Similar Datasets
Project description:Precise definition of porin profiles is of critical importance to understand the role of porins in antimicrobial resistance. In this study, the outer membrane proteins (OMP) profiles of 26 clinical isolates of Klebsiella pneumoniae and of strain ATCC 13883 (wild-type) and ATCC 700603 (producing SHV-18) have been determined using both sodium-dodecyl-sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization–time of flight/mass spectrometry (MALDI-TOF/MS). SDS-PAGE was performed using both homemade and commercial gels, and protein bands were identified by liquid chromatography coupled to mass spectrometry. A rapid extraction method was used to analyse OMPs by MALDI-TOF/MS. The sequences of porin genes were obtained by whole genome sequencing (WGS) and mutations were defined by BLAST. Same results were obtained for all strains either using SDS-PAGE or MALDI-TOF/MS. SDS-PAGE showed protein bands of ~35, ~36, and ~37 KDa, identified as OmpA, OmpK36 and OmpK35, respectively. By MALDI-TOF/MS, peaks at ~35700 (OmpA), ~37000 (OmpK35), and ~38000 (OmpK36) m/z were detected. ompK35 was intact in nine wild-type isolates and was truncated in 13 isolates, but OmpK35 was not observed in 3 isolates without mutations in ompK35. One point mutation was detected in another isolate and multiple mutations were detected in the remaining isolate. ompK36 was truncated in two isolates lacking this protein and presented one point mutation (n=1) or multiple mutations in the remaining isolates. In conclusion, MALDI-TOF/MS was reliable for porin detection, but because of the complex regulation of porin genes, WGS cannot always anticipate protein expression, as observed with SDS-PAGE and MALDI-TOF/MS.
2025-05-07 | PXD053879 | Pride
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:Antimicrobial resistance (AMR) arises from complex genetic and regulatory changes, including single mutations, gene acquisitions or cumulative effects. Advancements in genomics and proteomics facilitate more comprehensive understanding of the mechanisms behind antimicrobial resistance. In this study, 74 clinically obtained Klebsiella pneumoniae isolates with increased meropenem and/or imipenem MICs were characterized by broth microdilution and PCR to check for the presence of carbapenemase genes. Subsequently, a representative subset of 15 isolates was selected for whole genome sequencing (WGS) by Illumina and Nanopore sequencing, and proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) to investigate the mechanisms underlying the differences in carbapenem susceptibility of Klebsiella pneumoniae isolates. Identical techniques were applied to characterize 4 mutants obtained after sequential meropenem exposure. We demonstrated that in clinically obtained isolates, increased copy numbers of blaOXA-48 containing plasmids, combined with OmpK36 loss, contributed to high carbapenem MICs without involvement of OmpK35 or other porins or efflux systems. In the meropenem exposed mutants, increased copy numbers of blaCTX-M-15 or blaOXA-48 containing plasmids, combined with OmpK36 loss was demonstrated. The OmpK36 loss resulted from the insertion of IS1 transposable elements or partial deletion of the ompK36 gene. Additionally, we identified two mutations, C59A and C58A, in the DNA coding the copA antisense RNA of IncFII plasmids and multiple mutations of an IncR plasmid, associated with increased plasmid copy numbers. This study demonstrates that by combining WGS and LC-MS/MS, the effect of genomic changes on protein expression related to antibiotic resistance and the mechanisms behind antibiotic resistance can be elucidated.
2025-06-06 | PXD061983 | Pride
Project description:New and rapid diagnostic methods are needed for the detection of antimicrobial resistance to aid in the curbing of drug-resistant infections. Targeted LC-MS/MS is a method that could serve this purpose, as it can detect specific peptides of resistance mechanisms with high accuracy. In the current study, we aimed to develop an accurate, rapid and high-throughput targeted LC-MS/MS assay based on parallel reaction monitoring for detection of the most prevalent aminoglycoside modifying enzymes and 16S ribosomal RNA methyltransferases in E. coli and K. pneumoniae that confer resistance to the most commonly used aminoglycosides. Specific tryptic peptides needed for detection were selected and validated for AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6’)-Ib, AAC(6’)-Ib-cr, ANT(2”)-I, APH(3’)-VI, ArmA, RmtB, RmtC and RmtF. In total, 205 different isolates containing different aminoglycoside resistance mechanisms that consisted mostly of E. coli and K. pneumoniae were selected for assay development and validation. MS results were automatically analyzed and were compared to WGS results which were regarded as the reference. The average sensitivity and specificity for the detection of the different mechanisms by LC-MS/MS compared to WGS was 95.1 % and 98.0 %, respectively. Furthermore, MS results were also used to predict resistance and susceptibility to gentamicin, tobramycin and amikacin in only the E. coli and K. pneumoniae isolates (n=191). The category interpretations were correctly predicted for gentamicin in 97.4 % of the isolates, for tobramycin in 97.4 % of the isolates, and for amikacin in 82.7 % of the isolates. The current study shows that targeted LC-MS/MS can be applied for accurate and rapid detection of aminoglycoside resistance mechanisms.
2021-04-30 | PXD024339 | Pride
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
2018-06-26 | GSE105092 | GEO
Project description:We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
2020-03-02 | GSE117693 | GEO
Project description:We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
2020-03-02 | GSE117692 | GEO
Project description:We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
2020-03-02 | GSE116057 | GEO