Single-cell RNA sequencing (scRNA-Seq) enables researchers to quantify the transcriptomes of individual cells. The capacity of researchers to perform this type of analysis has allowed researchers to undertake new scientific goals. The usefulness of scRNA-Seq has depended on the development of new computational biology methods, which have been designed to meeting challenges associated with scRNA-Seq analysis. However, the proper application of these computational methods requires extensive bioinformatics expertise. Otherwise, it is often difficult to obtain reliable and reproducible results. We have developed SingleCAnalyzer, a cloud platform that provides a means to perform full scRNA-Seq analysis from FASTQ within an easy-to-use and self-exploratory web interface. Its analysis pipeline includes the demultiplexing and alignment of FASTQ files, read trimming, sample quality control, feature selection, empty droplets detection, dimensional reduction, cellular type prediction, unsupervised clustering of cells, pseudotime/trajectory analysis, expression comparisons between groups, functional enrichment of differentially expressed genes and gene set expression analysis. Results are presented with interactive graphs, which provide exploratory and analytical features. SingleCAnalyzer is freely available at https://singleCAnalyzer.eu.
Trisomy 8 (+8) is the most frequent trisomy in myelodysplastic syndromes (MDS) and is associated to clinical heterogeneity and intermediate cytogenetic risk when found isolated. The presence of gene mutations in this group of patients and the prognostic significance has not been extensively analyzed. Targeted-deep sequencing was performed in a cohort of 79 MDS patients showing isolated +8. The more frequent mutated genes were: TET2 (38%), STAG2 (34.2%), SRSF2 (29.1%) and RUNX1 (26.6%). The mutational profile identified a high risk subgroup with mutations in STAG2, SRSF2 and/or RUNX1, resulting in shorter time to acute myeloid leukemia progression (14 months while not reached in patients without these mutations, p<0.0001) and shorter overall survival (23.7 vs 46.3 months, p=0.001). Multivariate analyses revealed the presence of mutations in these genes as an independent prognostic factor in MDS showing +8i (HR: 3.1; p<0.01). Moreover, 39.5% and 15.4% of patients classified as low/intermediate risk by the IPSS-R and IPSS-M, respectively were re-stratified as high risk subgroup based on the mutational status of STAG2, SRSF2 and RUNX1. Results were validated in an external cohort. In summary, the mutational profile in isolated +8 MDS patients could offer new insights for the correct management of these patients.
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