FBW29-09-2011

Wim Van Criekinge

What is Bioinformatics ?

• Application of information technology to the storage, management and analysis of biological information (Facilitated by the use of computers)– Sequence analysis?– Molecular modeling (HTX) ?– Phylogeny/evolution?– Ecology and population studies?– Medical informatics?– Image Analysis ?– Statistics ? AI ?– Sterkstroom of zwakstroom ?

• Medicine (Pharma)– Genome analysis allows the targeting of genetic

diseases– The effect of a disease or of a therapeutic on RNA and

protein levels can be elucidated– Knowledge of protein structure facilitates drug design– Understanding of genomic variation allows the tailoring

of medical treatment to the individual’s genetic make-up

• The same techniques can be applied to crop (Agro) and livestock improvement (Animal Health)

Promises of genomics and bioinformatics

Bioinformatics: What’s in a name ?

• Begin 1990’s• “Bio-informatics”:

Computing PowerGenbank(Log)

Time (years)

Bioinformatics: What’s in a name ?

• Begin 1990’s• “Bio-informatics”:

– convergence of explosive growth in biotechnology, paralled by the explosive growth in information technology

• Not new: > 30 years that people use “computers” in biology

• In silico biology, database biology, ...

Time (years)

Happy Birthday …

PCR + dye termination

Suddenly, a flash of insight caused him to pull the car off the road and stop. He awakened his friend dozing in the passenger seat and excitedly explained to her that he had hit upon a solution - not to his original problem, but to one of even greater significance. Kary Mullis had just conceived of a simple method for producing virtually unlimited copies of a specific DNA sequence in a test tube - the polymerase chain reaction (PCR)

Math

Informatics

Bioinformatics, a scientific discipline …

Theoretical Biology

Computational Biology

(Molecular)Biology

Computer Science

Bioinformatics

Math Algorithm Development

Informatics

Interface Design

Bioinformatics, a scientific discipline …

AI, Image Analysisstructure prediction (HTX)

Theoretical Biology

Sequence Analysis

Computational Biology

(Molecular)Biology

Expert Annotation

Computer Science

NPDatamining

Bioinformatics

Math Algorithm Development

Informatics

Interface Design

Bioinformatics, a scientific discipline …

AI, Image Analysisstructure prediction (HTX)

Theoretical Biology

Sequence Analysis

Computational Biology

(Molecular)Biology

Expert Annotation

Computer Science

NPDatamining

BioinformaticsDiscovery Informatics – Computational Genomics

Doel van de cursus

• Meer dan een inleiding tot ... het is de bedoeling van de cursus een onderliggend inzicht te verschaffen achter de verschillende technieken.

• Naast het gebruik van recepten, wat terug te vinden is in delen van de syllabus laat een inzicht in – de werking van databanken – en de achterliggende algoritmen

• toe – om wisselende interfaces op nieuwe

problemen toe te passen.

Inhoud Lessen: Bioinformatica

• don 29-09-2011: 1* Bioinformatics (practicum 8.30-11.00) • don 06-10-2011: 2* Biological Databases (practicum 9.00-

11.30) • don 20-10-2011: 3 Sequence Similarity (Scoring Matrices)• don 27-10-2011: 4 Sequence Alignments• don 10-11-2011: 5 Database Searching Fasta/Blast• don 17-11-2011: 6 Phylogenetics• don 24-11-2011: 7 Protein Structure • don 01-12-2011: 8 Gene Prediction, Gene Ontologies &

HMM• don 08-12-2011: 9 ncRNA, Chip Data Analysis, AI• don 15-12-2011: 10 Bio- & Cheminformatics in Drug

Discovery (inhaalweek)• Opgelet: Geen les op don 13-10-2010 en don 3-11-2010

Examen

• Theorie – Deel rond een zelf te kiezen publicatie die in

verband staat met de cursus • Bv Bioinformatics of Computational Biology

– Drie inzichtsvragen over de cursus (inclusief !!)

