Single Nucleotide Polymorphisms Analysis of Noise-Induced Hearing Loss Using Three-Dimensional Polyacrylamide Gel-Based Microarray Method

Hereditary hearing loss is one of the most common human neurosensory disorder, and there is a great need for early intervention methods such as genetically screening newborns. Single nucleotide polymorphisms...

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Highlights from the 15th International Congress of Twin Studies/Twin Research: Differentiating MZ Co-twins Via SNPs; Mistaken Infant Twin-Singleton Hospital Registration; Narcolepsy With Cataplexy; Hearing Loss and Language Learning/Media Mentions: Broadway Musical Recalls Conjoined Hilton Twins; High Fashion Pair; Twins Turn 102; Insights From a Conjoined Twin Survivor

Twin Research and Human Genetics ◽

10.1017/thg.2014.84 ◽

2015 ◽

Vol 18 (1) ◽

pp. 108-115

Author(s):

Nancy L. Segal

Keyword(s):

Hearing Loss ◽

Single Nucleotide Polymorphisms ◽

Language Learning ◽

Twin Studies ◽

Conjoined Twins ◽

International Congress ◽

Nucleotide Polymorphisms ◽

Childhood Onset ◽

Single Nucleotide ◽

Broadway Musical

Highlights from the 15th International Congress of Twin Studies are presented. The congress was held November 16–19, 2014 in Budapest, Hungary. This report is followed by summaries of research addressing the differentiation of MZ co-twins by single nucleotide polymorphisms (SNPs), an unusual error in infant twin-singleton hospital registration, twins with childhood-onset narcolepsy with cataplexy, and the parenting effects of hearing loss in one co-twin. Media interest in twins covers a new Broadway musical based on the conjoined twins Violet and Daisy Hilton, male twins becoming famous in fashion, twins who turned 102 and unique insights from a conjoined twin survivor.

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A STRUCTURAL BIOINFORMATICS APPROACH TO THE ANALYSIS OF NONSYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS (nsSNPs) AND THEIR RELATION TO DISEASE

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720007003120 ◽

2007 ◽

Vol 05 (06) ◽

pp. 1297-1318 ◽

Cited By ~ 44

Author(s):

CATHERINE L. WORTH ◽

G. RICHARD J. BICKERTON ◽

ADRIAN SCHREYER ◽

JULIA R. FORMAN ◽

TAMMY M. K. CHENG ◽

...

Keyword(s):

Amino Acid ◽

Single Nucleotide Polymorphisms ◽

Structure Prediction ◽

Three Dimensional ◽

Comparative Modeling ◽

Divergent Evolution ◽

Amino Acid Substitutions ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Human Proteins

The prediction of the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) on function depends critically on exploiting all information available on the three-dimensional structures of proteins. We describe software and databases for the analysis of nsSNPs that allow a user to move from SNP to sequence to structure to function. In both structure prediction and the analysis of the effects of nsSNPs, we exploit information about protein evolution, in particular, that derived from investigations on the relation of sequence to structure gained from the study of amino acid substitutions in divergent evolution. The techniques developed in our laboratory have allowed fast and automated sequence-structure homology recognition to identify templates and to perform comparative modeling; as well as simple, robust, and generally applicable algorithms to assess the likely impact of amino acid substitutions on structure and interactions. We describe our strategy for approaching the relationship between SNPs and disease, and the results of benchmarking our approach — human proteins of known structure and recognized mutation.

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Single-Nucleotide Polymorphisms in XPO5 are Associated with Noise-Induced Hearing Loss in a Chinese Population

Biochemistry Research International ◽

10.1155/2020/9589310 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Ning Wang ◽

Boshen Wang ◽

Jiadi Guo ◽

Suhao Zhang ◽

Lei Han ◽

...

Keyword(s):

Hearing Loss ◽

Chinese Population ◽

Luciferase Reporter ◽

Noise Induced Hearing Loss ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Increased Risk ◽

Polymerase Chain ◽

Control Study ◽

Dual Luciferase Reporter Assay

Objectives.The purpose of this study was to investigate the correlation between single-nucleotide polymorphism (SNP) in 3′UTR of XPO5 gene and the occurrence of noise-induced hearing loss (NIHL), and to further explore the regulatory mechanism of miRNAs in NIHL on XPO5 gene. Methods.We conducted a case-control study involving 1040 cases and 1060 controls. The effects of SNPs on XPO5 expression were studied by genotyping, real-time polymerase chain reaction (qPCR), cell transfection, and the dual-luciferase reporter assay. Results.We genotyped four SNPs (rs2257082, rs11077, rs7755135, and rs1106841) in the XPO5 gene. The rs2257082 AG/GG carriers have special connection to an increased risk of noise-induced hearing loss compared to the AA carriers. The rs11077TG/GG carriers had a significantly increased association with NIHL susceptibility than the TT carriers. There was a higher risk of NIHL in the XPO5 gene rs7755135 CC carriers than in the TT carriers. No statistically significant correlation was obtained with respect to SNPrs1106841. Functional experiments showed that the rs11077 change might inhibit the interaction between miRNAs (miRNA-4763-5p, miRNA-5002-3p, and miRNA-617) and XPO5, with rs11077G allele resulting in overexpression of XPO5. Conclusion. The genetic polymorphism, rs11077, within XPO5 is associated with the risk of noise-induced hearing loss in a Chinese population.

