1
ITMO Genetics, Genomics and Bioinformatics
Personalized medicine in the Next Generation Sequencing
(NGS) era: Scientific and Medical challenges, Ethical
considerations
September 24, 2013 / Bruxelles
Thierry Frebourg
CEA
CHRU CNRS CPU INRA INRIA INSERM INSTITUT PASTEUR IRDARIIS EFS INERIS INSTITUT CURIE INSTITUT MINES-TELECOM UNICANCERIRBA IRSNCIRAD
FONDATION MERIEUX
1985 PCR
(Mullis)
2004-Genomic era
2004End of
sequencing of the human
genome
2007Whole genome analyses: CGH
1865 – 1975Pre-molecular era
1975 – 2004Molecular era
1865 Mendel
1953 DNA
Structure Watson and
Crick
1959 Trisomy 21 LejeuneTurpin Jacobs
A SHORT HISTORY OF HUMAN GENETICS 1975
Southern 1993
Automated sequencers
Beginning of sequencing
of the human genome
Sanger sequencing
2009New generation
Sequencing(NGS)
THE NGS REVOLUTION : FROM TARGETED TO GLOBAL SEQUENCING
Human exome sequencing 160.000 exons = 30 Mb (30 106)
1.2% of the human genome 3 Gb 100x 3000 Mb = 3 Gb
50 Gb (50. 109 pb) sequenced within 7 days
Sanger sequencing on amplicons : 500 bp1000 Kb (106 bp) sequenced within 7 days
X 100 000
The human genome : 3 Gb (3.109 )
NGS : BIOINFORMATICS EXPERTISE
Quality - Alignment - Annotation - Filtration - Comparison - Storage
pb -Kb
Gb
X 1 000 000
Per exome 34 Mb : 1.2% of the total genome :
17000 Single Nucleotide Variations (SNV)50% non synonymous
500 rare (<0.1%) SNVs not present in the data bases 1 de novo SNV with potential impact per generation
UNDERESTIMATED VARIABILITY OF THE HUMAN GENOME
MAIN CHALLENGE OF NGS : INTERPRETATION OF GENETIC VARIATIONS
1995-2010Detection of mutations
Since 2010Interpretation of mutations
Discovery of the DNA polymorphism complexity SNV, SNP, CNV…..
Biological and medical interpretation
Phenotypic evaluationStatistical analyses Animal models
EXTENSIVE CHARACTERIZATION OF THE GENETIC DETERMINISM OF DISEASES
Single case Extreme phenotype
17000 SNVsExclusion of non genic– intronic – synonymous SNPs : 5000 SNVs
Exclusion of SNVs from dbSNP131 -1000 genome project - in house exomes - 5379 exomes*400 non-synonymous/splice acceptor donor site/frameshift coding indels
Substractive exomes in trio
Comparative exomesinter-families
Familial cases
III.12°III.5° III.7° III.8° III.9°
II.5
III.16° III.17 III.18° III.19
?III.23°
?
II.9°
III.29° III.30° III.31° III.32°
? ?
II.8°
????
??
? ? ? ? ??III.26° III.27° III.28°
?
56 (52) (51) (48)
?
(43) (46) (41) (36)
I.1 I.2
II.2 II.4 II.7°
III.4 III.6 III.11 III.13 III.14 III.15 III.22° III.24° III.25
IV.1° IV.2° IV.3
Comparative exomesbetween relatives
Subtraction of inherited SNVs
De novo mutations : 0-10
Genes affected by identical variations : 20
Altered genes in common
*NHLBI Grand Opportunity Exome Sequencing Project
September 2013 : 900 publications
Colon cancer 62 years
WT/ mt Wt/ Wt WT/WT
Suppression of an illegitimate anxiety and inappropriate medical follow-up
in non mutation carriers
WT/ mt
Colonoscopy since 20 years of age every 2 years
Colon cancer 32 years Colon cancer 36 years
OPTIMIZATION OF PERSONALIZED MEDICINE
Hereditary colorectal cancer : 1/500High throughputSimultaneous analysis of genes
Reduction of delay
MSH2, MLH1, MSH6 ,PMS2, APC, MUTYH,
SMAD4, BMPR1A,STK11, PTEN
Risk
of d
isea
se
100%
40%
60%
80%
Number of genetic variations100
Oligogenicdiseases
Age
Multigenicdiseases
Monogenic diseases
Biol
ogic
al to
lera
nce
NGS HIGHLIGHTS THE COMPLEXITY OF THE GENETIC DETERMINISM OF DISEASES
Personalized medicine
1 5
Mis-interpretation of the medical significance of the genetic variations- Genomic reductionism “and tomorrow, everyone in this room will be
able to hold their genome in their iPad and You will be able to surf your genome and find out everything about yourself.“ Senior VP , Illumina, June 2013
- Development of Direct-to-consumer (DTC) genetic testing services- No medical value of genetic analyses without clinical evaluation
Access to genome data : the global alliance white paper“Cancers, rare diseases, common diseases infectious diseases” “Serving the needs of the entire biomedical ecosystems: patients, researchers hospitals, biopharma, institutions, clinical trials, governments”
Cloud computing for storage controlled access
ETHICAL ISSUES OF NGS IN THE CONTEXT OF PERSONALIZED MEDICINE
10CEA
CHRU CNRS CPU INRA INRIA INSERM INSTITUT PASTEUR IRDARIIS EFS INERIS INSTITUT CURIE INSTITUT MINES-TELECOM UNICANCERIRBA IRSNCIRAD
FONDATION MERIEUX
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