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1 Supplementary Information Two new susceptibility loci for Kawasaki disease identified through genome-wide association analysis Yi-Ching Lee 1,2, Ho-Chang Kuo 3,4, Jeng-Sheng Chang,Luan-Yin Chang 6,1, Li-Min Huang 6,1, Ming-Ren Chen 7, Chi-Di Liang 3,4, Hsin Chi 7,1, Fu-Yuan Huang 7, Meng-Luen Lee 8, Yhu-Chering Huang 9,10,1, Betau Hwang 11, Nan-Chang Chiu 7,1, Kao-Pin Hwang 3,12,13,1, Pi-Chang Lee 14, Li-Ching Chang 1, Yi-Min Liu 1, Ying-Ju Chen 1, Chien-Hsiun Chen 1,13, Taiwan Pediatric ID Alliance 1, Yuan-Tsong Chen 1,16*, Fuu-Jen Tsai 13,17,18* 1, 13*, Jer-Yuarn Wu 1 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 2 Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan 3 Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan 4 Graduate Institute of Clinical Medical Science, Chang Gung University College of Medicine, Kaohsiung, Taiwan. Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan 6 Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan 7 Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan 8 Department of Pediatrics and Divisions of Pediatric Cardiology, Changhua Christian Hospital, Changhua, Taiwan 9 Division of Pediatric Infectious Diseases, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan 10 Chang Gung University College of Medicine, Taoyuan, Taiwan 11 Department of Pediatrics, Taipei City Hospital, ZhongXiao Branch, Taipei, Taiwan 12 Division of Pediatrics Infectious Diseases, Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan 13 School of Chinese Medicine, China Medical University, Taichung, Taiwan 14 Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan. 1 Taiwan Pediatric ID Alliance. A complete list of the Alliance and affiliations appears at the Supplementary Note. 16 Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of American 17 Department of Medical Genetics, China Medical University Hospital, Taichung, Taiwan 18 Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan 1

2 Supplementary Note Taiwan Pediatric ID Alliance: Luan-Yin Chang, Chun-Yi Lu, Pei-Lan Shao, Li-Min Huang (Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan) Nan-Chang Chiu, Hsin Chi, Daniel Tsung-Ning Huang (Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan) Hsiao-Chuan Lin, Kao-Pin Hwang, Ting-Yu Yen, Tsung-Hsueh Hsieh (Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan) Yungling Leo Lee (Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan) Ching-Chuan Liu, Shih-Min Wang (Department of Pediatrics, National Cheng-Kung University Hospital, Tainan, Taiwan) Shun-Cheng Yang (Department of Pediatrics, Changhua Christian Hospital, Changhua, Taiwan) Yu-Chia Hsieh, Yhu-Chering Huang, Cheng-Hsun Chiu (Department of Pediatrics,Chang Gung Hospital, Taoyuan, Taiwan) Jin-Town Wang (Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan) Yu-Huai Ho (Department of Pediatrics, Tzu Chi University, Hualien, Taiwan) Jung-Jung Mu (Research and Diagnostic Center, Centers for Disease Control, Taiwan) Yi-Chuan Huang (Department of Pediatrics, Chang Gung Hospital, Kaohsiung, Taiwan) Supplementary Figures 2

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5 Supplementary Figure 1: Principal components analysis and Q Q plot for the trend test. (a) We used EIGENSTRAT 2.0 to conduct principal components analysis (PCA) with HapMap III data to correct our data for population stratification in GWAS. PCA was carried out based on the genotype data of 40,000 SNPs, roughly equal spacing across the human genome and selected from 716,93 high-quality SNPs in KD

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Supplementary Figure 2: The LD structure and logistic regression analyses in BLK region. (a) LD patterns, D value and r 2 among the disease-associated SNPs (P < 2.7 10-6 ) in BLK region.

7 Supplementary Figure 2: The LD structure and logistic regression analyses in BLK region. (a) LD patterns, D value and r 2 among the disease-associated SNPs (P < ) in BLK region. (b) The P-values for the rs and the linked SNPs in logistic regression models conditioned on rs The insignificant effects of the linked SNPs in the logistic regression models conditioned on rs indicated the linked SNPs were individually confounded with rs due to the strong LD with rs In particular, rs and rs were confounded that one showed 7

an insignificant association when conditioned on the other. Supplementary Figure 3: The LD structure and logistic regression analyses in CD40 region.

