AI for clinical Genomics

Syllabus Overview

NGS data analysis – FIVE weeks program

About the course: NGS has brought a paradigm shift in the field of medicine and agriculture. It enabled to look into whole genome of an organism to identify impact of variants on disease. It became necessary for a biologist to understand NGS technology in order to have better understanding on disease pathology, diagnosis and suggesting a therapeutic recommendation.

The course aims to provide glimpse of NGS analysis tools with live examples on open source data.

Week 1

Theory

·        Introduction NGS data analysis (What is NGS? Applications – Genomics, Transcriptomics, Metagenomics and Epigenomics. Basic infrastructure requirement for NGS; NGS Data and analysis tools resources on Web – NCBI; NGS analysis steps)

·        NGS raw data  retrieval from SRA and ENA and Quality Control

Practical

·        NGS Data retrieval from SRA/ENA

·        Linux commands and R

·        Quality control: FastQC, fastp, MultiQC and Trimmomatic

·        Galaxy sever – NGS QC

Assignment 1

NGS data retrieval for a disease of interest and QC report of reads

Week 2

Theory

·        Read mapping, coverage analysis and visualization

·        Variant Calling and annotation

Practical

·        Read alignment and coverage analysis BWA and deeptools

·        Variant Calling and annotation: Genome Analysis Tool Kit and SNPSIFT

Assignment 2

Perform read mapping with reference, coverage analysis, variant calling

Week 3

Theory

·        Variant from NGS studies and its applications

·        Whole exome – Germline variant calling

·        Somatic variant calling

Practical

·        Variant impact prediction, filtering and visualization in IGV

Assignment 3

·        Call germline variants from an exome sample of your interest and visualize in IGV.

Week 4 Genome Assembly and annotation

Theory

·        De novo genome assembly, annotation, draft genome construction.

·        Multiple sequence alignment and extracting cold spot regions in the consensus genome.

·        Metagenomics

Practical

·        De novo genome assembly, annotation

·        Consensus genome construction and genome annotation – prokka

·        In silico vaccine design and drug target identification

·        QIIME

Assignment 4 – Perform de novo assembly on a virus/bacteria NGS sample

Week 5 Gene expression analysis - RNAseq

Theory

·        RNAseq concept.

·        Identifying potential drug targets/biomarkers from gene expression data

Practical

·        Bioconductor

·        Differential gene expression analysis – hisat2, stringtie and limma

·        Protein-protein interaction analysis

·        Gene ontology and pathway enrichment

QUIZ

Projects