Frida Lundmark, Kristina Duvefelt, Ellen Iacobaeus, Ingrid Kockum, Erik Wallström,

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1 Title Variations in the interleukin 7 receptor α chain gene influence the risk of multiple sclerosis Authors Frida Lundmark, Kristina Duvefelt, Ellen Iacobaeus, Ingrid Kockum, Erik Wallström, Mohsen Khademi, Annette Oturai, Lars P Ryder, Janna Saarela, Hanne F Harbo, Elisabeth G Celius, Hugh Salter, Tomas Olsson, Jan Hillert

2 Supplementary Table 1. Numbers of patients and controls included in the confirmatory study and the following tag- SNP fine-mapping study. Sweden 1 refers to the patients included in the paper by Zhang et al. Country MS CTR Confirmation study tagsnp study Denmark yes no Finland yes no Norway yes no Sweden Group 1 * no yes Sweden Group yes yes

3 Supplementary Table 2. Estimation of haplotype frequencies was performed in Haploview. We chose to describe the haplotypes consistently by the allelic nucleotides carried by the + strand, whereas in the previous report 4 haplotypes were described by a mixture of + and strand nucleotides. Global P-values were obtained performing 10,000 permutations of haplotype-count distributions and haplotype P-values were calculated using a chi-square test, as implemented in Haploview. Permutation tests with 10,000 permutations showed significant P-values for both associated haplotypes. Haplotype MS patients Controls Global P Haplotype P Haplotype P permutation Haplotype 1 CAA Haplotype 2 TTG Haplotype 3 CTA

4 Supplementary Table 3. Tagging properties of SNP markers used.. SNP Location Alleles Capture Location of captured SNPS 1 2 rs ' C T X X rs intron 3 C T rs intron 1 rs intron 1 G T rs intron 1 rs intron 2 rs intron 1 rs intron 1 G T rs intron 4 rs intron 5 rs intron 6 rs intron 6 rs exon 8, nonsyn rs rs rs rs rs X X rs intron 3 G T rs rs A C rs intron 2 rs intron 4 rs intron 4 rs intron 6 rs rs rs rs rs rs rs X X rs A T rs intron1, rs intron 3 A T rs intron 1 rs intron1, rs exon2, nonsyn rs intron 2 rs intron 2 rs intron 2 rs intron 2 rs intron 2 rs intron 3 rs intron 3 rs intron 3

5 rs intron 3 rs intron 3 rs intron 3 rs intron 3 rs exon 4, nonsyn rs rs rs rs rs rs intron 4 rs A G rs rs rs rs rs rs rs C T rs intron 1 rs intron 1 rs intron 2 rs exon 6 rs rs rs rs rs rs rs rs exon 6 C T rs exon 4 C T

6 Supplementary Table 4. Results from the logistic regression analysis, to determine the best logistic regression model. The analysis included one SNP in each model for six associated SNPs. Forward, stepwise and backward selection was used to determine the best fit. Model -2logL P-value Intercept only rs co-dominant rs dominant rs recessive rs co-dominant rs dominant rs recessive rs co-domiant ns rs domiant rs recessive ns rs co-domiant rs dominant rs recessive ns rs co-domiant rs dominant rs recessive ns rs co-domiant ns rs dominant rs recessive ns

7 Supplementary Table 5. Haplotype frequencies were estimated using Haploview, and haplotype P-values were calculated using a chi-square test. A permutation test based on 10,000 permutations was performed in order to correct for multiple testing. Haplotypes were constructed using SNPs 1-12, i.e. the markers within the LD block (Table 2). The 3-marker haplotype presented in Supplementary table 2 are indicated in bold. Number Haplotype MS patients Controls Haplotype P Haplotype P permutation 1 TGTAGTTCTATC TTTAGTCTTGTT ns 3 TGCTGCCCAACT ns 4 TGTAGTCCAATT ns 5 GGTTGCCCAACT ns

