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Pedroza Matute S, Turvey K, Iyavoo S. Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study. Forensic Sci Int Genet 2024; 71:103049. [PMID: 38653142 DOI: 10.1016/j.fsigen.2024.103049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel's performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.
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Affiliation(s)
| | - Kiera Turvey
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom
| | - Sasitaran Iyavoo
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom; School of Chemistry, College of Health and Science, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, United Kingdom.
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Passos-Silva AM, Silva EDCE, Borzacov LMP, Araújo A, Porto AS, Salcedo JMV, Vieira D. Molecular genetic association of rs8099917 and rs1800795 polymorphisms in the progression of hepatitis Delta virus liver disease. J Venom Anim Toxins Incl Trop Dis 2024; 30:e20230025. [PMID: 38221914 PMCID: PMC10786575 DOI: 10.1590/1678-9199-jvatitd-2023-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/23/2023] [Indexed: 01/16/2024] Open
Abstract
Background The relationship between viral infections and host factors holds high hopes for identifying the role of Interferon Lambda 3 (IFNL3) and Interleukin 6 (IL-6) polymorphisms in the development of Chronic Liver Disease (CLD) in patients infected with hepatitis Delta virus (HDV) in the Western Brazilian Amazon. Methods Cross-sectional study conducted with a cohort of 40 chronic HDV patients, 27 with CLD and 13 without evident liver damage. Biological samples from the participants were analyzed using the polymerase chain reaction (PCR) technique, followed by sequencing by the automated Sanger method. Results The rs8099917 T allele, from the IFNL3 gene, showed a higher frequency in both groups; however, it was not possible to establish an association with HDV infection [OR = 1.42 (0.42 - 4.75; p = 0.556 (95% CI). For IL-6, the rs1800795 G allele was superior to rs1800795 C. Analyzing both distributions in the studied groups, any association with HDV was absent (p > 0.05). Conclusion The results suggest that the rs8099917 T/G (IFNL3) and rs1800795 G/C (IL-6) polymorphisms are not associated with the evolution of HDV in the studied population.
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Affiliation(s)
- Ana Maísa Passos-Silva
- Molecular Virology Laboratory, Oswaldo Cruz Foundation Rondonia -
FIOCRUZ/RO, Porto Velho, RO, Brazil
- Postgraduate Program in Experimental Biology, Federal University of
Rondonia, UNIR/FIOCRUZ-RO, Porto Velho, RO, Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
| | | | | | - Adrhyan Araújo
- Molecular Virology Laboratory, Oswaldo Cruz Foundation Rondonia -
FIOCRUZ/RO, Porto Velho, RO, Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
| | - Anita Sperandio Porto
- Federal University of Rondonia, UNIR, Porto Velho, RO,
Brazil
- Unir Pathology Laboratory, UNIR/RO, Porto Velho, RO, Brazil
| | - Juan Miguel Villalobos Salcedo
- Federal University of Rondonia, UNIR, Porto Velho, RO,
Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
| | - Deusilene Vieira
- Molecular Virology Laboratory, Oswaldo Cruz Foundation Rondonia -
FIOCRUZ/RO, Porto Velho, RO, Brazil
- Postgraduate Program in Experimental Biology, Federal University of
Rondonia, UNIR/FIOCRUZ-RO, Porto Velho, RO, Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
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Siddique A, Bashir S, Abbas M. Pharmacogenetics of Anticancer Drugs: Clinical Response and Toxicity. Cancer Treat Res 2023; 185:141-175. [PMID: 37306909 DOI: 10.1007/978-3-031-27156-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cancer is the most challenging disease for medical professionals to treat. The factors underlying the complicated situation include anticancer drug-associated toxicity, non-specific response, low therapeutic window, variable treatment outcomes, development of drug resistance, treatment complications, and cancer recurrence. The remarkable advancement in biomedical sciences and genetics, over the past few decades, however, is changing the dire situation. The discovery of gene polymorphism, gene expression, biomarkers, particular molecular targets and pathways, and drug-metabolizing enzymes have paved the way for the development and provision of targeted and individualized anticancer treatment. Pharmacogenetics is the study of genetic factors having the potential to affect clinical responses and pharmacokinetic and pharmacodynamic behaviors of drugs. This chapter emphasizes pharmacogenetics of anticancer drugs and its applications in improving treatment outcomes, selectivity, toxicity of the drugs, and discovering and developing personalized anticancer drugs and genetic methods for prediction of drug response and toxicity.
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Affiliation(s)
- Ammara Siddique
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Samra Bashir
- Faculty of Pharmacy, Capital University of Science and Technology, Islamabad, Pakistan.
| | - Mateen Abbas
- Faculty of Pharmacy, Capital University of Science and Technology, Islamabad, Pakistan
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Beheshti M, Rabiei N, Taghizadieh M, Eskandari P, Mollazadeh S, Dadgostar E, Hamblin MR, Salmaninejad A, Emadi R, Mohammadi AH, Mirazei H. Correlations between single nucleotide polymorphisms in obsessive-compulsive disorder with the clinical features or response to therapy. J Psychiatr Res 2023; 157:223-238. [PMID: 36508934 DOI: 10.1016/j.jpsychires.2022.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Obsessive-compulsive disorder (OCD) is a debilitating neuropsychiatric disorder, in which the patient endures intrusive thoughts or is compelled to perform repetitive or ritualized actions. Many cases of OCD are considered to be familial or heritable in nature. It has been shown that a variety of internal and external risk factors are involved in the pathogenesis of OCD. Among the internal factors, genetic modifications play a critical role in the pathophysiological process. Despite many investigations performed to determine the candidate genes, the precise genetic factors involved in the disease remain largely undetermined. The present review summarizes the single nucleotide polymorphisms that have been proposed to be associated with OCD symptoms, early onset disease, neuroimaging results, and response to therapy. This information could help us to draw connections between genetics and OCD symptoms, better characterize OCD in individual patients, understand OCD prognosis, and design more targeted personalized treatment approaches.
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Affiliation(s)
- Masoumeh Beheshti
- Pathophysiology Laboratory, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nikta Rabiei
- School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, School of Medicine, Center for Women's Health Research Zahra, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pariya Eskandari
- Department of Biology, School of Basic Sciences, University of Guilan, Rasht, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran; Student Research Committee, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | - Arash Salmaninejad
- Regenerative Medicine, Organ Procurement and Transplantation Multi Disciplinary Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Raziye Emadi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
| | - Amir Hossein Mohammadi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamed Mirazei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Mitochondrial uncoupling protein 2 (UCP2) gene polymorphism - 866 G/A in the promoter region is associated with type 2 diabetes mellitus among Kashmiri population of Northern India. Mol Biol Rep 2023; 50:475-483. [PMID: 36346492 DOI: 10.1007/s11033-022-08055-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE The study aimed to evaluate the association of UCP2 gene polymorphism - 866 G/A and its expression with diabetes predisposition in the North Indian population. METHODS The study involved 850 subjects, including 425 each T2DM and control subjects. The serum metabolic and clinical parameters were estimated using standard protocols. The PCR-RFLP based genotyping was performed to determine UCP2 gene polymorphism, while the expression was measured by real-time quantitative PCR. RESULTS The genotypic and allelic frequencies showed a significant difference in cases compared to controls (p < 0.05). The diabetes patients had a 4.2-fold decrease in UCP2 gene expression. The expression was 29.8 and 8.4 fold lower in diabetes patients with homozygous (AA) and heterozygous (GA) mutation at - 866 locus of UCP2 nucleotide sequence, respectively. When categorized according to age and BMI, the T2DM subjects with age ≥ 50 and BMI ≥ 25 had a 5.53 and 8.2-fold decrease in UCP2 expression, respectively. The diabetes subjects with homozygous and heterozygous mutation demonstrated a pathological increase in serum metabolic and clinical parameters, which corroborated with UCP2 gene expression, indicating a strong association between the two. Intriguingly, we did not find any association between - 866 G/A polymorphism of UCP2 with serum insulin levels. CONCLUSION Our investigation is the first among the studies conducted in Jammu and Kashmir to work on adipose tissue and UCP2 gene polymorphism. The association of - 866 G/A SNP of the UCP2 gene with its expression in diabetes patients appears to be an important genetic determinant in the progression of T2DM. Moreover, age ≥ 50 years and BMI ≥ 25 could be considered risk factors for developing T2DM in the studied population.
