An Introduction to the Analysis of the Next-generation Sequencing Data [EL019]

Detailed information about this course:

Description

This course introduces working with Next-Generation Sequencing (NGS) data. It targets individuals who have access to NGS data and want to learn how to work with this data and what the possibilities and limitations of NGS are. Lectures will be complemented with practical sessions in which the student will gain hands-on experience with various tools and techniques. Subjects that will be covered include:

• NGS: an introduction to methodology and techniques;
• Basic statistics of NGS data, e.g. coverage;
• Aligning the sequence reads;
• Calling and interpreting DNA variants;
• Dealing with common NGS tools (samtools, VCFtools, GATK);
• Evaluating functional effects of the genetic variants on proteins;
• Single variant and Collapsed genotype analyses with various tools (e.g. seqMeta, RAREMETAL and RVtest);
• Analyze rare variants in families and population based studies for complex phenotypes;
• Imputation of sequence variants.
• Introduction and examples of NGS applications outside of DNA sequencing, such as in epigenomics, transcriptomics, and microbiomics

See 'how to apply' for the course registration period.

Objectives

• Understand the main principles of genome sequencing technologies, data preparation, control and data analysis.
• Acquire tools and skills in Linux to analyze NGS data through the command line using dedicated tools and software for NGS data processing, variant calling, and quality control.
• Learn the principles of NGS data analysis in family-based studies and clinical case collections of monogenic and oligogenic disorders.
• Grasp the potential and drawbacks of applying genome sequencing technologies in population-based studies of complex traits.
• Understand the main principles of NGS data generation and analysis across other "–omics" layers, transcriptome, epigenome, microbiome.

Participant profile

Clinical researchers, clinical epidemiologists, molecular biologists, bioinformaticians and biostatisticians aspiring to run sequencing-based data analyses by themselves, or work with next-generation sequencing data and want to know how this is typically created. Affinity with scripts is suggested, as the practical sessions cover technical topics. Basic understanding of genetics is required, such as the different types of DNA variants, inheritance patterns, the concept of gene regulation and expression. These topics will be repeats briefly in class but not explained at length. Contact the coordinator for details.

Assessment

Assignment(s), Attendance