Supplementary Material to. Genome-wide association study identifies new HLA Class II haplotypes strongly protective against narcolepsy

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1 Supplementary Material to Genome-wide association study identifies new HLA Class II haplotypes strongly protective against narcolepsy Hyun Hor, 1,2, Zoltán Kutalik, 3,4, Yves Dauvilliers, 2,5 Armand Valsesia, 3,4,6 Gert J. Lammers, 7 Claire E.H.M. Donjacour, 7 Alex Iranzo, 8 Joan Santamaria, 8 Rosa Peraita Adrados, 9 José L. Vicario, 10 Sebastiaan Overeem, 11,12 Isabelle Arnulf, 13 Ioannis Theodorou, 14 Poul Jennum, 15 Stine Knudsen, 15 Claudio Bassetti, 16 Johannes Mathis, 17 Michel Lecendreux, 18 Geert Mayer, 19 Peter Geisler, 20 Antonio Benetó, 21 Brice Petit, 1 Corinne Pfister, 1 Julie Vienne Bürki, 1 Gérard Didelot, 1 Michel Billiard, 5 Guadalupe Ercilla, 22 Willem Verduijn, 23 Frans H.J. Claas, 23 Peter Vollenwider, 24 Gerard Waeber, 24 Dawn M. Waterworth, 25 Vincent Mooser, 25 Raphaël Heinzer, 26 Jacques S. Beckmann, 3,27 Sven Bergmann, 3,4 and Mehdi Tafti 1,26 *

2 Supplementary Note Extended 8.1 haplotype analysis We estimated the extent of the discovered protective haplotype (DRB1*1301-DQB1*0603) by phasing our genotype data (using PLINK 1 ) to reveal all HLA 8.1 ancestral haplotypes present in our population. We then selected individuals that carried exactly one copy of the DRB1*1301-DQB1*0603 haplotype and one copy of the DRB1*1501-DQB1*0602. Next we examined whether they carry shared HLA-A*0101-HLA-B*0801 haplotype, in which case the DRB1*1301-DQB1*0603 signal could extend to the full 8.1 extended ancestry haplotype. Tagging SNPs rs , rs and rs , rs were used for HLA-A and HLA-B, respectively. Only the CATT haplotype was shared among the DRB1*1301-DQB1*0603 controls, but this haplotype was frequently found also in non- DRB1*1301-DQB1*0603 carriers (Supplementary Figure 2a). This excludes that the protective signal extends beyond the HLA Class II region. For the DRB1*0301-DQB1*0200, we found that CACT is the only haplotype that is found in (almost) all DRB1*0301-DQB1*0200 carriers, but this haplotype is frequent amongst DRB1*0301-DQB1*0200 non-carriers too. This again, illustrates that the newly discovered signal cannot extend beyond the HLA Class II region. CNV analysis For the CNV analysis we derived copy number (CN) ratios from the raw CEL files. These ratios allowed us to estimate whether a genomic region is duplicated or deleted compared to a reference. All the normalization steps were done using the Aroma.affymetrix framework 1 and included Allelic Cross-talk calibration 2 to correct for differences between SNP s and offset in CN probes; intensity summarization using Robust Median Average and correction for any PCR amplification bias inherent to the Affymetrix SNP platform. To estimate the CN ratios for a given sample at a given SNP or CN probe, we computed the log 2 ratio of the normalized intensity of this probe divided by the median across all the samples from the same batch.

3 Raw copy number ratios were smoothed along physical position using Loess filtering with a 41-probe window size. Next, four component Gaussian mixture model (one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy) was fitted to the smoothed copy number ratios with a constraint on the difference between the mixture means. Next, for a given individual we determined the probabilities for each copy number states. The copy number was finally determined as the expected copy number (dosage) and rounded to the nearest integer. Since CNV calls showed batch-specific hybridization efficiency, we used the batch-incidence matrix as covariate in addition to the principal components to correct for the batch effect. This substantially reduced the effective sample size, since batches with only case/control subjects were ignored. The subsequent genome-wide search for association between narcolepsy and CNVs revealed three genomic regions within the HLA class II region (best hit probe CN_425606, P = 4 x ). These CNV regions are part of previously identified CNVs 3-8 : (1) the first region extends approximately 40kb ( ) and contains HLA-DRB5; (2) the second region ( ) is 25kb long and contains the HLA-DQA1 gene; (3) the last region ( ) is 10kb long and is in between DQB1 and DQA2 (Supplementary Figure 1). No other genomic region showed significant (P < 10-6 ) association with narcolepsy in our sample. However, considering that genomic reorganizations within the HLA Class II region, due to the presence or absence of different DRB1 gens and several pseudogenes, give rise to at least 8 different haplotypes, the 3 identified CNVs may not be independent of HLA class II haplotypes. Accordingly, qpcr analysis indicated that the first CNV mainly tags the presence of DRB5, which is only present within the DRB51 (DRB1*15 and DRB1*16) haplotype. Note that more cases are DRB1*1501 homozygous and that among DRB1*1501 heterozygous, DRB1*1601 is significantly increased in cases. The second CNV could not be confirmed by qpcr and did not yield any multiple copy number. This apparent/pseudo CNV might stem from the high polymorphism of the region resulting in different hybridization signals. The third CNV corresponds to a hot spot of recombination immediately centromeric to DQB1. Note that SNP rs (32,808,061) is located just 2.5kb centromeric of this CNV region. Again this CNV could not be confirmed to be independent of HLA haplotypes, indicating that these CNVs are common genomic reorganizations reliably tagged by SNPs and HLA haplotypes, as recently found also in several other HLA-associated disorders 9.