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Sattarzadeh Bardsiri M, Zehtab S, Karami N, Farsinejad A, Ehsan M, Fatemi A. Association of IKZF1 and CDKN2A gene polymorphisms with childhood acute lymphoblastic leukemia: a high-resolution melting analysis. BMC Med Genomics 2022; 15:171. [PMID: 35932035 PMCID: PMC9354342 DOI: 10.1186/s12920-022-01325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Acute lymphoblastic leukemia is the most prevailing pediatric hematologic malignancy, and various factors such as environmental exposures and genetic variation affect ALL susceptibility and patients outcome. According to genome-wide association studies, several single nucleotide polymorphisms (SNPs) in IKZF1 (rs4132601) and CDKN2A (rs3731249 and rs3731217) genes are associated with ALL susceptibility. Hereupon, this study aimed to discover the association between these SNPs and the risk of childhood ALL among a sample of the Iranian population.
Methods A total of fifty children with ALL were included in this case–control study, along with an additional fifty healthy children, matched for age and gender. High-resolution melting (HRM) analysis was employed to genotyping rs4132601, rs3731249, and rs3731217.
Results In the patient group, the CT genotype and T allele frequency of rs3731249 were significantly greater than controls (p = 0.01 and p = 0.005, respectively). Moreover, the positive association of CT and dominant model (CT + TT) genotypes and T allele at rs3731249 with the risk of ALL was confirmed (OR = 9.56, OR = 10.76 and OR = 11.00, respectively). There was no significant relation between rs4132601 (IKZF1), rs3731217 (CDKN2A), and childhood ALL. Conclusion The present study indicates that CT genotype and T allele at rs3731249 (CDKN2A) can significantly increase the risk of ALL among children.
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Affiliation(s)
- Mahla Sattarzadeh Bardsiri
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahrzad Zehtab
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Najibe Karami
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Farsinejad
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Ehsan
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran
| | - Ahmad Fatemi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran. .,Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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Nasirigerdeh R, Torkzadehmahani R, Matschinske J, Frisch T, List M, Späth J, Weiss S, Völker U, Pitkänen E, Heider D, Wenke NK, Kaissis G, Rueckert D, Kacprowski T, Baumbach J. sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies. Genome Biol 2022; 23:32. [PMID: 35073941 PMCID: PMC8785575 DOI: 10.1186/s13059-021-02562-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/02/2021] [Indexed: 11/10/2022] Open
Abstract
Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies (GWAS). However, the accuracy of meta-analysis can be attenuated in the presence of cross-study heterogeneity. We present sPLINK, a hybrid federated and user-friendly tool, which performs privacy-aware GWAS on distributed datasets while preserving the accuracy of the results. sPLINK is robust against heterogeneous distributions of data across cohorts while meta-analysis considerably loses accuracy in such scenarios. sPLINK achieves practical runtime and acceptable network usage for chi-square and linear/logistic regression tests. sPLINK is available at https://exbio.wzw.tum.de/splink .
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Affiliation(s)
- Reza Nasirigerdeh
- AI in Medicine and Healthcare, Technical University of Munich, Munich, Germany.
- Klinikum rechts der Isar, Munich, Germany.
| | | | - Julian Matschinske
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Tobias Frisch
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Julian Späth
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Stefan Weiss
- Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Nina Kerstin Wenke
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Georgios Kaissis
- AI in Medicine and Healthcare, Technical University of Munich, Munich, Germany
- Klinikum rechts der Isar, Munich, Germany
- Biomedical Image Analysis Group, Imperial College London, London, UK
- OpenMined, Oxford, UK
| | - Daniel Rueckert
- AI in Medicine and Healthcare, Technical University of Munich, Munich, Germany
- Klinikum rechts der Isar, Munich, Germany
- Biomedical Image Analysis Group, Imperial College London, London, UK
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Brunswick, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Brunswick, Germany
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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Higgins O, Smith TJ. Loop-Primer Endonuclease Cleavage-Loop-Mediated Isothermal Amplification Technology for Multiplex Pathogen Detection and Single-Nucleotide Polymorphism Identification. J Mol Diagn 2021; 22:640-651. [PMID: 32409120 DOI: 10.1016/j.jmoldx.2020.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/15/2019] [Accepted: 02/03/2020] [Indexed: 12/27/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) provides effective diagnostic technology for infectious disease pathogen identification and is compatible with inexpensive instrumentation for use in disease-prevalent developing regions. However, simultaneous multiple-target detection and single-nucleotide polymorphism (SNP) identification, essential properties of nucleic acid diagnostics, are difficult to achieve using LAMP. This study introduces loop-primer endonuclease cleavage (LEC)-LAMP, a singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification. We developed a singleplex LEC-LAMP Neisseria meningitidis assay that demonstrated complete analytical specificity and a limit of detection of 3.1 genome copies per reaction. Small-scale clinical testing of this assay demonstrated 100% diagnostic specificity and sensitivity when assessed with anonymized DNA extracts from confirmed cases of bacterial meningitis infection. The single-base specificity of this assay indicated effective SNP identification properties when challenged with DNA templates containing SNPs located within a specific six-base region. This assay was modified to generate an allele-specific LEC-LAMP N. meningitidis assay that successfully demonstrated single-tube differentiation of wild-type and mutant allele templates. The singleplex assay was further modified to generate a multiplex LEC-LAMP assay that successfully demonstrated simultaneous multiple-target detection of three bacterial targets, N. meningitidis, Streptococcus pneumonia, and Hemophilus influenzae. LEC-LAMP is the first report of single-tube, real-time, singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | - Terry J Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland
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Higgins O, Smith TJ. 3' Tth Endonuclease Cleavage Polymerase Chain Reaction (3TEC-PCR) Technology for Single-Base-Specific Multiplex Pathogen Detection using a Two-Oligonucleotide System. Int J Mol Sci 2021; 22:6061. [PMID: 34199760 PMCID: PMC8199996 DOI: 10.3390/ijms22116061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
Polymerase chain reaction (PCR) is the standard in nucleic acid amplification technology for infectious disease pathogen detection and has been the primary diagnostic tool employed during the global COVID-19 pandemic. Various PCR technology adaptations, typically using two-oligonucleotide dye-binding methods or three-oligonucleotide hydrolysis probe systems, enable real-time multiplex target detection or single-base specificity for the identification of single-nucleotide polymorphisms (SNPs). A small number of two-oligonucleotide PCR systems facilitating both multiplex detection and SNP identification have been reported; however, these methods often have limitations in terms of target specificity, production of variable or false-positive results, and the requirement for extensive optimisation or post-amplification analysis. This study introduces 3' Tth endonuclease cleavage PCR (3TEC-PCR), a two-oligonucleotide PCR system incorporating a modified primer/probe and a thermostable cleavage enzyme, Tth endonuclease IV, for real-time multiplex detection and SNP identification. Complete analytical specificity, low limits of detection, single-base specificity, and simultaneous multiple target detection have been demonstrated in this study using 3TEC-PCR to identify bacterial meningitis associated pathogens. This is the first report of a two-oligonucleotide, real-time multiplex PCR technology with single-base specificity using Tth endonuclease IV.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland;
- Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Terry J. Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland;
- Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
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Sivaprakasam B, Sadagopan P. Development of shiny dashboard application for “genome-wide association study on analysis of SNPs injected in Homo sapiens genome (snips-HsG)”. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Aslam R, Shahid M, Bano I, Ayoub M, Sabar MF, Altaf S, Kousar S, Ghani MU, Husnain T, Shahid AA. Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan. THE CLINICAL RESPIRATORY JOURNAL 2021; 15:374-381. [PMID: 33211378 DOI: 10.1111/crj.13309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/09/2020] [Accepted: 11/13/2020] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Various genome wide association studies have manifested that Major Histocompatibility Complex (MHC) region on chromosome 6p21 houses many potential candidate genes for asthma. OBJECTIVE This Case-Control association study was planned to determine the association of 10 Single Nucleotide Polymorphisms (SNPs), residing within and around MHC genes' region on chromosome 6p21, with Asthma in Punjabi population of Lahore, Pakistan. METHODS A total of 161 subjects, 61 physician-diagnosed asthma patients and 100 age-matched healthy controls, were recruited from Lahore, a city in Punjab. Ten single nucleotide polymorphisms (SNPs) (rs9378249, rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049225, rs1049219, rs7773955 and rs928976) located within or near AGER, NOTCH and HLA genes in MHC region, were genotyped in both patients and controls using single base extension reaction and capillary electrophoresis-based genetic analyser. Statistical models were applied using SHEsis Plus. Results were adjusted for various cofactors (age, gender and environment) and by applying multiple corrections. Haplotype and linkage disequilibrium analyses were performed on Haploview software v4.1. RESULTS Three of the studied SNPs rs1049124, rs1049219 and rs7773955 show independent significant association with asthma under allelic and genotypic models. Two of the haplotypes, H7 and H13, "CTAATTT" and "CCACTAT", respectively, for rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049219 and rs7773955, are found to be significantly associated with the disease. CONCLUSION This study reports association of SNP variants residing on HLA-DQB1 and HLA-DQA2 genes and haplotypes H7 and H13 on genomic region 6p21 with Asthma in the Punjabi population of Lahore, Pakistan.
