2014 11 03_bioinformatics_case_studies
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Bioinformatics case studiesTranslating epigenetics, Personal genomics
Wim Van CriekingeAmsterdam, 3rd November 2014
wvcrieki
Overview
Epigenetics– Introduction– DNA Methylation & Oncology
Translating Epigenetics– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic UsePersonal/Recreational Genomics
Overview
Epigenetics– Introduction– DNA Methylation & Oncology
Translating Epigenetics– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic Use Personal Genomics
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
Gene Expression
Epigenome
Chromatin
Phenotype
Chromatin, a Key Component of Epigenetic Regulation
nucleosomehistoneDNA
chromatin
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
Epigenetics I Intoduction | Oncology | Biomarker
DNA Methylation Prevents Gene Expression
DNA methylation involves the transfer of methyl groups to cytosine residues in DNA by DNA methyltransferases (DNMTs)
Hypo <-> Hyper
MeMeMe Me
MeMe
MeAc
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
Ac
DNMT DNMT
DNMT DNMT
Geneexpression
Geneexpression
TF
TF
Historically, Cancer Was Considered to be Driven Mostly by Genetic Changes
Example: Replication errors
GENETIC
Altered DNA/mRNA/proteins
Altered DNA sequence
X X
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
Epigenetic Changes are Important in Causing Cancer
Example: Replication errors
GENETIC EPIGENETIC
Example: Chromatin modification errors
Altered DNA/mRNA/proteins
Altered DNA sequence
Altered levels ofmRNA/proteins
Alteredchromatin structure
X X
Oncogenesis
Tumor
Source: Schuebel et al 2007
SYNE1
APC2
GPNMB
MM
P2EVL
STARD8
PTPRDCD109
LGR6
RETCHD%
RNF182
ICAM5
0
20
40
60
80
100
120
Methylated Mutated
76-100 51-75 21-50 1-20
Dx
CDx
Example of Methylation vs Mutation: Colon & Breast Cancer
ActionableEpigenome
OutsideOncology ?
Evolutionary Perspectiveepigenetic (meta)information = stem cells
Cellular programming
Overview
Epigenetics– Introduction– DNA Methylation & Oncology
Translating Epigenetics– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic Use – Implementation
MGMT BiologyO6 Methyl-Guanine Methyl Transferase
Essential DNA Repair Enzyme
Removes alkyl groups from damaged guanine bases
Healthy individual: - MGMT is an essential DNA repair enzymeLoss 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
# samples
# markers
Discovery Verification Validation
3 000 000
5
6 000
50
<50 only models
and fresh frozen
> 50 All sample types
Incl. FFPE
Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
Next GenerationEpigenetic Profiling
# samples
# markers
MethylCap_Seq
Discovery Verification Validation
3 000 000
5
6 000
50
<50 only models
and fresh frozen
> 50 All sample types
Incl. FFPE
Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
Next GenerationEpigenetic Profiling
MethylCap_Seq
DNA Sheared
Immobilized Methyl Binding Domain
Condensed Chromatin
DNA Sheared
Immobilized Methyl binding domain
MgCl2
Next Gen SequencingGA Illumina: 100 million reads
MethylCap_Seq
Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Quality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing
MGMT = dual core
Data integrationCorrelation tracks
methylation methylation
expression expression
Corr =-1 Corr = 1
Correlation trackin GBM @ MGMT
+1
-1
# samples
# markers
MethylCap_Seq
Discovery Verification Validation
3 000 000
5
6 000
50
EpiHealth
<50 only models
and fresh frozen
> 50 All sample types
Incl. FFPE
Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
Next GenerationEpigenetic Profiling
Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
440 cancer-related genes genes are known to be epigenetically altered in human solid cancers based on recent scientific and clinical literature.
Coverage and allelic strans specific methylation signals
Dual strands accounts for genetic variant identification
# samples
# markers
MethylCap_Seq
Deep_Seq
Discovery Verification Validation
3 000 000
5
6 000
50
EpiHealth
<50 only models
and fresh frozen
> 50 All sample types
Incl. FFPE
Methylation Specific Seq
Enrichment Sequencing (RUO) Targeted Sequencing (IVD)
Next GenerationEpigenetic Profiling
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
25% 50% 25%
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
Dense methylated needed for transcriptional silencingAre there alleles with all three positions methylated ?
GCATCGTGACTTACGACTGATCGATGGATGCTAGCAT
unmethylated alleles
less methylationmethylated alleles
more methylation
Deep Sequencing
Deep Sequencing MGMT Heterogenic complexity
Data integration with
DEEP Sequencing, Infinium, Reactivation, (directional) Expression …
Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
DeepSeq
Molecular Unificationgenetic + epigenetic testing
107 106 105 104 103 102 101 1108109
Full genome bp
Whole-genomeBisulphite seq
EPI
GENETIC
Whole-genomesequencing
Enrichment seq(MBD, RRBS)
Enrichment seq(Exome)
Probes(450-27K)
Enrichment Targeted Panels
Enrichment Targeted Panels
UltraDeep
SequencingRUO Clinical
Overview
Epigenetics– Introduction– DNA Methylation & Oncology
Translating Epigenetics– NEXT-GENeration (Epi)genetic biomarkers
for Clinical and Prognostic UsePersonal/Recreational Genomics
Lab for Bioinformatics and computational genomics
107 106 105 104 103 102 101 1108109
Full genome bp
GENETIC
Whole-genomesequencing
Enrichment seq(Exome)
PCREnrichment
Targeted Panels
Instrument and Assay providers
CLIA Lab service providers
The genome fits as an e-mail attachment
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
The Technical Feasibility Argument
The Quality Argument
The Price Argument
The Logistics Argument
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Recreational genomics
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
Lab for Bioinformatics and computational genomics
Recreational genomics
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 ?
Lab for Bioinformatics and computational genomics
Recreational genomics
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”
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Recreational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
Recreational genomics
Lab for Bioinformatics and computational genomics
Recreational genomics
Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and computational genomics
my genome is too important (for me) to leave it (only) to doctors
Lab for Bioinformatics and computational genomics
NXTGNT biohackerspace …
Lab for Bioinformatics and computational genomics
PGMv2: Personal Genomics Manifesto
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 topush the boundaries of knowledge are a basic human right.
PGMv2: Personal Genomics Manifesto
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
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
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
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
Lab for Bioinformatics and computational genomics
Genomeslikemine
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