Profiling Deleterious Non-synonymous SNPs of Smoker's Gene CYP1A1

Introduction. Changes in the body of children and adolescents aimed at adapting to environmental factors are determined by genetic polymorphism in xenobiotic biotransformation genes, determining the degree of susceptibility of the child’s body to pollutants, which is the basis of modern personalized preventive medicine when managing risks to the health of the child population under the influence of environmental factors. Material and methods. Trace elements, including heavy metals, lead and cadmium, were determined in the hair of 256 practically healthy teenagers by atomic absorption spectrophotometry. Depending on the level of content of the latter, two groups of adolescents were formed to determine six genes of the cytochrome P-450 family. Group 1 consisted of adolescents whose cadmium lead content exceeded the average Russian indices. The second group included adolescents whose heavy metals were above the level of average Russian standards. Results. Studies have shown that in adolescents of the 1st group, compared with the data of adolescents of the 2nd group, an increase in the number of carriers of two mutant alleles at the locus rs 1048943 (gene CYP1A1) is 3.08 times, rs 464621 (gene CYP1A1) is 1. 8 times; locus rs 2069522 (CYP1A2 gene) 3.63 times; locus rs 1799853 (CYP2C9 * 2 gene) 4.5 times; locus rs 1057910 (gene CYP2C9 * 3) 3.8 times and locus rs 2279343 (gene CYP2B6) 4.25 times. Moreover, carriers of two normal alleles in adolescents of the first group at the locus rs 1048943 (gene CYP1A1) were 5.14 times; locus rs 2279343 (CYP2B6 gene) was 6.5 fold less than among adolescents of the 2nd group; and at the locus rs 464621 (gene CYP1A1), rs 2069522 (gene CYP1A2), rs 1799853 (gene CYP2C9 * 2), rs 1057910 (gene CYP2C9 * 3) there were no carriers of normal homozygotes. Conclusion. Group 1 adolescents with heavy metal contamination of the body are carriers significantly in a greater number of pathological mutations in the genes of the cytochrome P-450 detoxification system in comparison with data from group 2 adolescents.

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Comprehensive in-silico Analysis of High-risk Non-synonymous SNPs in Dectin-1 Gene of Human and their Impact on Protein Structure

Current Pharmacogenomics and Personalized Medicine ◽

10.2174/1875692116666180115142706 ◽

2018 ◽

Vol 15 (2) ◽

pp. 144-155 ◽

Cited By ~ 2

Author(s):

Raman Thakur ◽

Jata Shankar

Keyword(s):

Protein Structure ◽

High Risk ◽

In Silico ◽

In Silico Analysis ◽

Synonymous Snps ◽

Silico Analysis

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In-silico analysis of non- synonymous SNPs of human LDLR gene and their impact on familial hypercholesterolemia

Gene Reports ◽

10.1016/j.genrep.2021.101127 ◽

2021 ◽

pp. 101127

Author(s):

Pratik Ghosh ◽

Samarpita Ghosh ◽

Bhaskar Behera ◽

Jiban Kumar Behera ◽

Manojit Bhattacharya ◽

...

Keyword(s):

Familial Hypercholesterolemia ◽

In Silico ◽

In Silico Analysis ◽

Ldlr Gene ◽

Synonymous Snps ◽

Silico Analysis

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In silico approach to identify non-synonymous SNPs with highest predicted deleterious effect on protein function in human obesity related gene, neuronal growth regulator 1 (NEGR1)

3 Biotech ◽

10.1007/s13205-018-1463-0 ◽

2018 ◽

Vol 8 (11) ◽

Cited By ~ 4

Author(s):

Permendra Kumar ◽

Kulandaivelu Mahalingam

Keyword(s):

Growth Regulator ◽

Protein Function ◽

In Silico ◽

Deleterious Effect ◽

Related Gene ◽

Neuronal Growth ◽

Human Obesity ◽

Synonymous Snps

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Chromosomal rearrangements and protein globularity changes inMycobacterium tuberculosisisolates from cerebrospinal fluid

PeerJ ◽

10.7717/peerj.2484 ◽

2016 ◽

Vol 4 ◽

pp. e2484 ◽

Cited By ~ 4

Author(s):

Seow Hoon Saw ◽

Joon Liang Tan ◽

Xin Yue Chan ◽

Kok Gan Chan ◽

Yun Fong Ngeow

Keyword(s):

Cerebrospinal Fluid ◽

Chromosomal Rearrangements ◽

Genome Sequences ◽

Genetic Traits ◽

Genomic Features ◽

Synonymous Snps ◽

Genome Wide ◽

Genes Encoding ◽

Transcription Regulators ◽

Central Nervous System Invasion

BackgroundMeningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains ofMycobacterium tuberculosis(Mtb) might have genetic traits associated with neurotropism.MethodsIn this study, we generated whole genome sequences of eight clinical strains ofMtbthat were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratoryMtbgenomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratoryMtb.ResultsGenome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratoryMtbgenomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated withStreptococcus pneumoniaemeningitis andNeisseria meningitidisvirulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study.DiscussionThe occurrence of in silico genetic differences in CSF-derived but not respiratoryMtbsuggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal infection is more likely to be related to the expression of multiple virulence factors on interaction with host defences than to CNS tropism associated with specific genetic traits.

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Associação dos polimorfismos A4889G e T6235C do gene CYP1A1 com características clínicas e epidemiológicas do câncer de mama

10.47749/t/unicamp.2012.881711 ◽

2012 ◽

Author(s):

Cassio Cardoso Filho

Keyword(s):

Cáncer De Mama ◽

Gene Cyp1a1

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Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP

PLoS ONE ◽

10.1371/journal.pone.0068370 ◽

2013 ◽

Vol 8 (7) ◽

pp. e68370 ◽

Cited By ~ 12

Author(s):

Morten Bo Johansen ◽

Jose M. G. Izarzugaza ◽

Søren Brunak ◽

Thomas Nordahl Petersen ◽

Ramneek Gupta

Keyword(s):

Neural Network ◽

Artificial Neural Network ◽

Synonymous Snps ◽

Artificial Neural

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Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice

Plants ◽

10.3390/plants9121653 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1653

Author(s):

Hayba Badro ◽

Marie-Noelle Ndjiondjop ◽

Agnelo Furtado ◽

Robert Henry

Keyword(s):

Association Analysis ◽

Agronomic Traits ◽

Heading Date ◽

Sucrose Metabolism ◽

Interspecific Crosses ◽

Oryza Glaberrima ◽

Gene Pools ◽

Synonymous Snps ◽

African Rice ◽

Asian Rice

Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.

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