Supplementary Note Additional contributors are presented in the following order: the data

coordinating center, the two genotyping teams (SLEGEN GWA and LLAS), and

then by center in the order of the number of case samples contributed:

= Data Analysis: Carl D. Langefeld, Ph.D., Wake Forest University

Paula Ramos, Ph.D. Matt L. Stiegert, M.A. Julie T. Ziegler, M.A.

= Genotyping: Stacey Gabriel, Ph.D., Broad Institute

Jamie Moore Amy Camargo Nicole Beattie Lauren Young Jason Carey

= Genotyping: Kenneth M. Kaufman, Ph.D., Oklahoma Medical Research Foundation Adam J. Adler

Trevor M. Rhoads Joshua W. Cavett Michelle M. Calvo Jeannie L. Te Tamiko L. Cabatic Keri B. Sherman Amanda J. Stramski Christen N. Gravlin Kim L. Nguyen Sofia I. Dozmorova

= Robert P. Kimberly, M.D. University of Alabama at Birmingham Graciela Alarcón, MD Gerald McGwin, Jr, MPH, PhD James M. Kelley, PhD Michelle Petri, MD, MPH (Johns Hopkins University, Baltimore, Maryland) Rosalind Ramsey-Goldman, MD, MPH (Northwestern University Feinberg School of Medicine, Chicago, Illinois) John Reveille, MD (University of Texas Health Science Center at Houston, Houston, Texas) Luis Vila, MD (University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico)

= John B. Harley, M.D. Ph.D. Oklahoma Medical Research Foundation

Teresa J. Aberle, PA-C Tena F. Broyles, RN Carisa M. Cooney Amanda B. Crosbie, MS Wesley E. Daniel Mark C. Drexel Lourdes M. Feo Stuart B. Glenn Ellen L. Goodmon Patti A. Grounds, MS Erica L. Jaramillo Sharon R. Johnson Jeffrey R. Kilpatrick Jean Morrisey, RN Monica Nall Jared W. Ning Tiny C. Powe Sandra G. Thayer, MS Joanne M. Tesiram, RN Courtney W. Weese Dominique B. Williams Jonathan D. Wren, PhD. Past contributors: Ida M. Adams Neeraj Asundi Drew Avery Kay Davis Sarah Dawson, MS Kurt Downing Marie H. Flesch, MS Phillip C. Garriott Debra Gentry Courtney Gray-McGuire, PhD Bryan Harris David C. Hutchings, MS Tuong Lam Jessica Lombard Catherine Pongratz Jeffrey Reid Roy Rindler Kimberly A. Rossacci Jonathan Stone Carrie Thornton Parvathi Vinod Joshua Weese Daniel Williams Hua Yu, MD

= Kathy L. Moser, University of Minnesota Jill Novitzke, RN Ward A. Ortmann (present address Genentech, Inc.) Peter R. Rodine Catherine A. Slattery

= Timothy J. Vyse, PhD, MRCP, Imperial College, London

Andrew K. Wong, PhD = Marta Alarcón-Riquelme, Uppsala University, Uppsala, Sweden

Gunnar Sturfelt (Lund University, Lund Sweden) Andreas Jönsen (Lund University, Lund Sweden) Lennart Truedsson (Lund University, Lund Sweden) Iva Gunnarsson (Karolinska University Hospital, Solna, Sweden) Elisabet Svenungsson (Karolinska University Hospital, Solna, Sweden) Kristjan Steinsson (Landspitali Hospital, Reykjavik, Iceland) Gerdur Gröndal (Landspitali Hospital, Reykjavik, Iceland) Helga Kristjansdottir (Landspitali Hospital, Reykjavik, Iceland) Ralph Williams Jr (University of New Mexico, Albuquerque, NM) Mauro Galeazzi (Policlinico LeScotte, Siena, Italy) Sergio Migliaresi (Second University of Naples, Naples, Italy) Gian Domenico Sebastiani (San Camilo Hospital, Rome, Italy) Alessandro Mathieu (University of Cagliari, Sardinia) Haralampos Moutsopoulos (University of Athens, Athens, Greece) Caroline Gordon (University of Birmingham, Birmingham, United

Kingdom) Roland Jonsson (University of Bergen, Bergen, Norway)

