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Galaxy Molecular Pathology: Adaptive Analysis & Image Algorithms

Explore quantitative image analysis methods for Adrenocortical Carcinoma (ACC) using Galaxy's Adaptive Step Finding Algorithm. Develop new Ki67 evaluation practices & hotspot detection tools.

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Galaxy Molecular Pathology: Adaptive Analysis & Image Algorithms

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  1. Molecular Diagnostics Digital Pathology Molecular Pathology

  2. Galaxy ...... a Data Analysis Platform for end users…. http://galaxyproject.org/

  3. Quantitative Digital Image Analysis Adaptive Step Finding Algorithm • Adrenocortical Carcinoma (ACC) Ki67 • Determine best practice for Ki67 evaluation • Develop Galaxy Digital Hotspot Detection and • Quantitation • Science Driven PoC Adrenocortical Carcinoma Thomas Popathomas & WinandDinjens

  4. Galaxy: Adaptive Selection of Hotspots Adrenocortical Carcinoma Thomas Popathomas & WinandDinjens

  5. Trait over view Scientifc problems – n is one and cohort analysis and cell line use case NGS Bioinformatics Adapt and Adopt (Bio)informatics Solutions Transcriptome Informatics technology Data Production Technology Genome Transcriptome sequencing (RNAseq) Whole Genome (DNAseq) Map Sequence Reads Identify Fusions [Reference set] Select variants [Reference set] Quantify Expression Identify Fusions Call variants Gene Fusions Copy Number (Somatic) Variants Gene / Transcript expression Gene Fusions (Somatic) Variants

  6. Genome Analysis Genome Whole Genome (DNAseq) http://bioinf-galaxian.erasmusmc.nl/galaxy Identify Fusions [Reference set] Select variants [Reference set] Fusion Genes Copy Number (Somatic) Variants (Somatic) Variants Fusion Genes Copy Number

  7. Practical Session Aims Assess read quality NGS Mapping Variant calling Exonic Variant Selection Prioritization by impact

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