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Affiliation(s)
- Raheela Aslam
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Iqbal Bano
- The Children's Hospital and The Institute of Child Health, Pediatric Pulmonology, Lahore, Pakistan
| | - Muhammad Ayoub
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Saba Altaf
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samra Kousar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Aslam R, Shahid M, Bano I, Ayoub M, Sabar MF, Altaf S, Kousar S, Ghani MU, Husnain T, Shahid AA. Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan. THE CLINICAL RESPIRATORY JOURNAL 2021. [DOI: https:/doi.org/10.1111/crj.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Raheela Aslam
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Iqbal Bano
- The Children’s Hospital and The Institute of Child Health, Pediatric Pulmonology Lahore Pakistan
| | - Muhammad Ayoub
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Saba Altaf
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Samra Kousar
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Tayyab Husnain
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
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13
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Aslam R, Shahid M, Bano I, Ayoub M, Sabar MF, Altaf S, Kousar S, Ghani MU, Husnain T, Shahid AA. Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan. THE CLINICAL RESPIRATORY JOURNAL 2020. [DOI: https://doi.org/10.1111/crj.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Raheela Aslam
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Iqbal Bano
- The Children’s Hospital and The Institute of Child Health, Pediatric Pulmonology Lahore Pakistan
| | - Muhammad Ayoub
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Saba Altaf
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Samra Kousar
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Tayyab Husnain
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
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14
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Hu S, Zhan W, Wang J, Xie J, Zhou W, Yang X, Zeng Y, Hu T, Duan L, Chen K, Du L, Yin A, Luo M. Establishment and application of a novel method based on single nucleotide polymorphism analysis for detecting β-globin gene cluster deletions. Sci Rep 2020; 10:18298. [PMID: 33106596 PMCID: PMC7588424 DOI: 10.1038/s41598-020-75507-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/12/2020] [Indexed: 12/03/2022] Open
Abstract
β-Globin gene mutations reduce or terminate the production of beta globin chains, of which approximately 10% are large deletions within the β-globin gene cluster. Because gene deletion leads to loss of heterozygosity at single nucleotide polymorphism (SNP), a novel method for detecting β-globin gene cluster deletions based on SNP heterozygosity analysis was established in this study. The location range of SNPs was selected according to the breakpoint of β-globin gene cluster deletions. SNPs were screened using bioinformatics analysis and population sequencing data. A novel method which enables genotyping of multiplex SNPs based on tetra-primer ARMS-PCR was designed and optimized. Forty clinical samples were tested in parallel by this method and MLPA to verify the performance of this method for detecting β-globin gene cluster deletion. Six informative SNPs were obtained, achieving heterozygote coverage of 93.3% in normal individuals. Genotyping of six SNPs were successfully integrated into two multiplex tetra-primer ARMS-PCR reactions. The sensitivity, specificity, positive predictive value and negative predictive value of the method for detecting β-globin gene cluster deletion were 100%, 96.30%, 92.86%, and 100%, respectively. This is a simple, cost-effective and novel method for detecting β-globin gene cluster deletions, which may be suitable for use in combination with MLPA for thalassemia molecular testing.
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Affiliation(s)
- Siqi Hu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetics Center, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Wenli Zhan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jicheng Wang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jia Xie
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China
| | - Weiping Zhou
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiaohan Yang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yukun Zeng
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Tingting Hu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lei Duan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China
| | - Keyi Chen
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Li Du
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Aihua Yin
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Mingyong Luo
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China. .,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China.
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15
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Schmidt N, Schücker K, Krause I, Dörk T, Klintschar M, Hummel S. Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:99-109. [DOI: 10.1002/ajpa.23996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Nicole Schmidt
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
| | - Katharina Schücker
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
- Max‐Planck‐Institute for Biophysical Chemistry Göttingen Germany
| | - Ina Krause
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
| | - Thilo Dörk
- Gynaecological Research UnitHannover Medical School Hannover Germany
| | | | - Susanne Hummel
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
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16
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ROLE OF SINGLE NUCLEOTIDE GENE POLYMORPHISMS IN THE DEVELOPMENT OF ULCERATIVE COLITIS. WORLD OF MEDICINE AND BIOLOGY 2020. [DOI: 10.26724/2079-8334-2020-3-73-52-56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Poma A, Cesare P, Bonfigli A, Vecchiotti G, Colafarina S, Savini F, Redi F, Zarivi O. Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy. Heliyon 2019; 5:e02586. [PMID: 31646208 PMCID: PMC6804371 DOI: 10.1016/j.heliyon.2019.e02586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy. The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.
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Affiliation(s)
- Anna Poma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Corresponding author.
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giulia Vecchiotti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Savini
- Department of Human Sciences, University of L'Aquila, L'Aquila, Italy
| | - Fabio Redi
- Department of Human Sciences, University of L'Aquila, L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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18
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Abd El Hamid MM, Mabrouk MS, Omar YMK. DEVELOPING AN EARLY PREDICTIVE SYSTEM FOR IDENTIFYING GENETIC BIOMARKERS ASSOCIATED TO ALZHEIMER’S DISEASE USING MACHINE LEARNING TECHNIQUES. BIOMEDICAL ENGINEERING: APPLICATIONS, BASIS AND COMMUNICATIONS 2019. [DOI: 10.4015/s1016237219500406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Alzheimer’s disease (AD) is an irreversible, progressive disorder that assaults the nerve cells of the brain. It is the most widely recognized kind of dementia among older adults. Apolipoprotein E (APOE), is one of the most common genetic risk factors for AD whose significant association with AD is observed in various genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among individuals. SNPs related to many common diseases like AD. SNPs are recognized as significant biomarkers for this disease, they help in understanding and detecting the disease in its early stages. Detecting SNPs biomarkers associated to the disease with high classification accuracy leads to early prediction and diagnosis. Machine learning techniques are utilized to discover new biomarkers of the disease. Sequential minimal optimization (SMO) algorithm with different kernels, Naive Bayes (NB), tree augmented Naive Bayes (TAN) and K2 learning algorithm have been applied on all genetic data of Alzheimer’s disease neuroimaging initiative phase 1 (ADNI-1)/Whole genome sequencing (WGS) datasets. The highest classification accuracy was achieved using 500 SNPs based on the [Formula: see text]-value threshold ([Formula: see text]-value [Formula: see text]). In whole genome approach ADNI-1, results revealed that NB and K2 learning algorithms scored an overall accuracy of 98% and 98.40%, respectively. In whole genome approach WGS, NB and K2 learning algorithms scored an overall accuracy of 99.63% and 99.75%, respectively.
