian 116027, China.
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Moonesinghe R, Yang Q, Khoury MJ. Sample size requirements to detect the effect of a group of genetic variants in case-control studies. Emerg Themes Epidemiol 2008; 5:24. [PMID: 19055767 PMCID: PMC2651869 DOI: 10.1186/1742-7622-5-24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 12/03/2008] [Indexed: 11/17/2022] Open
Abstract
Background Because common diseases are caused by complex interactions among many genetic variants along with environmental risk factors, very large sample sizes are usually needed to detect such effects in case-control studies. Nevertheless, many genetic variants act in well defined biologic systems or metabolic pathways. Therefore, a reasonable first step may be to detect the effect of a group of genetic variants before assessing specific variants. Methods We present a simple method for determining approximate sample sizes required to detect the average joint effect of a group of genetic variants in a case-control study for multiplicative models. Results For a range of reasonable numbers of genetic variants, the sample size requirements for the test statistic proposed here are generally not larger than those needed for assessing marginal effects of individual variants and actually decline with increasing number of genetic variants in many situations considered in the group. Conclusion When a significant effect of the group of genetic variants is detected, subsequent multiple tests could be conducted to detect which individual genetic variants and their combinations are associated with disease risk. When testing for an effect size in a group of genetic variants, one can use our global test described in this paper, because the sample size required to detect an effect size in the group is comparatively small. Our method could be viewed as a screening tool for assessing groups of genetic variants involved in pathogenesis and etiology of common complex human diseases.
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Affiliation(s)
- Ramal Moonesinghe
- Office of Minority Health and Health Disparities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Bombell S, McGuire W. Cytokine polymorphisms in women with recurrent pregnancy loss: meta-analysis. Aust N Z J Obstet Gynaecol 2008; 48:147-54. [PMID: 18366487 DOI: 10.1111/j.1479-828x.2008.00843.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Inflammatory cytokine cascades have been implicated in the pathogenesis of recurrent pregnancy loss (RPL). Polymorphisms in cytokine genes may affect the risk of RPL, but genetic association studies are often limited by small sample sizes. Meta-analysis of all available studies can increase the precision of these estimates. AIMS To assess and synthesise the available data from association studies of inflammatory cytokine polymorphisms with RPL. METHODS Systematic review and random effects meta-analysis of genetic association studies. RESULTS Sixteen reports of genetic association studies of cytokine polymorphisms with RPL were identified. Meta-analyses did not identify any significant associations with tumour necrosis factor (-308A, or -238A), interferon-gamma (+874T), interleukin (IL)-1beta (-511T), IL-6 (-174G), or IL-10 (-1082A, or -819T, or -592A). Significant associations were found with IL-1B (-31T) (two studies: pooled odds ratio (OR) 2.12 (95% confidence interval (CI) 1.04 to 4.33)) and IL-6 (-634G) (one study: OR 0.22 (95% CI 0.09 to 0.57)). CONCLUSIONS The available data are not consistent with more than modest associations between these candidate cytokine polymorphisms and RPL. Data from future association studies may be added to the meta-analyses to obtain more precise estimates of effect sizes.
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Affiliation(s)
- Sarah Bombell
- Australian National University Medical School, The Canberra Hospital, Woden, Australian Capital Territory, Australia
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The continuum of translation research in genomic medicine: how can we accelerate the appropriate integration of human genome discoveries into health care and disease prevention? Genet Med 2008; 9:665-74. [PMID: 18073579 DOI: 10.1097/gim.0b013e31815699d0] [Citation(s) in RCA: 458] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Advances in genomics have led to mounting expectations in regard to their impact on health care and disease prevention. In light of this fact, a comprehensive research agenda is needed to move human genome discoveries into health practice in a way that maximizes health benefits and minimizes harm to individuals and populations. We present a framework for the continuum of multidisciplinary translation research that builds on previous characterization efforts in genomics and other areas in health care and prevention. The continuum includes four phases of translation research that revolve around the development of evidence-based guidelines. Phase 1 translation (T1) research seeks to move a basic genome-based discovery into a candidate health application (e.g., genetic test/intervention). Phase 2 translation (T2) research assesses the value of a genomic application for health practice leading to the development of evidence-based guidelines. Phase 3 translation (T3) research attempts to move evidence-based guidelines into health practice, through delivery, dissemination, and diffusion research. Phase 4 translation (T4) research seeks to evaluate the "real world" health outcomes of a genomic application in practice. Because the development of evidence-based guidelines is a moving target, the types of translation research can overlap and provide feedback loops to allow integration of new knowledge. Although it is difficult to quantify how much of genomics research is T1, we estimate that no more than 3% of published research focuses on T2 and beyond. Indeed, evidence-based guidelines and T3 and T4 research currently are rare. With continued advances in genomic applications, however, the full continuum of translation research needs adequate support to realize the promise of genomics for human health.
