scholarly journals Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue

2019 ◽  
Vol 36 (12) ◽  
pp. 2525-2531
Author(s):  
Qian Geng ◽  
Xiaoli Cui ◽  
Yaqi Zhang ◽  
Lijuan Zhang ◽  
Cai Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Uniparental Disomy ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Quadratic Curve ◽  
Low Coverage

Abstract Purpose To establish a single-nucleotide polymorphism-based analysis (SBA) method to identify triploidy in the miscarriage tissue by using low-coverage whole-genome sequencing (LC-WGS). Methods The method was established by fitting a quadratic curve model by counting the distribution of three heterozygous mutation content intervals. The triploid test result was mainly determined by the opening direction and the axis of symmetry of the quadratic curve, and Z test between the same batch samples was also used for auxiliary judgment. Results Two hundred thirteen diploid samples and 8 triploid samples were used for establishment of the analytical method and 203 unknown samples were used for blind testing. In the blind testing, we found 2 cases positive for triploidy. After chromosome microarray analysis (CMA) and mass spectrometry verification, we found that both samples were true positives. We randomly selected 5 samples from the negative samples for mass spectrometry verification, and the results showed that these samples were all true negatives. Conclusions Our method achieved accurate detection of triploidy in the miscarriage tissue and has the potential to detect more chromosomal abnormality types such as uniparental disomy (UPD) using a single LC-WGS approach.

scholarly journals Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

2009 ◽  
Vol 10 (8) ◽  
pp. R82 ◽  
Author(s):  
Sebastian H Eck ◽  
Anna Benet-Pagès ◽  
Krzysztof Flisikowski ◽  
Thomas Meitinger ◽  
Ruedi Fries ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bos Taurus ◽  
Single Nucleotide Polymorphism Discovery ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polymorphism Discovery

scholarly journals Single nucleotide polymorphism in the rpoB gene Mycobacterium tuberculosis from Papua-Indonesia and its impact on rifampicin resistance: A whole genome sequencing analysis

2021 ◽  
Vol 15 (2) ◽  
pp. 1
Author(s):  
Yustinus Maladan ◽  
Tri Wahyuni ◽  
Hana Krismawati
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Rna Polymerase ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

In the antibiotic era, Tuberculosis (TB) drugs resistance especially Rifampicin (RIF) is highly reported around the world. Resistance of RIF is caused by the mutation of genes that associated with RIF receptor. The aims of this study are detecting the Single Nucleotide Polymorphism of Rifampicin resistant genes using Whole Genome Sequencing (WGS) and analysing the profile of protein changing caused by SNP. Twenty Mycobacterium tuberculosis culture samples were passed on WGS procedure and 19 samples were adequate to further bioinformatics analysis. Single Nucleotide Polymorphisms Analysis was done using TBprofiler. Based on TBProfiler, seventeen samples were resistant to rifampicin. The mutations that cause the resistance are S450L, D435Y, H445Y, 430P, Q432K. Other Single Nucleotide Polymorphisms H835R, V534M and R224C were also found. The H835R mutants are present together with the S450L, V534M with S450L mutants, and R224C with Q432K mutants. Native protein for RNA Polymerase Subunit β used was the result of separation from the crystal structure of Mycobacterium tuberculosis H37Rv RNA polymerase (PDB: 5UHB). Binding affinity RIF to RNA Polymerase Subunit β calculated using AutoDock vina. Construction of mutant 3D structures using FoldX5. From the analysis, it was found that seventeen samples were resistant to rifampicin and two samples did not contain SNP which could cause resistance to rifampicin.

scholarly journals Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

2015 ◽  
Vol 53 (10) ◽  
pp. 3334-3340 ◽  
Author(s):  
Angela J. Taylor ◽  
Victoria Lappi ◽  
William J. Wolfgang ◽  
Pascal Lapierre ◽  
Michael J. Palumbo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Molecular Subtyping ◽  
Foodborne Outbreaks