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Affiliation(s)
| | - Mai S. Mabrouk
- Biomedical Engineering Department, Misr University for Science and Technology (MUST), Egypt
| | - Yasser M. K. Omar
- College of Computing and Information Technology AASTMT, Cairo Branch, Egypt
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19
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Bisciotti GN, Chamari K, Cena E, Bisciotti A, Bisciotti A, Corsini A, Volpi P. Anterior cruciate ligament injury risk factors in football. J Sports Med Phys Fitness 2019; 59:1724-1738. [PMID: 31062538 DOI: 10.23736/s0022-4707.19.09563-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Anterior cruciate ligament (ACL) lesion represents one of the most dramatic injuries in a football (soccer) player's career. There are many injury risk factors related to intrinsic (non-modifiable) and/or extrinsic (modifiable) factors of ACL injury. EVIDENCE ACQUISITION Research of the studies was conducted until September 2018 without publication data limitation or language restriction on the following databases: PubMed/MEDLINE, Scopus, ISI, EXCERPTA. EVIDENCE SYNTHESIS To date, evidence from the literature suggests that the risk of ACL injury is multifactorial and involves biomechanical, anatomical, hormonal, and neuromuscular factors. Despite this relative complexity, the mechanisms of injury are well known and rationally classified into two categories: mechanisms of injury based on contact or on non-contact with another player, with the non-contact injury mechanisms clearly prevailing over the mechanisms of contact injury. One of the most frequent biomechanical risk factors, associated with ACL non-contact injury, is represented by the valgus knee in the pivoting and cutting movements and in the landing phase after jumping. Gender-related risk factors show female populations to have a higher predisposition to ACL injury than males However, there are still some theoretical and practical aspects that need further investigation such as; genetic risks together with the role of estrogen and progesterone receptors in female populations, and the in-vivo interaction shoe-playing surface. In particular, the genetic risk factors of ACL lesion seem to be an interesting and promising field of investigation, where considerable progress has still to be made. CONCLUSIONS This narrative review provides an insight into the risk factors of ACL injury that could be used by practitioners for preventing injury in football (soccer).
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Affiliation(s)
- Gian Nicola Bisciotti
- Qatar Orthopedic and Sport Medicine Hospital, FIFA Center of Excellence, Doha, Qatar -
| | - Karim Chamari
- Qatar Orthopedic and Sport Medicine Hospital, FIFA Center of Excellence, Doha, Qatar
| | - Emanuele Cena
- Qatar Orthopedic and Sport Medicine Hospital, FIFA Center of Excellence, Doha, Qatar
| | | | | | | | - Piero Volpi
- FC Internazionale Milano, Milan, Italy.,Unit of Traumatology, Department of Knee Orthopedic and Sports, Humanitas Research Hospital, Rozzano, Milan, Italy
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20
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Ad'hiah AH, Al-naseri MA, Ahmed ZA, Salman ED, Al-saffar OB, Ahmed HS, Hussain TA, Idan EM. Cytokine gene variations and their impact on serum levels of IFN-γ, IL-2, IL-4, IL-10 and IL-12 among Iraqi Arabs. Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Shin S, Kim K, Lee JM, Kim EJ, Kim SJ, Kim IJ, Pak K, Lee MJ. Effect of Single-Nucleotide Polymorphisms on Decline of Dopamine Transporter Availability in Parkinson's Disease. J Clin Neurol 2019; 15:102-107. [PMID: 30618224 PMCID: PMC6325373 DOI: 10.3988/jcn.2019.15.1.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND PURPOSE We aimed to determine the association between the annual changes in dopamine transporter (DAT) availability as measured by ¹²³I-ioflupane (¹²³I-FP-CIT) single-photon-emission computed tomography and single-nucleotide polymorphisms (SNPs) known to be risk factors in Parkinson's disease (PD). METHODS In total, 150 PD patients were included from the Parkinson's Progression Markers Initiative database. Specific SNPs that are associated with PD were selected for genotyping. SNPs that were not in Hardy-Weinberg equilibrium or whose minor allele frequency was less than 0.05 were excluded. Twenty-three SNPs met the inclusion criteria for this study. The Kruskal-Wallis test was used to compare annual percentage changes in DAT availability for three subgroups of SNP. RESULTS None of the 23 SNPs exerted a statistically significant effect (p<0.0022) on the decline of DAT availability in PD patients. However, we observed trends of association (p<0.05) between three SNPs of two genes with the annual percentage change in DAT availability: 1) rs199347 on the putamen (p=0.0138), 2) rs356181 on the caudate nucleus (p=0.0105), and 3) rs3910105 on the caudate nucleus (p=0.0374). A post-hoc analysis revealed that DAT availability was reduced the most for 1) the putamen in the CC genotype of rs199347 (vs. CT, p=0.0199; vs. TT, p=0.0164), 2) the caudate nucleus in the TT genotype of rs356181 (vs. CC, p=0.0081), and 3) the caudate nucleus in the CC genotype of rs3910105 (vs. TT, p=0.0317). CONCLUSIONS Significant trends in the associations between three SNPs and decline of DAT availability in PD patients have been discovered.
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Affiliation(s)
- Seunghyeon Shin
- Department of Nuclear Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Keunyoung Kim
- Department of Nuclear Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Jae Meen Lee
- Department of Neurosurgery, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Eun Joo Kim
- Department of Neurology, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Seong Jang Kim
- Department of Nuclear Medicine and Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - In Joo Kim
- Department of Nuclear Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.
| | - Kyoungjune Pak
- Department of Nuclear Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.
| | - Myung Jun Lee
- Department of Neurology, Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.
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22
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An introduction to the role of immunology in medical anthropology and molecular epidemiology. Biomed Pharmacother 2019; 109:2203-2209. [DOI: 10.1016/j.biopha.2018.11.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
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23
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Single Nucleotide Polymorphism in SMAD7 and CHI3L1 and Colorectal Cancer Risk. Mediators Inflamm 2018; 2018:9853192. [PMID: 30498395 PMCID: PMC6222239 DOI: 10.1155/2018/9853192] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/01/2018] [Accepted: 08/16/2018] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the leading cancers throughout the world. It represents the third most common cancer and the fourth in mortality. Most of CRC are sporadic, arise with no known high-penetrant genetic variation and with no previous family history. The etiology of sporadic CRC is considered to be multifactorial and arises from the interaction of genetic variants of low-penetrant genes and environmental risk factors. The most common well-studied genetic variation is single nucleotide polymorphisms (SNPs). SNP arises as a point mutation. If the frequency of the sequence variation reaches 1% or more in the population, it is referred to as polymorphism, but if it is lower than 1%, the allele is typically considered as a mutation. Lots of SNPs have been associated with CRC development and progression, for example, genes of TGF-β1 and CHI3L1 pathways. TGF-β1 is a pleiotropic cytokine with a dual role in cancer development and progression. TGF-β1 mediates its actions through canonical and noncanonical pathways. The most important negative regulatory protein for TGF-β1 activity is termed SMAD7. The production of TGF-β can be controlled by another protein called YKL-40. YKL-40 is a glycoprotein with an important role in cancer initiation and metastasis. YKL-40 is encoded by the CHI3L1 gene. The aim of the present review is to give a brief introduction of CRC, SNP, and examples of some SNPs that have been documented to be associated with CRC. We also discuss two important signaling pathways TGF-β1 and CHI3L1 that influence the incidence and progression of CRC.
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24
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Naidoo P, Naidoo RN, Ramkaran P, Muttoo S, Asharam K, Chuturgoon AA. Maternal miRNA-146a G/C rs2910164 variation, HIV/AIDS and nitrogen oxide pollution exposure collectively affects foetal growth. Hum Exp Toxicol 2018; 38:82-94. [PMID: 29896975 DOI: 10.1177/0960327118781902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE: Nitrogen oxide (NOx) pollution and human immunodeficiency virus (HIV)/AIDS intensify inflammation during pregnancy and linked with adverse birth outcomes (ABOs). MicroRNA (miRNA)-146a plays a crucial role in regulating inflammation in the NF-κB pathway. The G/C rs2910164 dampens miRNA-146a activity and linked with inflammatory diseases. The present study investigated whether HIV/AIDS and NOx exposure throughout pregnancy further intensifies ABO in Black South African women genotyped for the rs2910164. METHODS: Pregnant women ( n = 300) were subdivided into low, medium and high NOx exposure groups, genotyped for the miRNA-146a G/C rs2910164 using polymerase chain reaction-restriction fragment length polymorphism, and further stratified based on HIV status. RESULTS: Unstratified data (HIV+ and HIV- mothers combined): Mothers from the high NOx group with the variant C-allele had low blood iron levels ( p = 0.0238), and had babies with reduced birthweights ( p = 0.0283). As NOx increased, the prevalence of preterm birth and low birth weight also increased in mothers with the variant C-allele versus wildtype G-allele. HIV-infected mothers: In all NOx exposure groups, mothers with the variant C-allele had higher systolic blood pressure (low: p = 0.0386, medium: p = 0.0367 and high: p = 0.0109) and had babies with lower Appearance, Pulse, Grimace, Activity and Respiration scores at 1 min (low: p = 0.0190, medium: p = 0.0301 and high: p = 0.0361). CONCLUSION: Maternal rs2910164 variant C-allele, NOx pollution and HIV/AIDS might collectively play a role in intensifying gestational hypertension and ABO.
