Genetic variations associated with long noncoding RNAs

2020 ◽  
Vol 64 (6) ◽  
pp. 867-873 ◽  
Author(s):  
Jianjun Luo ◽  
Runsheng Chen
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Development Process ◽  
Noncoding Rnas ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Immune Disease ◽  
Single Nucleotide

Abstract Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including the long noncoding RNA (lncRNA) regions. The changes at locus might produce numerous effects in a variety of aspects. Multiple bioinformatics resources and tools were also developed for systematically dealing with genetic variations associated with lncRNAs. Moreover, correlation of the genetic variations in lncRNAs with immune disease, cancers, and other disease as well as development process were all included for discussion. In this essay, we summarized how and in what aspects these changes would affect lncRNA functions.

scholarly journals Single Nucleotide Polymorphisms in HOTAIR Are Related to Breast Cancer Risk and Prognosis in the Northeastern Chinese Population

2021 ◽  
Vol 11 ◽  
Author(s):  
Zheng Lv ◽  
Changgui Kou ◽  
Naifei Chen ◽  
Lin Jia ◽  
Xu Sun ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Chinese Population ◽  
Noncoding Rna ◽  
Disease Free Survival ◽  
Population Based ◽  
Clinicopathological Characteristics ◽  
Nucleotide Polymorphisms ◽  
Binary Logistic Regression Model ◽  
Single Nucleotide

BackgroundThe long noncoding RNA HOX transcript antisense RNA (HOTAIR) is highly expressed in breast cancer (BC) tissues and is associated with the recurrence and metastasis of BC. Until now, the results of studies on associations between several functional single nucleotide polymorphisms(SNPs) (rs920778, rs1899663, and rs4759314) in HOTAIR with BC susceptibility carried out in different regions of China are still inconsistent. There is no study on correlation between HOTAIR SNPs and prognosis of Chinese population. Therefore, we investigated the relationship between HOTAIR SNPs and susceptibility to and prognosis of BC.MethodWe conducted a population-based case-control study involving 828 BC cases and 905 healthy controls. Peripheral blood DNA was used for genotyping. The association between HOTAIR genotypes and BC risk were estimated by odds ratios (ORs) computed using the binary logistic regression model. The relationships between HOTAIR SNPs and clinicopathological features were tested by Pearson’s chi-square test or Fisher’s exact test. Survival was analyzed using the Kaplan-Meier method.ResultsThe functional rs920778 genetic variant increased BC risk in the codominant model. Individuals with the rs920778 GG genotype had an OR of 2.426 (95% confidence interval [CI] = 1.491–3.947, P < 0.001) for developing BC compared to individuals with the AA genotype. Individuals with the AG genotype had an OR of 1.296 (95% CI = 1.040–1.614, P = 0.021) for developing BC compared to individuals with the AA genotype. Individuals with the rs4759314 GA genotype had a lower BC risk than individuals with the rs4759314 AA/GG genotype (OR = 0.566, 95% CI = 0.398–0.803, P = 0.001). The rs1899663 genotype had no correlation with BC susceptibility. Haplotypes composed of rs920778–rs1899663 and rs920778–rs1899663–rs4759314 could increase BC risk (all P < 0.001). There were no statistically significant associations between HOTAIR SNPs and clinicopathological characteristics. The rs920778 GG/AG genotypes were associated with worse disease-free survival (DFS) (p = 0.012), and the rs4759314 GA genotype was associated with worse DFS and overall survival (OS) (p = 0.011).ConclusionHOTAIR SNPs(rs920778 and rs4759314) are significantly related to BC susceptibility and prognosis in the northeastern Chinese population, indicating the significance in the occurrence and development of BC.

Functional nonsynonymous single nucleotide polymorphisms from the TGF-β protein interaction network

2007 ◽  
Vol 29 (2) ◽  
pp. 109-117 ◽  
Author(s):  
Sevtap Savas ◽  
Ian W. Taylor ◽  
Jeff L. Wrana ◽  
Hilmi Ozcelik
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Protein Interactions ◽  
Transforming Growth Factor ◽  
Conservation Status ◽  
Genetic Variations ◽  
Phosphorylation Sites ◽  
Nucleotide Polymorphisms ◽  
Protein Protein Interactions ◽  
Single Nucleotide ◽  
Putative Protein

Protein complexes mediated by protein-protein interactions are essential for many cellular functions. Transforming growth factor (TGF)-β signaling involves a cascade of protein-protein interactions and malfunctioning of this pathway has been implicated in human diseases. Using an in silico approach, we analyzed the naturally occurring human genetic variations from the proteins involved in the TGF-β signaling (10 TGF-β proteins and 242 other proteins interacting with them) to identify the ones that have potential biological consequences. All proteins were searched in the dbSNP database for the presence of nonsynonymous single nucleotide polymorphisms (nsSNPs). A total of 118 validated nsSNPs from 63 proteins were retrieved and analyzed in terms of 1) evolutionary conservation status, 2) being located in a functional protein domain or motif, and 3) altering putative protein motif or phosphorylation sites. Our results indicated the presence of 31 nsSNPs that occurred at evolutionarily conserved residues, 37 nsSNPs were located in protein domains, motifs, or repeats, and 46 nsSNPs were predicted to either create or abolish putative protein motifs or phosphorylation sites. We undertook this study to analyze the human genetic variations that can affect the protein function and the TGF-β signaling. The nsSNPs reported in here can be characterized by experimental approaches to elucidate their exact biological roles and whether they are related to human disease.

scholarly journals Single Nucleotide Polymorphisms in PEMT and MTHFR Genes are Associated with Omega 3 and 6 Fatty Acid Levels in the Red Blood Cells of Children with Obesity

