Transcriptome sequencing (RNA-seq) is widely used to detect gene rearrangements and quantitate gene expression in acute lymphoblastic leukemia (ALL), but its utility and accuracy in identifying copy number variations (CNVs) has not been well described. CNV information inferred from RNA-seq can be highly informative to guide disease classification and risk stratification in ALL due to the high incidence of aneuploid subtypes within this disease. Here we describe RNAseqCNV, a method to detect large scale CNVs from RNA-seq data. We used models based on normalized gene expression and minor allele frequency to classify arm level CNVs with high accuracy in ALL (99.1% overall and 98.3% for non-diploid chromosome arms, respectively), and the models were further validated with excellent performance in acute myeloid leukemia (accuracy 99.8% overall and 99.4% for non-diploid chromosome arms). RNAseqCNV outperforms alternative RNA-seq based algorithms in calling CNVs in the ALL dataset, especially in samples with a high proportion of CNVs. The CNV calls were highly concordant with DNA-based CNV results and more reliable than conventional cytogenetic-based karyotypes. RNAseqCNV provides a method to robustly identify copy number alterations in the absence of DNA-based analyses, further enhancing the utility of RNA-seq to classify ALL subtype.
- MeSH
- algoritmy MeSH
- karyotypizace MeSH
- lidé MeSH
- sekvenování transkriptomu MeSH
- variabilita počtu kopií segmentů DNA * genetika MeSH
- vysoce účinné nukleotidové sekvenování * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Maskovaná hypertenze je definována jako normální hodnota krevního tlaku při měření v ordinaci a hypertenzní hodnoty zachycené mimo ni. Její prevalence bývá uváděna kolem 15 %. Častěji bývá přítomna u osob, které měly v ordinaci naměřený tlak krve v pásmu vysokého normálního tlaku krve, tedy 130–139/80–89 mmHg. Dále je její výskyt častější u mužů, kuřáků. Pojí se rovněž s konzumací alkoholu, stresem na pracovišti, obezitou, diabetem nebo chronickým onemocněním ledvin. Kardiovaskulární morbidita a mortalita pacientů s maskovanou hypertenzí se téměř blíží té při setrvalé hypertenzi. Vhodnou metodou pro její screening je ambulantní 24hodinové monitorování krevního tlaku. Doporučení Evropské kardiologické společnosti a American College of Cardiology/American Heart Association uvádí jako jednoznačnou indikaci ke screeningu maskované hypertenze přítomnost orgánových komplikací spojených s hypertenzí u jedinců, kterým hypertenze dosud diagnostikována nebyla. Jasná doporučení stran terapie maskované hypertenze prozatím vydána nejsou, terapie je tedy empirická.
Masked hypertension is defined as normal level of blood pressure when measured in doctor's office and hypertension levels outside of it. Prevalence is usually reported to be around 15%. It is more often detected among patients who had pressure measured in the office at the upper limit of normal blood pressure, or 130–139/80–89 mmHg. More common occurrence is among men, smokers. It is associated with alcohol consumption, stress in workplace, obesity, diabetes or chronic kidney disease. Cardiovascular morbidity and mortality in patients with masked hypertension are almost close to those with persistent hypertension. The recommendations of the European Society of Cardiology and the American College of Cardiology/American Heart Association state that the presence of organ complications associated with hypertension in individuals who have not yet been diagnosed with hypertension as a clear indication for screening of masked hypertension. There haven't been issued any clear recommendation for masked hypertension, hence therapy is empirical.
- Publikační typ
- abstrakt z konference MeSH
