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
Lab for Bioinformatics and
computational genomics
10 “genome hackers”
mostly engineers (statistics)
42 scientists
technicians, geneticists, clinicians

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 Analysis
structure prediction (HTX)
Theoretical Biology
Sequence Analysis
(Molecular)
Biology
Expert Annotation
Computer Science
NP
Datamining
Bioinformatics

Math Algorithm
Development
Informatics
Interface Design
AI, Image Analysis
structure prediction (HTX)
Theoretical Biology
Sequence Analysis
(Molecular)
Biology
Expert Annotation
Computer Science
NP
Datamining
Bioinformatics
Discovery Informatics – Computational Genomics

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 code
DNA

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)
Genome
DNA
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!

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

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 to
push 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)

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

Prototyping
Low 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

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Viewers also liked

Viewers also liked (8)

Similar to 2015 03 13_puurs_v_public

Similar to 2015 03 13_puurs_v_public (20)

More from Prof. Wim Van Criekinge

More from Prof. Wim Van Criekinge (20)

Recently uploaded

Recently uploaded (20)

2015 03 13_puurs_v_public

Editor's Notes