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2600 ◽  
Author(s):  
Vlad Serafim ◽  
Adela Chirita-Emandi ◽  
Nicoleta Andreescu ◽  
Diana-Andreea Tiugan ◽  
Paul Tutac ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Methylenetetrahydrofolate Reductase ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Dietary Intakes ◽  
Omega 3 ◽  
Single Nucleotide ◽  
Pufa Composition

Polyunsaturated fatty acids (PUFAs) play important roles in health and disease. PUFA levels are influenced by nutrition and genetic factors. The relationship between PUFA composition in red blood cells (RBCs) and genetic variations involved in PUFA metabolism has not been investigated in children with obesity. This study evaluated the association between several genetic variations and PUFA levels in RBCs in children with obesity. One hundred ninety-six children with obesity (101 females, 95 males) were evaluated using anthropometric measurements, dietary intakes, plasma and RBC PUFA quantification, blood biochemistry, and 55 single nucleotide polymorphisms within 14 genes. phosphatidylethanolamine N-methyltransferase (PEMT) rs1109859 and methylenetetrahydrofolate reductase gene (MTHFR) rs4846052 genotypes were associated with PUFA levels in RBCs. PUFA intake did not influence the RBC eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) levels. Higher RBC DHA and EPA levels were observed for PEMT rs1109859 GG and GA genotypes versus the AA genotype. Higher levels of RBC DHA, EPA, arachidonic acid (ARA), and linoleic acid (LA) and were observed for MTHFR rs4846052 TT genotype versus TC and CC genotypes. Genetic variations in PEMT rs1109859 and MTHFR rs4846052 were associated with different PUFA levels in RBC membranes and are estimators for PUFA species in RBCs. Further research is needed to establish whether these genotype-specific alterations are specific to overweight children.

scholarly journals Genetic Variations and Frequencies of the Two Functional Single Nucleotide Polymorphisms of SLCO1B1 in the Thai Population

2020 ◽  
Vol 11 ◽  
Author(s):  
Chalitpon Na nakorn ◽  
Jariya Waisayarat ◽  
Charungthai Dejthevaporn ◽  
Pornpen Srisawasdi ◽  
Sansanee Wongwaisayawan ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Thai Population ◽  
Single Nucleotide

scholarly journals Association of genetic variations in genes involved in glutathione metabolism with risk of development of uterine fibroids

2020 ◽  
pp. 52-54
Author(s):  
О.К. Кудрявцева ◽  
Е.М. Барышева ◽  
И.Н. Вдовина ◽  
А.А. Клиновская ◽  
Е.А. Новикова ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Multiplex Pcr ◽  
Uterine Fibroids ◽  
Genetic Variations ◽  
Glutathione Metabolism ◽  
Healthy Controls ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Increased Risk ◽  
Risk Of Disease

В исследование были включены 552 пациентки с миомой матки (ММ) и 337 женщин контрольной группы соответствующего возраста. Генотипирование однонуклеотидных полиморфизмов (rs713041 GPX4, rs4902346 GPX2, rs41303970 GCLM, rs17883901 GCLC, rs1050450 GPX1, rs1799811 и rs1695 GSTP1, rs2551715 GSR, rs1801310 GSS, rs4820599 GGT1, rs7674870 SLC7A11) было проведено методом ПЦР в режиме реального времени; генотипирование делеционных полиморфизмов (+/0 GSTM1 и +/0 GSTT1) было проведено методом мультиплексной ПЦР. С повышенным риском развития ММ ассоциировался rs7674870 SLC7A11 (OR=1,25, 95%CI=1,03-1,50; p=0,02). Полиморфизм rs2551715 GSR обладал протективным эффектом относительно развития заболевания (OR=0,83, 95%CI=0,70-0,99; p=0,04). A total of 552 females with uterine fibroids and 337 age-matched healthy controls were recruited for the study. Genotyping of single nucleotide polymorphisms (SNPs) of rs713041 GPX4, rs4902346 GPX2, rs41303970 GCLM, rs17883901 GCLC, rs1050450 GPX1, rs1799811 and rs1695 GSTP1, rs2551715 GSR, rs1801310 GSS, rs4820599 GGT1, rs7674870 SLC7A11 were done using Taq-Man-based assays. Genotyping of +/0 GSTM1 and +/0 GSTT1 polymorphisms were done using multiplex PCR. Polymorphism rs7674870 SLC7A11 was associated with increased risk of uterine fibroids (OR=1.25, 95%CI=1.03-1.50; p=0.02); rs2551715 GSR was associated with decreased risk of disease (OR=0.83, 95% CI=0.70-0.99; p=0.04)

The genomic basis of medicine

2020 ◽  
pp. 218-235
Author(s):  
Paweł Stankiewicz ◽  
James R. Lupski
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Complex Traits ◽  
Copy Number ◽  
Clinical Medicine ◽  
Association Studies ◽  
Copy Number Variants ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Practical Applications

The first phase of the studies on genetic variation in humans has been focused on single nucleotide polymorphisms and common variation. The large number of single nucleotide polymorphisms identified has enabled successful genome-wide association studies for disease susceptibility risk of complex traits (e.g. diabetes and cancer), but for the most part has had limited practical applications in clinical medicine. This chapter examines the recent technological developments which have enabled a higher-resolution analysis of the human genome and its extensive submicroscopic structural variation, including copy-number variants. Copy-number variants involving dosage-sensitive genes result in several diseases and contribute to human diversity and evolution. An emerging group of genetic diseases have been described that result from DNA rearrangements (e.g. copy-number variants and other structural variations including copy-number neutral inversions and translocations), rather than from single nucleotide changes.

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