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Pajič T. Testing for Factor V Leiden (FVL) and Prothrombin G20210A Genetic Variants. Methods Mol Biol 2023; 2663:233-251. [PMID: 37204714 DOI: 10.1007/978-1-0716-3175-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Laboratory testing for Factor V Leiden and Prothrombin G20210A genetic variants permits defining the increased relative risk for venous thromboembolism in selected patients. Laboratory DNA testing for these variants may be undertaken by a variety of methods, including fluorescence-based quantitative real-time PCR (qPCR). This is a rapid, simple, robust, and reliable method to identify genotypes of interest. This chapter describes the method that employs PCR amplification of the patient DNA region of interest and genotyping by allele-specific discrimination technology on a quantitative real-time PCR (qPCR) instrument.
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Affiliation(s)
- Tadej Pajič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
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Ong J, Bennett A. A review of laboratory considerations in thrombophilia testing. Pathology 2022; 54:835-841. [DOI: 10.1016/j.pathol.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/29/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
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Label-Free Oligonucleotide-Based SPR Biosensor for the Detection of the Gene Mutation Causing Prothrombin-Related Thrombophilia. SENSORS 2020; 20:s20216240. [PMID: 33142935 PMCID: PMC7663036 DOI: 10.3390/s20216240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022]
Abstract
Prothrombin-related thrombophilia is a genetic disorder produced by a substitution of a single DNA base pair, replacing guanine with adenine, and is detected mainly by polymerase chain reaction (PCR). A suitable alternative that could detect the single point mutation without requiring sample amplification is the surface plasmon resonance (SPR) technique. SPR biosensors are of great interest: they offer a platform to monitor biomolecular interactions, are highly selective, and enable rapid analysis in real time. Oligonucleotide-based SPR biosensors can be used to differentiate complementary sequences from partially complementary or noncomplementary strands. In this work, a glass chip covered with an ultrathin (50 nm) gold film was modified with oligonucleotide strands complementary to the mutated or normal (nonmutated) DNA responsible for prothrombin-related thrombophilia, forming two detection platforms called mutated thrombophilia (MT) biosensor and normal thrombophilia (NT) biosensor. The results show that the hybridization response is obtained in 30 min, label free and with high reproducibility. The sensitivity obtained in both systems was approximately 4 ΔμRIU/nM. The dissociation constant and limits of detection calculated were 12.2 nM and 20 pM (3 fmol), respectively, for the MT biosensor, and 8.5 nM and 30 pM (4.5 fmol) for the NT biosensor. The two biosensors selectively recognize their complementary strand (mutated or normal) in buffer solution. In addition, each platform can be reused up to 24 times when the surface is regenerated with HCl. This work contributes to the design of the first SPR biosensor for the detection of prothrombin-related thrombophilia based on oligonucleotides with single point mutations, label-free and without the need to apply an amplification method.
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Yu P, Dai Y, Dong J, Zhang L, Ping Y, Wang X, Wang D, Tao Z. ARMS TaqMan real-time PCR for genotyping factor V Leiden mutation in Han Chinese. Electrophoresis 2020; 41:2015-2020. [PMID: 32839994 DOI: 10.1002/elps.202000193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/05/2020] [Indexed: 11/07/2022]
Abstract
Factor V Leiden (FVLeiden ) is a missense mutation of 1691 position (G1691A) in exon 10 of FV gene, and being a genetic risk for venous thrombosis. Currently, there are several PCR-based methods for detecting FVLeiden mutation; however, these methods have disadvantages such as time-consuming, cumbersome steps and potentially hazardous gels. The aims of present study were to develop a simple, time-saving, accurate, and gel-free method, called amplification refractory mutation system (ARMS) TaqMan real-time PCR, for detecting FVLeiden mutation. We severally designed two specific reverse primers for mutant and wild-type through intentional introduction of mismatched nucleotide at the penultimate 3' position. Although target amplicon amplification efficiency is reduced, but another corresponding amplicon is almost completely inhibited. Then, specific TaqMan-probe was designed to detect target amplicon. Established method was used to detect 500 unselected samples in Han Chinese, the results showed 499 cases of wild-type and one heterozygote. Afterward, 50 randomly picked wild-type cases and one heterozygote were reexamined by bidirectional DNA sequencing, which is considered as "Gold standard method." Exhilaratingly, the results detected by the two methods were completely consistent. At last, allelic frequency of FVLeiden was calculated the in Han Chinese. Given the above results, A FVLeiden heterozygote has been found in 500 random samples in Han Chinese, and the allelic frequency was 0.1%. In conclusion, the ARMS TaqMan real-time PCR is an ideal detecting system for genotyping FVLeiden mutation in clinical application, and FVLeiden mutation exists in Han Chinese despite extremely low prevalence.
