Introduction to Complex Genetics: Concepts and Tools Andr G - PowerPoint PPT Presentation

MolMed Course “ Genetics for Dummies ” Rotterdam, 1 November, 2017 Introduction to Complex Genetics: Concepts and Tools André G Uitterlinden Genetic Laboratory Department of Internal Medicine Department of Epidemiology Department of Clinical Chemistry www.glimdna.org Our website… Professor Trifonius Zonnebloem Professor Cuthbert Calculus Professeur Tryphon Tournesol

ROTTERDAM – OLDEBARNEVELDSTRAAT - MULTATULI Viewed from the moon we are all equal Portret gemaakt door Mathieu Ficheroux, 1974

DNA Differences cause Phenotype Differences

AGING RESEARCH

Genetics of Ageing…… 1953 1990 James Watson : 1928- Francis Crick : 1916-2004

From DNA to RNA to Protein.... . . . . A A C C G C A T A A G G DNA base pair . . . . T T G G C G T A T T C C “Genetics” sequence exon Gene structure “Genomics” mRNA “Proteomics” Protein

Why do we study DNA variation ? *Biology: - Mechanism : understand cause of disease - Treatment : finding new potential drug targets *Prediction: - (Early) diagnostics with a stable marker : understand how DNA variation contributes to variation in: - Risk of disease (vulnarability): “personalized medicine” - “Response -to- treatment” (medication, diet): “pharmacogenetics”

“The Human Genome Project” What will DNA tell about this stain in a dress Bill Clinton Tony Blair Craig Venter Francis Collins * 26 Juni 2000: Press conference Bill Clinton & Tony Blair: "working draft“, 95% gesequenced * 14 april 2003: finished: 99% gesequenced. >>Cheaper and Faster!! Costs: $ 2.7 miljard (instead of $ 3 billion estimated costs) Timing: 1990 - 2003 (instead of 2005)

AGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATT AGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGAC GTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGAT HUMAN DNA IS HIGHLY VARIABLE CGATGCTAGTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTA GTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGGAGTCTGACTGACCATTGGAC TAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGC GATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGAGTCT DNA Variants are: “SNP= Single Nucleotide Polymorphism ” GACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGA CGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTG *Frequent in the Genome (50k WGS/250k WES): CGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTA GTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGT - >150 million variable loci in genome (~3%) GGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGGAGTCTGACTGACCATTGGA C TAGGGGATT - “ SNPs ” , in/del, CNV, VNTR GACCAGTA G GCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGGA CTGAACGCCCCTCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGAGGAGTCTGACTGACCATTGGACTA - dbSNP, HapMap , 1KG, “ local ” NGS efforts,.. GGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGCGA “IN/DEL= Insertion Deletion ” TGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTAC CTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCT A GCTGATC GATCATCGATAACCG TAT AAGGGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATGC *Frequent in the Population: GATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGA TCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAAGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCTG > 5 % = common polymorphism CGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCC 1 – 5 % CGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGT = less common variant “CNV=Copy Number Variation ” CGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAGC < 1 % = rare variant/mutation TAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAAC AAAATAGC GGTATTTTGGAGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGAC GATTAAAAAGGAT TACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCT GACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTA GCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATC GATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGCTA GCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGG GGGTTAAATG CACACACACACACACACACACACACACACACACA GATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGGT GCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAG CTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTT “VNTR= Variable Nunber of Repeats ” AAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGAGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGG CTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCC CCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCA GTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGA

AGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATT AAAA AGGATTACGATT AGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGAC GTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGAT CGATGCTAGTAG C TAGCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTA GTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGGAGTCTGACTGACCATTGGAC TAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGC GATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGAGTCT GACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGAC G ATTAAAAAGGATTACGATTAGCTGTGA “SNP” CGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTG CGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTA GTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGT GGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGGAGTCTGACTGACCATTGGACTAGGGGATT GACCAGT A GGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGG ACTGAACGCCCCCCGGGCTTCTTTATTA G CT G CTGACGTGCCAGATGCTGACGTGCAGTGAGGAGTCTGACTGACCATTGGACT AGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGC GATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTA CCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGAT CGATCATCGATAACCG T ATAAGGGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATG CGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCG ATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAAGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCT GCGATTCGGATGCGGATTGACGATTAAAAAGGATTACGATTAGCTGTGAC G TGCAGGATGCTGCGATGCTGGACTGAACGCCCC T- C “HAPLOTYPE” CCGGGCTTCTTTATTAGCTGCTGACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAG TCGAT C GATCGATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAG CTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAA CAAAATAGCGGTATTTTGGAGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGAC GATTAAAAAGGATTACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTA G CTGCT GACGTGCCAGATGCTGACGTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTA GCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATC GATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGCTA GCTAGCTGA TCG ATCATCGATCGTAGCTAGCTAGCTAGCTAGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGG GGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCGGTATTTTGGGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATC GATCGTAGCGTAGCGTATGCTAGCTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGATCATCGATCGT A GCTAGCTAGCTAGCT AGCTGATCGATCGATGCTAGCTAGCTAGCTAGTCATCTGTGGTGGGGGGTTAAATGCGATTGCCGCTAGCTAGAACAAAATAGCG GTATTTTGGAGGAGTCTGACTGACCATTGGACTAGGGGATTGACCAGTAGGCTGCGATTCGGATGCGGATTGACGATTAAAAAGG ATTACGATTAGCTGTGACGTGCAGGATGCTGCGATGCTGGACTGAACGCCCCCCGGGCTTCTTTATTAGCTGCTGACGTGCCAGA TGCT G ACGTGCAGTGCGGCTGACGGTGCTTACCTGGATCGGATGCTACCAGTCGATCGATCGATCGTAGCGTAGCGTATGCTAG CTAGTGATCGATGCTAGTAGCTAGCTAGCTGATCGA

SNPs, alleles, genotypes and haplotypes SNP= Single Nucleotide Polymorphism Chromosomes: strand Allele A A C G from Father + + from Mother C G A T Genotype Haplotype Allele A A C G C G A T

Single Nucleotide Polymorphisms (SNPs) are common and have subtle effects Codon 222 Codon 222 ..AACCG C ATAAGG.. ..AACCG T ATAAGG.. ..TTGGC G TATTCC.. ..TTGGC A TATTCC.. DNA: C677T Alanine Valine protein: Ala222Val c u enzyme activity Ala Val Hcy level Population frequency: 65% 35% Disease risk

“Simple” versus “Complex” Disease Simple/Monogenic Disease Complex Disease • severe phenotype • mild phenotype • early onset • late onset • rare • common • Mendelian inheritance • complex inheritance • e.g.: cystic fibrosis, • e.g.: diabetes, asthma, osteogenesis imperfecta osteoporosis Mutations Polymorphisms Cause: (  1%) (< 1%)