scholarly journals Pathogenesis of atherosclerosis of arteries of the lower extremities: candidate genes and their polymorphism

2012 ◽  
Vol 93 (2) ◽  
pp. 311-314
Author(s):  
M N Katina ◽  
R F Gayfullina ◽  
V V Valiullin ◽  
A A Rizvanov
Keyword(s):  
Personalized Medicine ◽  
Early Diagnosis ◽  
Human Genome ◽  
Literature Search ◽  
Lower Extremities ◽  
Disease Course ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Genes ◽  
The Individual

Personalized medicine involves the use of genetic methods 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 different varieties of alleles of human genes (polymorphism) and predisposition to certain diseases. Currently there are more than 10 million single-nucleotide polymorphisms in the human genome, but 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 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 Using human demographic history to infer natural selection reveals contrasting patterns on different families of immune genes

2010 ◽  
Vol 278 (1711) ◽  
pp. 1587-1594 ◽  
Author(s):  
William Amos ◽  
Clare Bryant
Keyword(s):  
Natural Selection ◽  
Human Genome ◽  
Demographic History ◽  
Time Interval ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Immune Genes ◽  
Geographical Patterns ◽  
Human Genes ◽  
The Relationship

Detecting regions of the human genome that are, or have been, influenced by natural selection remains an important goal for geneticists. Many methods are used to infer selection, but there is a general reliance on an accurate understanding of how mutation and recombination events are distributed, and the well-known link between these processes and their evolutionary transience introduces uncertainty into inferences. Here, we present and apply two new, independent approaches; one based on single nucleotide polymorphisms (SNPs) that exploits geographical patterns in how humans lost variability as we colonized the world, the other based on the relationship between microsatellite repeat number and heterozygosity. We show that the two methods give concordant results. Of these, the SNP-based method is both widely applicable and detects selection over a well-defined time interval, the last 50 000 years. Analysis of all human genes by their Gene Ontology codes reveals how accelerated and decelerated loss of variability are both preferentially associated with immune genes. Applied to 168 immune genes used as the focus of a previous study, we show that members of the same gene family tend to yield similar indices of selection, even when located on different chromosomes. We hope our approach will provide a useful tool with which to infer where selection has acted to shape the human genome.

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 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

Characterization of single-nucleotide polymorphisms in coding regions of human genes

10.1038/10290 ◽  
1999 ◽  
Vol 22 (3) ◽  
pp. 231-238 ◽  
Author(s):  
Michele Cargill ◽  
David Altshuler ◽  
James Ireland ◽  
Pamela Sklar ◽  
Kristin Ardlie ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Human Genes

scholarly journals BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs

2020 ◽  
Author(s):  
Nina Luhmann ◽  
Guillaume Holley ◽  
Mark Achtman
Keyword(s):  
Data Structure ◽  
Fluoroquinolone Resistance ◽  
Nucleotide Polymorphisms ◽  
Bacterial Genomes ◽  
Single Nucleotide ◽  
De Bruijn Graphs ◽  
Practical Applications ◽  
The Individual ◽  
Dynamic Data Structure ◽  
Genome Assemblies

AbstractBlastFrost is a highly efficient method for querying 100,000s of genome assemblies. It builds on Bifrost, a recently developed dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants. Here we describe the algorithms and implementation of BlastFrost. We also present two exemplar practical applications. In the first, we determined the presence of the individual genes within the SPI-2 Salmonella pathogenicity island within a collection of 926 representative genomes in minutes. In the second application, we determined the existence of known single nucleotide polymorphisms associated with fluoroquinolone resistance in the genes gyrA, gyrB and parE among 190, 209 Salmonella genomes. BlastFrost is available for download at https://github.com/nluhmann/BlastFrost.

scholarly journals Associations between Genotype–Diet Interactions and Weight Loss—A Systematic Review

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2891
Author(s):  
Sandra Bayer ◽  
Vincent Winkler ◽  
Hans Hauner ◽  
Christina Holzapfel
Keyword(s):  
Weight Loss ◽  
Literature Search ◽  
Treatment Success ◽  
Systematic Literature Search ◽  
Fat Intake ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Main Determinant ◽  
Future Studies ◽  
Special Groups

Studies on the interactions between single nucleotide polymorphisms (SNPs) and macronutrient consumption on weight loss are rare and heterogeneous. This review aimed to conduct a systematic literature search to investigate genotype–diet interactions on weight loss. Four databases were searched with keywords on genetics, nutrition, and weight loss (PROSPERO: CRD42019139571). Articles in languages other than English and trials investigating special groups (e.g., pregnant women, people with severe diseases) were excluded. In total, 20,542 articles were identified, and, after removal of duplicates and further screening steps, 27 articles were included. Eligible articles were based on eight trials with 91 SNPs in 63 genetic loci. All articles examined the interaction between genotype and macronutrients (carbohydrates, fat, protein) on the extent of weight loss. However, in most cases, the interaction results were not significant and represented single findings that lack replication. The publications most frequently analyzed genotype–fat intake interaction on weight loss. Since the majority of interactions were not significant and not replicated, a final evaluation of the genotype–diet interactions on weight loss was not possible. In conclusion, no evidence was found that genotype–diet interaction is a main determinant of obesity treatment success, but this needs to be addressed in future studies.

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