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Affiliation(s)
- Pan Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Yibei Dai
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Jiantao Dong
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Luyan Zhang
- Department of Laboratory Medicine, Ningbo Mingzhou Hospital, Ningbo, 315104, P. R. China
| | - Ying Ping
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Danhua Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Zhihua Tao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
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Luca Tiscia G, Colaizzo D, Vergura P, Favuzzi G, Chinni E, Vandermeulen C, Detemmerman L, Grandone E. Loop-mediated isothermal amplification (LAMP)-based method for detecting factor V Leiden and factor II G20210A common variants. J Thromb Thrombolysis 2020; 50:908-912. [PMID: 32557225 DOI: 10.1007/s11239-020-02183-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Automated methodologies allowing for rapid detection of Factor V Leiden and Factor II G20210A variants are desirable, due to a high number of tested patients. Here, we report a preliminary validation of a CE-marked in vitro diagnostic (IVD) certified method for simultaneous detection of Factor V Leiden and Factor II G20210A variants on whole blood samples. The novel method is based on Loop-mediated isothermal AMPlification (LAMP) applied for a duplex detection of Factor V Leiden and Factor II G20210A variants without requiring prior DNA extraction, whereas the routine one is a TaqMan SNP genotyping targeting genomic DNA. We tested routine patients for both variants using novel and current methods and estimated concordance rate. Patients were tested under similar laboratory procedures. One hundred and eight patients referred for the thrombophilia testing in the period between 9th December 2019 to 27th February 2020 represented the study population. We routinely identified for the Factor V Leiden variant 163 wild-type, 17 heterozygotes and no homozygote. Concerning the Factor II G20210A variant, we identified 170 wild-type, nine heterozygotes and one homozygous carrier. Two heterozygotes carried both variants (double heterozygotes). The LAMP method showed a 100% concordance rate, detecting rightly all genotypes. The LAMP for a duplex detection of common thrombophilia variants shows analytic performances as good as those of the standard method.
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Affiliation(s)
- Giovanni Luca Tiscia
- UOSD e di Ricerca di Emostasi e Trombosi, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Donatella Colaizzo
- UOSD e di Ricerca di Emostasi e Trombosi, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Patrizia Vergura
- UOSD e di Ricerca di Emostasi e Trombosi, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Giovanni Favuzzi
- UOSD e di Ricerca di Emostasi e Trombosi, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Elena Chinni
- UOSD e di Ricerca di Emostasi e Trombosi, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | | | | | - Elvira Grandone
- UOSD e di Ricerca di Emostasi e Trombosi, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy. .,Department of Obstetrics and Gynecology, First Moscow State Medical University, Moscow, Russia.
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Glotov AS, Sinitsyna ES, Danilova MM, Vashukova ES, Walter JG, Stahl F, Baranov VS, Vlakh EG, Tennikova TB. Detection of human genome mutations associated with pregnancy complications using 3-D microarray based on macroporous polymer monoliths. Talanta 2015; 147:537-46. [PMID: 26592644 DOI: 10.1016/j.talanta.2015.09.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/21/2015] [Accepted: 09/27/2015] [Indexed: 01/13/2023]
Abstract
Analysis of variations in DNA structure using a low-density microarray technology for routine diagnostic in evidence-based medicine is still relevant. In this work the applicability of 3-D macroporous monolithic methacrylate-based platforms for detection of different pathogenic genomic substitutions was studied. The detection of nucleotide replacements in F5 (Leiden G/A, rs6025), MTHFR (C/T, rs1801133) and ITGB3 (T/C, rs5918), involved in coagulation, and COMT (C/G, rs4818), TPH2 (T/A, rs11178997), PON1 (T/A rs854560), AGTR2 (C/A, rs11091046) and SERPINE1 (5G/4G, rs1799889), associated with pregnancy complications, was performed. The effect of such parameters as amount and type of oligonucleotide probe, amount of PCR product on signal-to-noise ratio, as well as mismatch discrimination was analyzed. Sensitivity and specificity of mutation detections were coincided and equal to 98.6%. The analysis of SERPINE1 and MTHFR genotypes by both NGS and developed microarray was performed and compared.