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Affiliation(s)
- P Naidoo
- 1 Discipline of Medical Biochemistry and Chemical Pathology, University of KwaZulu-Natal, Durban, South Africa
| | - R N Naidoo
- 2 Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, Durban, South Africa
| | - P Ramkaran
- 1 Discipline of Medical Biochemistry and Chemical Pathology, University of KwaZulu-Natal, Durban, South Africa
| | - S Muttoo
- 2 Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, Durban, South Africa
| | - K Asharam
- 2 Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, Durban, South Africa
| | - A A Chuturgoon
- 1 Discipline of Medical Biochemistry and Chemical Pathology, University of KwaZulu-Natal, Durban, South Africa
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25
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Fleury A, Alaez C, Dessein A, Rosetti M, Saenz B, Hernández M, Bobes RJ, Ramírez-Aquino R, Sciutto E, Gorodezky C, Fragoso G. No association of IL2, IL4, IL6, TNF, and IFNG gene polymorphisms was found with Taenia solium human infection or neurocysticercosis severity in a family-based study. Hum Immunol 2018; 79:578-582. [PMID: 29684412 DOI: 10.1016/j.humimm.2018.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 11/19/2022]
Abstract
Neurocysticercosis (NC) is caused by the establishment of the metacestode stage of Taenia solium in the human central nervous system. A great heterogeneity in the susceptibility to the infection and to the disease has been reported. While the factors involved in this heterogeneity are not completely understood, clearly different immune-inflammatory profiles have been associated to each condition. This study evaluated the association of cytokine single nucleotide polymorphisms (SNPs) with susceptibility to infection and disease severity in NC patients. Blood samples from 92 NC cases and their parents (trios) were genotyped for SNPs in five cytokines relevant for the immune response: IL4 (-589C/T), IL6 (-174C/G), IFNG (+874T/A), TNF (-238G/A), and IL2 (-330G/T). Specific DNA fragments were amplified by the polymerase chain reaction, using the 5'-nuclease Taqman assay on a 7500 platform, allowing the detection of the polymorphism genotypes. No association between the polymorphisms evaluated neither with susceptibility to infection nor with disease severity was found, although previous studies reported variations in the levels of these cytokines among different NC clinical pictures. These results, nevertheless, add new elements to our understanding of the complex pathogenic mechanisms involved in susceptibility to infection by T. solium cysticerci and the severity of the ensuing disease.
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Affiliation(s)
- A Fleury
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; Unidad Periférica del Instituto de Investigaciones Biomédicas en el Instituto Nacional de Neurología y Neurocirugía, Mexico.
| | - C Alaez
- Dept of Immunology & Immunogenetics, Instituto de Diagnóstico y Referencia Epidemiológicos-InDRE, Secretaria de Salud, Ciudad de México, Mexico; Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico.
| | - A Dessein
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR906, GIMP, Labex ParaFrap, Aix-Marseille Université, 13005 Marseille, France.
| | - M Rosetti
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
| | - B Saenz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - M Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - R J Bobes
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
| | - R Ramírez-Aquino
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - E Sciutto
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
| | - C Gorodezky
- Dept of Immunology & Immunogenetics, Instituto de Diagnóstico y Referencia Epidemiológicos-InDRE, Secretaria de Salud, Ciudad de México, Mexico.
| | - G Fragoso
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
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Zulfiqar HF, Javed A, Sumbal, Afroze B, Ali Q, Akbar K, Nadeem T, Rana MA, Nazar ZA, Nasir IA, Husnain T. HIV Diagnosis and Treatment through Advanced Technologies. Front Public Health 2017; 5:32. [PMID: 28326304 PMCID: PMC5339269 DOI: 10.3389/fpubh.2017.00032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) is the chief contributor to global burden of disease. In 2010, HIV was the fifth leading cause of disability-adjusted life years in people of all ages and leading cause for people aged 30-44 years. It is classified as a member of the family Retroviridae and genus Lentivirus based on the biological, morphological, and genetic properties. It infects different cells of the immune system, such as CD4+ T cells (T-helper cells), dendritic cells, and macrophages. HIV has two subtypes: HIV-1 and HIV-2. Among these strains, HIV-1 is the most virulent and pathogenic. Advanced diagnostic methods are exploring new ways of treatment and contributing in the reduction of HIV cases. The diagnostic techniques like PCR, rapid test, EIA, p24 antigen, and western blot have markedly upgraded the diagnosis of HIV. Antiretroviral therapy and vaccines are promising candidates in providing therapeutic and preventive regimes, respectively. Invention of CRISPR/Cas9 is a breakthrough in the field of HIV disease management.
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Affiliation(s)
| | - Aneeqa Javed
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Sumbal
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Bakht Afroze
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Khadija Akbar
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Tariq Nadeem
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | | | - Zaheer Ahmad Nazar
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
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Abstract
CONTEXT Inbreeding increases the level of homozygotes for autosomal recessive disorders and is the major objective in clinical studies. The prevalence of consanguinity and the degree of inbreeding vary from one population to another depending on ethnicity, religion, culture and geography. Global epidemiological studies have revealed that consanguineous unions have been significantly associated with increased susceptibility to various forms of inherited diseases. OBJECTIVE The study aimed to determine the role of consanguinity in human health and to highlight the associated risks for various diseases or disorders. METHODS PubMed and Google Scholar search engines were used to explore the published literature on consanguinity and its associated risks using the key words "consanguinity", "prevalence", "inbreeding depression", "coefficient of inbreeding", "child health", "mortality", "human health", "homozygosity" and "complex diseases" in different combinations. The studies were screened for eligibility on the basis of their epidemiological relevance. RESULTS This comprehensive assessment highlights the deleterious consequences in populations with a higher prevalence of consanguinity among different countries worldwide. CONCLUSIONS To avoid the inbreeding load there is the need to improve socioeconomic and educational status and to increase public awareness of reproductive health and anticipated deleterious effects. Pre-marital and pre-conception counselling of consanguineous populations should be an integral part of health policy to train people and make people aware of its harmful consequences. Furthermore, runs of homozygosity (ROH) and whole-exome sequencing (WES) are useful tools in exploring new genomic signatures for the cause of inbreeding depression.
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Affiliation(s)
- Mohd Fareed
- a Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences , Aligarh Muslim University , Aligarh , Uttar Pradesh , India.,b Centre for Biodiversity Studies, School of Biosciences and Biotechnology , Baba Ghulam Shah Badshah University , Rajouri , Jammu and Kashmir , India
| | - Mohammad Afzal
- a Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences , Aligarh Muslim University , Aligarh , Uttar Pradesh , India
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John R, Dhillon MS, Sharma S, Prabhakar S, Bhandari M. Is There a Genetic Predisposition to Anterior Cruciate Ligament Tear? A Systematic Review. Am J Sports Med 2016; 44:3262-3269. [PMID: 26842309 DOI: 10.1177/0363546515624467] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Injuries to the anterior cruciate ligament (ACL) are among the most common knee ligament injuries and frequently warrant reconstruction. The etiopathogenesis of these injuries has focused mainly on mechanism of trauma, patient sex, and anatomic factors as predisposing causes. Several genetic factors that could predispose to an ACL tear have recently been reported. PURPOSE This systematic review summarizes the current evidence for a genetic predisposition to ACL tears. The principal research question was to identify genetic factors, based on the available literature, that could predispose an individual to an ACL tear. STUDY DESIGN Systematic review. METHODS The PubMed, EMBASE, Cochrane, and HuGE databases were searched; the search was run from the period of inception until June 21, 2015. A secondary search was performed by screening the references of full-text articles obtained and by manually searching selected journals. Articles were screened with prespecified inclusion criteria. The quality of studies included in the review was assessed for risk of bias by 2 reviewers using the Newcastle-Ottawa Scale. RESULTS A total of 994 records were identified by the search, out of which 17 studies (16 case-control studies and 1 cross-sectional study) were included in the final review. Two studies observed a familial predisposition to an ACL tear. Fourteen studies looked at specific gene polymorphisms in 20 genes, from which different polymorphisms in 10 genes were positively associated with an ACL tear. In addition to these polymorphisms, 8 haplotypes were associated with ACL tear. One study looked at gene expression analysis. CONCLUSION Although specific gene polymorphisms and haplotypes have been identified, it is difficult to come to a conclusion on the basis of the existing literature. Several sources of bias have been identified in these studies, and the results cannot be extrapolated to the general population. More studies are needed in larger populations of different ethnicities. Gene-gene interactions and gene expression studies in the future may delineate the exact role of these gene polymorphisms in ACL tears.
