Supplementary Information IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy.
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1 Supplementary Information IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Vijayaprakash Suppiah, Max Moldovan, Golo Ahlenstiel, Thomas Berg, Martin Weltman, Maria Lorena Abate, Margaret Bassendine, Ulrich Spengler, Gregory J. Dore, Elizabeth Powell, Stephen Riordan, David Sheridan, Antonina Smedile, Vincenzo Fragomeli, Tobias Müller, Melanie Bahlo, Graeme J. Stewart, David R. Booth and Jacob George for the Hepatitis C Study Page(s) Description 1 Index Supplementary Index 2-5 Supplementary Table 1 SNPs genotyped in the replication phase of the study. 6 Supplementary Table 2 Distribution of genotypes of rs for responders and non-responders. 7 Supplementary Table 3 Fine mapping of SNPs from the IL28A/B and IL29 region. 8 Supplementary Table 4 Distribution of haplotypes within chromosome 19 region containing IL28A/B and IL29 genes for responders and nonresponders. 9 Supplementary Figure 1 Genome-wide association results (a) P values are shown in signal-intensity (Manhattan) plot relative to their genomic position comparing 162 nonresponders and 131 responders (Stage 1). Within each chromosome, the results are plotted left to right from the p- terminal end. (b) Quantile-Quantile plot of allelic association analysis of expected versus observed p-values calculated from these genotypes. 10 Supplementary Figure 2 Haplotype distribution within the study population. Blocks 1 (markers 1-2), 2 (markers 4-7, 9-11) and 3 (markers 16-17) correspond to SNPs rs , rs , rs , rs , rs , rs , rs , rs , rs , rs and rs respectively. 11 Supplementary Note Membership list of the Hepatitis C Study Team 1
2 Supplementary table 1. SNPs genotyped in the replication phase of the study. SNP Chr Position P values* Reason for choosing rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Viral genome replication rs Viral genome replication rs Immune related gene rs dysregulation in gene expression rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Lipid metabolism rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs E-06 p<10-5 rs Immune related gene 2
3 rs Lipid metabolism rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs dysregulation in gene expression rs Lipid metabolism rs Lipid metabolism rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs E-08 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs E-06 p<10-5 rs E-05 p<10-5 rs Immune related gene rs Lipid metabolism rs Lipid metabolism rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs dysregulation in gene expression rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene 3
4 rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Lipid metabolism rs Lipid metabolism rs Lipid metabolism rs Lipid metabolism rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs dysregulation in gene expression rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs dysregulation in gene expression rs Immune related gene rs Immune related gene 4
5 rs Immune related gene rs Immune related gene rs Immune related gene rs Regulation of virion penetration into host cell rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs E-05 p<10-5 rs E-07 p<10-5 rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs E-05 p<10-5 rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene rs Immune related gene * P value of Cochrane-Armitage trend test. 5
6 Supplementary Table 2. Distribution of genotypes of rs for responders and non-responders. Genotype Responders Non-responders OR (95% CI)* GG 15 (3.8) 34 (7.5) 2.39 ( ) GT 130 (33.2) 227 (49.8) 1.64 ( ) TT 247 (63) 195 (42.7) - * OR and 95% CI calculated as carriage of G allele(s) as compared to T homozygotes. 6
