NGS bioinformatics quality control and variant annotation for cancer diagnosis - November 2019
Section outline
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NGS bioinformatics quality control and variant annotation for cancer diagnosis
Bern, 12 November 2019
This page is addressed to registered participants. To access course description and application form, please click here. For any assistance, please contact training@sib.swiss. -
Venue: University of Bern, Hochschulstrasse 4, main building, classroom 028 (ground floor)
Schedule: from 9h15 to 17h15, with a lunch break and 2 coffee breaks.PARTS I & II: NGS BIOINFORMATICS PIPELINE & QUALITY CONTROL (QC)
09:15-10:30 - Why are we doing this?
- Overview of a bioinformatics analysis pipeline:- FASTQ and PHRED scores
- Reference genome, alignment concepts, and the BAM file format
- Sequencing depth, coverage
- VCF, BED formats
- Variant annotation (from DNA to HGVS)
- QC throughout the NGS pipeline
- Variant-level QC: common measures and thresholds for IonTorrent and Illumina10:30-10:45 Coffee break
10:45-11:15 Example study case presented on OncoBenchTM
11:15-12:15 Hands-on: Spotting data artifacts among true variants (in groups of 2-3 people, 2 patients)
12:15-12:45 Presentation/Discussion of the results
12:45-13:45 Lunch break
PART III: ANNOTATION
13:45-15:00
- Clinical significance: pathogenicity & actionability
- Annotation using literature and other public databases: essentials and extras
- From variant to gene, assessing functional impact:- Existing tools and when (not) to use them
- Variant effects on the protein
- Genes, transcripts and HGVS nomenclature
15:00-15:15 Coffee break
15:15-16:15 Study case – Annotation using bioinformatics tools and public databases (in groups of 2-3 people, 2 patients)
16:15-17:00 Presentation/Discussion of the results
17:00-17:15 Wrap-up of the course and take-home messages
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Download slides below
Additional reading
- The Association for Molecular Pathology together with the American Society of Clinical Pathology and the College of American Pathologists recently released a set of guidelines for the interpretation and annotation of somatic variant in cancer: Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer
- How much depth is enough? This is explained in Figure 2 of the Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels.
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OncoBench interface: https://oncobench-demo.vital-it.ch/#/loginHANDS-ON SESSION - Quality controlHANDS-ON SESSION - AnnotationUSER: g13password: Lziexa64suvQ0OW