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Fareed M, Afzal M. Genetic structure of human populations based on 5 gene loci: A preliminary report from Northern India. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sadaf T, John P, Bhatti A, Jahangir S, Kiani AK, Gill FA, Malik JM. Lack of tumor necrosis factor alpha gene polymorphism -857c/t (rs1799724) association in Pakistani rheumatoid arthritis patients. Int J Rheum Dis 2016; 19:1119-1125. [PMID: 27126784 DOI: 10.1111/1756-185x.12857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a common systemic autoimmune disease, influenced greatly by the pro-inflammatory cytokine tumor necrosis factor- alpha (TNF-α). Single nucleotide polymorphisms (SNPs) in regulatory regions of the TNF-α gene play a significant role in disease development and pathogenesis. The aim of this study was to investigate the association of TNF-α -857C/T (rs1799724) SNP with RA activity or severity in our Pakistani study group. METHODS The study included 134 (116 women, 18 men) patients with RA and 134 ethnically matched healthy controls (108 women, 26 men). Each patient's disease activity was measured by Disease Activity Score of 28 joints. The genotypes were determined in all included individuals following allele-specific polymerase chain reaction along with the prerequisite internal amplification controls. Statistical analysis including chi-square/Fischer exact test and one-way analysis of variance; nonparametric Kruskal-Wallis test was employed using Graphpad Prism 6 software for association study. RESULTS The prevalence of TNF-α -857C/T (rs1799724) polymorphism was not differentially distributed between RA patients and controls in either allele frequency, with odds ratio (95% CI) of 0.9661 (0.6714-1.390) and P-value of 0.8527, or genotype frequency with χ2 of 0.5015 and P-value of 0.7782. Moreover, no correlation was found when genotype frequency distribution was analyzed with disease severity (P = 0.6321 and Kruskal-Wallis statistics of 1.098). CONCLUSION The study demonstrated -857C/T (rs1799724) polymorphism may not have influenced RA susceptibility in our study group. However, investigations of genetic variability influence on disease outcome in large prospective cohorts are required, so the complicated interconnection of genetic and environmental elements can be emulated for better understanding.
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Affiliation(s)
- Tayyaba Sadaf
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Peter John
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Attya Bhatti
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Sidrah Jahangir
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Aysha K Kiani
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Farah A Gill
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Javed M Malik
- Arthritis Research Center, Rahmat Noor Clinic, Rawalpindi, Pakistan
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Kasim NB, Huri HZ, Vethakkan SR, Ibrahim L, Abdullah BM. Genetic polymorphisms associated with overweight and obesity in uncontrolled Type 2 diabetes mellitus. Biomark Med 2016; 10:403-15. [DOI: 10.2217/bmm-2015-0037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Generally, obese and overweight individuals display higher free fatty acid levels, which stimulate insulin resistance. The combination of overweight or obesity with insulin resistance can trigger Type 2 diabetes mellitus (T2DM) and are primary contributing factors to the development of uncontrolled T2DM. Genetic polymorphisms also play an important role as they can impact a population's susceptibility to becoming overweight or obese and developing related chronic complications, such as uncontrolled T2DM. This review specifically examines the genetic polymorphisms associated with overweight and obesity in patients with uncontrolled T2DM. Particularly, gene polymorphisms in ADIPOQ (rs1501299 and rs17300539), LepR (rs1137101 and rs1045895), IRS2 (rs1805092), GRB14 (rs10195252 and rs3923113) and PPARG (rs1801282) have been associated with overweight and obesity in uncontrolled T2DM.
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Affiliation(s)
- Nor Bahirah Kasim
- Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hasniza Zaman Huri
- Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Clinical Investigation Centre, Faculty of Medicine, 13th Floor Main Tower, University Malaya Medical Centre, 59100 Lembah Pantai Kuala Lumpur, Malaysia
| | | | - Luqman Ibrahim
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Bashar Mudhaffar Abdullah
- Clinical Investigation Centre, Faculty of Medicine, 13th Floor Main Tower, University Malaya Medical Centre, 59100 Lembah Pantai Kuala Lumpur, Malaysia
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Abd El-Fattah AA, Sadik NAH, Shaker OG, Kamal AM. Are SMAD7 rs4939827 and CHI3L1 rs4950928 polymorphisms associated with colorectal cancer in Egyptian patients? Tumour Biol 2016; 37:9387-97. [PMID: 26779637 DOI: 10.1007/s13277-016-4813-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/06/2016] [Indexed: 02/07/2023] Open
Abstract
A wide variety of genes have been associated with colorectal cancer (CRC) development and progression. The SMAD7 gene encodes an intracellular protein, which inhibits the transforming growth factor beta (TGF-β) signaling pathway, thereby having a key role in the control of neoplastic processes in various organs. The CHI3L1 gene encodes glycoprotein YKL-40, which plays a role in cell proliferation, anti-apoptosis, and angiogenesis. The present study aimed to evaluate the association of single nucleotide polymorphisms (SNPs) SMAD7 rs4939827 and CHI3L1 rs4950928, as well as circulating TGFβ-1 and YKL-40 levels with CRC in an Egyptian population of 77 CRC patients and 36 healthy controls. Polymorphisms in the SMAD7 rs4939827 and the CHI3L1 rs4950928 genes were determined using the real-time polymerase chain reaction (RT-PCR). Both the SMAD7 rs4939827 TT genotype and the CHI3L1 rs4950928 C allele were associated with the rectal but not the colon cancer. In addition, the C allele of both SMAD7 rs4939827 and CHI3L1 rs4950928 was associated with increased serum levels of TGF-β1 and YKL-40, respectively. In conclusion, our data suggest that SMAD7 rs4939827 and CHI3L1 rs4950928 SNPs have no significant association with CRC. A significant association of SNP in SMAD7 rs4939827 and CHI3L1 rs4950928 was revealed between the rectal cancer and colon cancer patients.
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Affiliation(s)
- Amal Ahmed Abd El-Fattah
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Eini Street, Cairo, 11562, Egypt
| | - Nermin Abdel Hamid Sadik
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Eini Street, Cairo, 11562, Egypt
| | - Olfat Gamil Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Kasr El-Eini Street, Cairo, Egypt
| | - Amal Mohamed Kamal
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Eini Street, Cairo, 11562, Egypt.
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BABADEMEZ MA, ÖZDAŞ T, ÖZDAŞ S. The common genetic variants of toll-like receptor and susceptibilityto adenoid hypertrophy: a hospital-based cohort study. Turk J Med Sci 2016; 46:1449-1458. [DOI: 10.3906/sag-1511-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/14/2016] [Indexed: 11/03/2022] Open
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Abstract
Interleukin (IL-)23 is a central cytokine controlling TH17 development. Overshooting IL-23 signaling contribute to autoimmune diseases. Moreover, GWAS studies have identified several SNPs within the IL-23 receptor, which are associated with autoimmune diseases. IL-23 is a member of the IL-12-type cytokine family and consists of IL-23p19 and p40. Within the IL-12 family, IL-12 and IL-23 share the p40 cytokine subunit and the IL-12Rβ1 as one chain of the receptor complex. For signaling, IL-23 triggers heterodimerization of IL-12Rβ1 and the IL-23R. Subsequently, signal transduction pathways including JAK/STAT, MAPK and PI3K are activated. Most studies have investigated the biological relevance of IL-23 in the development of TH17 cells and autoimmunity, whereas less is known about the molecular context of IL-23 biology. Therefore, we focused on IL-23 receptor complex assembly, signal transduction and functional relevance of IL-23R SNPs in the context of IL-23-inhibitory principles.