Salmonella entericaserovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis ofS. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmentalS. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of theS. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method forS. Enteritidis.

scholarly journals Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis

2015 ◽  
Vol 54 (3) ◽  
pp. 556-564 ◽  
Author(s):  
Célia Leão ◽  
Robert J. Goldstone ◽  
Josephine Bryant ◽  
Joyce McLuckie ◽  
João Inácio ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mycobacterium Avium ◽  
Discriminatory Power ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Phylogenetic Groups ◽  
Single Nucleotide ◽  
Content Type

Typing ofMycobacterium aviumsubspeciesparatuberculosisstrains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization ofMycobacterium aviumsubspeciesparatuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133Mycobacterium aviumsubspeciesparatuberculosisisolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPsMycobacterium aviumsubspeciesparatuberculosisisolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing ofMycobacterium aviumsubspeciesparatuberculosisisolates.

scholarly journals 1436. Use of Whole Genome Sequencing to Characterize Antimicrobial-resistant Salmonella Berta Isolates from Clinical and Retail Meat Sources

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S722-S723
Author(s):  
Nkuchia M M’ikanatha ◽  
Rachael Jacques ◽  
David Faucette ◽  
Dettinger Lisa ◽  
Kevin Libuit ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Isolates ◽  
Health Concern ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Retail Meat

Abstract Background Antimicrobial resistance (AMR) in foodborne pathogens of animal origin, including non-typhoidal Salmonella (NTS) are a public health concern. Pennsylvania conducts integrated surveillance for AMR in NTS isolates from human and animal sources in collaboration with the National Antimicrobial Resistance Monitoring System (NARMS). Methods During 2009-2014, Salmonella enterica isolates from various types of meat purchased from randomly selected retail outlets in southeastern Pennsylvania were analyzed by pulsed-field gel electrophoresis (PFGE). We compared PFGE patterns from meat with clinical isolates in the Pennsylvania surveillance database. All meat isolates and a subset of matched clinical isolates were tested for susceptibility to antimicrobial agents. Eleven isolates with indistinguishable PFGE patterns were analyzed by whole genome sequencing (WGS). Sequence data were uploaded to the FDA’s GalaxyTrakr platform for quality assessment, genome assembly, AMR gene detection, and phylogenetic inference via single-nucleotide polymorphism (SNP) analysis. Results PFGE patterns of 86 (48.6%) of 177 meat isolates had PFGE matches to 1,665 clinical isolates; 40 distinct PFGE patterns were represented among the shared patterns. Seventeen (43%) of the 40 shared PFGE patterns (with ≥1 isolate(s) from both sources) were considered multi-drug resistant (MDR). Among the 48 S. Berta pattern JAXX01.0001 isolates, 5 (10.9%) and 2 (100%) from human and meat sources respectively were MDR including resistance to amoxicillin and ceftriaxone. WGS analysis of one isolate from ground turkey meat (PNUSAS061602) was genetically related to clinical isolates including two within 9 and 11 SNPs [Figure]. Presence of genes that hydrolyze extended spectrum cephalosporins (ESC), [blaCMY, blaHERA, or blaTEM], was identified in eight (two meat and six clinical) isolates. One meat isolate was resistant to six antibiotics including ceftriaxone. Figure 2. Single nucleotide polymorphism (SNP) distance matrix showing relatedness in non-typhoidal Salmonella isolates from retail meat (n=2) and human (n=9) sources — Pennsylvania, 2010-2014. One S Berta from retail meat was separated from two clinical two clinical isolates by 9 and 11 SNPs. Second isolate from meat was separated from those associated with human infections by 14 (n=1), 17 (n=1) and ≥20 (n=7). Conclusion WGS analysis revealed clinically relevant ESCs genes in closely related S. Berta isolates from human and animal sources. Presence of these genes in NTS highlights the need for enhanced One-Health surveillance and judicious use of antibiotics in humans and food-animal production. Disclosures All Authors: No reported disclosures

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