1. No category

Whole Genome Medicine: Concepts,
Technologies & Challenges
ÖGO Symposium: “Orthopädie im Wandel”, Donauspital Wien
Christoph Bock
25 April 2015
http://epigenomics.cemm.oeaw.ac.at
lab
http://biomedical-sequencing.at
Epigenome research
Sequencing platform
Outline
1. Genes and genomes: Widespread
relevance for medical practice
2. Personal genomes: Genetic
information in science & society
3. Epigenome research: A case study
focusing on Ewing sarcoma
4. Outlook: How is the genetics clinic
of the future going to look like?
Page 1 of 29
Genomes define us as individuals
Monozygotic twins
Dizygotic twins
Unrelated
100% genetically identical 50% genetically identical
A similarity that lasts a lifetime
Page 2 of 29
Most traits have a genetic component – not only diseases
Monozygotic twins
Dizygotic twins
Heritability is
calculated by
comparing MZ &
DZ twin pairs
50% genetically identical
100% genetically identical
Examples for the heritability of traits and disease
Height (90%)
Weight (70%)
Type 1 diabetes (90%)
Colon cancer (30%) Type 2 diabetes (60%)
Eating behavior (45%)
Smoking (50%)
Schizophrenia (80%)
Alcohol abuse (60%)
Doing sports (60%)
Major depression (40%)
Life expectancy (25%)
http://www.nature.com/nrg/journal/v13/n9/full/nrg3243.html
Page 3 of 29
80% of rare diseases have genetic causes
Genetic methods are essential for clinical diagnostics & precision medicine
Page 4 of 29
Striking parallels between the computing revolution & sequencing
High-performance computing
1979
2014
Who has a computer?
Genome sequencing
2006
2014
Whose genome has been sequenced?
1960s: Major research institutes
1996: First bacterium (E. coli)
1970s: University departments
2001: Human reference genome
1980s: Companies and schools
2007: First personal genomes
2014: Almost everybody & always
2014: Many thousand personal genomes
Like computers, DNA sequencing is a platform technology with many applications
Page 5 of 29
Next generation sequencing in medicine
Cancer: Somatic mutations
Tumor
DNA extraction
Blood
Next generation
sequencing
Mendelian diseases: Germline mutations
Patient(s)
Relatives
Genome data
analysis
Page 6 of 29
Experimental workflow for detecting disease-relevant mutations
Patient DNA
Fragmentation
Adapter
ligation
Genomic region
enrichment
Sequencing
by synthesis
Library preparation
Advantages of automation
Higher throughout (96 samples /
run)
Higher consistency & data quality
Technical reliability  lower cost
HiSeq
MiSeq
Ion Proton
Page 7 of 29
Bioinformatic workflow for detecting disease-relevant mutations
Base Calling
Alignment
Genotyping
Prioritization
of findings
Page 8 of 29
CeMM’s response: The Biomedical Sequencing Facility (jointly with MUW)
Biomedical Sequencing Facility (BSF)
Technology platform for biomedical sequencing at CeMM and MedUni Wien
Focus on genome/epigenome/transcriptome sequencing for biomedicine
Bioinformatics & supercomputing infrastructure and expertise
Supported assays
Grade 1 (diagnostics-near): Exome-seq
Grade 2 (96-well robotics): RNA-seq,
personal genomes, DNA methylation
Grade 3 (pilot projects): Massive-scale
RNA-seq fingerprinting, 96-well ChIPseq
Grade 4 (testing phase): Single-cell
genome/epigenome/transcriptome
BSF: http://biomedical-sequencing.at
Page 9 of 29
CeMM’s response: The Biomedical Sequencing Facility (jointly with MUW)
Infrastructure of the Biomedical Sequencing Facility (BSF)
Next Generation Sequencing
Robotic Library Preparation
Single-cell Technology
PerkinElmer Sciclone NGS
Fluidigm C1
PerkinElmer Zephyr
DEPArray
Illumina HiSeq
2000/2500 (2x)
Illumina HiSeq
3000/4000
MiSeq
Page 10 of 29
Outline
1. Genes and genomes: Widespread
relevance for medical practice
2. Personal genomes: Genetic
information in science & society
3. Epigenome research: A case study
focusing on Ewing sarcoma
4. Outlook: How is the genetics clinic
of the future going to look like?
