1. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX 1 ITMO Génétique, génomique et bioinformatique From population genetics to cellular genomics: a path towards personalised medicine Lluis Quintana-Murci, Institut Pasteur-CNRS CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX

2. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Genetic variation in health and disease 2 ACGTGTACAGAAGGGCCATGAACACTGTTATTACTCTTAC A C AATTGTGAGGCAGCCCTCGAGCCACAGGCGGGTCCAG CTGTTGGCTATAAACGGATAGCCTAC C GGTCTCTGATCGG AGATCACCATGTTTCTGGGTCCCTTGTACCCTGGATGCAG TACCTCGCCCCAGTTTCGCATACAAATTCGCATACAAAAC GTGTACAGAAGGGC C ATGAACACTGTTATTACTCTTACAC AATTGTGAGGCAGCCCTCGAGCCACAGGCGGGTCCA G CT GTTGGCTATAAACGGATAGCCTACCGGTCTCTGATCGGA GATCACCATGTTTCTGGGTCCC T TGTACCCTGGATGCAGT ACCTCGCCCCAGTTTCGCATACAAATTTCGCATACAAAAA Genetic Diversity Inter-Population Variation Phenotypic Diversity Inter-Individual Variation Personal genomics Personalised medicine

3. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX The last decade in human genomics 3 1. The complete sequence of the human genome 2. SNP Discovery and the HapMap Project 3. The 1,000 Genomes Project

4. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Lessons from genome diversity 4 tttctccatttgtcgtgacacctttgttgacaccttcatttctgcattctcaattctatttcactggtctatggcagagaacacaaaatat ggccagtggcctaaatccagcctactaccttttttttttttttgtaacattttactaacatagccattcccatgtgtttccatgtgtctgg gctgcttttgcactctaatggcagagttaagaaattgtagcagagaccacaatgcctcaaatatttactctacagccctttataaaa acagtgtgccaactcctgatttatgaacttatcattatgtcaataccatactgtctttattactgtagttttataagtcatgacatcaga taatgtaaatcctccaactttgtttttaatcaaaagtgttttggccatcctagatatactttgtattgccacataaatttgaagatcag cctgtcagtgtctacaaaatagcatgctaggattttgatagggattgtgtagaatctatagattaattagaggagaatgactatctt gacaatactgctgcccctctgtattcgtgggggattggttccacaacaacacccaccccccactcggcaacccctgaaacccccac atcccccagcttttttcccctgctaccaaaatccatggatgctcaagtccatataaaatgccatactatttgcatataacctctgcaat cctcccctatagtttagatcatctctagattacttataatactaataaaatctaaatgctatgtaaatagttgctatactgtgttgagg gttttttgttttgttttgttttatttgtttgtttgtttgtattttaagagatggtgtcttgctttgttgcccaggctggagtgcagtggtgag atcatagcttactgcagcctcaaactcctggactcaaacagtcctcccacctcagcctcccaaagtgctgggatacaggtgtgacc cactgtgcccagttattattttttatttgtattattttactgttgtattatttttaattattttttctgaatattttccatctatagttggttga atcatggatgtggaacaggcaaatatggagggctaactgtattgcatcttccagttcatgagtatgcagtctctctgtttatttaaag ttttagtttttctcaaccatgtttacttttcagtatacaagactttgacgttttttgttaaatgtatttgtaagtattttattatttgtgatgt tatttaaaaagaaattgttgactgggcacagtggctcacgcctgtaatcccagcactttgggaggctgaggcgggcagatcacga ggtcaggagatcaagaccatcctggctaacatggtaaaaccccgtctctactaaaaatagaaaaaaattagccaggcg 3 million differences between individuals

5. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Lessons from genome diversity 5 tttctccatttgtcgtgacacctttgttgacaccttcatttctgcattctcaattctatttcactggtctatggcagagaacacaaaatat ggccagtggcctaaatccagcctactaccttttttttttttttgtaacattttactaacatagccattcccatgtgtttccatgtgtctgg gctgcttttgcactctaatggcagagttaagaaattgtagcagagaccacaatgcctcaaatatttactctacagccctttataaaa acagtgtgccaactcctgatttatgaacttatcattatgtcaataccatactgtctttattactgtagttttataagtcatgacatcaga taatgtaaatcctccaactttgtttttaatcaaaagtgttttggccatcctagatatactttgtattgccacataaatttgaagatcag cctgtcagtgtctacaaaatagcatgctaggattttgatagggattgtgtagaatctatagattaattagaggagaatgactatctt gacaatactgctgcccctctgtattcgtgggggattggttccacaacaacacccaccccccactcggcaacccctgaaacccccac atcccccagcttttttcccctgctaccaaaatccatggatgctcaagtccatataaaatgccatactatttgcatataacctctgcaat cctcccctatagtttagatcatctctagattacttataatactaataaaatctaaatgctatgtaaatagttgctatactgtgttgagg gttttttgttttgttttgttttatttgtttgtttgtttgtattttaagagatggtgtcttgctttgttgcccaggctggagtgcagtggtgag atcatagcttactgcagcctcaaactcctggactcaaacagtcctcccacctcagcctcccaaagtgctgggatacaggtgtgacc cactgtgcccagttattattttttatttgtattattttactgttgtattatttttaattattttttctgaatattttccatctatagttggttga atcatggatgtggaacaggcaaatatggagggctaactgtattgcatcttccagttcatgagtatgcagtctctctgtttatttaaag ttttagtttttctcaaccatgtttacttttcagtatacaagactttgacgttttttgttaaatgtatttgtaagtattttattatttgtgatgt tatttaaaaagaaattgttgactgggcacagtggctcacgcctgtaatcccagcactttgggaggctgaggcgggcagatcacga ggtcaggagatcaagaccatcctggctaacatggtaaaaccccgtctctactaaaaatagaaaaaaattagccaggcg gaga gcgc gcgc gaga gaga gaga gaga tctc tctc tctc gaga gaga gcgc tctc tctc tctc Most mutations have no (known) phenotypic effects

6. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Lessons from genome diversity 6 tttctccatttgtcgtgacacctttgttgacaccttcatttctgcattctcaattctatttcactggtctatggcagagaacacaaaatat ggccagtggcctaaatccagcctactaccttttttttttttttgtaacattttactaacatagccattcccatgtgtttccatgtgtctgg gctgcttttgcactctaatggcagagttaagaaattgtagcagagaccacaatgcctcaaatatttactctacagccctttataaaa acagtgtgccaactcctgatttatgaacttatcattatgtcaataccatactgtctttattactgtagttttataagtcatgacatcaga taatgtaaatcctccaactttgtttttaatcaaaagtgttttggccatcctagatatactttgtattgccacataaatttgaagatcag cctgtcagtgtctacaaaatagcatgctaggattttgatagggattgtgtagaatctatagattaattagaggagaatgactatctt gacaatactgctgcccctctgtattcgtgggggattggttccacaacaacacccaccccccactcggcaacccctgaaacccccac atcccccagcttttttcccctgctaccaaaatccatggatgctcaagtccatataaaatgccatactatttgcatataacctctgcaat cctcccctatagtttagatcatctctagattacttataatactaataaaatctaaatgctatgtaaatagttgctatactgtgttgagg gttttttgttttgttttgttttatttgtttgtttgtttgtattttaagagatggtgtcttgctttgttgcccaggctggagtgcagtggtgag atcatagcttactgcagcctcaaactcctggactcaaacagtcctcccacctcagcctcccaaagtgctgggatacaggtgtgacc cactgtgcccagttattattttttatttgtattattttactgttgtattatttttaattattttttctgaatattttccatctatagttggttga atcatggatgtggaacaggcaaatatggagggctaactgtattgcatcttccagttcatgagtatgcagtctctctgtttatttaaag ttttagtttttctcaaccatgtttacttttcagtatacaagactttgacgttttttgttaaatgtatttgtaagtattttattatttgtgatgt tatttaaaaagaaattgttgactgggcacagtggctcacgcctgtaatcccagcactttgggaggctgaggcgggcagatcacga ggtcaggagatcaagaccatcctggctaacatggtaaaaccccgtctctactaaaaatagaaaaaaattagccaggcg gaga gcgc gcgc gaga gaga gaga gaga tctc tctc tctc gaga gaga gcgc tctc tctc tctc Some variants can explain phenotypic variation (in health and disease)

7. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX 7 Lessons from genome diversity The burden of deleterious mutations in the human genome 10,000 amino-acid altering mutations 300-400 stop/splice/indels disrupting 200-300 genes heterozygous at 50-100 mutations associated with an inherited disorder

8. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Impact of genetic variation on phenotypes 8 ACGTGTACAGAAGGGCCATGAACACTGTTATTACTCTTAC A C AATTGTGAGGCAGCCCTCGAGCCACAGGCGGGTCCAG CTGTTGGCTATAAACGGATAGCCTAC C GGTCTCTGATCGG AGATCACCATGTTTCTGGGTCCCTTGTACCCTGGATGCAG TACCTCGCCCCAGTTTCGCATACAAATTCGCATACAAAAC GTGTACAGAAGGGC C ATGAACACTGTTATTACTCTTACAC AATTGTGAGGCAGCCCTCGAGCCACAGGCGGGTCCA G CT GTTGGCTATAAACGGATAGCCTACCGGTCTCTGATCGGA GATCACCATGTTTCTGGGTCCC T TGTACCCTGGATGCAGT ACCTCGCCCCAGTTTCGCATACAAATTTCGCATACAAAAA Genetic Diversity Inter-Population Variation Phenotypic Diversity Inter-Individual Variation Personal genomics Personalised medicine

9. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Genome-wide association studies - GWAS 9 By September 2013: 11,304 SNPs associated with 891 traits/diseases (1,701 studies)

10. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX GWAS results in personalised medicine 10 Thomas et al. Nature. 2009 High p-values do not translate to clinically useful diagnostic assays Strong population variation (only useful in European populations)

11. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Healthy-based population approaches 11 Understanding patterns of population variation of our genomes Searching for the signatures of selection in the genome

12. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Population and evolutionary genetics 12 Variation in biological relevance in host defence of immune receptors Positive selection targeting protective mutations in Europeans Type-III IFNs and hepatitis CInnate immunity to infection Quintana-Murci & Clark. Nat Rev Immunol, 2013 Manry et al., J Exp Med, 2011

13. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Principles of cellular genomics Infection Drugs Radiation Untreated cellsTreated cells Variation in gene expression Genetic/epigenetic markers Gene-environment interactions Complex phenotypes Lack of mechanistic understanding Simpler phenotypes Focus on mechanisms

14. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Cellular genomics complementing GWAS 14 GWAS of TB have mostly failed in identifying susceptibility genes A recent cellular genomics study has identified >100 mutations that affect expression only after infection (response eQTLs) These mutations may contribute in an additive manner to susceptibility to develop TB - > added value of cellular genomics

15. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Integrative genomics Importance of taking first basic science approaches Need for understanding how genotypes affect phenotypes in BOTH health and disease Need for complementary approaches based on model systems Opportunities to tackle these questions at the highest resolution (e.g., NGS, rare variants, epigenetics) Improve methods in statistical genetics and computational biology (e.g., epistasis) 15

16. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX A path towards personalised medicine 16 ENVIRONMENTSLIFESTYLE GENETICS complete sequences EPIGENETICS Methylation, Histone modification HEALTH and DISEASE BIOMARKERS Responses to treatment Vaccine efficiency, doses PHENOTYPES Molecular phenotypes (expression) Cellular phenotypes Organismal phenotypes (traits or diseases) Model systems

17. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX 17

18. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Population and evolutionary genetics 18 Barreiro & Quintana-Murci, Nat Rev Genet, 2010 180 immunity-related genes targeted by positive selection

19. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Disease-based approaches 19 ApproachClinical geneticsEpidemiological genetics Phenotype Severe/acute (children) Milder/chronic (adults) ToolsMendelian GeneticsLinkage/association SampleSmallLarge Rare mutations Strong individual effect Common polymorphisms Modest individual effect Little public health impactStrong public health impact

20. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Limitations of disease-only-based approaches Associations based on strict statistic thresholds Disease is a complex phenotype Odds ratios remain rather low Assumption of genes acting alone Causal mutations remain mostly unidentified - > Need for complementary approaches 20

21. CEACHRUCNRSCPUINRAINRIAINSERMINSTITUT PASTEURIRD ARIISEFSINERISINSTITUT CURIEINSTITUT MINES-TELECOMUNICANCERIRBAIRSNCIRADFONDATION MERIEUX Using simpler phenotypes (molecular) Expression is a molecular phenotype that varies between individuals and populations Levels of expression can be under genetic control (eQTL) 21 GenotypemRNA M. tuberculosis 1/3 of the worlds population infected with Mycobacterium tuberculosis (MTB) Only 10% of infected individuals will develop the active form of the disease Environment