2015 03 13_puurs_v_public

Lab for Bioinformatics and computational genomics

^…

@wvcrieki


13 maart 2015

• ^ Biobix: Who ? Where ?• Bioinformatics• Epigenetics• Personal Genomics• 3D printing

^[now][transl comput]ational⎮ [epi]genomic$

Ghent University at a glance

Department of Molecular Biotechnology


10 “genome hackers” mostly engineers (statistics)

42 scientiststechnicians, geneticists, clinicians

http://www.biolinux.org/


13 maart 2015




Bioinformatics ?

• Application of information technology to the storage, management and analysis of biological information

• Facilitated by the use of computers

Math

Informatics

Bioinformatics, a scientific discipline …

Theoretical Biology

Computational Biology

(Molecular)Biology

Computer Science

Bioinformatics

Math Algorithm Development

Informatics

Interface Design


AI, Image Analysisstructure prediction (HTX)

Theoretical Biology

Sequence Analysis


(Molecular)Biology

Expert Annotation

Computer Science

NPDatamining

Bioinformatics

Math Algorithm Development

Informatics

Interface Design


AI, Image Analysisstructure prediction (HTX)

Theoretical Biology

Sequence Analysis


(Molecular)Biology

Expert Annotation

Computer Science

NPDatamining

BioinformaticsDiscovery Informatics – Computational Genomics


13 maart 2015




Cell Theory• All organisms are

composed of one or more cells.

• Cells are the smallest living units of all living organisms.

• Cells arise only by division of a previously existing cell.


Cell Theory


Genetic codeDNA


The human genome comprises the information contained in one set of human chromosomes which themselves contain about 3 billion base pairs (bp) of DNA in 46 chromosomes (22 autosome pairs + 2 sex chromosomes). The total length of DNA present in one adult human is calculated by the multiplication of

(length of 1 bp)(number of bp per cell)(number of cells in the body)

DNA: Structure and Function




(0.34 × 10-9 m)(6 × 109)(1013)2.0 × 1013 meters





(0.34 × 10-9 m)(6 × 109)(1013)2.0 × 1013 meters

That is the equivalent of nearly 70 trips from the earth to the sun and back.



Defining Epigenetics

• Reversible changes in gene expression/function

• Without changes in DNA sequence

• Can be inherited from precursor cells

• Epigenetic information is included in the epigenome

• Allows to integrate intrinsic with environmental signals (including diet)

GenomeDNA

Gene Expression

Epigenome

Chromatin

Phenotype


Epigenetics

• Epigenetics is essentially the study of how our environment impacts traits acquired within our lifetimes, altering certain gene expressions which may then be passed on to future generations

• That is, what we do to our own bodies may affect our children & grandchildren more than we thought.

26

Actionable Epigenome

…. It is estimated that there are more microbes in your intestine than there are human cells in your body!


13 maart 2015



The genome fits as an e-mail attachment


Overview

• Who ? Where ?• > Genetics • Technology: Next Gen

Sequencing• Personal …. Medicine/Genomics• Manifesto• The App

Molecular Profiling

The study of specific patterns (fingerprints) of proteins, DNA, and/or mRNA and how these patterns correlate with an individual's physical characteristics or symptoms of disease.


Overview

• Who ? Where ?• > Genetics • Technology: Next Gen

Sequencing• … Personal Genomics• Manifesto• The App


Generic Health advice

•Exercise (Hypertrophic Cardiomyopathy)

•Drink your milk (MCM6 Lactose intolarance)

•Eat your green beans (glucose-6-phosphate dehydrogenase Deficiency)

•& your grains (HLA-DQ2 – Celiac disease)

•& your iron (HFE - Hemochromatosis)

•Get more rest (HLA-DR2 - Narcolepsy)

Generic Health advice (UNLESS)


•Drink your milk (MCM6 Lactose intolarance)





Generic Health advice (UNLESS)


•Drink your milk (MCM6 Lactose intolerance)






my genome is too important (for me) to leave it (only) to doctors


NXTGNT biohackerspace …


PGMv2: Personal Genomics Manifesto


Everyone should have the power and legitimacy to be able to discover, develop and find new things about their own genome data.

Intelligent exploration, experimentation and trial topush the boundaries of knowledge are a basic human right.



Personal genome data access should be affordable to all irrespective of nationality, gender, social background or any other circumstance.

Not having access to a personal genetic test is in itself a new kind of discrimination.



Whether one wants to share genome data or keep it private should be a matter of personal choice.

Whatever attitude a person has towards personal genome privacy, it should be utterly respected.

Corporate interest can never compromise any human right. Laws must fully protect individual human rights of equality for every person, irrespective of predicted risks from genetic data.



Stating that genetic tests merely provide non-clinical information misses the point of what personal genomics is all about.

Most genomic information is uninterpretable and may well be meaningless. But those are not reasons to deny it to people.

Genetic test results are not unrelated to someone’s health, one’s ability to respond to certain drugs and one’s ethnic ancestry.



Education in risks and opportunities for personal genetic testing should be the primary aim of policy makers.

Restricting access to interested people makes no sense and it is virtually impossible to ensure.

Access to personal genomics data and tools for its interpretation should become accessible to everyone.



Epigenome(s)


13 maart 2015




What is 3D Printing?

Technical Definition

Process of joining materials to make objects from 3D model data, usually layer upon

layer as opposed to subtractive manufacturing methodologies

Okay…but in English please


Let’s Start with 2D Printing

Digital to Physical


Now 3D Printing

Digital to Physical


Material Extrusion (FDM)

• Most common technology• Desktop models are

widespread


Cont…


Powder Based System (SLS)

• Wider range of materials• Very strength• Functional parts• Base material is powder• Still at the industrial scale


How do people use 3D Printing?

• Prototyping • Low volume manufacturing• Tooling • Consumer products• Customization + personalization• Art/design• Education• Medical


PrototypingLow barrier to create a physical model

– Limited risk if it fails– Get products into the customers

hands– Streamlined development

process– Save money and time on tooling – Ability to iterate and incorporate

new feedback


• Developed by WWII vets• Highly visible Paralympic

sport

Challenge• Range of abilities and no

one size fits all chair

Task• Personalized solution to

maximize performance

Customization-Case Study


Design What You Print


3D Printed Seat

The Customized Outcome


Design Freedom


Geometric Freedom


Low Volume Manufacturing


Getting started with 3D Printing

• Thingiverse


Getting started with 3D Printing

• Thingiverse• Autodesk App• Printcraft• Blender


… $

2015 03 13_puurs_v_public

Education

set of human chromosomes

adult human

sex chromosomes

computational genomics13

base pairs bp of dna

bpnumber of bp

autosome pairs

cellnumber of cells