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Association of Interleukin-10 gene promoter polymorphisms with obstructive sleep apnea. Sleep Breath 2015; 20:855-66. [PMID: 26139223 DOI: 10.1007/s11325-015-1216-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/02/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Interleukin-10 (IL) is an anti-inflammatory cytokine that regulates normal sleep patterns, and recent studies have reported that it is a potential useful biomarker to identify presence and severity of sleep apnea syndrome (OSAS). Promoter polymorphisms of IL-10 gene have been associated with altered expression levels, which contributes to OSAS. OBJECTIVE The aim of this study was to determine the prevalence of -1082 G/A, -819 C/T, and -592 C/A promoter polymorphisms of IL-10 gene in individuals with OSAS and controls. SUBJECTS AND METHODS An open-label study was performed in the Otorhinolaryngology and Sleep Disorders Outpatient Clinics. One hundred four cases with OSAS were included as the study group, and 78 individuals without OSAS were included as the controls. DNAs were extracted from peripheral blood leukocytes, and the sites that encompassed those polymorphisms were identified by DNA sequencing analyses. Data were analyzed with SNPStats and multifactor dimensionality reduction (MDR) software. RESULTS The prevalence of OSAS was higher in males in the study group when compared to controls (P = 0.0003). The IL-10-1082 G/A, -819 C/T, and -592 C/A SNPs, and their minor alleles were associated with a significantly increased risk for OSAS compared to the controls (P ˂ 0.05 for all). Furthermore, ATA haplotype frequency was significantly higher in the study group compared to the control group, but the GCC haplotype frequency was lower (P = 0.0001 and P = 0.0001). As indicated in MDR analysis, combinations of IL-10 gene were associated with OSAS in single-, double-, and triple-locus analyses. CONCLUSION The prevalences of the IL-10 gene promoter polymorphisms were different in OSAS patients and the controls in Turkish population. IL-10 gene polymorphisms may lead to altered inflammatory cascade, which might contribute to OSAS. Further studies on larger cohorts are needed to validate our findings.
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Kitakaze M, Asakura M, Nakano A, Takashima S, Washio T. Data Mining as a Powerful Tool for Creating Novel Drugs in Cardiovascular Medicine: The Importance of a “Back-and-Forth Loop” Between Clinical Data and Basic Research. Cardiovasc Drugs Ther 2015; 29:309-15. [DOI: 10.1007/s10557-015-6602-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Effect of MTHFR, TGFβ1, and TNFB polymorphisms on osteoporosis in rheumatoid arthritis patients. Gene 2015; 568:124-8. [PMID: 25981594 DOI: 10.1016/j.gene.2015.05.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/17/2015] [Accepted: 05/12/2015] [Indexed: 01/07/2023]
Abstract
Diseases of the immune and the skeletal systems should be studied together for the deep interaction between them. Many studies consider osteoporosis (OP) as a risk factor for the prediction of disease progression in rheumatoid arthritis (RA). The aim of this research is to study the effect of four single nucleotide polymorphisms (SNPs) on RA patients with and without OP. The examined SNPs (MTHFR (C677T, and A1298C), TGFβ1 (T869C), and TNFB (A252G)) were tested by genotyping 17 RA patients with OP and 72 RA patients without OP. Associations were tested using four models (multiplicative, dominant, recessive, and co-dominant). The studied SNPs were not significantly associated with the risk of OP in RA. MTHFR, TGFβ1, and TNFB polymorphisms don't appear to be clinically useful genetic markers for predicting RA severity in Egyptian women population.
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Affiliation(s)
- Mohamed N Saad
- Biomedical Engineering Department, Minia University, Minia, Egypt.
| | - Mai S Mabrouk
- Biomedical Engineering Department, MUST, 6th of October, Egypt
| | - Ayman M Eldeib
- Systems and Biomedical Engineering Department, Cairo University, Giza, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Cairo University, Cairo, Egypt
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: A systematic review and meta-analysis. J Adv Res 2015; 7:1-16. [PMID: 26843965 PMCID: PMC4703421 DOI: 10.1016/j.jare.2015.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 01/13/2015] [Accepted: 01/20/2015] [Indexed: 12/30/2022] Open
Abstract
Genetics of autoimmune diseases represent a growing domain with surpassing biomarker results with rapid progress. The exact cause of Rheumatoid Arthritis (RA) is unknown, but it is thought to have both a genetic and an environmental bases. Genetic biomarkers are capable of changing the supervision of RA by allowing not only the detection of susceptible individuals, but also early diagnosis, evaluation of disease severity, selection of therapy, and monitoring of response to therapy. This review is concerned with not only the genetic biomarkers of RA but also the methods of identifying them. Many of the identified genetic biomarkers of RA were identified in populations of European and Asian ancestries. The study of additional human populations may yield novel results. Most of the researchers in the field of identifying RA biomarkers use single nucleotide polymorphism (SNP) approaches to express the significance of their results. Although, haplotype block methods are expected to play a complementary role in the future of that field.
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Affiliation(s)
- Mohamed N Saad
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology, 6th of October City, Egypt
| | - Mai S Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology, 6th of October City, Egypt
| | - Ayman M Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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Fareed M, Afzal M. Estimating the inbreeding depression on cognitive behavior: a population based study of child cohort. PLoS One 2014; 9:e109585. [PMID: 25313490 PMCID: PMC4196914 DOI: 10.1371/journal.pone.0109585] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cognitive ability tests are widely assumed to measure maximal intellectual performance and predictive associations between intelligence quotient (IQ) scores and later mental health problems. Very few epidemiologic studies have been done to demonstrate the relationship between familial inbreeding and modest cognitive impairments in children. OBJECTIVE We aimed to estimate the effect of inbreeding on children's cognitive behavior in comparison with non-inbred children. METHODOLOGY A cohort of 408 children (6 to 15 years of age) was selected from inbred and non-inbred families of five Muslim populations of Jammu region. The Wechsler Intelligence Scales for Children (WISC) was used to measure the verbal IQ (VIQ), performance IQ (PIQ) and full scale IQ (FSIQ). Family pedigrees were drawn to access the family history and children's inbred status in terms of coefficient of inbreeding (F). RESULTS We found significant decline in child cognitive abilities due to inbreeding and high frequency of mental retardation among offspring from inbred families. The mean differences (95% C.I.) were reported for the VIQ, being -22.00 (-24.82, -19.17), PIQ -26.92 (-29.96, -23.87) and FSIQ -24.47 (-27.35,-21.59) for inbred as compared to non-inbred children (p<0.001) [corrected].The higher risk of being mentally retarded was found to be more obvious among inbred categories corresponding to the degree of inbreeding and the same accounts least for non-inbred children (p<0.0001). We observed an increase in the difference in mean values for VIQ, PIQ and FSIQ with the increase of inbreeding coefficient and these were found to be statistically significant (p<0.05). The regression analysis showed a fitness decline (depression) for VIQ (R2 = 0.436), PIQ (R2 = 0.468) and FSIQ (R2 = 0.464) with increasing inbreeding coefficients (p<0.01). CONCLUSIONS Our comprehensive assessment provides the evidence for inbreeding depression on cognitive abilities among children.
