DOI: 10.5061/dryad.fbg79cp56
title: Single nucleotide polymorphisms related to vitamin D metabolism in patients with chronic obstructive pulmonary disease

description: Introduction: Chronic obstructive pulmonary disease (COPD) is one of the
 world's major public health problems. It is characterized by a major
 inflammatory response, where vitamin D, due to its role in
 regulating the immune system, and genetic variants involved in its
 metabolism may play an essential role. The aim of this study is
 to evaluate the association between 13 polymorphisms related to
 vitamin D metabolism and the COPD risk. Material and methods: A
 retrospective longitudinal study was designed in which 152 cases of COPD
 diagnosed at the University Hospital Virgen de las Nieves and 456 controls
 without the pathology, matched by age and sex, were included. The
 determination of the 13 polymorphisms was carried out using TaqMan™
 probes. Results: Statistical analysis showed that the AA genotype and the
 A allele of the CYP27B1 rs4646536 polymorphism may be associated with an
 increased risk of developing COPD according to genotypic models (OR = 2.6;
 95% CI = 1.38-5.22; p = 0.004), dominant (OR = 1.69; 95% CI = 1.15-2.5; p
 = 0.008), recessive (OR = 2.24; 95% CI = 1.22-4.41; p = 0.013) and
 additive (OR = 1.56; 95% CI = 1.18-2.08; p =0.020) models. Likewise, the
 AA genotype and the A allele of the CYP2R1 rs10741657 polymorphism were
 also associated with the risk of developing COPD according to the
 genotypic (OR = 1.9; 95% CI = 1.06-3.36; p = 0.028) and additive (OR =
 1.37; 95% CI = 1.04-1.81; p = 0.027) models. Likewise, an association was
 found between GATG (p = 0.002; OR = 2.05; 95%CI = 1.32-3.20) and AGGT (p
 &lt; 0.0001; OR = 2.1e46; 95%CI = 2.1e46-2.1e46) haplotypes and an
 increased risk of COPD. Conclusions: We can therefore conclude that those
 variants could be used in the early detection of the disease in the
 future.
description: This study was approved by the Ethical Committee of the
 Andalusian Health System and conducted in accordance with the Declaration
 of Helsinki (code: 0201-N-23). All subjects participating in the study
 signed a written informed consent for the collection of saliva or blood
 samples and their donation to the biobank. The samples were encoded and
 treated confidentially throughout the study. This study
 included 152 patients with COPD and 456 controls of Caucasian origin from
 southern Spain. The cases were diagnosed and recruited at the Virgen de
 las Nieves University Hospital, Granada (Spain), between 2017 and 2023.
 All sociodemographic and clinical variables were collected through Diraya
 clinical software. <br>The Biobank of the Virgen de las Nieves
 University Hospital, which is part of the Biobank of the Andalusian Public
 Health System, provided DNA samples isolated from saliva or blood. Saliva
 samples were collected in 50 mL BD Falcon conical tubes (BD, Plymouth,
 United Kingdom). Blood samples were collected in 3 mL BD Vacutainer® tubes
 with EDTA K3 as an anticoagulant. DNA extraction was performed using the
 QlAamp DNA Mini extraction kit (Qiagen GmbH, Hilden, Germany), following
 the specifications provided by the manufacturer for DNA purification from
 saliva or blood. Purified DNA samples were stored at −80°C in the Biobank
 of the Virgen de las Nieves University Hospital. DNA concentration and
 purity were measured with the NanoDrop 2000™ UV-visible spectrophotometer
 using the ratio of the absorbance at 260/280 and 260/230.
 The 13 polymorphisms (rs1544410 (BsmI), rs11568820 (Cdx-2),
 rs2228570 (FokI), rs7975232 (ApaI), rs731236 (TaqI), rs4646536, rs3782130,
 rs10877012, rs703842, rs6068816, rs4809957, rs7041, rs10741657) were
 determined by real-time polymerase chain reaction for allele
 discrimination using TaqMan® probes (ABI Applied Biosystems, Quant Studio
 3 Real-Time PCR System, 96 wells), following the manufacturer’s
 instructions. The polymorphisms VDR-Bsml (rs1544410), CYP27B1 rs703842,
 and CYP27B1 rs3782130 were analyzed using an assay customized by
 ThermoFisher Scientific (Waltham, Massachusetts, United States) encoded as
 AN324M4, AN9HX2K, and ANPRYR9, respectively. Sanger sequencing was
 performed in 10% of the samples and used to confirm of the results.
 Real-time PCR and Sanger sequencing were performed in the Pharmacogenetics
 Unit of the Virgen de las Nieves University Hospital and the Department of
 Biochemistry and Molecular Biology II of the University of Granada. The
 criteria for SNPs quality control were: 1) missing genotype rate per SNP
 &lt; 0.05; 2) minor allele frequency &gt; 0.01; 3) p-value
 &gt; 0.05 in Hardy Weinberg equilibrium test; 4) missing genotype rate
 between cases and controls &lt; 0.05.
description: # Single nucleotide polymorphisms related to vitamin D metabolism in
 patients with chronic obstructive pulmonary disease. 