7 Supplementary Table 3. Fine mapping of SNPs from the IL28A and IL28B region (Chr 19: ). P values* SNP Position Stage 1 Stage 2 Merged rs E-01 x x rs E-01 x x rs E-01 x x rs E-01 x x rs E E E-10 rs x 3.70E-04 x rs x 3.83E-04 x rs E E E-01 rs E E E-04 rs E E E-09 rs E E E-02 rs E-03 x x rs E E E-03 rs E E E-01 rs E-02 x x rs E-02 x x rs E-01 x x rs E-02 x x rs E-01 x x * P value from Cochrane-Armitage trend test In bold: SNPs with P values significant after correction for multiple testing 7
8 Supplementary Table 4. Distribution of haplotypes within chromosome 19 region containing IL28A/B and IL29 genes for responders and non-responders. Haplotype Marker nos. Freq. Responder:Non-responder Ratio Counts Responder:Non-responder Frequencies Block 1 Chi Square P Value ATC 1, 2, : 139.1, : , GGT : 150.1, : , GGC : 240.0, 46.0 : , AGC : 260.0, 4.1 : , Block 2* ATTTCT 5, 6, 7, 9, 10, : 392.5, : , E-03 GCCTAG : 630.1, : , E-09 GTCCAT : 693.0, : , ATTTAT : 675.1, 74.8 : , E-03 ATCTAT : 757.1, 17.5 : , GCCTAT : 765.2, 18.9 : , GTTTCT : 765.5, 8.4 : , Block 3 CG 16, : 50.1, : , TA : 225.0, 62.9 : , TG : 250.9, 13.2 : , * Block 2 clearly shows the association with response to treatment to be within IL28B (interferon lambda-3) gene region. In bold: Haplotype significantly associated with treatment response. Markers 1-2, 4-7, 9-11 and correspond to SNPs rs , rs , rs , rs , rs , rs , rs , rs , rs , rs and rs respectively. 8
9 Supplementary Figure 1. Genome-wide association results a. b. 9
10 Supplementary Figure 2. Haplotype distribution within the study population. 10
11 Supplementary Note Membership list of the Hepatitis C Study Team Study design and management: Vijayaprakash Suppiah 1,2, Graeme J. Stewart 2, David R. Booth 2, Jacob George 1 Sample processing, Data handling and genotyping: Vijayaprakash Suppiah 1,2, Lee Russell 1, Najwa Marmash 2, Monika Michalk 4, Barbara Malik 5, Vincenzo Fragomeli 6, Elizabeth Snape 6, David Sheridan 8, Richard Norris 10, Dianne How- Chow 10, Helen Barrie 11, Shona Fletcher 13 Data Analysis: Vijayaprakash Suppiah 1,2, Max Moldovan 3, Melanie Bahlo 3 Phenotyping: Golo Ahlenstiel 4, Ulrich Spengler 4, Tobias Müller 5, Thomas Berg 5, Martin Weltman 6, Maria Lorena Abate 7, Antonina Smedile 7, Margaret Bassendine 8, David Sheridan 8, Gregory J. Dore 9, 10, Julie R. Jonsson 11, Elizabeth Powell 11,12, Stephen Riordan 13, Sacha Stelzer-Braid 13, Jacob George 1 Affiliations: 1 Storr Liver Unit, and 2 Institute for Immunology and Allergy Research, Westmead Millennium Institute, University of Sydney, Sydney, Australia. 3 The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Victoria, Australia. 4 Department of Internal Medicine I, University of Bonn, Sigmund-Freud-Strasse 25, Bonn, Germany. 5 Medizinische Klinik m.s. Hepatologie und Gastroenterologie, Charité, Campus Virchow-Klinikum, Universitätsmedizin Berlin, Germany. 6 Department of Gastroenterology and Hepatology, Nepean Hospital, Penrith, Sydney, Australia. 7 University of Turin, Department of Internal Medicine, Liver Physiopathology Lab., Torino, Italy. 8 Liver Research Group, Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom. 9 National Centre in HIV Epidemiology and Clinical Research, University of New South Wales, Sydney, Australia and 10 St Vincent s Hospital, Sydney, Australia. 11 Princess Alexandra Hospital, Dept of Gastroenterology and Hepatology, Ipswich Rd, Woolloongabba, and 12 The University of Queensland, School of Medicine, Princess Alexandra Hospital, Ipswich Rd, Woolloongabba, Queensland, Australia. 13 Gastrointestinal and Liver Unit, Prince of Wales Hospital and University of New South Wales, Sydney, Australia. 11
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