Page 11 of 29
Genes and genomes are broadly relevant beyond medicine
Genes and genomes in society and everyday life:
Inheritance: Many traits are shared with among relatives
Family: Paternity testing routinely affects social relations
Crime: DNA testing convicts many criminals – and frees innocent suspects
Privacy: We leave a trace of unique DNA wherever we go (and can’t help it)
Nutrition: Recent surge of “functional food” and lactose-free milk
Need to build “genetic literacy” in society to handle genetic information responsibly
Page 12 of 29
Genom Austria: Personal genome sequencing & open discussion
Project summary
Citizen science project on personal genomes
Open discussion of ethical, social, etc. implications
2015: Sequence & share 20 pioneer genomes
Focus on education – not on medicine / diagnostics
www.genomaustria.at | personalgenomes.org/austria
Collaboration partners
CeMM & Biomedical Sequencing Facility
Medical University of Vienna
Personal Genome Project at Harvard
PersonalGenomes.org foundation
Many individuals who donate their time
Page 13 of 29
Genom Austria is backed by an interdisciplinary team
Ehrenschutz
• Margit Fischer
Projektteam
Steering Board
• Christoph Bock (Projektleitung &
• Christiane Druml (Bioethikkommission beim
Genomanalyse)
Bundeskanzler & MedUni Wien)
• Christoph Binder (Labordiagnostik)
• Markus Hengstschläger (MedUni Wien)
• Kaan Boztug (Seltene Erkrankungen)
• Helga Nowotny (ERA Council Forum)
• Ulrich Jäger (Hämatologische Ambulanz)
• Michael Speicher (ÖGH & MedUni Graz)
• Franco Laccone (Humangenetik)
• Giulio Superti-Furga (CeMM Direktor,
• Thomas Perkmann (Biobank)
Projektverantwortlicher, Steering Board
• Eva Schweng (Öffentlichkeitsarbeit)
Chair)
Beirat für wissenschaftliche, ethische und gesellschaftliche Fragen
Matthias Beck (Uni Wien): Bioethik und Theologie | Walter Berka (Uni Salzburg): Öffentliches
Recht |
Meinrad Busslinger (IMP): Molekularbiologie | Hans-Christoph Duba (Landes- Frauen- und
Kinderklinik Linz): Humangenetik | Ulrike Felt (Uni Wien): Wissenschaftsforschung | Gabriele
Fischer (MedUni Wien): Psychiatrie | Barbara Horejs (ÖAW): Geschichtswissenschaften | Ulrich
Körtner (MedUni Wien): Bioethik und Theologie | Christine Mannhalter (MedUni Wien):
Labordiagnostik | Markus Müller (MedUni Wien): Pharmakologie | Peter Pakesch
(Universalmuseum Joanneum) | Christina Peters (St. Anna Kinderspital): Kinderheilkunde |
Barbara Prainsack (King‘s College): Wissenschaftsforschung | Eva Schlegel: Künstlerin |
Barbara Streicher (Science Center Netzwerk): Wissenschaftskommunikation | Johannes Zschocke
(MedUni Innsbruck): Humangenetik
Page 14 of 29
Principles for personal genome sequencing in Genom Austria
Principles of Genom Austria
Public data & open access
Anonymity not guaranteed
Non-commercial & transparent
Public dialog & ethical oversight
Project workflow
Volunteers register via www.genomaustria.at website
Selection of candidates for personal genome sequencing
Detailed consent form (19 pages) & “entrance exam” to test understanding
Genome sequencing and initial reporting – genetic counselling available on
request
Participant tasks us to share the genome on the Internet (or leaves project at any
time)
Page 15 of 29
Genom Austria timeline
Preparation
May 2013: Interaction & invitation by PGP Harvard to launch PGP Austria
Oct 2013:
Submission of ethics package to MedUni Wien Ethikkommission
Feb 2014:
Ethical approval received
Mar – Nov: Stakeholder meetings, feedback, refinement of plans & materials
Nov 2014: Project launch, press conference (including Ms Margit Fischer)
The first year
Mar 2015:
>600 volunteer registrations, 10 participants randomly selected
Apr – Dec: Participants invited for genome sequencing
Apr – Sep: School project and video workshop with Open Science, Vienna
Aug 2015: Selecting 10 additional participants from all registrations
Sep 2015: 10th Anniversary Meeting of the Personal Genome Project at
CeMM
Page 16 of 29
The personal genome of Genom Austria pioneer PGA-1
Top-5 of ~500 manually reviewed associations:
Carrier status for genetic diseases: β
thalassemia, hemochromatosis, DIDMOAD
syndrome
Various risk variants for cardiovascular diseases
Clearly increased MPN risk: rs12340895(C;G)
Olcaydu D et al. (2009). Nat Genet 41(4):450-4.
