scholarly journals Synonymous SNP: Rare versus frequent codon can cause Phenotypic changes in the human genome

2019 ◽  
Author(s):  
Ashu Srivastav
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Phenotypic Effect ◽  
Single Nucleotide ◽  
Coding Sequences ◽  
Phenotypic Changes ◽  
Genome Variability ◽  
The Individual

ABSTRACTSince the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation and phenotypic changes between individuals. Single nucleotide polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. Synonymous Single Nucleotide Polymorphisms (sSNP) is an important source of human genome variability. It does not produce altered coding sequences therefore expected not to change the function of protein in which they occur. Examination of synonymous SNPs that change a rarely used codon into a frequently used one or vice versa may help in predicting their phenotypic effect on the individual carrying the change. Detail information of Human Synonymous Single-nucleotide-polymorphism may accelerate the research of personalized medicine since it has the crucial impact in the field of non-synonymous SNP.

scholarly journals Quantitative Analysis of Single-Nucleotide Polymorphism for Rapid Detection of TR34/L98H- and TR46/Y121F/T289A-Positive Aspergillus fumigatus Isolates Obtained from Patients in Iran from 2010 to 2014

2015 ◽  
Vol 60 (1) ◽  
pp. 387-392 ◽  
Author(s):  
Faezeh Mohammadi ◽  
Seyed Jamal Hashemi ◽  
Jan Zoll ◽  
Willem J. G. Melchers ◽  
Haleh Rafati ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Aspergillus Fumigatus ◽  
Tandem Repeat ◽  
Promoter Region ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACTWe employed an endpoint genotyping method to update the prevalence rate of positivity for the TR34/L98H mutation (a 34-bp tandem repeat mutation in the promoter region of thecyp51Agene in combination with a substitution at codon L98) and the TR46/Y121F/T289A mutation (a 46-bp tandem repeat mutation in the promoter region of thecyp51Agene in combination with substitutions at codons Y121 and T289) among clinicalAspergillus fumigatusisolates obtained from different regions of Iran over a recent 5-year period (2010 to 2014). The antifungal activities of itraconazole, voriconazole, and posaconazole against 172 clinicalA. fumigatusisolates were investigated using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution method. For the isolates with an azole resistance phenotype, thecyp51Agene and its promoter were amplified and sequenced. In addition, using a LightCycler 480 real-time PCR system, a novel endpoint genotyping analysis method targeting single-nucleotide polymorphisms was evaluated to detect the L98H and Y121F mutations in thecyp51Agene of all isolates. Of the 172A. fumigatusisolates tested, the MIC values of itraconazole (≥16 mg/liter) and voriconazole (>4 mg/liter) were high for 6 (3.5%). Quantitative analysis of single-nucleotide polymorphisms showed the TR34/L98H mutation in thecyp51Agenes of six isolates. No isolates harboring the TR46/Y121F/T289A mutation were detected. DNA sequencing of thecyp51Agene confirmed the results of the novel endpoint genotyping method. By microsatellite typing, all of the azole-resistant isolates had genotypes different from those previously recovered from Iran and from the Dutch TR34/L98H controls. In conclusion, there was not a significant increase in the prevalence of azole-resistantA. fumigatusisolates harboring the TR34/L98H resistance mechanism among isolates recovered over a recent 5-year period (2010 to 2014) in Iran. A quantitative assay detecting a single-nucleotide polymorphism in thecyp51Agene ofA. fumigatusis a reliable tool for the rapid screening and monitoring of TR34/L98H- and TR46/Y121F/T289A-positive isolates and can easily be incorporated into clinical mycology algorithms.

scholarly journals EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 455 ◽  
Author(s):  
Shuai Zeng ◽  
Jing Yang ◽  
Brian Hon-Yin Chung ◽  
Yu Lau ◽  
Wanling Yang
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Impact

NIASGBsnp: integration of single nucleotide polymorphism data of rice (Oryzasativa L.) genetic resources

