The document discusses a lab for bioinformatics and computational genomics at Ghent University. The lab has 10 "genome hackers" who are mostly engineers and 42 scientists, technicians, geneticists and clinicians. The lab focuses on bioinformatics, epigenetics, personal genomics and 3D printing. Bioinformatics is defined as the application of information technology to biological information, facilitated by computers. The document then discusses various topics related to genetics, genomics and personalized medicine.

1. Lab for Bioinformatics and computational genomics
^…
@wvcrieki

2. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

3. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

4. 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

5. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

6. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

7. Lab for Bioinformatics and computational genomics
Bioinformatics ?
• Application of information
technology to the storage,
management and analysis of
biological information
• Facilitated by the use of computers

8. Math
Informatics
Bioinformatics, a scientific discipline …
Theoretical Biology
Computational Biology
(Molecular)
Biology
Computer Science
Bioinformatics

9. Math Algorithm
Development
Informatics
Interface Design
Bioinformatics, a scientific discipline …
AI, Image Analysis
structure prediction (HTX)
Theoretical Biology
Sequence Analysis
Computational Biology
(Molecular)
Biology
Expert Annotation
Computer Science
NP
Datamining
Bioinformatics

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

12. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

13. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

14. Lab for Bioinformatics and 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.

15. Lab for Bioinformatics and computational genomics
Cell Theory

16. Lab for Bioinformatics and computational genomics
Genetic code
DNA

17. Lab for Bioinformatics and computational genomics

18. Lab for Bioinformatics and computational genomics
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

19. Lab for Bioinformatics and computational genomics
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)
(0.34 × 10-9
m)(6 × 109
)(1013
)
2.0 × 1013
meters
DNA: Structure and Function

20. Lab for Bioinformatics and computational genomics
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)
(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.
DNA: Structure and Function

21. Lab for Bioinformatics and computational genomics
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

24. Lab for Bioinformatics and computational genomics

26. Lab for Bioinformatics and computational genomics
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

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

30. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

31. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

32. Lab for Bioinformatics and computational genomics

33. The genome fits as an e-mail attachment

34. Lab for Bioinformatics and computational genomics

35. Lab for Bioinformatics and computational genomics

36. Lab for Bioinformatics and computational genomics
Overview
• Who ? Where ?
• > Genetics
• Technology: Next Gen
Sequencing
• Personal …. Medicine/Genomics
• Manifesto
• The App

37. 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.

38. Lab for Bioinformatics and computational genomics
Overview
• Who ? Where ?
• > Genetics
• Technology: Next Gen
Sequencing
• … Personal Genomics
• Manifesto
• The App
^[now][transl comput]ational⎮ [epi]genomic$

39. 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)

40. Generic Health advice (UNLESS)
•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)

41. Generic Health advice (UNLESS)
•Exercise (Hypertrophic Cardiomyopathy)
•Drink your milk (MCM6 Lactose intolerance)
•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)

42. Generic Health advice (UNLESS)
•Exercise (Hypertrophic Cardiomyopathy)
•Drink your milk (MCM6 Lactose intolerance)
•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)

43. Lab for Bioinformatics and computational genomics

45. Lab for Bioinformatics and computational genomics

46. Lab for Bioinformatics and computational genomics

47. Lab for Bioinformatics and computational genomics

48. Lab for Bioinformatics and computational genomics

49. Lab for Bioinformatics and computational genomics

50. Lab for Bioinformatics and computational genomics

51. Lab for Bioinformatics and computational genomics
my genome is too important (for me)
to leave it (only) to doctors

53. Lab for Bioinformatics and computational genomics
NXTGNT biohackerspace …

54. Lab for Bioinformatics and computational genomics
PGMv2: Personal Genomics Manifesto

55. Lab for Bioinformatics and computational genomics
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.
PGMv2: Personal Genomics Manifesto

56. Lab for Bioinformatics and computational genomics
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.
PGMv2: Personal Genomics Manifesto

57. Lab for Bioinformatics and computational genomics
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.
PGMv2: Personal Genomics Manifesto

58. Lab for Bioinformatics and computational genomics
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.
PGMv2: Personal Genomics Manifesto

59. Lab for Bioinformatics and computational genomics
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.
PGMv2: Personal Genomics Manifesto

60. Lab for Bioinformatics and computational genomics

65. Lab for Bioinformatics and computational genomics

66. Lab for Bioinformatics and computational genomics
Epigenome(s)

67. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

68. Lab for Bioinformatics and computational genomics
13 maart 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Epigenetics
• Personal Genomics
• 3D printing
^[now][transl comput]ational⎮ [epi]genomic$

69. Lab for Bioinformatics and computational genomics
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

70. Lab for Bioinformatics and computational genomics
Let’s Start with 2D Printing
Digital to Physical

71. Lab for Bioinformatics and computational genomics
Now 3D Printing
Digital to Physical

72. Lab for Bioinformatics and computational genomics
Material Extrusion (FDM)
• Most common technology
• Desktop models are
widespread

73. Lab for Bioinformatics and computational genomics
Cont…

74. Lab for Bioinformatics and computational genomics
Powder Based System (SLS)
• Wider range of materials
• Very strength
• Functional parts
• Base material is powder
• Still at the industrial scale

75. Lab for Bioinformatics and computational genomics
How do people use 3D Printing?
• Prototyping
• Low volume manufacturing
• Tooling
• Consumer products
• Customization + personalization
• Art/design
• Education
• Medical

76. Lab for Bioinformatics and computational genomics
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

77. Lab for Bioinformatics and computational genomics
• 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

78. Lab for Bioinformatics and computational genomics
Design What You Print

79. Lab for Bioinformatics and computational genomics
3D Printed
Seat
The Customized Outcome

80. Lab for Bioinformatics and computational genomics
Design Freedom

81. Lab for Bioinformatics and computational genomics
Geometric Freedom

82. Lab for Bioinformatics and computational genomics
Low Volume Manufacturing

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86. Lab for Bioinformatics and computational genomics
Getting started with 3D Printing
• Thingiverse

87. Lab for Bioinformatics and computational genomics

88. Lab for Bioinformatics and computational genomics
Getting started with 3D Printing
• Thingiverse
• Autodesk App
• Printcraft
• Blender

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… $