8 an insignificant association when conditioned on the other. Supplementary Figure 3: The LD structure and logistic regression analyses in CD40 region. (a) LD patterns, D value and r 2 among the disease-associated SNPs (P < ) in CD40 region. (b) The P values for the rs and the linked SNPs in logistic regression models conditioned on rs The insignificant effects of the linked SNPs in the logistic regression models conditioned on rs indicated all of the linked SNPs were individually confounded with rs due to the strong LD with rs

9 Supplementary Figure 4: Regional association, recombination rate, and linkage disequilibrium plots at the Chr 19 ITPKC/MIA regions. Top panel: regional association plot and recombination rate for the associated region, with gene annotations superimposed. The log 10 P values (left y-axis) for the trend test from the primary GWAS scan are shown as blue diamonds, and the red squares represent joint analysis of the GWAS and replication study. The estimated recombination rates (right y-axis) based on the Chinese HapMap population are plotted in light green across the region. Bottom panel: Regional LD plot (using D algorithm) for all SNPs in the top panel using data from the GWAS. Gene annotations are based on NCBI Build

10 Supplementary Figure : Regional association plots at the Chr 6 MHC region. The log 10 P values (y-axis) for the trend test from the primary GWAS scan are shown as blue diamonds. 10

11 Supplementary Table 1: Quality control of participant data. Number at start of QC 90,38 SNPs SNPs dropped during exclusion steps: Nonpolymorphic in patients and controls Call rate in patients or controls <9% Overall MAF < % and total call rate <99% HWE for control (P < 10 4 ) with polymorphic in control Number at end of QC 66,429 SNPs 66,46 SNPs 23,130 SNPs 32,318 SNPs 716,93 SNPs HWE, Hardy Weinberg equilibrium; MAF, minor allele frequency; QC, quality control. 11

12 Supplementary Table 2: All SNPs (n = 101) with P trend < 10 4 in the GWAS. Risk RAF RAF Risk allele OR Chr SNP Position Gene Allele Allele Controls Patients Trend P (9%CI) 1 rs no gene AC A E ( ) 1 rs RNF187 CT T E ( ) 2 rs no gene CT T E ( ) 2 rs no gene AG G E ( ) 2 rs no gene CT C E ( ) 3 rs LOC AC A E ( ) 3 rs SLC6A6 AG A E ( ) 3 rs SLC12A8 CG C E ( ) 3 rs COPB2 CG G E ( ) 3 rs COPB2 AC A E ( ) 3 rs COPB2 AG G E ( ) 3 rs COPB2 CT C E ( ) 3 rs PPM1L AG G E ( ) 4 rs SRDA2L2 AG G E ( ) 4 rs SRDA2L2 AC A E ( ) 4 rs SRDA2L2 CT T E ( ) 4 rs LOC64699 GT T E ( ) 4 rs LOC64699 AG G E ( ) 4 rs LOC64699 CT T E ( ) 4 rs LOC64699 GT T E ( ) 4 rs DDX60L AG A E ( ) 4 rs DDX60L GT T E ( ) rs LOC7283 AG A E ( ) rs no gene AT A E ( ) 6 rs LOC CT C E ( ) 6 rs LOC CG C E ( ) 6 rs LOC AG G E ( ) 6 rs LOC CG G E ( ) 6 rs LRRC16 AG G E ( ) 6 rs LRRC16 CG C E ( ) 6 rs PARK2 AG A E ( ) 6 rs PARK2 AC A E ( ) 7 rs no gene AT T E ( ) 7 rs BMPER AC A E ( ) 7 rs FLJ23834 CG G E ( ) 12

13 7 rs no gene CT T E ( ) 8 rs no gene AT A E ( ) 8 rs BLK CT T E ( ) 8 rs BLK CT T E ( ) 8 rs BLK AG G E ( ) 8 rs BLK AG A E ( ) 8 rs BLK AG G E ( ) 8 rs BLK CG G E ( ) 8 rs BLK CT C E ( ) 8 rs BLK AG G E ( ) 8 rs BLK AC A E ( ) 8 rs BLK CG G E ( ) 8 rs BLK CT C E ( ) 8 rs BLK AT T E ( ) 8 rs no gene CT C E ( ) 8 rs no gene CT C E ( ) 8 rs MED30 AG G E ( ) 8 rs MED30 CT C E ( ) 9 rs ROR2 CT T E ( ) 10 rs no gene CT T E ( ) 11 rs no gene AG G E ( ) 11 rs SPI1 AC A E ( ) 11 rs SPI1 CG G E ( ) 11 rs SPI1 AG A E ( ) 11 rs SPI1 CT T E ( ) 11 rs MTCH2 AG G E ( ) 11 rs no gene AG A E ( ) 11 rs no gene AG G E ( ) 11 rs no gene AG G E ( ) 11 rs CADM1 CT T E ( ) 12 rs CLEC4A GT G E ( ) 13 rs HS6ST3 GT T E ( ) 13 rs COL4A2 CT T E rs KNS2 CT C E ( ) 1 rs ARPP-19 AG G E rs no gene AC C E ( ) 1 rs BTBD1 CT C E ( ) 1 rs BTBD1 AG G E ( ) 13