4 Supplementary Table 1. Genome-wide association top hit SNPs (p<10-5 ) Chr Pos rs# A B r-sqhat AF 9 AF (case) odds ratio odds ratio CI95 P Gene Distance (kb)* rs A G [ ] 6.50E-06 UGT2B rs A G [ ] 1.44E-06 OR12D rs A G [ ] 2.04E-06 GABBR rs A C [ ] 7.37E-06 SORCS rs C T [ ] 7.32E-06 SORCS rs C T [ ] 7.54E-06 ATP12A rs C T [ ] 3.38E-06 LAMA1 0 Chr: chromosome, Pos: physical map position, r-sq-hat: imputation quality, AF: frequency, CI95: 95% confidence interval, * 0 indicate that the SNP maps within the indicated gene. In case when multiple hits are all below the threshold and are within 10kb from each other, only the one with the lowest p-value is reported.

5 Supplementary Table 2. Replication attempt of two selected top hits from Supplementary Table 1 Chr Pos rs# Gene Distance to Gene (kb) risk other r-sq-hat rs ATP12A 8 T C rs LAMA1 0 C T 1 stage effect freq controls cases odds ratio odds ratio CI95 discovery [ ] 7.54x10-6 replication [ ] 0.9 combined [ ] 1.89x10-5 discovery [ ] 3.38x10-6 replication [ ] 0.8 combined [ ] 2.01x10-5 P Abbreviations as in Supplementary Table 1. Supplementary Table 3. Genome-wide analysis of SNP associations (p<10-5 ) in HLA-DRB1*1501 positive individuals. Chr Pos rs# A B r-sqhat AF 9 AF (case) odds ratio odds ratio CI95 P Gene Distance (kb) rs A T [ ] 5.14E-06 SLC2A rs A G [ ] 5.68E-06 NOTCH rs G T [ ] 1.14E-07 C6orf rs C G [ ] 8.62E-07 BTNL rs A C [ ] 4.65E-08 HLA-DQA rs A G [ ] 2.31E-06 FLJ rs A G [ ] 5.98E-06 NTF rs C T [ ] 8.94E-06 BTG rs A G [ ] 4.67E-06 HAL rs G T [ ] 5.81E-06 SNX rs C T [ ] 2.90E-06 CACNG5 27 Abbreviations as in Supplementary Table 1.

6 Supplementary Figure 1. Phased extended 8.1 haplotype structure of the HLA-DRB1*1501/HLA- DRB1*03-DQB1*02 (a) (b) (a) Extended 8.1 haplotype configurations for DRB1*1301-DQB1*0603 carriers and non-carriers. No single HLA-A-HLA-B haplotype can distinguish between DRB1*1301-DQB1*0603 carriers and non-carriers. (b) Extended 8.1 haplotype configurations for DRB1*03-DQB1*02 carriers and non-carriers. Here, again, no single HLA-A-HLA-B haplotype can distinguish between DRB1*03-DQB1*02 carriers and non-carriers.

7 Supplementary Figure 2. Manhattan plot for CNV and SNP associations in the HLA region (a) (b) (a) Manhattan plot for SNP and CNV associations in the HLA region. For this analysis we used the batch incidence matrix as covariates in the logistic regression (both for SNPs and CNVs to retain comparability of the results). One can observe that the top CNV and SNPs signals are of the same strength hence one cannot determine causality. (b) Manhattan plot for SNP and CNV associations in the HLA region for HLA positive individuals only corrected for the copy number of the HLA-DRB1 haplotype. For this analysis we used the batch incidence matrix and the rs genotype as covariates in the logistic regression (both for SNPs and CNVs to retain comparability of the results). HLA-DRB1*1501 independent CNV signals emerge in the DRB5 and DQA1 regions.

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