Quality Assurance of Samples and Processes in the Spanish Renal Research Network (REDinREN) Biobank

Calleros-Basilio, Laura; Cortés, María Alicia; García-Jérez, Andrea; Luengo-Rodríguez, Alicia; Orozco-Agudo, Ana; Valdivielso, José M.; Rodríguez‐Puyol, Diego; Rodrı́guez-Puyol, Manuel

doi:10.1089/bio.2015.0095

Cited by 15 publications

(5 citation statements)

References 49 publications

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“…DNA samples were then stored at 4 °C in sterile plastic vials. In the case of participants recruited in the NEFRONA study, genetic material was obtained from biological samples stored at the REDinREN biobank [ 10 ] using QIAamp DNA Blood Kits (Qiagen, Hilden, Germany).…”

Section: Methodsmentioning

confidence: 99%

A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease

Mota-Zamorano

González

Robles

et al. 2021

Genes

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Diabetic kidney disease (DKD) has been pointed out as a prominent cause of chronic and end-stage renal disease (ESRD). There is a genetic predisposition to DKD, although clinically relevant loci are yet to be identified. We utilized a custom target next-generation sequencing 70-gene panel to screen a discovery cohort of 150 controls, DKD and DKD-ESRD patients. Relevant SNPs for the susceptibility and clinical evolution of DKD were replicated in an independent validation cohort of 824 controls and patients. A network analysis aiming to assess the impact of variability along specific pathways was also conducted. Forty-eight SNPs displayed significantly different frequencies in the study groups. Of these, 28 with p-values lower than 0.01 were selected for replication. MYH9 rs710181 was inversely associated with the risk of DKD (OR = 0.52 (0.28–0.97), p = 0.033), whilst SOWAHB rs13140552 and CNDP1 rs4891564 were not carried by cases or controls, respectively (p = 0.044 and 0.023). In addition, the RGMA rs1969589 CC genotype was significantly correlated with lower albumin-to-creatinine ratios in the DKD patients (711.8 ± 113.0 vs. 1375.9 ± 474.1 mg/g for TC/TT; mean difference = 823.5 (84.46–1563.0); p = 0.030). No biological pathway stood out as more significantly affected by genetic variability. Our findings reveal new variants that could be useful as biomarkers of DKD onset and/or evolution.

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Section: Methodsmentioning

confidence: 99%

A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease

Mota-Zamorano

González

Robles

et al. 2021

Genes

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“…We used blood samples from the NEFRONA study stored in the Biobank of the REDinREN (Calleros-Basilio et al, 2016) in Alcala de Henares, Madrid, for DNA extraction from all 2,445 CKD cases and 559 controls. Seventy-nine SNPs located in twenty-nine genes (Supplementary Table S1) related with CKD-MBD and vascular calcification that have been reported in the scientific literature (Rong et al, 2014; Tuñón-Le Poultel et al, 2014; Ammirati et al, 2015; Higgins et al, 2015; Xu and Sun, 2015) were genotyped.…”

Section: Methodsmentioning

confidence: 99%

Association of Candidate Gene Polymorphisms With Chronic Kidney Disease: Results of a Case-Control Analysis in the Nefrona Cohort