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Affiliation(s)
- A S Glotov
- Faculty of Biology, Saint-Petersburg State University, St. Petersburg, Russia; D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - E S Sinitsyna
- Institute of Chemistry, Saint-Petersburg State University, St. Petersburg, Russia; Institute of Macromolecular Compound, Russian Academy of Sciences, St. Petersburg, Russia
| | - M M Danilova
- D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - E S Vashukova
- D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - J G Walter
- Institute for Technical Chemistry, Leibniz University, Hannover, Germany
| | - F Stahl
- Institute for Technical Chemistry, Leibniz University, Hannover, Germany
| | - V S Baranov
- Faculty of Biology, Saint-Petersburg State University, St. Petersburg, Russia; D.O. Ott Research Institute of Obstetrics and Gynecology, Russian Academy of Medical Sciences, St. Petersburg, Russia
| | - E G Vlakh
- Institute of Chemistry, Saint-Petersburg State University, St. Petersburg, Russia; Institute of Macromolecular Compound, Russian Academy of Sciences, St. Petersburg, Russia
| | - T B Tennikova
- Institute of Chemistry, Saint-Petersburg State University, St. Petersburg, Russia; Institute of Macromolecular Compound, Russian Academy of Sciences, St. Petersburg, Russia.
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Davydov DM, Zhdanov RI, Dvoenosov VG, Kravtsova OA, Voronina EN, Filipenko ML. Resilience to orthostasis and haemorrhage: A pilot study of common genetic and conditioning mechanisms. Sci Rep 2015; 5:10703. [PMID: 26024428 PMCID: PMC4650686 DOI: 10.1038/srep10703] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 04/27/2015] [Indexed: 01/15/2023] Open
Abstract
A major challenge presently is not only to identify the genetic polymorphisms increasing risk to diseases, but to also find out factors and mechanisms, which can counteract a risk genotype by developing a resilient phenotype. The objective of this study was to examine acquired and innate vagal mechanisms that protect against physical challenges and haemorrhages in 19 athletes and 61 non-athletes. These include examining change in heart rate variability (HF-HRV; an indicator of vagus activity) in response to orthostatic challenge, platelet count (PLT), mean platelet volume (MPV), and single-nucleotide polymorphisms in genes that encode several coagulation factors, PAI-1, and MTHFR. Individual differences in PLT and MPV were significant predictors, with opposite effects, of the profiles of the HF-HRV changes in response to orthostasis. Regular physical training of athletes indirectly (through MPV) modifies the genetic predisposing effects of some haemostatic factors (PAI-1 and MTHFR) on vagal tone and reactivity. Individual differences in vagal tone were also associated with relationships between Factor 12 C46T and Factor 11 C22771T genes polymorphisms. This study showed that genetic predispositions for coagulation are modifiable. Its potential significance is promoting advanced protection against haemorrhages in a variety of traumas and injuries, especially in individuals with coagulation deficits.
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Affiliation(s)
- Dmitry M Davydov
- 1] Sholokhov Moscow State University for the Humanities, the Russian Institute for Advanced Study and Institute of Neurosciences and Cognitive Research, Verkhnyaya Radishevskaya 16-18, Moscow, 109240 [2] Laboratory of Neuroimmunopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 8 Baltiyskaia ul., Moscow, 125315, Russia
| | - Renad I Zhdanov
- 1] Sholokhov Moscow State University for the Humanities, the Russian Institute for Advanced Study and Institute of Neurosciences and Cognitive Research, Verkhnyaya Radishevskaya 16-18, Moscow, 109240 [2] Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, 18 Kremlin ul., Kazan, 420008, Russia
| | - Vladimir G Dvoenosov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, 18 Kremlin ul., Kazan, 420008, Russia
| | - Olga A Kravtsova
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, 18 Kremlin ul., Kazan, 420008, Russia
| | - Elena N Voronina
- Pharmacogenomics laboratory, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maxim L Filipenko
- Pharmacogenomics laboratory, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
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Rajatileka S, Luyt K, Williams M, Harding D, Odd D, Molnár E, Váradi A. Detection of three closely located single nucleotide polymorphisms in the EAAT2 promoter: comparison of single-strand conformational polymorphism (SSCP), pyrosequencing and Sanger sequencing. BMC Genet 2014; 15:80. [PMID: 24996834 PMCID: PMC4112986 DOI: 10.1186/1471-2156-15-80] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 07/02/2014] [Indexed: 11/15/2022] Open
Abstract
Background Single-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs) due to its simplicity, requirement for basic equipment accessible in most laboratories and low cost. This technique was previously used to detect rs4354668:A > C (g.-181A > C) SNP in the promoter of astroglial glutamate transporter (EAAT2) and the same approach was initially used here to investigate this promoter region in a cohort of newborns. Results Unexpectedly, four distinct DNA migration patterns were identified by SSCP. Sanger sequencing revealed two additional SNPs: g.-200C > A and g.-168C > T giving a rise to a total of ten EAAT2 promoter variants. SSCP failed to distinguish these variants reliably and thus pyrosequencing assays were developed. g.-168C > T was found in heterozygous form in one infant only with minor allele frequency (MAF) of 0.0023. In contrast, g.-200C > A and -181A > C were more common (with MAF of 0.46 and 0.49, respectively) and showed string evidence of linkage disequilibrium (LD). In a systematic comparison, 16% of samples were miss-classified by SSCP with 25-31% errors in the identification of the wild-type and homozygote mutant genotypes compared to pyrosequencing or Sanger sequencing. In contrast, SSCP and pyrosequencing of an unrelated single SNP (rs1835740:C > T), showed 94% concordance. Conclusion Our data suggest that SSCP cannot always detect reliably several closely located SNPs. Furthermore, caution is needed in the interpretation of the association studies linking only one of the co-inherited SNPs in the EAAT2 promoter to human diseases.
