scholarly journals A novel system for forensic SNP analysis through PCR–ligase detection reaction

2015 ◽  
Vol 5 ◽  
pp. e231-e232
Author(s):  
W. He ◽  
J. Mao ◽  
T. Feng ◽  
L. Wang ◽  
Z. Li ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Ligase Detection Reaction

Genetic polymorphisms as the predictors of response to antiviral treatment in chronic hepatitis C virus infection

2011 ◽  
Vol 152 (22) ◽  
pp. 876-881
Author(s):  
Alajos Pár
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Genetic Polymorphisms ◽  
Chronic Hepatitis C ◽  
Genome Wide Association Study ◽  
Antiviral Treatment ◽  
Hcv Infection ◽  
Snp Analysis ◽  
Chronic Hcv

The review discusses the genetic polymorphisms involved in the pathogenesis of hepatitis C virus (HCV) infection, that may determine the outcome of disease. In this field earlier both certain major histocompatibility complex (MHC) alleles and some cytokine gene variants have also been studied. Recently, the genome-wide association study (GWAS) and targeted single nucleotide polymorphism (SNP) analysis have revealed that a variant in the promoter region of interleukin-28B (IL-28B) gene is strongly linked to viral clearance and it may be the strongest pretreatment predictor of treatment response in chronic hepatitis C. Last year it was shown that two genetic variants leading to inosine triphosphatase deficiency protect against haemolytic anemia in patients receiving ribavirin during antiviral treatment for chronic HCV infection. Orv. Hetil., 2011, 152, 876–881.

Genome-wide SNP analysis suggests male heterogamety in bighead catfish (Clarias macrocephalus, )

Aquaculture ◽  
2021 ◽  
pp. 737005
Author(s):  
Dung Ho My Nguyen ◽  
Jatupong Ponjarat ◽  
Nararat Laopichienpong ◽  
Ekaphan Kraichak ◽  
Thitipong Panthum ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Genome Wide ◽  
Clarias Macrocephalus ◽  
Male Heterogamety

scholarly journals The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xue Zhu ◽  
Jiyue Qin ◽  
Chongyang Tan ◽  
Kang Ning
Keyword(s):  
Gut Microbiome ◽  
Seasonal Changes ◽  
Dry Season ◽  
Urban Setting ◽  
Snp Analysis ◽  
Wet Season ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Genome Level ◽  
Prevalent Species

Abstract Background Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level. Results In this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis. Conclusions Eight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets.

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

scholarly journals Synergistic effect of genetic polymorphisms in TLR6 and TLR10 genes on the risk of pulmonary tuberculosis in a Moldavian population

2021 ◽  
pp. 175342592110299
Author(s):  
Alexander Varzari ◽  
Igor V. Deyneko ◽  
Elena Tudor ◽  
Harald Grallert ◽  
Thomas Illig
Keyword(s):  
Pulmonary Tuberculosis ◽  
Interaction Analysis ◽  
P Value ◽  
Fisher Exact Test ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exact Test ◽  
Pulmonary Tb ◽  
The Republic

Polymorphisms in genes that control immune function and regulation may influence susceptibility to pulmonary tuberculosis (TB). In this study, 14 polymorphisms in 12 key genes involved in the immune response ( VDR, MR1, TLR1, TLR2, TLR10, SLC11A1, IL1B, IL10, IFNG, TNF, IRAK1, and FOXP3) were tested for their association with pulmonary TB in 271 patients with TB and 251 community-matched controls from the Republic of Moldova. In addition, gene–gene interactions involved in TB susceptibility were analyzed for a total of 43 genetic loci. Single nucleotide polymorphism (SNP) analysis revealed a nominal association between TNF rs1800629 and pulmonary TB (Fisher exact test P = 0.01843). In the pairwise interaction analysis, the combination of the genotypes TLR6 rs5743810 GA and TLR10 rs11096957 GT was significantly associated with an increased genetic risk of pulmonary TB (OR = 2.48, 95% CI = 1.62–3.85; Fisher exact test P value = 1.5 × 10−5, significant after Bonferroni correction). In conclusion, the TLR6 rs5743810 and TLR10 rs11096957 two-locus interaction confers a significantly higher risk for pulmonary TB; due to its high frequency in the population, this SNP combination may serve as a novel biomarker for predicting TB susceptibility.

scholarly journals Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

2014 ◽  
Vol 80 (7) ◽  
pp. 2125-2132 ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
Ruth Timme ◽  
Brian H. Raphael ◽  
Donald Zink ◽  
Shashi K. Sharma
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Clostridium Botulinum ◽  
Toxin Gene ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

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