University of Lausanne

VIC Tech forms i-Seq Biotechnology to develop broad-spectrum vaccines and therapeutics using CRISPRi-Seq, aiming to address global infectious disease challenges.

NeoDisc installation requires registration and manual guidance. DNA reads are aligned using GATK best practices, processed with bwa, and quality assessed. CNV and tumor content are estimated with Sequenza, using PCAWG CNV frequencies. Variant calling is performed with Mutect, VarScan, and GATK tools. High-confidence variants are defined by consensus among multiple algorithms. Clonality analysis uses SAMtools mpileup for VAF calculation. RNA reads are aligned with STAR for gene expression quantification. HLA typing is done with HLA-HD, and HLA LOH analysis involves CN estimation and statistical tests. Noncanonical genes are defined based on expression levels. TAAs and HC-TSAs are identified and prioritized using specific algorithms. Viral peptides are predicted and filtered for tumor specificity. Sample-specific proteomes are created, and neoantigen prediction relies on personalized proteome filtering. Prioritization of TSAs uses ML and rule-based algorithms. APPM analysis assesses HLA presentation machinery gene expression. Inflammation scores are calculated from RNAseq data. MS/MS spectra are converted and peptides are identified with Comet, NewAnce, and FragPipe. Combined peptide identifications are filtered and annotated. Tools for NeoDisc benchmarking include pTuneos, pVACtools, and LOHHLA. Sample collection and preparation for sequencing are detailed. Flow cytometry and FACS are used for tumor cell isolation. Peptide purification, LC-MS, and immunogenicity assessment of TIL cultures are described. Antigen and tumor reactivity are validated by TCR cloning. mIF staining and CD8+ T cell infiltration assessment are detailed. A reporting summary provides further research design information.

One in three former NFL players believe they have CTE, reporting more brain function issues, depression, and suicidal thoughts, compared to those without such beliefs.