• Practicum (“open-book”)– Viertal oefeningen die meestal het schrijven van een

programma veronderstellen

• Puntenverdeling 50/50

• Timelin: Magaret Dayhoff …

Nexus > FAQ > Bioinformatics Milestones

• http://www.sciencemag.org/cgi/content/full/291/5507/1195

• Printed version in cursus

naturetheHumangenome

Setting the stage …

Genome Meters

• Genomes Online Database (GOLD 1.0)– http://geta.life.uiuc.edu/~nikos/genomes.html– http://www.ebi.ac.uk/research/cgg/genomes.html

• NCBI– http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.ht

ml• INFOBIOGEN

– http://www.infobiogen.fr/doc/data/complete_genome.html

Genome Size

DOGS: Database Of Genome Sizes

E. coli = 4.2 x 106

Yeast = 18 x 106

Arabidopsis = 80 x 106

C.elegans = 100 x 106

Drosophila = 180 x 106

Human/Rat/Mouse = 3000 x 106

Lily = 300 000 x 106

With ... : 99.9 %To primates: 99%

Biological Research

Adapted from John McPherson, OICRAdapted from John McPherson, OICR

And this is just the beginning ….

Next Generation Sequencing is here

Basics of the “old” technology

• Clone the DNA.• Generate a ladder of labeled (colored) molecules

that are different by 1 nucleotide.• Separate mixture on some matrix.• Detect fluorochrome by laser.• Interpret peaks as string of DNA.• Strings are 500 to 1,000 letters long• 1 machine generates 57,000 nucleotides/run• Assemble all strings into a genome.

Basics of the “new” technology

• Get DNA.• Attach it to something.• Extend and amplify signal with some color

scheme.• Detect fluorochrome by microscopy.• Interpret series of spots as short strings of DNA.• Strings are 30-300 letters long• Multiple images are interpreted as 0.4 to 1.2

GB/run (1,200,000,000 letters/day). • Map or align strings to one or many genome.

Next Generation Technologies

• 454–Emulsion PCR–Polymerase–Natural Nucleotides

• 20-100Mb for 5-15k –1% error rate–Homopolymers

One additional insight ...

Read Length is Not As Important For Resequencing

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

8 10 12 14 16 18 20

Length of K-mer Reads (bp)

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Jay Shendure

Two Short Read Techologies

• Illumina GA

• ABI SOLID

Technology Overview: Solexa/Illumina Sequencing

ABI Solid

Dressman 2003

ABI SOLID

ABI SOLID

Paired End Reads are Important!

Repetitive DNAUnique DNA

Single read maps to multiple positions

Paired read maps uniquely

Read 1 Read 2

Known Distance

Single Molecule Sequencing

Helicos Biosciences Corp.

Microscope slide

Single DNA molecule

dNTP-Cy3

* * *

*

primer

Super-cooledTIRF microscope

Adapted from: Barak Cohen, Washington University, Bio5488 http://tinyurl.com/6zttuq http://tinyurl.com/6k26nh

Introducing

NXT GNT DXSNext Generation Diagnostics

18th september 2009

Wim Van Criekinge

develop in shortest time frame best assay for most relevant

clinical application

NXT GNT DXS

• GNT– Dedicated Team & Network– Operational: Location– Professionalized

• DXS– Content engine– Product 1 established– Pipeline for n+1

• NXT– Workflow management– Bioinformatics– Epigenetics

Next next generation sequencing

Third generation sequencing

Now sequencing

Complete genomics

Complete genomics

Pacific Biosciences: A Third Generation Sequencing Technology

Eid et al 2008

Pacific Biosciences: A Third Generation Sequencing Technology

Nanopore Sequencing

NCBI (educational resources)

Weblems

• What ?– Web-based problemes (over de huidige les

en/of voorbereiding op volgende les)• When ?

– Einde van elke les• How ?

– Oplossingen online via screencasts– Practicum– Voorbedereiding op het practicum examen ...

Niet alle problemen vereisen noodzakelijk programmacode ...

Weblems

W1.1: To which phyla do the following species belong (a) starfish (b) ginko tree (c) scorpion

W1.2: What are the common names for the following species (a) Orycterophus afer (b) Beta vulagaris (c) macrocystis pyrifera

W1.3: What species has the smallest known genome ? And is genome size related to number of genes ?

W1.4: What are the 5 latest genomes published ? How complete is “coverage” ?

W1.5: For approximately 10% of europeans, the painkiller codeine is ineffective because the patients lack the enzyme that converts codeine into the active molecule, morphine. What is the most common mutation that causes this condition ?