2013 ◽  
Vol 11 (3) ◽  
pp. 221-224
Author(s):  
Masaru Takeya ◽  
Fukuhiro Yamasaki ◽  
Sachiko Hattori ◽  
Kaworu Ebana
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Pathology ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Resources ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Data ◽  
Polymorphism Data

The NIASGBsnp system manages data on single nucleotide polymorphisms (SNPs) of rice (Oryzasativa L.) genetic resources in the National Institute of Agrobiological Science (NIAS) Genebank. NIASGBsnp currently holds data on 768 SNP markers for 301 rice accessions and plans to add the SNP data of active rice accessions in the NIAS Genebank. It can show differences between accessions by graphical genotyping. Passport, characteristics and evaluation data of accessions can be retrieved to allow phenotype to be associated with genotype. NIASGBsnp will support various research purposes such as genomic selection and plant pathology research.

scholarly journals The role of genetic polymorphism in the formation of atherosclerosis in the vessels of lower extremities

2012 ◽  
Vol 93 (3) ◽  
pp. 513-516
Author(s):  
M N Katina ◽  
R F Gayfullina ◽  
V V Valiullin ◽  
A A Rizvanov ◽  
R F Khamitov ◽  
...  
Keyword(s):  
Human Genome ◽  
Literature Search ◽  
Lower Extremities ◽  
Disease Course ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Genes ◽  
Genomics And Proteomics ◽  
The Individual

Personalized medicine involves the use of methods of genomics and proteomics by physicians for early diagnosis, prediction of the nature of the disease course and the choice of medicines and their doses based on personalized characteristics of the individual patient. Advances in the study of the human genome make it possible to reveal the interrelation between the individual mutations in the human genes (polymorphisms) and predisposition to certain diseases. Currently there are more than 10 million single-nucleotide polymorphisms in the human genome, however their biological role remains poorly understood. On the basis of a literature search of electronic full-text and abstract-only versions of articles, which was conducted in the PUBMED, OMIM and GENE databases, collected was the information on genetic predisposition to systemic atherosclerosis. The review is dedicated to polymorphisms of the major genes that play a role in the pathophysiology of atherosclerosis of the lower extremities.

scholarly journals Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome

2003 ◽  
Vol 13 (3) ◽  
pp. 335-342 ◽  
Author(s):  
Thomas G. Schulze ◽  
Kui Zhang ◽  
Yu-Sheng Chen ◽  
Nirmala Akula ◽  
Fengzhu Sun ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Haplotype Blocks

scholarly journals Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold?

2006 ◽  
Vol 123 (3) ◽  
pp. 145-151 ◽  
Author(s):  
L. Grapes ◽  
S. Rudd ◽  
R.L. Fernando ◽  
K. Megy ◽  
D. Rocha ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals (6) Highly Polymorphic Genesin Cultivated Tomato

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 999A-999
Author(s):  
Angela Baldo ◽  
Larry Robertson ◽  
Joanne Labate
Keyword(s):  
Amino Acid ◽  
Single Nucleotide Polymorphisms ◽  
Germplasm Conservation ◽  
Wild Relatives ◽  
Nonsynonymous Snps ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Tomato Genome ◽  
Single Nucleotide

Cultivated tomato varieties are genetically extremely similar. We identified 764 Unigenes with potential single nucleotide polymorphisms (SNPs) among more than 15 cultivars from public expressed tomato data. By sequencing regions from 53 of these Unigenes in two to three cultivars, we discovered an unexpected wealth of nucleotide polymorphism (62 SNPs and 12 indels in 21 Unigenes). This included a high proportion of predicted nonsynonymous nucleotide (17 of 33 SNPs in exons) and nonconservative amino acid (6 of 16 nonsynonymous SNPs) changes. We hypothesize that five of these regions are associated with introgressions from wild relatives. Identifying polymorphic, expressed genes in the tomato genome will be useful for both tomato improvement and germplasm conservation.

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