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Salt-Inducible Kinase 3 Haplotypes Associated with Noise-Induced Hearing Loss in Chinese Workers

Audiology and Neurotology ◽

10.1159/000506066 ◽

2020 ◽

Vol 25 (4) ◽

pp. 200-208

Author(s):

Haoyang Yin ◽

Jiadi Guo ◽

Enmin Ding ◽

Hengdong Zhang ◽

Lei Han ◽

...

Keyword(s):

Hearing Loss ◽

Noise Exposure ◽

Noise Induced Hearing Loss ◽

Nucleotide Polymorphisms ◽

Multifactor Dimensionality Reduction Analysis ◽

Work Time ◽

Single Nucleotide ◽

Chinese Workers ◽

Hearing Damage ◽

Textile Factory

Introduction: Noise-induced hearing loss (NIHL) is a common occupational disease that represents an irreversible hearing damage to the auditory system. It has been identified as a complicated disease involving both environmental and genetic factors. More efforts need to be made to explore the genes associated with susceptibility to NIHL. The main aim of this research is to detect the associations between SIK3 polymorphisms and NIHL susceptibility in Han people in China. Methods: A case-control study was performed in 586 cases and 639 controls in a textile factory matched for sex, age, smoking, drinking, work time with noise, and intensity of noise exposure. Three single nucleotide polymorphisms (SNPs) (rs493134, rs6589574, and rs7121898) of SIK3 were genotyped in the participants. Then, the main influences of the SNPs on and their interactions with NIHL were assessed. Results: Under the allelic model, distributions of rs493134 T, rs6589574 G, and rs7121898 A in the NIHL group are statistically different from those of the normal group (p = 0.001, p < 0.001, and p = 0.019, respectively). The following haplotype analysis shows that TAA (rs493134-rs6589574-rs7121898) may have a protective effect, while TGA (rs493134-rs6589574-rs7121898) (OR = 1.49, 95% CI = 1.25–1.79) may be a risk factor for NIHL. Multifactor dimensionality reduction analysis shows that the interaction of the 3 selected SNPs is associated with NIHL susceptibility (OR = 1.88, 95% CI = 1.50–2.36). Conclusion: The results suggest that 3 SNPs (rs493134, rs6589574, and rs7121898) of SIK3 may be an important part of NIHL susceptibility and can be applied in the prevention, early diagnosis, and treatment of NIHL in noise-exposed Chinese workers.

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Electrochemical single nucleotide polymorphisms genotyping on surface immobilized three-dimensional branched DNA nanostructure

Science China Chemistry ◽

10.1007/s11426-011-4327-6 ◽

2011 ◽

Vol 54 (8) ◽

pp. 1273-1276 ◽

Cited By ~ 72

Author(s):

ZhiLei Ge ◽

Hao Pei ◽

LiHua Wang ◽

ShiPing Song ◽

ChunHai Fan

Keyword(s):

Single Nucleotide Polymorphisms ◽

Three Dimensional ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Dna Nanostructure ◽

Branched Dna

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A survey of proteins encoded by non-synonymous single nucleotide polymorphisms reveals a significant fraction with altered stability and activity

Biochemical Journal ◽

10.1042/bj20090723 ◽

2009 ◽

Vol 424 (1) ◽

pp. 15-26 ◽

Cited By ~ 31

Author(s):

Abdellah Allali-Hassani ◽

Gregory A. Wasney ◽

Irene Chau ◽

Bum Soo Hong ◽

Guillermo Senisterra ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Three Dimensional ◽

Catalytic Efficiency ◽

Nucleotide Polymorphisms ◽

Wild Type ◽

Coding Region ◽

Wild Type Enzyme ◽

Single Nucleotide ◽

The Stability ◽

And Function

On average, each human gene has approximately four SNPs (single nucleotide polymorphisms) in the coding region, half of which are nsSNPs (non-synonymous SNPs) or missense SNPs. Current attention is focused on those that are known to perturb function and are strongly linked to disease. However, the vast majority of SNPs have not been investigated for the possibility of causing disease. We set out to assess the fraction of nsSNPs that encode proteins that have altered stability and activity, for this class of variants would be candidates to perturb cellular function. We tested the thermostability and, where possible, the catalytic activity for the most common variant (wild-type) and minor variants (total of 46 SNPs) for 16 human enzymes for which the three-dimensional structures were known. There were significant differences in the stability of almost half of the variants (48%) compared with their wild-type counterparts. The catalytic efficiency of approx. 14 variants was significantly altered, including several variants of human PKM2 (pyruvate kinase muscle 2). Two PKM2 variants, S437Y and E28K, also exhibited changes in their allosteric regulation compared with the wild-type enzyme. The high proportion of nsSNPs that affect protein stability and function, albeit subtly, underscores the need for experimental analysis of the diverse human proteome.

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