 [https://doi.org/10.5061/dryad.fbg79cp56](https://doi.org/10.5061/dryad.fbg79cp56) ## Description of the data and file structure The data file contains a basic description of our study population of Caucasian origin from southern Spain, including sample coding, participant sex, case or control status, age at COPD diagnosis and the corresponding genotype for each of the 13 polymorphisms that were evaluated (rs1544410 (BsmI), rs11568820 (Cdx-2), rs2228570 (FokI), rs7975232 (ApaI), rs731236 (TaqI), rs4646536, rs3782130, rs10877012, rs703842, rs6068816, rs4809957, rs7041, rs10741657). This information is useful, for example, for COPD risk analysis, to establish some relationship between the frequency of the genotype in each of the polymorphisms evaluated and the sex of the participant. Thus, as well as to feed the frequency data of the polymorphisms in the Caucasian population of southern Spain. The cases met the following inclusion criteria to enter the study: Age ≥ 18 years and a diagnosis of COPD according to the guidelines of the Spanish COPD Guidelines (GesEPOC). The 13 polymorphisms were determined by real-time polymerase chain reaction for allele discrimination using TaqMan® probes (ABI Applied Biosystems, Quant Studio 3 Real-Time PCR System, 96 wells), following the manufacturer’s instructions. Note: Empty cells correspond to missing information. Files and variables #### File: Dataset\_.csv **Description:**  ##### Variables * Code: sample coding * Sex: female or male * Case or control: Case: COPD diagnosis - Control: Healthy patients at time of analysis. Both of Caucasian origin from southern Spain.  * Age: Case: age at COPD diagnosis or Control: age at time of analysis * VDR-BmsI rs1544410: Gene location: 12q13.11 - SNP location: Intron 8, G &gt; A. The data take the values of wild type (GG), Heterozygous (AG or GA) or homozygous mutated (AA). * VDR-Cdx-2 rs11568820: Gene location: 12q13.11 - SNP location: Intron 1, G &gt; A . The data take the values of wild type (GG), Heterozygous (AG or GA) or homozygous mutated (AA). * VDR-FokI rs2228570: Gene location: 12q13.11 - SNP location: Exon 2, C &gt; T . The data take the values of wild type (CC), Heterozygous (CT or TC) or homozygous mutated (TT). * VDR-ApaI rs7975232: Gene location: 12q13.11 - SNP location: Intron 8, C &gt; A . The data take the values of wild type (CC), Heterozygous (AC or CA) or homozygous mutated (AA). * VDR-TaqI rs731236: Gene location: 12q13.11 - SNP location: Exon 9, T &gt; C . The data take the values of wild type (TT), Heterozygous (CT or TC) or homozygous mutated (CC). * CYP27B1 rs4646536: Gene location: 12q14.1 - SNP location: Intron 6, A &gt; G . The data take the values of wild type (AA), Heterozygous (AG or GA) or homozygous mutated (GG). * CYP27B1 rs703842: Gene location: 12q14.1 - SNP location: 3’UTR, A &gt; G . The data take the values of wild type (AA), Heterozygous (AG or GA) or homozygous mutated (GG). * CYP27B1rs3782130: Gene location: 12q14.1 - SNP location: Promotor 5’, G &gt; C . The data take the values of wild type (GG), Heterozygous (CG or GC) or homozygous mutated (CC). * CYP27B1 rs10877012: Gene location: 12q14.1 - SNP location: 5’UTR, T &gt; G . The data take the values of wild type (TT), Heterozygous (GT or TG) or homozygous mutated (TT). * CYP24A1 rs6068816: Gene location: 20q13.2 - SNP location: Exon 6, G &gt; A. The data take the values of wild type (GG), Heterozygous (AG or GA) or homozygous mutated (AA). * CYP24A1rs4809957:  Gene location: 20q13.2 - SNP location: 3’UTR, G &gt; C. The data take the values of wild type (GG), Heterozygous (CG or GC) or homozygous mutated (CC). * GC rs7041: Gene location: 4q13.3 - SNP location: Exon 11, T &gt; G. The data take the values of wild type (TT), Heterozygous (GT or TG) or homozygous mutated (TT). * CYP2R1 rs10741657: Gene location: 11p15.2 - SNP location: 5’UTR, A &gt; G. The data take the values of wild type (AA), Heterozygous (AG or GA) or homozygous mutated (GG). ## Code/software CSV files: Compatible with Microsoft Excel, NeoOffice, EditPlus, Corel WordPerfect Office X6, Microsoft Works, Google Sheets, Numbers for Mac and OpenOffice. ## Access information Data was derived from the following sources: * The Biobank of the Virgen de las Nieves University Hospital, which is part of the Biobank of the Andalusian Public Health System, provided DNA samples isolated from saliva or blood.