Module lead: Prof Jean-Baptiste Cazier

Module code: 01 27584

Credits: 15

Attendance: Teaching delivered on Mondays for five consecutive weeks

Module dates: 11 June – 9 July 2018

Learning hours: 150 hours – teaching and private study

The module will cover the fundamental principles of informatics and bioinformatics applied to clinical genomics, find and use major genomic and genetic data resources; use software packages, in silico tools, databases and literature searches to align sequence data to the reference genome, critically assess, annotate and interpret findings from genetic and genomic analyses. Theoretical sessions will be coupled with practical assignments of analysing and annotating predefined data sets. This is a core module that is central to the MSc programme in Genomic Medicine as it will provide the student with the skills to analyse genomic data. Upon completion of this module students will be eligible to base their MSc research project on data from the 100,000 Genomes Project data set.

By the end of the module students should be able to:

  • Analyse the principles applied to quality control of sequencing data, alignment of sequence to the reference genome, calling and annotating sequence variants, and filtering strategies to identify pathogenic mutations in sequencing data
  • Interrogate major data sources, e.g. of genomic sequence, protein sequences, variation, pathways, (e.g. EVS, dbSNP, ClinVar, etc.) and be able to integrate with clinical data, to assess the pathogenic and clinical significance of the genome result
  • Acquire relevant basic computational skills and understanding of statistical methods for handling and analysing sequencing data for application in both diagnostic and research settings
  • Gain practical experience of the bioinformatics pipeline through the Genomics England programme
  • Justify and defend the place of Professional Best Practice Guidelines in the diagnostic setting for the reporting of genomic variation

Assessment: The module will be assessed via a short presentation and an exam made up of multiple-choice questions and a choice of essay (essay submission date and exam, typically around five-six weeks after the teaching).