Minigene splicing assay of patients synonymous substitutions.

<p>Effect of synonymous <i>BRCA1</i> substitutions on splicing products full-length, D(11q) and D(11). RT-PCR products from transfection experiments using mutated minigenes are shown.</p

Minigene splicing assay of BRCA1 exon 11.

<p><b>A</b>. Sequence of the critical region in exon 11 showing the deletion 1,2,3,4 (highlighted). The donor site (5′ss) generating D11q isoform is boxed. Arrows indicate nucleotide positions of the variations reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037255#pone-0037255-g002" target="_blank">Figure 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037255#pone-0037255-g003" target="_blank">3</a> to affect splicing. <b>B</b>. Transient transfection results for the hybrid minigenes carrying deletions.</p

Minigene splicing assay of BRCA1 exon 11.

<p><b>A</b>. The pB1 wild type (WT) version of the minigene is shown. PCMV = promoter of the pCDNA3 vector. ATG = start codon. TAG = stop codon. +3C = insertion of cytosine as the third nucleotide in exon 8. pA = poly A signal. 1 = exon 1 of the alfa globin gene. BRCA1 exons from 8 to 12 are numbered. The black solid line represents introns. Dotted lines show alternative splicing of exon 11. <b>B</b>. The three splicing isoforms FL, D11q and D11 and the position of specific oligos used for detection, are shown. <b>C</b>. Detection of BRCA1 exon 11 splicing isoforms for: _MCF7 endogenous BRCA1 (endogenous WT). _pB1 WT minigene transfected in MCF7 (pB1 WT). _pB1 minigene carrying the c.696G>A nucleotide substitution transfected in MCF7 (pB1 c.696G>A).</p

DataSheet_1_Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19.docx

BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.</p