Anne-Isine Bolstad (University of Bergen, Bergen, Norway) Carmen Gutierrez (Universidad de Oviedo, Oviedo, Spain) Ana Suarez (Universidad de Oviedo, Oviedo, Spain) Jesús Gómez-Arbesú (Universidad de Oviedo, Oviedo, Spain) Helle Laustrup (Odense University Hospital, Odense, Denmark) Anne Voss (Odense University Hospital, Odense, Denmark) Peter Junker Odense University Hospital, Odense, Denmark) Bernardo Pons-Estel (Sanatorio Parque, Rosario, Argentina) The Argentine collaboration on SLE:

Hugo R. Scherbarth MD, Pilar C. Marino MD, Estela L. Motta MD Servicio de Reumatología, Hospital Interzonal General de Agudos "Dr. Oscar Alende", Mar del Plata, Argentina; Susana Gamron MD, Cristina Drenkard MD, Emilia Menso MD Servicio de Reumatología de la UHMI 1, Hospital Nacional de Clínicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Alberto Allievi MD, Guillermo A. Tate MD Organización Médica de Investigación, Buenos Aires, Argentina; Jose L. Presas MD Hospital General de Agudos Dr. Juán A. Fernandez, Buenos Aires, Argentina; Simon A. Palatnik MD, Marcelo Abdala MD, Mariela Bearzotti PhD Facultad de Ciencias Medicas, Universidad Nacional de

Rosario y Hospital Provincial del Centenario, Rosario, Argentina; Alejandro Alvarellos MD, Francisco Caeiro MD, Ana Bertoli MD Servicio de Reumatología, Hospital Privado, Centro Medico de Córdoba, Córdoba, Argentina; Sergio Paira MD, Susana Roverano MD, Hospital José M. Cullen, Santa Fe, Argentina; Cesar E. Graf MD, Estela Bertero PhD Hospital San Martín, Paraná; Cesar Caprarulo MD, Griselda Buchanan PhD Hospital Felipe Heras, Concordia, Entre Ríos, Argentina; Carolina Guillerón MD, Sebastian Grimaudo PhD, Jorge Manni MD Departamento de Inmunología, Instituto de Investigaciones Médicas "Alfredo Lanari", Buenos Aires, Argentina; Luis J. Catoggio MD, Enrique R. Soriano MD, Carlos D. Santos MD Sección Reumatología, Servicio de Clínica Medica, Hospital Italiano de Buenos Aires y Fundación Dr. Pedro M. Catoggio para el Progreso de la Reumatología, Buenos Aires, Argentina; Cristina Prigione MD, Fernando A. Ramos MD, Sandra M. Navarro MD Servicio de Reumatología, Hospital Provincial de Rosario, Rosario, Argentina; Guillermo A. Berbotto MD, Marisa Jorfen MD, Elisa J. Romero PhD Servicio de Reumatología Hospital Escuela Eva Perón. Granadero Baigorria, Rosario, Argentina; Mercedes A. Garcia MD, Juan C Marcos MD, Ana I. Marcos MD Servicio de Reumatología, Hospital Interzonal General de Agudos General San Martín, La Plata; Carlos E. Perandones MD, Alicia Eimon MD Centro de Educación Médica e Investigaciones Clínicas (CEMIC), Buenos Aires, Argentina; Cristina G. Battagliotti MD Hospital de Niños Dr. Orlando Alassia, Santa Fe, Argentina.

= Lindsey A. Criswell, M.D., M.P.H., University of California, San Francisco

Sharon A. Chung, M.D Kirsten A. Sterba, B.A. Joanne S. Nititham, B.A.

= Betty P. Tsao, Ph.D., University of California at Los Angeles Hui Wu, MD Punchong Hanvivadhanakul, MD (present address: Chulalongkorn University, Bankok, Thailand) Jennifer M. Grossman, MD Daniel J. Wallace, MD., Cedars Sinai Research Institute Rita M. Cantor, Ph.D.