Reduced risk for nicotine addiction
Increased risk for obesity
Page 17 of 29
http://www.genomaustria.at/
Page 18 of 29
Outline
1. Genes and genomes: Widespread
relevance for medical practice
2. Personal genomes: Genetic
information in science & society
3. Epigenome research: A case study
focusing on Ewing sarcoma
4. Outlook: How is the genetics clinic
of the future going to look like?
Page 19 of 29
The genome utilizes multiple regulatory layers
1D: Genome sequence
Protein-coding genes
DNA binding motifs
“2D”: Epigenetic marks
DNA methylation
Histone modifications
3D: Nuclear organization
Spatial proximity
Transcription factories
Page 20 of 29
Comprehensive genome/epigenome/transcriptome profiling
Genome sequence
Fragmentation
of the DNA
Custom
enrichment
Epigenetic marks
Sequencing
library
preparation
…
…
…
…
…
…
…
…
Treating DNA
with bisulfite
Chromatin
immunoprecipitation
Nuclear organization
Cross-linking
adjacent DNA
Next generation
sequencing
Bock (2012) Nature Reviews Genetics (http://dx.doi.org/10.1038/nrg3273)
Page 21 of 29
Bioinformatic inference of epigenomic cell state dynamics
Genome data
Large-scale data
integration &
analysis
Epigenome data
…
…
…
…
…
…
…
…
3D interactions
Examples from our previous work:
Bock et al. (2011) Cell (http://dx.doi.org/10.1016/j.cell.2010.12.032)
Bock et al. (2012) Molecular Cell (http://dx.doi.org/10.1038/nrg3273)
Page 22 of 29
Case study: Oncogene-driven epigenome changes in Ewing sarcoma
EWS/FLI1 High
shRNA
mediated
knockdown
DNA Methylation
WGBS + RRBS
Gene Expression
RNA-seq
Histone Marks
H3K4me3 H3K4me1
H3K27me3 H3K27ac
H3K9me3 H3K36me3
H3K56ac
EWS/FLI1
Low
DNA Methylation
WGBS + RRBS
Gene Expression
RNA-seq
Histone Marks
H3K4me3 H3K4me1
H3K27me3 H3K27ac
H3K9me3 H3K36me3
H3K56ac
Reference epigenome mapping done according to the International Human
Epigenome Consortium’s criteria for full epigenomes (http://ihec-epigenomes.org)
Tomazou, Sheffield et al. (2015) Cell Reports (http://www.cell.com/cell-reports/abstract/S2211-1247(15)00067-4)
Page 23 of 29
Reference epigenome map of an EWS-FLI1 dependent cell line
Tomazou, Sheffield et al. (2015) Cell Reports, in press
Page 24 of 29
Promoter-centric view on EWS-FLI1 dependent chromatin changes
Differential gene expression
Chromatin-based promoter clustering
Page 25 of 29
Widespread enhancer and super-enhancer reprogramming
Tomazou, Sheffield et al. (2015) Cell Reports (http://www.cell.com/cell-reports/abstract/S2211-1247(15)00067-4)
Page 26 of 29
Outline
1. Genes and genomes: Widespread
relevance for medical practice
2. Personal genomes: Genetic
information in science & society
3. Epigenome research: A case study
focusing on Ewing sarcoma
4. Outlook: How is the genetics clinic
of the future going to look like?
Page 27 of 29
EU project (coordination action): Genetics Clinic of the Future
Vrijenhoek et al.: Stepping stones towards the genetics clinic of the future,
Page 28 of 29
Whole Genome Medicine: Perspectives & Challenges
Impact of next generation sequencing on clinical practice
1. Exome sequencing as an a last-resort diagnostic method
2. Sequencing-first approach for faster & more accurate diagnostics
3. Each aspect of clinical care cross-checked with personal genome
Challenges
Technology: Accuracy, efficiency, scale, bioinformatics
Organization: Integration into clinical practice
Ethics & data protection: Who owns the data?
Education: Medical personnel, but also patients/population
Cost: Already cost-effective when done well
Page 29 of 29
Acknowledgements
Lab: Paul Datlinger, Matthias Farlik, Florian Halbritter,
Johanna Klughammer, Andre Rendeiro, Andreas
Schönegger, Christian Schmidl, Nathan Sheffield
BSF: Johanna Hadler, Angelo Nuzzo, Thomas Penz,
Michael Schuster
All our national and international collaborators
Funding
Austrian Academy of Sciences & New Frontiers Programme
European projects: BLUEPRINT, EpiMark, CINOCA, BERG, GCOF
Collaborative research grants & infrastructure grants
Websites
http://www.cemm.oeaw.ac.at
http://epigenomics.cemm.oeaw.ac.at
http://www.biomedical-sequencing.at
(institute website)
(lab website)
(NGS website)