Association Analysis Between the rs1899663 Polymorphism of HOTAIR and Risk of Psychiatric Conditions in an Iranian Population

Sayad, Arezou; Badrlou, Elham; Ghafouri‐Fard, Soudeh; Taheri, Mohammad

doi:10.1007/s12031-020-01499-7

Cited by 17 publications

(10 citation statements)

References 22 publications

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“…Our results show that the allelic frequencies of the rs1899663 and rs7958904 SNPs were significantly different between the control and CAD groups in genotype frequencies. These variants have previously been reported in association with other diseases, including various cancers, sclerosis, and psychiatric conditions [ 7 , 19 , 23 , 24 ]. Amongst metabolic syndrome patients, rs1899663 and rs12826786 were found to be associated with CAD risk.…”

Section: Discussionmentioning

confidence: 99%

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Association between HOTAIR lncRNA Polymorphisms and Coronary Artery Disease Susceptibility

Kim

Lee

Park

et al. 2021

JPM

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Coronary artery disease (CAD), one of the most frequent causes of mortality, is the most common type of cardiovascular disease. This condition is characterized by the accumulation of plaques in the coronary artery, leading to blockage of blood flow to the heart. The main symptom of CAD is chest pain caused by blockage of the coronary artery and shortness of breath. HOX transcript antisense RNA gene (HOTAIR) is a long non-coding RNA which is well-known as an oncogene involved in various cancers, such as lung, breast, colorectal, and gastric cancer. We selected six single nucleotide polymorphisms, rs4759314 A>G, rs1899663 G>T, rs920778 T>C, rs7958904 G>C, rs12826786 C>T, and rs874945 C>T, for genotype frequency analysis and assessed the frequency of HOTAIR gene polymorphisms in 442 CAD patients and 418 randomly selected control subjects. To analyze the differences between these two populations, we performed a Student’s t-test, adjusted odds ratio (AOR), 95% confidence intervals (CIs), and ANOVA analysis. According to our baseline characteristic analysis, control subjects and CAD patients were significantly different in hypertension and diabetes mellitus. We also found that the rs4759314 A>G, rs1899663 G>T, and rs12826786 C>T genotypes were strongly associated with CAD susceptibility (AA vs. AG+GG: AOR = 0.608, 95% CI = 0.393−0.940, p = 0.025; GG vs. TT: AOR = 2.276, 95% CI = 1.125−4.607, p = 0.022; CC vs. CT+TT: AOR = 1.366, 95% CI = 1.027−1.818, p = 0.032, respectively). Our data also demonstrated that the genotype of HOTAIR polymorphisms, genotype combination, and haplotype analysis affect disease occurrence. Moreover, these polymorphisms are linked to clinical factors that contribute to disease susceptibility. In conclusion, results from our study suggest that HOTAIR polymorphisms may be useful novel biomarkers for diagnosing CAD.

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Section: Discussionmentioning

confidence: 99%

“…Single nucleotide polymorphisms (SNPs) are associated with many disease occurrences [ 18 , 19 , 20 ], and HOTAIR SNPs have been associated with recurrent implant failure and various cancers. However, the association between HOTAIR SNPs and CAD remains poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Association between HOTAIR lncRNA Polymorphisms and Coronary Artery Disease Susceptibility

Kim

Lee

Park

et al. 2021

JPM

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“…The MESTIT1 gene is associated with the cognitive disease as reported in 55 . Finally, the DAOA-AS1 gene is extracted for bipolar disorder as reported in 56 .…”

Section: /23mentioning

confidence: 99%

Predicting Parkinson’s Disease Related Genes Based on PyFeat and Gradient Boosted Decision Tree (GBDT)