et al. 2019

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Chronic kidney disease (CKD) is a major risk factor for end-stage renal disease, cardiovascular disease and premature death. Despite classical clinical risk factors for CKD and some genetic risk factors have been identified, the residual risk observed in prediction models is still high. Therefore, new risk factors need to be identified in order to better predict the risk of CKD in the population. Here, we analyzed the genetic association of 79 SNPs of proteins associated with mineral metabolism disturbances with CKD in a cohort that includes 2,445 CKD cases and 559 controls. Genotyping was performed with matrix assisted laser desorption ionization–time of flight mass spectrometry. We used logistic regression models considering different genetic inheritance models to assess the association of the SNPs with the prevalence of CKD, adjusting for known risk factors. Eight SNPs (rs1126616, rs35068180, rs2238135, rs1800247, rs385564, rs4236, rs2248359, and rs1564858) were associated with CKD even after adjusting by sex, age and race. A model containing five of these SNPs (rs1126616, rs35068180, rs1800247, rs4236, and rs2248359), diabetes and hypertension showed better performance than models considering only clinical risk factors, significantly increasing the area under the curve of the model without polymorphisms. Furthermore, one of the SNPs (the rs2248359) showed an interaction with hypertension, being the risk genotype affecting only hypertensive patients. We conclude that 5 SNPs related to proteins implicated in mineral metabolism disturbances (Osteopontin, osteocalcin, matrix gla protein, matrix metalloprotease 3 and 24 hydroxylase) are associated to an increased risk of suffering CKD.

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“…DNA was obtained from blood samples stored at the Biobank of the Spanish Renal Research Network (REDinREN) [29] using the QIAamp DNA Blood Kit and following manufacturer instructions. Genotyping was performed with matrix assisted laser desorption ionization time-of-flight mass spectrometry in the Sequenom MassARRAY platform ® , in Centro de Genotipado-Plataforma de Recursos Biomoleculares y Bioinformáticos (CEGEN-PRB2) del Instituto de Salud Carlos III (Nodo de la Universidad de Santiago de Compostela, A Coruña, Spain).…”

Section: Methodsmentioning

confidence: 99%

The rs1126616 Single Nucleotide Polymorphism of the Osteopontin Gene Is Independently Associated with Cardiovascular Events in a Chronic Kidney Disease Cohort

Cambray

Galimudi

Božić

et al. 2019

JCM

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Chronic kidney disease (CKD) is associated with a higher risk of cardiovascular events (CVE), partly due to the higher burden of atherosclerosis. Circulating Osteopontin (OPN) levels have been also shown to have a potential role in the development of atherosclerosis. Indeed, CKD patients show an increase in circulating OPN levels, but their effect of CKD-related atherosclerosis is not clear. Polymorphisms in the OPN gene (SPP1) have been studied in atheromatous disease, but reported results show conflictive findings. Thus, the main aim of the present study is to analyze the influence of SPP1 polymorphisms in CVE in CKD patients, taking into account circulating OPN levels. We followed 559 healthy controls and 2445 CKD patients without previous CVE from the National Observatory of Atherosclerosis in Nephrology study (NEFRONA study). After 48 months of follow-up 206 CVE were recorded. Genotyping for rs9138, rs1126616, rs1126772, rs11730582 and rs28357094 polymorphisms of the SPP1 gene was performed along with the measurements of plasma OPN levels. The group of patients with CVE showed higher incidence of atherosclerotic plaque (90.3% vs 64.5%; p < 0.001) and higher OPN levels (p < 0.001) at baseline. Patients with the heterozygous genotype of the rs1126616 polymorphism showed a higher hazard ratio of having a CVE, even after adjustment for multiple potential confounders. After adjustment, OPN levels were no longer associated with the incidence of CVE. We found that the rs1126616 single nucleotide polymorphism (SNP) of the SPP1 gene is independently associated with a higher incidence of CVE in a cohort of CKD patients and that it could be used to predict CVE risk.

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Quality Assurance of Samples and Processes in the Spanish Renal Research Network (REDinREN) Biobank

Abstract: These results clearly indicate that our PBMC, DNA, and RNA stored samples meet the required quality standards to be used for biomedical research, ensuring their long-term preservation.

Cited by 15 publications

References 49 publications

A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease

A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease

Association of Candidate Gene Polymorphisms With Chronic Kidney Disease: Results of a Case-Control Analysis in the Nefrona Cohort

The rs1126616 Single Nucleotide Polymorphism of the Osteopontin Gene Is Independently Associated with Cardiovascular Events in a Chronic Kidney Disease Cohort

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