Introduction to NGS

Innovation Scholar UK:

Omics Pillar
Alexandre Thiery
Eva Hamrud
Centre for Craniofacial and Regenerative Biology
What are the applications of NGS?
Learning Objectives:
• Refresher on the central dogma of biology and its main players: DNA,
RNA and proteins
• Understand the difference between de novo genome assembly and
reference-based genome assembly
• Appreciate the advantage of having a reference genome
• Explore some of the potential applications of resequencing genomes
Sequencing: identifying the sequence of
nucleotides in a length of DNA

https://www.genome.gov/genetics-glossary/acgt
Refresher: Central Dogma of Biology
Applications of whole genome sequencing (WGS)
- De novo genome assembly

https://www.hudsonalpha.org/sequencing-from-scratch-reference-genomes-and-de-novo-sequence-assembly/
Reference genomes

https://www.yourgenome.org/facts/timeline-organisms-that-have-had-their-genomes-sequenced/
WGS applications that make use of reference genomes
Genome assembly can make use of a reference

https://www.futurelearn.com/info/courses/making-sense-of-genomic-data-covid-19-web-based-bioinformatics/0/steps/319527
Some applications of resequencing

Investigating evolutionary relationships Variant detection

https://www.ebi.ac.uk/training/online/courses/human-genetic-
variation-introduction/variant-identification-and-analysis/

https://www.yourgenome.org/facts/what-is-phylogenetics/
WGS often generates too much data!

https://www.nature.com/articles/478022a
Central Dogma of Biology – what else can NGS help
us study?
If you culture cells in different conditions, they
change which genes they express
Whole transcriptome sequencing – RNA-seq

https://www.1010genome.com/transcriptome-analysis-applications/
Some examples of RNA-seq applications

Differentiating cells Drug testing Disease progression

Addition of drug
Central Dogma of Biology – what else can NGS help
us study?
Refresher: Transcription
Refresher: Transcription
Refresher: DNA packaging

https://evolutionnews.org/2021/09/hierarchical-systems-in-biology-dna-packaging/
Central Dogma of Biology – what else can NGS help
us study?
Looking for open chromatin: ATAC-seq
Looking for proteins bound to DNA: CUT&TAG

https://www.nature.com/articles/s41596-020-0373-x
Combining different modalities
Summary of NGS approaches and potential uses:
• To look at genetic differences between samples:
• Whole genome sequencing
• Exome sequencing
• Single gene sequencing

• To look for gene expression differences between samples:

• RNA-seq

• To look for transcriptional control differences between samples:

• CUT&TAG
• ATAC-seq
Resources
• Organisms that have had their genomes sequenced: https://www.yourgenome.org/facts/timeline-
organisms-that-have-had-their-genomes-sequenced/
• Genome assembly: https://www.futurelearn.com/info/courses/making-sense-of-genomic-data-covid-19-
web-based-bioinformatics/0/steps/319527
• Phylogenetic trees: https://www.yourgenome.org/facts/what-is-phylogenetics/
• Variant calling: https://www.ebi.ac.uk/training/online/courses/human-genetic-variation-
introduction/variant-identification-and-analysis/
• Nature article about genome sequencing in medicine: https://www.nature.com/articles/478022a
• ATAC-seq: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/
• CUT&TAG: https://www.nature.com/articles/s41596-020-0373-x