Bevra H. Hahn, MD = Chaim O. Jacob, M.D., Ph.D., University of Southern California

Voicu Ciobanu Don Armostrong

Francisco P. Quismorio = SLEGEN Administration Fumi Ota Kimberly L. Ewing Winnie Oliver Paula A. Slaughter Cheryl M. Guest Laurie Russell = SLEGEN Advisory Committee Joseph Craft, MD, Yale University Edward K. Wakeland, PhD, University of Texas Southwestern Medical Center

The work has also been supported by the Rosalind Russell Medical Research

Center for Arthritis (LAC), the Gustaf V 80th-Year Jubilee (MEAR) and the

Swedish Rheumatism Association (MEAR). This work was carried out in part at

the General Clinical Research Center, Moffitt Hospital, University of California,

San Francisco with a grant from the National Center for Research Resources,

Public Health Service, 5-M01 RR00079 (LAC), and at the The University of

Alabama at Birmingham, MO1-RR00032 (JCE). The Broad Institute Center for

Genotyping and Analysis is supported by grant U54 RR020278-01 from the

National Center for Research Resources. SLEGEN received a subsidy from the

Broad Institute Center for Genotyping and Analysis and the National Center for

Research Resources.

Supplementary Methods

Quality Control of Genotyping Data.

GWA. Despite strong laboratory genotyping quality control procedures,

some SNPs may remain problematic for statistical inference. A SNP

classification scheme was developed based on the assumptions of the

statistical tests. Statistical analyses were computed on all 317,451 SNPs. The

265,648 (84%) SNPs that met the following criteria were used for statistical

inference: 1) No statistically significant differences in the proportions of missing

genotype data between cases and controls (i.e., p>0.05); 2) overall <5%

missing genotype data; 3) Hardy-Weinberg Expectations (HWE) in controls

p>0.01, HWE in cases p>0.0001; and 4) allele frequencies of controls

statistically consistent with expectations for ethnicity matched HapMap sample

(p>0.01). There were 265,648 (84%) GWA SNPs that met these criteria and

were included in the analysis of Sets 1 & 2.

LLAS: Genotype data were only used from samples with a call rate

greater than 90% (all samples), and from SNPs with a call frequency greater

than 90% (removed 27 SNPs) and an Illumina GenTrain score greater than 0.7

(removed 152 SNPs). In order to minimize sample misidentification, 91 SNPs

that had been previously genotyped on 42% of the samples were used to verify

sample identity. In addition, at least one sample previously genotyped was

randomly placed on each Illumina Infinium™ BeadChip and used to track

samples throughout the genotyping process. A total of 8230 SNPs produced

acceptable data and were analyzed in the LLAS (Sets 3 & 4) samples.

These quality control measures established a minimal effect of potential

population stratification-admixture effects and the reported associations appear

robust. The quantile-quantile plots (Q-Q plots), computed without the HLA

region, show little deviation from the expected (see Supplementary Figure 2

online) and most of the outliers are from clearly established associations,

IRF5/TNPO3 and ITGAM, or are not related to any of the other associations

reported herein. Genomic control shows that the inflation factor is modest (see

Supplementary Table 2 online) and does not alter the inferences made. The

incorporation of the first principal component and genomic control models also

do not alter our reported associations (see Supplementary Table 2 online).

Finally, the inferences remain whether data are analyzed jointly or as individual

replication samples.

Supplementary Table 1. Power analysis of split sample design assuming prevalence (Kp)=0.001260, complete linkage

disequilibrium between SNP and predisposing loci and an additive genetic model. MAF=minor allele frequency,

OR=odds ratio.

Set 1 Set 2 Set 3 Set 4 Intersection Combined

Case

(N=366)

Control

(N=1164)

Case

(N=354)

Control

(N=1173)

Case

(N=906)

Control

(N=819)

Case

(N=926)

Control

(N=1006)

Probability

(Product)

Case

(N=2552)

Control

(N=4162)

OR = 1.25

MAF = 0.15 0.50 0.49 0.68 0.73 0.12 0.25

MAF = 0.30 0.70 0.68 0.86 0.90 0.37 0.71

MAF = 0.45 0.75 0.74 0.90 0.93 0.47 0.82

OR = 1.5

MAF = 0.15 0.96 0.95 0.99 0.99 0.92 0.99

MAF = 0.30 0.99 0.99 0.99 0.99 0.99 0.99

MAF = 0.45 0.99 0.99 0.99 0.99 0.99 0.99

Alpha = 0.05 two-sided

Alpha = 1E-7

two-sided

Supplementary Table 2. Statistical significance of SNPs using the Genomic

Control correction factor.