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Liu H, Yu W, Wang X, Fang F, Yang G, Zhou J, Liang X, An W. Number of STR repeats as a potential new quantitative genetic marker for complex diseases, illustrated by schizophrenia. Biochem Genet 2007; 45:683-9. [PMID: 17690978 DOI: 10.1007/s10528-007-9105-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 02/24/2007] [Indexed: 11/29/2022]
Abstract
It has proved difficult to find strong and replicable genetic linkages for complex diseases, since each susceptibility gene makes only a modest contribution to onset. This is partly because high-efficacy genetic markers are not usually available. The aim of this article is to explore the possibility that the total number of tandem repeats in one STR locus, rather than the frequencies of different alleles, is a higher efficacy quantitative genetic marker. DNA samples were collected from schizophrenic patients and from a control population. Alleles of the short tandem repeats (STR) loci D3S1358, vWA, and FGA were determined using the STR Profiler Plus PCR amplification kit. The two groups did not differ statistically in the frequencies of alleles at the D3S1358, vWA, or FGA loci. However, a significant difference was obtained in the vWA locus when the total number of core unit repeats was compared between the schizophrenia and control groups (33.28+/-2.61 vs. 32.35+/-2.58, P<0.05). It seems that the number of STR repeats may be a new, quantitative, and higher efficacy genetic marker for directly indicating genetic predisposition to complex hereditary diseases such as schizophrenia.
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Affiliation(s)
- Hui Liu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116027, P.R. China.
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Bertram L, McQueen MB, Mullin K, Blacker D, Tanzi RE. Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet 2007; 39:17-23. [PMID: 17192785 DOI: 10.1038/ng1934] [Citation(s) in RCA: 1257] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The past decade has witnessed hundreds of reports declaring or refuting genetic association with putative Alzheimer disease susceptibility genes. This wealth of information has become increasingly difficult to follow, much less interpret. We have created a publicly available, continuously updated database that comprehensively catalogs all genetic association studies in the field of Alzheimer disease (http://www.alzgene.org). We performed systematic meta-analyses for each polymorphism with available genotype data in at least three case-control samples. In addition to identifying the epsilon4 allele of APOE and related effects, we pinpointed over a dozen potential Alzheimer disease susceptibility genes (ACE, CHRNB2, CST3, ESR1, GAPDHS, IDE, MTHFR, NCSTN, PRNP, PSEN1, TF, TFAM and TNF) with statistically significant allelic summary odds ratios (ranging from 1.11-1.38 for risk alleles and 0.92-0.67 for protective alleles). Our database provides a powerful tool for deciphering the genetics of Alzheimer disease, and it serves as a potential model for tracking the most viable gene candidates in other genetically complex diseases.
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Affiliation(s)
- Lars Bertram
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease (MIND), Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA.
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Khoury MJ, Little J, Gwinn M, Ioannidis JPA. On the synthesis and interpretation of consistent but weak gene-disease associations in the era of genome-wide association studies. Int J Epidemiol 2006; 36:439-45. [PMID: 17182636 DOI: 10.1093/ije/dyl253] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Emerging technologies are allowing researchers to study hundreds of thousands of genetic variants simultaneously as risk factors for common complex diseases. Both theoretical considerations and empirical evidence suggest that specific genetic variants causally associated with common diseases will have small effects (risk ratios mostly <2.0). However, the combination of even a few small effects (e.g. effects of fewer than 20 common genetic variants) could account for a sizeable population attributable fraction of common diseases and shed important light on disease pathogenesis and environmental determinants. Nevertheless, the inauguration of genome-wide association studies only magnifies the challenge of differentiating between the expected, true weak associations from the numerous spurious effects caused by misclassification, confounding and significance-chasing biases. Standards are urgently needed for presenting and interpreting cumulative evidence on gene-disease associations, especially for consistent but weak associations. Criteria for synthesis of the evidence should include sound methods for study conduct and analysis, biological plausibility, experimental evidence and adequate replication in large-scale, collaborative studies. Efforts by the Human Genome Epidemiology Network (HuGENet) are currently ongoing to streamline and operationalize these criteria for data on genetic associations with common diseases.
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Affiliation(s)
- Muin J Khoury
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
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Burgner D, Jamieson SE, Blackwell JM. Genetic susceptibility to infectious diseases: big is beautiful, but will bigger be even better? THE LANCET. INFECTIOUS DISEASES 2006; 6:653-63. [PMID: 17008174 PMCID: PMC2330096 DOI: 10.1016/s1473-3099(06)70601-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genetic epidemiology, including twin studies, provides robust evidence that genetic variation in human populations contributes to susceptibility to infectious disease. One of the major limitations of studies that attempt to identify the genes and mechanisms that underlie this susceptibility has been lack of power caused by small sample size. With the development of novel technologies, burgeoning information on the human genome, the HapMap project, and human genetic diversity, we are at the beginning of a new era in the study of the genetics of complex diseases. This review looks afresh at the epidemiological evidence that supports a role for genetics in susceptibility to infectious disease, examines the somewhat limited achievements to date, and discusses current advances in methodology and technology that will potentially lead to translational data in the future.
