Introduction to NGS - Course list- DTU Health TechDTU Sundhedsteknologi Introduction to NGS Summary...

Introduction to NGS

Gisle VestergaardAssociate Professor

Section of BioinformaticsTechnical University of Denmark

[email protected]

DTU Health Technology Bioinformatics

DTU Sundhedsteknologi3. juni 2019 Introduction to NGS

Menu• Why are you all here today?• Why NGS?• How?• Why do we need bioinformatics for NGS?

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Life science data deluge

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• Massive unstructured data from several areas DNA, patient journals, proteomics, imaging, ...

• Impacts Industry, Environment, Health

• Societal grand challenges• Cheap sequencing technologies

results in explosion of DNA data

DTU Sundhedsteknologi3. juni 2019 Introduction to NGS 5

Reading the order of bases in DNA fragments

DNA sequencing


Why NGS?

Transforming how we are doing biological science (and bioinformatics)

By

allowing experiments that could not have beendone before, and perform experiments much faster

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How ?

by producing massive amounts of sequence data, really fast

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First generation: Sanger• Fragment DNA• Clone into plasmid and amplify• DNA polymerase and only 1 primer• Sequence using dNTP + labelled ddNTPs (stops reaction)• Early method used radioactive labels, later came fluorescent tags• Run capillary electrophoresis/gel and “read” DNA code• Low output, long reads (~800-1200 nt), high quality

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1st generation to NGS

• 454 Life Sciences. Bought by Roche 2007. Shut down 2013

• Illumina is currently cheapest per GB• Long-read sequencing outputs about 100 GB

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Sequencing costs

• Computer speed and storagecapacity is doubling every18 months and this rate is steady

• DNA sequence data is doubling faster thancomputer speeds!

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Human sequencing

• First draft genome of human in 2001, final 2004• Estimated costs $3 billion, time 13 years

• Today:–1000-2000$ for one genome–A couple of days!

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Storage and analysis• Cost of sequencing is comparable to cost of storage and

analysis• One Illumina HiSeq X Ten system: 18,000 human genomes

per year!• A standard human (30-40x) whole-genome sequencing exp.

would create 150 Gb of data

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Distributed data production

• World wide >900 centers• >60 Pb pr year (2014)• Data transfer and storage

becomes an issue

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The X Genomes projects

• Human population projects–1000 genomes project (2500 individuals)–Genomics England (100k individuals)–US Precisions medicine (1 million individuals)

• 100K pathogens project, Earth Microbiome project, Cancer genome project, Plants and animals, Insects,…

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NGS in the clinic• Diagnostics of patients (+ fetus)• Focused treatment of cancer patients• Sequencing of bacterial isolates• Country-wide projects:• UK, US, Qatar, Finland, China, …• DK: Danish regions want to sequence 100k individuals

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Personalized medicine

• Personalized medicine initiative in DK• Up to 70% of medicine does not work!• Sequence 100,000 patients on hospitals• Use extensive registry data• Current: 100 mill DKK (estimated 2 bill DKK)• National Genomics Institute

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NGS & bioinformatics

• Extreme data size causes problems• Just transferring and storing the data• Standard comparisons fail (N*N)• Standard/old tools can not be used• Think in fast and parallel programs

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Novel technology allows novel questions

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What can we use it for?

• Whole genome re-sequencing• Population genomics• Diagnostics • Cancer genomics• Ancient genomes• Metagenomics• RNA sequencing• Single cell sequencing• Genomic Epidemiology• anything with DNA

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Main pitfall of NGS• Finding a needle in a haystack is difficult…especially if you do not know that you are

looking for a needle

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Summary

• Bioinformatic knowledge is needed to handle the amount of data• Sequencing technology keeps getting better, both in wet and dry

labs• Metagenomic data does no longer just describe genetic potential

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How it works

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Slide Number 1Slide Number 2MenuLife science data delugeSlide Number 5Why NGS?How ?First generation: Sanger1st generation to NGSSequencing costsHuman sequencingStorage and analysisDistributed data productionThe X Genomes projectsNGS in the clinicPersonalized medicineNGS & bioinformaticsNovel technology allows novel questionsWhat can we use it for?Main pitfall of NGSSummaryHow it works

Introduction to NGS - Course list- DTU Health TechDTU Sundhedsteknologi Introduction to NGS Summary...

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