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Affiliation(s)
- Mohd Fareed
- Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- * E-mail: (MF); (MA)
| | - Mohammad Afzal
- Human Genetics and Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- * E-mail: (MF); (MA)
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He MY, Deng YX, Shi QZ, Zhang XJ, Lv Y. Comparative pharmacokinetic investigation on baicalin and wogonoside in type 2 diabetic and normal rats after oral administration of traditional Chinese medicine Huanglian Jiedu decoction. JOURNAL OF ETHNOPHARMACOLOGY 2014; 155:334-342. [PMID: 24910405 DOI: 10.1016/j.jep.2014.05.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 06/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Huanglian Jiedu decoction (HLJDD) is used traditionally in China for the treatment of diabetes mellitus in clinical practice, which has been proved to be effective. The purpose of this study was to investigate the pharmacokinetic characteristics (especially the area under the curve, AUC) of baicalin and wogonoside in type 2 diabetic rats after oral administration of HLJDD extract and to explore its possible mechanism. MATERIALS AND METHODS HLJDD extract and Radix scutellariae extract were prepared and the contents of baicalin and wogonoside contained in two extracts were assayed with high performance liquid chromatography (HPLC). Type 2 diabetic rats were induced by high fat diet and intraperitoneal injection of streptozotocin. Pharmacokinetics of baicalin and wogonoside in type 2 diabetic and normal control rats after oral administration of HLJDD extract or Radix scutellariae extract were investigated. Pharmacokinetics of baicalin in type 2 diabetic and normal rats after oral administration of pure baicalin was also investigated. RESULTS The pharmacokinetic parameters (especially AUCs) of baicalin and wogonoside in type 2 diabetic rats after oral administration of HLJDD extract were remarkably different from those in normal rats. And the alterations of the AUCs of baicalin and wogonoside in type 2 diabetic rats after oral administration of Radix scutellariae extract were similar to those after oral administration of HLJDD extract. Moreover, the increase of the AUC of baicalin in type 2 diabetic rats after oral administration of pure baicalin was similar to that after oral administration of HLJDD extract or Radix scutellariae extract. CONCLUSION The pharmacokinetic behaviors of baicalin and wogonoside (especially the systemic exposure [AUCs] of baicalin and wogonoside) were significantly altered in type 2 diabetic rats after orally administrated HLJDD extract. And the increased AUCs of baicalin and wogonoside in type 2 diabetic rats after oral administration of HLJDD extract resulted from neither the effects of other herbs contained in HLJDD nor the effects of other components contained in Radix scutellariae. It might result from the effects of the pathological status of type 2 diabetes mellitus.
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Affiliation(s)
- Meng-Yun He
- Department of Pharmaceutical Science, Medical College of Hunan Normal University, Changsha 410013, PR China
| | - Yuan-Xiong Deng
- Department of Pharmaceutical Science, Medical College of Hunan Normal University, Changsha 410013, PR China.
| | - Qun-Zhi Shi
- Department of Pharmaceutical Science, Medical College of Hunan Normal University, Changsha 410013, PR China
| | - Xiao-Jie Zhang
- Department of Pharmaceutical Science, Medical College of Hunan Normal University, Changsha 410013, PR China
| | - Yuan Lv
- Department of Pharmaceutical Science, Medical College of Hunan Normal University, Changsha 410013, PR China
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Wu XJ, Zhang ML, Cui XY, Paul Fawcett J, Gu JK. Comparative pharmacokinetics and the bioavailability of escin Ib and isoescin Ib following the administration of escin, pure escin Ib and isoescin Ib in rats. JOURNAL OF ETHNOPHARMACOLOGY 2014; 151:839-845. [PMID: 24334163 DOI: 10.1016/j.jep.2013.11.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/24/2013] [Accepted: 11/21/2013] [Indexed: 06/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Adequate pharmacokinetic data of escin, a natural mixture of triterpene saponins used for the treatment of chronic venous insufficiency, hemorrhoids, inflammation and edema, is of special interest in view of the growing use of escin agent in clinical medicine. However, pharmacokinetic data are inadequate to support their clinical indication. Escin Ib and isoescin Ib are the chief active ingredients in escin, pharmacokinetics study of them would be helpful for improving the practice of escin application. The goals of this study are to determine the plasma concentration of escin Ib and isoescin Ib using an established liquid chromatography tandem mass spectrometry (LC-MS/MS) method and to compare the pharmacokinetics and bioavailability of these compounds in rats when administered as pure isomers or as sodium escinate. MATERIALS AND METHODS Five groups of Wistar rats (n=6 per group) were treated with either an intravenous (IV) dose (2.78mg/kg) of sodium escinate (corresponding to 0.5mg/kg of escin Ib and 0.5mg/kg of isoescin Ib), an IV dose (0.5mg/kg) and an oral dose (4mg/kg) of pure escin Ib or isoescin Ib. The concentrations of escin Ib and isoescin Ib in rat plasma were determined by LC-MS/MS at various times following the administration of the drugs. The pharmacokinetic parameters were estimated by a non-compartmental analysis and then subjected to statistical analysis. RESULTS The administration of sodium escinate, which contains the two isomers, gave rise to higher terminal phase half-life (t1/2) and mean residence time (MRT) values for both escin Ib and isoescin Ib compared to the corresponding compounds administered alone. The absorption of escin Ib and isoescin Ib was very poor, with the oral bioavailability (F) values of <2% observed for both compounds. The two compounds were found to isomerize in vivo, wherein the conversion of escin Ib to isoescin Ib was much easier than that of isoescin Ib to escin Ib. CONCLUSIONS A comparison of the pharmacokinetics of escin Ib and isoescin Ib administered alone and together in rats suggests that the administration of herbal preparations of escin in a clinical setting may result in a longer duration of action than the administration of each isomer alone. The interconversion of escin Ib and isoescin Ib when administered alone indicates that the administration of one isomer results in exposure to the other isomer.
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Affiliation(s)
- Xiu-Jun Wu
- Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, 110032 Shenyang, China; Research Center for Drug Metabolism, Jilin University, 2699 Qianjin Road, 130012 Changchun, China
| | - Meng-Liang Zhang
- Research Center for Drug Metabolism, Jilin University, 2699 Qianjin Road, 130012 Changchun, China
| | - Xiang-Yong Cui
- Research Center for Drug Metabolism, Jilin University, 2699 Qianjin Road, 130012 Changchun, China
| | - J Paul Fawcett
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Jing-Kai Gu
- Research Center for Drug Metabolism, Jilin University, 2699 Qianjin Road, 130012 Changchun, China.
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The Relationship between ALA16VAL Single Gene Polymorphism and Renal Cell Carcinoma. Adv Urol 2014; 2014:932481. [PMID: 24587799 PMCID: PMC3920972 DOI: 10.1155/2014/932481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 12/02/2013] [Indexed: 12/12/2022] Open
Abstract
Objectives. The aim of this study was to investigate the association of RCC and Ala16Val polymorphism in Turkish patients with RCC. Materials and Methods. A total of 41 patients with RCC who underwent radical or partial nephrectomy in our clinic and 50 healthy volunteers living in the same geographic area were included in this study. DNA samples from serum of RCC patients and controls were genotyped for MnSOD polymorphism analysis. Genotype ratios and allele frequencies were compared between two groups and odd ratios with 95% confidence intervals were calculated statistically. A P value of <0.05 was considered statistically significant. Results. There was a significant difference in the MnSOD genotype distributions between the RCC patients and the controls in terms of Ala/Ala+Ala/Val and Val/Val genotypes (P = 0.039). The Ala/Ala+Ala/Val genotypes were found significantly suspicious for RCC with an OR of 2.64 (95% CI = 1.06–6.69, P = 0.039). In addition, Ala allele was found significantly suspicious for RCC with an OR of 2.26 (95% CI = 1.24–4.12, P = 0.009). Conclusion. Our study indicated that MnSOD Ala16Val polymorphism may be one of the many genetic factors for renal cancer susceptibility in Turkish patients.
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Sagong B, Bae JW, Rhyu MR, Kim UK, Ye MK. Multiplex minisequencing screening for PTC genotype associated with bitter taste perception. Mol Biol Rep 2014; 41:1563-7. [PMID: 24413990 DOI: 10.1007/s11033-013-3002-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 12/30/2013] [Indexed: 11/26/2022]
Abstract
Sensitivity to phenylthiocarbamide (PTC) has a bimodal distribution pattern and the genotype of the TAS2R38 gene, which is composed of combinations of three coding single nucleotide polymorphisms (SNPs), p.A49P (c.145G>C), p.V262A (c.785T>C) and p.I296 V (c.886A>G), determines the ability or inability to taste PTC. In this study, we developed a tool for genotyping of these SNPs in the TAS2R38 gene using SNaPshot minisequencing and investigated the accuracy of the tool in 100 subjects who were genotyped by Sanger sequencing. The minor allele frequencies of the three SNPs were 0.39, and these genotypes corresponded to those determined by direct sequencing. In conclusion, we successfully developed a precise and rapid genetic tool for analysis of PTC genotype associated with bitter taste perception.
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Affiliation(s)
- Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
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