Helmy

El-Daydamony

Mekky

et al. 2022

Preprint

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Identifying genes related to Parkinson's disease (PD) is an active and effective research topic in biomedical analysis, which plays a critical role in diagnosis and treatment. In recent years, many studies have proposed different techniques for predicting disease-related genes. However, a few of these techniques are designed or developed for PD gene prediction. Most of these PD techniques are developed to identify only protein genes and discard long non-coding (lncRNA) genes, which play an essential role in biological processes and the Transformation and development of diseases. This paper proposes a novel prediction system to identify protein and lncRNA genes related to PD that can aid in an early diagnosis. First, we preprocessed the genes into DNA FASTA sequences from the UCSC genome browser and removed the redundancies. Second, we extracted some significant features of DNA FASTA sequences using five numerical mapping techniques with Fourier transform and PyFeat method with Adaboost technique as feature selection. Finally, the features were fed to the gradient boosted decision tree (GBDT) to diagnose different tested cases. Seven performance metrics are used to evaluate the performance of the proposed system. The proposed system achieved an average accuracy (ACC) equals 78.1%, the area under the curve (AUC) equals 84.9%, the area under precision-recall (AUPR) equals 85.0%, F1-score equals 78.2%, Matthews correlation coefficient (MCC) equals 0.564, Sensitivity (SEN) equals 79.1%, and specificity (SPC) equals 77.1%. The experiments demonstrate promising results compared with other systems. The predicted top-rank protein and lncRNA genes are verified based on a literature review.

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“…24,25 Furthermore, SNPs in this gene have been linked to the onset and the progression of disorders with diverse etiology. [26][27][28][29] Evidence showed that genetics might play different roles in susceptibility to RSA. 16 Few studies have reported an association between SNPs in lncRNA genes and RSA 30,31 ; however, no study has investigated the relationship of HOTAIR gene polymorphisms to RSA development.…”

Section: Introductionmentioning

confidence: 99%

“…The HOTAIR gene is adequately expressed in placental tissue; however, it has been reported that HOTAIR is downregulated in patients with RSA compared to healthy women 24,25 . Furthermore, SNPs in this gene have been linked to the onset and the progression of disorders with diverse etiology 26–29 …”

Section: Introductionmentioning

confidence: 99%

Genetic variants of HOTAIR are associated with susceptibility to recurrent spontaneous abortion: A preliminary case–control study

Salimi

Sargazi

Nia

et al. 2021

J of Obstet and Gynaecol

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Aim To investigate the association between Hox transcript antisenses RNA (HOTAIR) polymorphisms, rs12826786 C/T, rs920778 T/C, rs4759314 A/G, and rs1899663 G/T, with recurrent spontaneous abortion (RSA) susceptibility in the Iranian women. Methods We enrolled 161 patients diagnosed with RSA and 177 healthy women with at least one live birth without a history of abortion. Genotyping of HOTAIR polymorphisms was carried out using both restriction fragment length polymorphism‐polymerase chain reaction and amplification refractory mutation system‐polymerase chain reaction methods. Odds ratios (ORs) with 95% confidence intervals (CIs) were assessed to estimate the strength of association. Results Different inheritance models of rs12826786 C/T, rs920778 T/C, and rs1899663 G/T polymorphisms significantly enhanced the risk of RSA (p < 0.05), whereas the rs4759314 A/G polymorphism was correlated with diminished risk of developing RSA under recessive AA versus GA + GG (OR 0.42 [95% CI = 0.19–0.91]), log‐additive GG versus GA vs. GG (OR 0.67 [95% CI = 0.48–0.93]), and allelic A versus G (OR 0.65 [95% CI = 0.47–0.92]) models. Moreover, the TGTC, TTCT, TTTC, CGTC, CGTT, CTCC, CTCT, CTTC, and CTTT haplotypes of rs920778/rs1899663/rs12826786/ significantly increased the risk of RSA. The studied variants were not in strong linkage disequilibrium. Conclusions Our results indicated that variations in the HOTAIR gene might serve as beneficial biomarkers for determining susceptibility to RSA. To confirm these findings, replication studies with a larger population and different races are needed.

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Association Analysis Between the rs1899663 Polymorphism of HOTAIR and Risk of Psychiatric Conditions in an Iranian Population

Cited by 17 publications

References 22 publications

Association between HOTAIR lncRNA Polymorphisms and Coronary Artery Disease Susceptibility

Association between HOTAIR lncRNA Polymorphisms and Coronary Artery Disease Susceptibility

Predicting Parkinson’s Disease Related Genes Based on PyFeat and Gradient Boosted Decision Tree (GBDT)

Genetic variants of HOTAIR are associated with susceptibility to recurrent spontaneous abortion: A preliminary case–control study

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