Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1136681 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29850855_1.fastq.gz | Fastqsanger.gz | |||
| SRR29850855_2.fastq.gz | Fastqsanger.gz | |||
| SRR29850856_1.fastq.gz | Fastqsanger.gz | |||
| SRR29850856_2.fastq.gz | Fastqsanger.gz | |||
| SRR29850857_1.fastq.gz | Fastqsanger.gz |
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Project description:Genetic abnormalities including copy number variants (CNVs, such as gains and losses), and gene mutations are important for diagnosis and treatment of myeloid malignances. In a routine clinical setting, somatic gene mutations are detected by targeted next generation sequencing (NGS), but CNVs are commonly detected by conventional chromosome analysis and fluorescence in situ hybridization (FISH). The aim of this proof-of-principle study was to investigate the feasibility of using a targeted NGS assay to simultaneously detect not only somatic mutations, but also CNVs. Here, we sequenced 406 consecutive patients with myeloid malignancies and performed a head-to-head comparison with the results from conventional clinical assays including conventional chromosome analysis and myeloid FISH to detect CNVs. The targeted NGS assay revealed all 120 CNVs detected by myeloid FISH panel including monosomy 5/5q deletions, monosomy 7/7q deletions, trisomy 8, and 20q deletions. Furthermore, the targeted NGS assay also detected 605 CNVs outsides targeted regions of the myeloid FISH panel, which were revealed by conventional cytogenetic testing. The targeted NGS assay achieved 100% concordance with the myeloid FISH for detection of these common myeloid CNVs, with a high clinical sensitivity (> 99%) and specificity (>99%). The lower limit of detection by the myeloid FISH and the targeted NGS assay was similar and was generally 5% variant allele fraction for DNA. This proof-of-principle study demonstrated that the targeted NGS assay can simultaneously detect both common myeloid CNVs and somatic mutations, which can provide more comprehensive genetic profiling for patients with myeloid malignancies using a single assay.
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Project description:Copy number alterations (CNAs) play a fundamental role in cancer development and constitute a potential tool for tailored treatments. The CNAs recognition in formalin fixed paraffin embedded (FFPE) material, to date, relies on fluorescence in situ hybridization, but the introduction of large-scale next-generation sequencing (NGS) has dramatically improved their discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. Herein, the CNAs detection by a widely used NGS assay (Oncomine Comprehensive Assay plus®, OCA+) were evaluated in 14 FFPE samples mirroring diagnostic daily practice and compared to a whole-genome assay. OCA+, a targeted DNA panel, showed lower CNAs detection sensitivity and equal specificity for gains and losses. According to proprietary software pipeline, OCA+ accurately identify gains characterized by CN ≥5,2. A much less robust threshold (CN ≤1.18) was identified that maximized the difference between true and false positive losses. Orthogonal FISH tests validated seven CNAs characterized by CN gain ≥6 or complete loss. Considering the CNAs growing significance in precision medicine, our findings further prompt towards a robust validation of NGS detection in FFPE materials.
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Project description:The present study was aimed at analyzing (i) the biological cost of RNA polymerase (rpoB) mutations conferring rifampin resistance on H.pylori, (ii) the relationship between the cost of rpoB mutations and the chromosomal mutaion, (iii) the relationship between the cost of rpoB mutations and the transcription profile of sensitive and resistantrif strains of H.pylori (iv) and rpoB mutations in view of the possible fitness burden associated with resistance to another antibiotics. H.pylori reference strain 26695 was routinely maintained on Columbia agar plates and H. pylori-selective antibiotic mix Dent. Liquid culture was grown in BHI broth. Both plates and broth cultures were incubated at 37C under atmosphere enriched with 5% CO2 for 2-3 days . Mutant strains were selected by culturing H. pylori 26695 on selective plates containing rifampicin. In 5 days resistant colonies were picked up and passed under rifampicin pressure. RNA isolated was reverse transcribed and used to probe H. pylori home-made arrays
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