Corrected p-values Principal Component

Adjusted Corrected P-

values

Gene SNP Set 1 Set 2 Set 1 Set 2

IRF5/TNPO3 rs10798269 5.37E-02 3.51E-03 1.06E-01 9.00E-03

ITGAM rs1143678 4.02E-02 1.77E-03 5.62E-04 9.48E-04

IRF5/TNPO3 rs12537284 5.38E-05 1.43E-06 1.13E-04 2.39E-05

HLA region rs3131379 1.42E-08 1.42E-08 6.47E-04 3.08E-04

ITGAM rs4548893 1.76E-02 8.81E-03 2.44E-04 2.90E-03

KIAA1542 rs4963128 4.98E-03 7.08E-03 2.16E-02 2.94E-02

PXK rs6445975 2.80E-02 5.63E-02 5.71E-02 2.91E-01

IRF5/TNPO3 rs729302 8.05E-02 6.51E-03 4.30E-02 5.66E-03

HLA region rs9275572 1.42E-08 9.04E-08 2.30E-04 2.87E-02

ITGAM rs9888739 3.24E-04 1.49E-06 2.18E-06 1.73E-06

mean(� 2) ±

SD

1.161

± 1.642

1.148

± 1.630

1.127

± 1.582

1.176

± 1.653

Results obtained after removing the HLA region and the IRF5 SNP (rs7808907).

Supplementary Table 3. Samples and sources for the Genome Wide Association (GWA) (Sets 1 & 2) and Replication

Sets (Sets 3 & 4).

Sets 1 & 2 Set 3 Set 4

Investigator Institution SLE

cases

Controls SLE

Cases

Controls SLE

Cases

Controls Reference

M. Alarcón U. Uppsala 50 0 83 0 78 0 S1,S2

L. Criswell UCSF 82 0 0 0 0 0 S3

G. Gilkeson MUSC 0 0 32 45 32 72 S4

P. Gregersen N. Shore U 0 261 0 0 0 93 S5

J. Harley OMRF 223 86 225 230 103 79 S6,S7

C. Jacob USC 36 8 0 0 33 45 S8

J. James OMRF 0 0 7 2 98 84

R. Kimberly UAB 0 0 327 250 245 508 S9,10

J. Merrill OMRF 0 0 0 40 95 0

K. Moser UMN 253 0 0 0 241 0 S11

B. Tsao UCLA 76 0 0 0 0 0 S12

T. Vyse I. College 0 0 246 0 1 0 S13

1958 Birth Cohort 0 0 0 252 0 125 S14

Illumina.com 0 1866 0 0 0 0 S15

IBD controls 0 116 0 0 0 0 S5

Supplementary Figure 1. Power Analyses for an Additive Model. The power is

calculated for the following case:control ratios: 360:1159, 916:912, 2551:4162.

The following assumptions were applied: D’=1, � =10-6 in 1A and D’=1, � =0.05 in

1B.

A.

Power Analysis for Additive Model Sample Size of 360 cases and 1169 Controls

Alpha = 10-6

Power Analysis for Additive Model

Sample Size of 916 cases and 912 Controls Alpha = 10-6

B.

Power Analysis for Additive Model

Sample Size of 2551 cases and 4162 Controls

Alpha = 10-6

Supplementary Figure 2. Q-Q plots. A delineation of the outliers for Sets 1

(panel A), 2 (panel B), and 3 (panel C). Plots are provided with and without the

principal component adjusted analysis for Sets 1 and 2. The observed and

expected values are given as the Z statistic. Those outliers at the bottom left of

the figure correspond to OR<1 and those in the top right correspond to OR>1.

A.

B.

Observed (Z-statistic)

Expected (Z-statistic)

Observed (Z-statistic)

Expected (Z-statistic)

C.

Outlying SNPs that are not in IRF5/TNP03, ITGAM, or in linkage disequilibrium with those in

Tables 1 or 2 are the following: Set 1: rs2302001 (OR>1, 7p15.3, LOC646468); Set 1 PC

adjusted: rs10513258 (OR>1, 9q32), rs2834618 (OR>1, 21q22.12); Set 2: rs12514473

(OR>1. 5q14.1, SSBP2), rs9303381 (OR>1, 17q22); Set 2 PC adjusted: rs10908907 (OR>1,

9q22.2).

Expected (Z-statistic)

Observed (Z-statistic)

B. B.

Supplementary Figure 3. Combined Sets 1,2,3 & 4 Results for Extended MHC Region

(Chromosome 6, 26-34 Mb). P-values <0.001 are represented, color coded by data source.

