GWAS GWAS GWAS 2 GWAS

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1 GWAS

2 GWAS GWAS GWAS 2 GWAS

Chapter 1 05 HapMap 06 GWAS 07 The Missing Heritability 08 Chapter 2

3 Chapter 1 05 HapMap 06 GWAS 07 The Missing Heritability 08 Chapter SNP 12 Chapter 3 GWAS Omni 15 GWAS Chapter

4 Chapter 1

5 Celera Genomics Human Genome Project HGP 1 HGP 30 25, SNP 5

6 HapMap HapMap HapMap Linkage Disequilibrium LD r 2 LD r 2 1 LD SNP tag SNP 6 GWAS

7 GWAS GWAS 2002 SNP DNA GWAS GWAS 5% Common Disease, Common Variant GWAS SNP 7

8 The Missing Heritability GWAS SNP GWAS SNP SNP 25% heritability 4 Missing Heritability GWAS Missing Heritability GWAS HapMap HapMap 5% 350 GWAS SNP 8 GWAS

$Heritability 100% Rare Common Disease \ Traits 80% 60%$

9 Heritability 100% Rare Common Disease \ Traits 80% 60% 40% 20% 0% Manolio et al 2009 SNP heritability SNP 9

10 Chapter 2

1000 1000 The 1000 Genomes Project: 1kGP HapMap

11 The 1000 Genomes Project: 1kGP HapMap MAF 1% SNP SNP SNP kGP kGP SNP GWAS 11

12 SNP 1000 SNP GWAS SNP SNP SNP SNP SNP GWAS SNP GWAS SNP SNP 1kGP SNP SNP Common Disease, Rare Variant GWAS 12 GWAS

13 ( SNP SNP GWAS ( 1 GWAS SNP SNP SNP ( ( SNP GWAS SNP SNP 13

14 Chapter 3 GWAS

15 Omni 1,000 SNP SNP Omni Omni GWAS Omni 1kGP GWAS 1% 500 SNP SNP Infinium Omni GWAS 500 SNP Omni Infinium tag SNP tag SNP InfiniumHD GWAS 15

16 GWAS Omni Omni Omni HumanOmni2.5 HumanOmni1 HumanOmniExpress 3 Omni2.5 Omni2.5 BeadChip 1kGP 4 2.5% 250 SNP Omni2.5 Omni2.5S BeadChip 1kGP 1% SNP Omni2.5 Multi-Use Omni2.5S Omni1 Multi-Use Omni1S Omni2.5S OmniExpress Multi-Use Omni1S Omni2.5S 16 GWAS

17 Omni1 Omni1 BeadChip HapMaptag SNP 1kGP MHC Omni1 Omni1S BeadChip120 SNP 1kGP 2.5% SNP 1kGP 1% SNP Omni2.5S BeadChip OmniExpress Omni1 OmniExpress BeadChip HapMaptag SNP 5% SNP 12 OmniExpress Omni1S BeadChip 1kGP 2.5% SNP Omni1 1kGP 1% SNP Omni2.5S BeadChip Omni OmniExpress Omni1 Omni 2.5 5% SNP 5% SNP CNV 1kGP 2.5% SNP CNV 17

18 r LD Omni SNP 2.5% S N P 1 k G P HapMap 1kGP HapMap 1kGP SNP Omni 1kGP Omni SNP 2.5% CEU 82% CHB/JPT 83% YRI 74% Omni SNP 50% r 2 > 0.8 % 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% CEU HapMap vs. 1KGP * 900K 660W Omni1 OmniExpress Omni2.5** r 2 > 0.8 % 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% CHB/JPT HapMap vs. 1KGP * 900K 660W Omni1 OmniExpress Omni2.5** r 2 > 0.8 % 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% YRI Coverage Estimates: HapMap vs. YRI HapMap vs. 1KGP Reference Data * 900K 660W Omni1 OmniExpress Omni2.5** HapMap > 5% MAF 1KGP > 5% MAF 1KGP > 2.5% MAF CEU: CEPH Utah; CHB: Chinese Han Beijing; JPT: Japanese Toyko; YRI: Yoruban * Coverage estimates represent the arraybase content ** Approximation based on preliminarymarker list 18 GWAS

19 Omni SNP SNP 5% SNP CNV Omni SNP InfiniumHD Omni 19

20 Chapter 4

21 SNP 21

22 Omni 1kGP SNP SNP 22 GWAS

23 GWAS1kGP Omni SNP CNV 23

24 References Manolio T, Collins F, Cox N, Goldstein D, Hindorff L, et al. (2009) Finding the missing heritability of complex diseases. Nature. 461(7265): Additional Resources Illumina GWAS Genotype Imputation Genotyping Rare Variants Multi-Use Sample Preparation Intelligent SNP Selection Illumina, Inc. All rights reserved. Illumina, IlluminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iselect, CSPro, GenomeStudio, Genetic Energy, HiSeq, HiScan Illumina, Inc Pub. No J015 15OCT10

Infinium BeadChip COGS BeadChip 4 * iselect 3 SNP 25 1 SNP NGS Sequencing by Synthesis SBS HiSeq MiSeq WGS 1 RNA-Seq ChIP-Seq 1 1 * icogs BCAC OCAC PR

Infinium BeadChip COGS BeadChip 4 * iselect 3 SNP 25 1 SNP NGS Sequencing by SynthesisSBSHiSeq MiSeq WGS 1 RNA-Seq ChIP-Seq 1 1 * icogs BCACOCAC PRACTICALBRCA1/2 CIMBA www.illuminakk.co.jp DNA CE DNA DNA