The document summarizes a presentation on bioinformatics case studies focusing on epigenetics and personal genomics. It discusses DNA methylation and its role in cancer development. It also describes how next-generation sequencing can be used to identify epigenetic biomarkers for clinical use. Finally, it addresses issues around personal and recreational genomics, including increasing access, educating users, and protecting individual privacy and rights.
ISYU TUNGKOL SA SEKSWLADIDA (ISSUE ABOUT SEXUALITY
2014 11 03_bioinformatics_case_studies
1. Bioinformatics case studies
Translating epigenetics, Personal genomics
Wim Van Criekinge
Amsterdam, 3rd November 2014
wvcrieki
2. Overview
Epigenetics
– Introduction
– DNA Methylation & Oncology
Translating Epigenetics
– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic Use
Personal/Recreational Genomics
3. Overview
Epigenetics
– Introduction
– DNA Methylation & Oncology
Translating Epigenetics
– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic Use
Personal Genomics
4. Defining Epigenetics
Reversible changes in gene
expression/function
Without changes in DNA
sequence
Can be inherited from
precursor cells
Allows to integrate intrinsic
with environmental signals
(including diet)
Genome
DNA
Epigenome
Gene Expression
Chromatin
Phenotype
5. Chromatin,
a Key Component of Epigenetic Regulation
Cellular DNA is packaged into a structure called
chromatin
The unit of chromatin is the nucleosome, a complex of a
histone tetramer with approx. 147 bp of DNA wound
around it
histone nucleosome
DNA
Epigenetics I Intoduction | Oncology | Biomarker
chromatin
6. DNA Methylation
Prevents Gene Expression
Me Me Me
DNA methylation involves the transfer of methyl groups to cytosine residues in DNA by DNA
methyltransferases (DNMTs)
Hypo <-> Hyper
Me
Me
Me
Me
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
DNMT DNMT
DNMT DNMT
Gene
expression
Gene
expression
TF
TF
7. Historically,
Cancer Was Considered
to be Driven Mostly by Genetic Changes
GENETIC
Example:
Replication errors
Altered
DNA sequence
X X
Altered
DNA/mRNA/proteins
Oncogenesis
Tumor
Mutations in p53
Activating mutations in RAS
Mutations or amplifications of the
HER-2 gene
Chromosomal translocations in
myeloid cells and the generation of
the BCR-ABL fusion protein
8. Epigenetic Changes are
Important in Causing Cancer
GENETIC EPIGENETIC
Example:
Replication errors
Example:
Chromatin modification errors
Altered
DNA sequence
Altered
DNA/mRNA/proteins
Altered
chromatin structure
Altered levels of
mRNA/proteins
X X
Oncogenesis
Tumor
9. Source: Schuebel et al 2007
120
100
80
60
40
20
0
Methylated Mutated
76-100 51-75 21-50 1-20
Dx
CDx
Example of Methylation
vs Mutation: Colon & Breast Cancer
13. Overview
Epigenetics
– Introduction
– DNA Methylation & Oncology
Translating Epigenetics
– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic Use
– Implementation
14. MGMT Biology
O6 Methyl-Guanine
Methyl Transferase
Essential DNA Repair Enzyme
Removes alkyl groups from damaged guanine
bases
Healthy individual:
- MGMT is an essential DNA repair enzyme
Loss of MGMT activity makes individuals susceptible
to DNA damage and prone to tumor development
Glioblastoma patient on alkylator chemotherapy:
- Patients with MGMT promoter methylation show
have longer PFS and OS with the use of alkylating
agents as chemotherapy
15. Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
# samples
# markers
Discovery Verification Validation
3 000 000
6 000
50
5
<50
only models
and fresh frozen
> 50
All sample types
Incl. FFPE
Next Generation
Epigenetic Profiling
16. Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
# samples
# markers
MethylCap_Seq
Discovery Verification Validation
3 000 000
6 000
50
5
<50
only models
and fresh frozen
> 50
All sample types
Incl. FFPE
Next Generation
Epigenetic Profiling
27. Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
# samples
# markers
MethylCap_Seq
Deep_Seq
Discovery Verification Validation
3 000 000
6 000
50
5
EpiHealth
<50
only models
and fresh frozen
> 50
All sample types
Incl. FFPE
Methylation Specific Seq
Next Generation
Epigenetic Profiling
28. GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
25% 50% 25%
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
Dense methylated needed for transcriptional silencing
Are there alleles with all three positions methylated ?
29. unmethylated alleles
methylated alleles less methylation
more methylation
Deep Sequencing
GCATCGTGACTTACGACTGATCGATGGATGCTAGCAT
33. Overview
Epigenetics
– Introduction
– DNA Methylation & Oncology
Translating Epigenetics
– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic Use
Personal/Recreational Genomics
34. Lab for Bioinformatics and computational genomics
Instrument and Assay providers
Full genome bp
109 108 107 106 105 104 103 102 101 1
G
E
N
E
T
I
C
Whole-genome
sequencing
Enrichment seq
(Exome)
PCR
Enrichment
Targeted Panels
CLIA Lab service providers
45. Lab for Bioinformatics and computational genomics
The Technical Feasibility Argument
The Quality Argument
The Logistics Argument
The Price Argument
48. Lab for Bioinformatics and computational genomics
Recreational genomics
• Experimental designs are outdated by technological advances
• Genetic background (reference genome) as a concept will need to be
updated
• Traits dependent on multiple loci are “complicated”: educate and
provide tools to deal with it
50. Lab for Bioinformatics and computational genomics
Recreational genomics
• Eye color … why not the ear wax/asparagus or unibrown example
• … metabolize nutrients (newborns ?)
• … metabolize drugs in case you need it urgently ?
52. Lab for Bioinformatics and computational genomics
Recreational genomics
“several 23andMe users have reported taking the FDA’s
advice of reviewing their genetic results with their
physicians, only to find the doctors unprepared, unwilling,
or downright hostile to helping interpret the data”
63. Lab for Bioinformatics and computational genomics
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.
64. Lab for Bioinformatics and computational genomics
PGMv2: Personal Genomics Manifesto
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.
65. Lab for Bioinformatics and computational genomics
PGMv2: Personal Genomics Manifesto
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.
66. Lab for Bioinformatics and computational genomics
PGMv2: Personal Genomics Manifesto
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.
67. Lab for Bioinformatics and computational genomics
PGMv2: Personal Genomics Manifesto
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.