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Affiliation(s)
- David Burgner
- School of Paediatrics and Child Health, University of Western Australia, Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Sarra E Jamieson
- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Jenefer M Blackwell
- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
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Ward K. Microarray technology in obstetrics and gynecology: a guide for clinicians. Am J Obstet Gynecol 2006; 195:364-72. [PMID: 16615920 PMCID: PMC7093878 DOI: 10.1016/j.ajog.2005.12.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 11/29/2005] [Accepted: 12/05/2005] [Indexed: 11/28/2022]
Abstract
Microarrays can be constructed with dozens to millions of probes on their surface to allow high-throughput analyses of many biologic processes to be performed simultaneously on the same sample. Microarrays are now widely used for gene expression analysis, deoxyribonucleic acid resequencing, single-nucleotide polymorphism genotyping, and comparative genomic hybridization. Microarray technology is accelerating research in many fields and now microarrays are moving into clinical application. This review discusses the emerging role of microarrays in molecular diagnostics, pathogen detection, oncology, and pharmacogenomics.
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Affiliation(s)
- Kenneth Ward
- Department of Obstetrics and Gynecology and Women's Health and the Pacific Research Center for Early Human Development, University of Hawaii, John A. Burns School of Medicine, Honolulu, HI 96826, USA.
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Lin BK, Clyne M, Walsh M, Gomez O, Yu W, Gwinn M, Khoury MJ. Tracking the epidemiology of human genes in the literature: the HuGE Published Literature database. Am J Epidemiol 2006; 164:1-4. [PMID: 16641305 DOI: 10.1093/aje/kwj175] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Completion of the human genome sequence has inspired a new wave of epidemiologic studies on the prevalence of gene variants and their associations with diseases in human populations. In 2001, the Human Genome Epidemiology (HuGE) Network launched the HuGE Published Literature database (HuGE Pub Lit), a searchable, online knowledge base of published, population-based epidemiologic studies of human genes. The database contains links to PubMed articles and can be searched by gene, disease, interacting factor, type of study design or analysis, or any combination of terms in these categories. The search output contains a link to each identified article, along with a table summarizing key features of the reported study. As of September 6, 2005, some 17,665 articles were indexed in the database. Most described gene-disease associations (86%); fewer evaluated gene-gene or gene-environment interactions (17%), the prevalence of gene variants (10%), or genetic tests (3%). Although not comprehensive, this database is a unique tool for epidemiologic researchers and others concerned with the role of genetic variation in population health. Here, the authors provide an overview of the database and its characteristics and uses.
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Affiliation(s)
- Bruce K Lin
- Office of Genomics and Disease Prevention, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
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Abstract
PURPOSE OF REVIEW Only two functionally validated susceptibility genes, CACNA1H and GABRD, have so far been identified in the common epilepsies using a candidate gene approach. The difficulty with the alternative statistical approach, where none of the suggested candidates has been functionally validated, may partly be due to the posited genetic architecture of the common epilepsies, such as the idiopathic generalized epilepsies. A subset of both rare and common variants from a much larger pool of susceptibility genes may contribute to disease risk. We review methods and designs for the genetic dissection of common epilepsies. RECENT FINDINGS Genetic association studies, though theoretically more powerful than linkage analysis, have not yet delivered validated susceptibility genes. Methodological flaws can undermine such studies but are correctable. Concerns remain, however, about the extent of underlying genetic heterogeneity in common epilepsies. Genome-wide association studies are increasingly feasible, but issues remain about their conduct and analysis. Meta-analysis may resolve conflicting association studies, facilitated by the establishment of databases of genetic association studies. Newer multi-locus and admixture mapping approaches are attractive alternatives to traditional association studies and may offer new insights into identifying epilepsy genes. SUMMARY We conclude by emphasizing the importance of deeper endophenotyping using electroclinical, imaging, and molecular approaches to dissect the common epilepsies.
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Affiliation(s)
- Nigel C K Tan
- Department of Neurology, National Neuroscience Institute, Singapore
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Davis RL, Khoury MJ. A public health approach to pharmacogenomics and gene-based diagnostic tests. Pharmacogenomics 2006; 7:331-7. [PMID: 16610943 DOI: 10.2217/14622416.7.3.331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
While the human genome project is likely to lead to fundamental changes in our understanding of disease causation and our ability to screen for disease predisposition and treatment responsiveness, the current healthcare system is not properly aligned to ensure the proper use of these advances. As the pace of genetic technology development increases and new pharmacogenetic drugs and gene-based diagnostic tests increasingly impact providers, patients, health plans, payers and employers, it will be crucial to develop an evidence-based framework by which to evaluate these new tests and treatments. In order to increase the level of evidence available and allow for informed decisions in the face of strong marketing and advocacy forces, the authors suggest the development of one (or more) large clinical networks with the purpose of systematically evaluating the clinical effectiveness of new genomic applications, including pharmaceuticals and gene-based diagnostic tests, in ‘real world’ settings.
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Affiliation(s)
- Robert L Davis
- Group Health Cooperative, Center for Health Studies, Seattle, Washington, USA
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