14 1 rs BTBD1 CT C E ( ) 16 rs CLEC3A AG G E ( ) 16 rs CLEC3A AC A E ( ) 16 rs CLEC3A AG G E ( ) 16 rs CLEC3A CT T E ( ) 16 rs CLEC3A AC A E ( ) 16 rs IRF8 CT T E ( ) 16 rs IRF8 CT T E ( ) 16 rs IRF8 AG A E ( ) 16 rs IRF8 GT T E ( ) 19 rs ITPKC AG A E ( ) 19 rs MIA AC C E ( ) 19 rs MIA CT T E ( ) 19 rs MIA AT A E ( ) 20 rs PROKR2 AG G E ( ) 20 rs PROKR2 AG G E ( ) 20 rs PROKR2 AG A E ( ) 20 rs CD40 CT C E ( ) 20 rs CD40 AC A E ( ) 20 rs CD40 CT C E ( ) 20 rs CD40 AC A E ( ) 20 rs CD40 GT G E ( ) 20 rs CD40 AC C E ( ) 20 rs CD40 CT C E ( ) 20 rs CD40 AG A E ( ) 20 rs CD40 GT T E ( ) 20 rs CD40 CT T E ( ) 21 rs no gene AT T E ( ) Chr, chromosome; RAF controls, risk allele frequency in controls; RAF patients, risk allele frequency in KD patients; risk allele OR: risk-allele odds ratio; Trend P, P value derived from a one-degree-of-freedom of Armitage trend test. SNPs failed assay design for Sequenom platform were highlighted in yellow; SNPs not reach 99% successful rate or not reach 99% concordance between Affymetrix and Sequenom platform were highlighted in pink; SNPs departed significantly from Hardy Weinberg equilibrium (P< 10 4 ) in replication cohort were highlighted in light green; SNPs successfully analyzed in the replication collection were remained in white background. 14

15 Supplementary Table 3. SNPs with P < 10-4 in the KD GWAS collection and P <0.0 in the KD replication collection and results of joint analysis. RAF Allele Risk Control RAF Chr. SNP Position Gene format Allele Stage s Patients TrendP Risk Allele OR (9% CI) 3 rs COPB2 CG G GWAS Replication rs PPM1L AG G GWAS Replication rs SRDA2L2 AC A GWAS Replication rs BLK CT T GWAS Replication rs BLK CT T GWAS Replication rs BLK AG G GWAS Replication ( ) ( ) ( ) ( ) 1.81 ( ) ( ) ( ) ( ) ( ) 1.14 ( ) 1.91 ( ) 1.38 ( ) ( ) 1.43 ( ) ( ) ( ) ( ) 1.24 ( ) 1

16 8 rs BLK AG A GWAS Replication rs BLK AG G GWAS Replication rs BLK CG G GWAS Replication rs BLK CT C GWAS Replication rs BLK AG G GWAS Replication rs BLK AC A GWAS replication rs BLK CG G GWAS Replication rs BLK CT C GWAS Replication ( ) 1.18 ( ) ( ) 1.48 ( ) 1.1 ( ) ( ) 1.49 ( ) 1.7 ( ) ( ) 1.43 ( ) 1.3 ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) 1.42 ( ) ( ) ( ) 1.96 ( ) 16

17 rs BLK AT T GWAS replication rs MED30 AG G GWAS replication rs MED30 CT C GWAS replication rs CD40 AC A GWAS replication rs CD40 CT C GWAS replication rs CD40 AC A GWAS replication rs CD40 AC C GWAS replication rs CD40 CT C GWAS ( ) ( ) 1.33 ( ) ( ) ( ) 2.31 ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) 1.41 ( ) ( ) ( ) 1.38 ( ) ( ) 17

18 replication ( ) 1.34 ( ) 20 rs CD40 AG A GWAS ( ) replication ( ) ( ) Gene, genes containing the SNP or the closest gene up to 0 kb up or downstream of the SNP; RAF controls, risk allele frequency in controls; RAF patients, risk allele frequency in KD patients; risk allele OR: risk-allele odds ratio; 9%CI, 9% confidence interval. The SNPs with genome-wide significance (P <10-8 in the joint analysis) were highlighted with bold typeface. 18