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Affiliation(s)
| | | | | | | | | | | | - Anikó Váradi
- Centre for Research in Biosciences, Department of Biological, Biomedical and Analytical Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK.
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Can Factor V Leiden and prothrombin G20210A testing in women with recurrent pregnancy loss result in improved pregnancy outcomes?: Results from a targeted evidence-based review. Genet Med 2011; 14:39-50. [PMID: 22237430 DOI: 10.1038/gim.0b013e31822e575b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Women with recurrent pregnancy loss are offered Factor V Leiden (F5) and/or prothrombin G20210A (F2) testing to identify candidates for anticoagulation to improve outcomes. A systematic literature review was performed to estimate test performance, effect sizes, and treatment effectiveness. Electronic searches were performed through April 2011, with review of references from included articles. English-language studies addressed analytic validity, clinical validity, and/or clinical utility and satisfied predefined inclusion criteria. Adequate evidence showed high analytic sensitivity and specificity for F5 and F2 testing. Evidence for clinical validity was adequate. The summary odds ratio for association of recurrent pregnancy loss with F5 in case-controlled studies was 2.02 (95% confidence interval, 1.60-2.55), with moderate heterogeneity and suggestion of publication bias. Longitudinal studies in women with recurrent pregnancy loss or unselected cohorts showed F5 carriers were more likely to have a subsequent loss than noncarriers (odds ratios: 1.93 and 2.03, respectively). Results for F2 testing were similar. For clinical utility, evidence was adequate that anticoagulation treatments were ineffective (except in antiphospholipid antibody syndrome) and had treatment-associated harms. The certainty of evidence is moderate (high, moderate, and low) that anticoagulation of women with recurrent pregnancy loss and F5/F2 variants would currently lead to net harms.
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Pajič T. Factor V Leiden and FII 20210 testing in thromboembolic disorders. Clin Chem Lab Med 2010; 48 Suppl 1:S79-87. [PMID: 21091236 DOI: 10.1515/cclm.2010.372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Factor V Leiden and prothrombin (F2) c.20210G>A mutation detection are very important in order to define the increased relative risk for venous thromboembolism in selected patients. Use of DNA-based methods to detect both mutations has become widely available in clinical diagnostic laboratories, including fluorescence-based quantitative real-time PCR (qPCR). The latter is a rapid, simple, robust and reliable method to identify genotypes of interest. There are several chemistries used for qPCR; this article describes their principles and applicability for Factor V Leiden and prothrombin (F2) c.20210G>A mutation detection.
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Affiliation(s)
- Tadej Pajič
- Department of Haematology, Division of Internal Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
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Liu H, Liu W, Liao Y, Cheng L, Liu Q, Ren X, Shi L, Tu X, Wang QK, Guo AY. CADgene: a comprehensive database for coronary artery disease genes. Nucleic Acids Res 2010; 39:D991-6. [PMID: 21045063 PMCID: PMC3013698 DOI: 10.1093/nar/gkq1106] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Coronary artery disease (CAD) is a complex, multifactorial disease and a leading cause of mortality world wide. Over the past decades, great efforts have been made to elucidate the underlying genetic basis of CAD and massive data have been accumulated. To integrate these data together and to provide a useful resource for researchers, we developed the CADgene, a comprehensive database for CAD genes. We manually extracted CAD-related evidence for more than 300 candidate genes for CAD from over 1300 publications of genetic studies. We classified these candidate genes into 12 functional categories based on their roles in CAD. For each gene, we extracted detailed information from related studies (e.g. the size of case–control, population, SNP, odds ratio, P-value, etc.) and made useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein–protein interactions and others. Besides the statistical number of studies for each gene, CADgene also provides tools to search and show the most frequently studied candidate genes. In addition, CADgene provides cumulative data from 11 publications of CAD-related genome-wide association studies. CADgene has a user-friendly web interface with multiple browse and search functions. It is freely available at http://www.bioguo.org/CADgene/.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan 430074, China
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