8 Supplementary Table 6. Primer sequences of primers used in the SNP genotyping and mrna expression assays. Assay Amplification primer 1 Amplification primer 2 Extension primer rs ACGTTGGATGCTTCCTGATAGCTCTCACTC ACGTTGGATGCAAAAGCTTATGAAGAGGGTC GAAGAGGGTCATATGACA rs ACGTTGGATGCATCACGGAAGGCAATCTAC ACGTTGGATGGCGAATAGGGAATGCTAAAAG gaaaagtatttttaagacatggtt rs ACGTTGGATGAAAGCTGGGTTTTCACTCC ACGTTGGATGGACGTAATCATGTGAATAGGG AGGGTAATTATACATCTTCTAAAA rs ACGTTGGATGCAAGGCTTTACACTGGAGAC ACGTTGGATGGAAAGTGCTATTCGGACAG GGTCTCTGGGACAATCAACT rs ACGTTGGATGTGAAGAAGAGTGAGCCTCAG ACGTTGGATGTTCAGGCCCCTGTAAAATGG gagggtttaaagggatccaaat rs ACGTTGGATGTCCAGTTACCAAAGAACCTC ACGTTGGATGTTTTTGTTGTAGAGGCAGAC TAGAGGCAGACCTCTTC rs ACGTTGGATGCACCACAAAGTCATTGGCTC ACGTTGGATGTTTCCAGTTAAACCTGAGGC cctctccttttgacctgagtgtc rs ACGTTGGATGTTCCACATGTGCATAAACAG ACGTTGGATGAAGCCCAGCCTTCAACCAAG TTTCCTACCAGAGGCACTT rs ACGTTGGATGCATCTTCCAACCCAGTAAGG ACGTTGGATGACTCTGCTAAGAGAAGTGGG GAAGTGGGAAGGCAGGA rs ACGTTGGATGATGAGCTTACTCAACGTAGG ACGTTGGATGAGATTCGAATCTGTCAGCCC ccccctccaagagtagatcca rs ACGTTGGATGGGTTGTGTCCTCAAATTAAA ACGTTGGATGGTGACTATTCCTGAAGAGTG tacatcttcaacttgatacattac rs ACGTTGGATGAAGATGACCAACAGAGCGAC ACGTTGGATGCAGGGGAGATGGATCCTAT GGAGATGGATCCTATCTTACTAA rs (hme) ACGTTGGATGGGCCATACGAAGGCTTAATC ACGTTGGATGAAGTGGGAAGACTCAGTGTG TGCCATTCACTTCATCT rs (iplex) ACGTTGGATGGCCATACGATAGGCTTAATC ACGTTGGATGAAGTGGGAAGACTCAGTGTG TGCCATTCACTTCATCT rs (hme) ACGTTGGATGGGATGAATCTCTTCCAAAGC ACGTTGGATGATCTGAGAAGCAGAGGCTTG CCATCTGAGGATGTAGTC rs (iplex) ACGTTGGATGGGATGAATCTCTTCCAAAGC ACGTTGGATGATCTGAGAAGCAGAGGCTTG GGGCCATCTGAGGATGTAGTC rs (iplex) ACGTTGGATGCCCCGTTGTTTACTCCCAAT ACGTTGGATGAATATTCCCCCACTTCCACC TAGCTGCCAGAGTTGCT rs (hme) ACGTTGGATGATATTCCCCCACTTCCACCA ACGTTGGATGTAACCCCGTTGTTTACTCCC CTTTTTATTTCTTCTCTTTACTGA IL7 (mrna) CCAGTTGCGGTCATCATGAC GGATGGATCGAACTTTAATCTCATACA IL7R (mrna) GATGAAAACAAATGGACGATGT GGATGGATCGAACTTTAATCTCATACA GAPDH (mrna) AGGGCTGCTTTTAACTCTGGTAAA CATATTGGAACATGTAAACCATGTAGTTG