19 Supplementary Table 4: The 4 P-values of 23 SNPs resulted from (1) the original association analysis (2) analysis with PCA justification (C1 to C10), (3) analysis after removing 4 outliers, and (4) analysis with PCA justification (C1 to C10) after removing 4 outliers. KW622SC1107 KW622SC1103 KW622SC1107 adjusted KW622SC1103 adjusted SNPs allele chr P trend P trend P trend P trend rs CG E E E E-04 rs AG E E E E-04 rs AC 4.726E E E E-0 rs CT E E E E-07 rs CT E E E E-0 rs AG E E E E-06 rs AG E E E E-06 rs AG E E E E-06 rs CG E E E E-06 rs CT E E E E-06 rs AG E E E E-0 rs AC E E E E-0 rs CG E E E E-0 rs CT E E E E-0 rs AT E E E E-0 rs AG E E E E-04 rs CT E E E E-04 rs AC E E E-0 rs CT E E E E-0 rs AC E E E E-07 rs AC E E E E-0 rs CT E E E E-0 rs AG E E E E-0 19

20 Supplementary Table : Results of heterogeneity test between GWAS and replication groups. Heterogeneity Trend-P Combined P a SNPs chr A1 A2 Q test I 2 GWAS Replicate rs G C E E E-0 rs G A E E E-0 rs A C E E-02.4E-07 rs C T E E E-09 rs C T E E E-07 rs A G E E E-09 rs G A E E E-08 rs A G E E E-08 rs C G E E E-08 rs T C E E E-08 rs A G E E E-07 rs C A E E E-07 rs C G E-0.62E E-07 rs T C E E E-08 rs A T E E E-06 rs G A E E E-07 rs C T E E E-07 rs C A E E E-06 rs T C E-0 3.9E E-06 rs C A E E E-09 rs A C E E E-07 rs T C E-0 3.9E E-07 rs G A E E E-06 a the combined P values were determined by Cochran-Mantel- Haenszel stratification analysis. 20

21 Supplementary Table 6: Association of the significant SNPs (P <10-4 ) in chromosome 19 q13 region in GWAS samples separated into previously reported GWAS samples and newly genotyped GWAS samples. SNP Allele Risk allele Stage RAF Controls RAF Patients Trend P rs AG A previous newly added total E-0 rs AC C previous newly added total E-06 rs CT T previous newly added total E-0 rs AT A previous newly added total E-0 RAF Controls: risk allele frequency in controls RAF Patients: risk allele frequency in KD cases Trend P: P-value derived from a 1 degree of freedom of Armitage trend test. Previous: The 20 KD samples and 446 control samples genotyped in previously report. (Tsai et al., PoLS ONE 6(2): e1683) New added: The newly genotyped samples including 372 KD samples and 661 controls Total: all 622 KD samples and 1107 samples. 21

22 Supplementary Table 7: The call rat, MAF, HWEP and association of SNPs, rs , rs , rs223312, within Chr.19q13 in GWAS and replication studies Stage Minor Call rate MAF HWEP Call rate MAF HWEP SNP Allele Allele Controls Controls Controls Patients Patients Patients Trend P rs GWAS AG A E-0 Rep rs GWAS AC C E-06 Rep rs GWAS CT T E-0 Rep Rep.: the replication stage MAF Controls: minor allele frequency in controls MAF Patients: minor allele frequency in KD cases Trend P: P-value derived from a 1 degree of freedom of Armitage trend test. 22

23 Supplementary Table 8: The SNPs in chromosome 1 FCGR2A region with P < 0.00 in the GWAS samples separated into previously reported GWAS samples and newly genotyped GWAS samples and their. SNP Allele Risk allele RAF Controls RAF Patients Trend P rs AG A previous newly added total rs CT C previous newly added total rs64279 AG G previous newly added total rs7347 AC C previous newly added total rs AG G previous newly added total rs CT T previous newly added total RAF Controls: risk allele frequency in controls RAF Patients: risk allele frequency in KD cases Trend P: P-value derived from a 1 degree of freedom of Armitage trend test. Previous: The 20 KD samples and 446 control samples genotyped in previously report. (Tsai et al., PoLS ONE 6(2): e1683) New added: The newly genotyped samples including 372 KD samples and 661 controls Total: all 622 KD samples and 1107 samples. 23

24 Supplementary Table 9: Demographic and clinical characteristics of participants in the GWAS and replication study. Characteristics GWAS cohort Follow-up cohort Patients (male%) 622 (64.31%) 261 (62.07%) CAA a / PE b (%) 16/86 (28.11%) 73/223 (32.74%) Control (male%) 1107 (48.87%) 0 (8.18 %) a CAA: significant coronary artery dilatation on echocardiogram at 4-8 weeks after the onset of the illness b PE: patients with echocardiographic data available 24

Supplementary Figure 1. Study design of a multi-stage GWAS of gout.

Supplementary Figure 1. Study design of a multi-stage GWAS of gout. Supplementary Figure 2. Plot of the first two principal components from the analysis of the genome-wide study (after QC) combined with