Characterising genomic and epigenomic variants in tumour-normal research samples: data analysis
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During this Knowledge Exchange, Philipp Rescheneder, Director, Genomic Applications Bioinformatics, and Andrea Talenti, Bioinformatics Workflow Developer, will describe how to analyse genomic and epigenomic variation in tumour-normal nanopore sequencing data from cancer research samples. Following on from the 'How to perform tumour-normal sequencing' masterclass, Philipp will begin by introducing how long nanopore sequencing reads of native DNA can be used to accurately identify structural variants (SVs), methylation differences, single nucleotide variants (SNVs), and copy number variants (CNVs) between matched tumour-normal research samples. He will also explain how long nanopore sequencing reads can be used to assign variants to a haplotype.
Andrea will then describe how data from a single sequencing run can be used to detect SVs, methylation, and SNVs using the dedicated EPI2ME analysis pipeline, wf-somatic-variation, from Oxford Nanopore. Starting from the beginning and including everything needed to begin your analyses, Andrea will demonstrate how to run a dataset using the command-line interface and explain both the basic and advanced features of the analysis pipeline, to suit different levels of expertise. He will also highlight the output files and reports generated at the end of the analysis, and discuss upcoming developments.
Meet the speakers
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Philipp Rescheneder, Director, Genomic Applications Bioinformatics, Oxford Nanopore TechnologiesPhilipp Rescheneder works as a bioinformatician in the Applications team at Oxford Nanopore. He and his teams identify, benchmark, and adapt the most appropriate tools and workflows for analysing Oxford Nanopore data in the context of a wide range of applications, including variant calling, assembly and modification calling. Furthermore, he is responsible for transferring this knowledge to enable pilot and proof of concept experiments showing the applicability of nanopore sequencing to existing and novel use cases.
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Andrea Talenti, Bioinformatic Workflow Developer, Oxford Nanopore TechnologiesAndrea Talenti works as a workflow developer in the Customer Analysis Workflows at Oxford Nanopore. Here, he contributes to the implementation of the life sciences workflows.
