Characterising cellular phenotypic heterogeneity is essential to understand the relationship between the molecular and morphological determinants of cellular state. Here we report that publicly available self-supervised vision transformers (ss-ViTs) accurately elucidate phenotypic stem cell heterogeneity out-of-the-box. Moreover, we introduce scDINO, an adapted ss-ViT trained on five-channel automated microscopy data, attaining excellent performance in delineating peripheral blood immune cell identity. Thus, ss-ViTs represent a leap forward in the unsupervised analysis of phenotypic heterogeneity.
Aligning protein isoform sequences is often performed in cancer diagnostics to homogenise mutation annotations from different diagnostic assays. However, most alignment tools are fitted for homologous sequences, leading often to alignments of non-identical exonic regions. Here, we present the interactive alignment webservice IsoAligner for exact mapping of exonic protein subsequences. The tool uses a customized Needleman-Wunsch algorithm including an open gap penalty combined with a gene-specific minimal exon length function and dynamically adjustable parameters. As an input, IsoAligner accepts either various gene/transcript/protein IDs from different databases (Ensembl, UniProt, RefSeq) or raw amino acid sequences. The output of IsoAligner consists of pairwise alignments and a table of mapped amino acid positions between the canonical or supplied isoform IDs and all alternative isoforms. IsoAligner’s human isoform library comprises of over 1.3 million IDs mapped on over 120,000 protein sequences. IsoAligner, is a fast and interactive alignment tool for retrieving amino acids positions between different protein isoforms. Its application will allow diagnostic and precision medicine labs to detect inconsistent variant annotations between different assays and databases. Availability: This tool is available as a Webservice on www.isoaligner.org. A REST API is available for programmatic access. The source code for both services can be found at https://github.com/mtp-usz/IsoAligner.
PURPOSE Comprehensive targeted next-generation sequencing (NGS) panels are routinely used in modern molecular cancer diagnostics. In molecular tumor boards, the detected genomic alterations are often discussed to decide the next treatment options for patients with cancer. With the increasing size and complexity of NGS panels, the discussion of these results becomes increasingly complex, especially if they are reported in a text-based form, as it is the standard in current molecular pathology. METHODS We have developed the Molecular Tumor Profiling pilot ( MTPpilot) webservice using HTML, PHP, JavaScript, and MySQL to support the clinical discussion of NGS results at molecular tumor boards. RESULTS MTPpilot integrates various public genome, network, and cancer mutation databases with interactive visualization tools to assess the functional impact of mutations and support clinical decision making at tumor boards. CONCLUSION MTPpilot is tailored for discussion of NGS gene panel results at molecular tumor boards. It is freely available as a webservice at MTPpilot.
Comprehensive targeted Next Generation Sequencing (NGS) panels are routinely used in modern molecular cancer diagnostics. In molecular tumor boards the detected genomic alterations are often discussed to decide the next treatment options for the cancer patient. With the increasing size and complexity of NGS panels, the discussion of these results becomes increasingly complex, especially if they are reported in a text-based form, as it is the standard in current molecular pathology. We developed the Molecular Tumor Profiling pilot (MTPpilot) software to enable an efficient and quick analysis and visualization of complex NGS results, thanks to a combination of automated annotations and interactive tools. The software is tailored for the use at molecular tumor boards to aid clinical decision making. It is freely available as a web-application at https://www.mtppilot.org.
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