De Bakker et al. (S16) report that r2=0.87 between rs2187668 and DRB1*0301 and in the

CEPH HapMap data this SNP has r2=1.0 with the DRB1*0301 tag rs2040410. Rs2187668 is ranked

tenth most significant in Sets 1 & 2. The SNP rs2187668 in our data has an r2=1.0 with the

DRB1*0301 tag SNP rs2040410 in the CEPH HapMap data. De Bakker et al. (S16) also report an

r2=0.97 for CEPH and r2=0.88 in the independent replication sample between rs3135388 and

DRB1*1501. Rs3135388 is not found on the 317K Illumina array but rs2395182 is in high LD

(r2=0.81) with rs3135388. In our sample rs2395182 was not consistently associated with SLE (p-

value=0.0031 and p-value=0.2861 in Set 1 and Set 2, respectively) and was not genotyped in Sets

3 & 4. The eighth-ranked SNP in the combined sample, rs7192, is in high LD with rs3135388 (D’=1)

but is not a tagging SNP (r2 = 0.46).

SNPs of interest are:

1) rs3131379 (position 31829012 Mb, gene MSH5), OR=2.36, p=1.7x10-52 ,

2) rs1270942 (position 32026839 Mb, gene RDBP), OR=2.35, p=1.3x10-51,

3) rs7775397 (position 32369230 Mb, gene C6orf10), OR=2.28, p=8.0x10-47 ,

4) rs9275572 (position 32786977 Mb, no gene known), OR=1.69, p=7.0x10-48 ,

5) rs1794282 (position 32774504 Mb, no gene known), OR=2.26, p=2.6x10-46 ,

6) rs7192 (position 32519624 Mb, gene HLA-DRA), OR=1.61, p=6.2x10-40 .

Rs1794282 is in high LD (r2=0.90) with DR3 tag SNP rs2187668 (S16) in CEU. Rs7192 is in high

LD (D’=1, r2=0.46) w/DR2 tag SNP rs3135388 in CEU (S16). Rs9275572 is at 32.787 Mb and is not

in a currently known gene but is between HLA-DQB1 and HLA_DQB2 (HLA-DQB1-44kb-

rs9275572- 45kb-HLA-DQB2).

Supplementary Figure 4. Haplotype block structure of reported associations in

Table 1 (excluding HLA).

ITGAM.

IRF5.

KIAA1542.

PXK.

Unknown gene (rs10798269).

Supplementary Figure 5. The -Log10(p value) with the p value taken from the

joint analysis of Set 1 and Set 2 as plotted against the L2 Norm, showing very

little difference in ranking by either measure.

|

References for Supplementary Figures, Tables and Methods

S1. Johanneson, B. et al. A major susceptibility locus for systemic lupus

erythemathosus maps to chromosome 1q31. Am. J. Hum. Genet. 71, 1060-

71 (2002).

S2. Johansson, C.M. et al. Chromosome 17p12-q11 harbors susceptibility loci

for systemic lupus erythematosus. Hum. Genet. 115, 230-238 (2004).

S3. Thorburn, C.M. et al. Association of PDCD1 genetic variation with risk and

clinical manifestations of systemic lupus erythematosus in a multiethnic

cohort. Genes Immun. 8, 279-287 (2007).

S4. Cooper, G.S. et al. Hormonal and reproductive risk factors for development

of systemic lupus erythematosus: results of a population-based, case-control

study. Arthritis Rheum. 46, 1830-1839 (2002).

S5. Mitchell, M.K. et al. The New York Cancer Project: rationale, organization,

design, and baseline characteristics. J Urban Health. 81, 301-310 (2004).

S6. Moser, K.L.. et al. Genome scan of human systemic lupus erythematosus:

evidence for linkage on chromosome 1q in African-American pedigrees.

Proc. Natl. Acad. Sci. U S A. 8, 14869-14874 (1998).

S7. Gray-McGuire, C.,et al. Genome scan of human systemic lupus

erythematosus by regression modeling: evidence of linkage and epistasis at

4p16-15.2. Am. J. Hum. Genet. 67, 1460-1469 (2000).

S8. Pricop, L., Li, L., Salmon, J.E., Jacob, C.O. Characterization of the

FcgammaRIIA promoter and 5'UTR sequences in patients with systemic

lupus erythematosus. Genes Immun. 3, S47-50 (2002).

S9. Alarcon, G.S. et al. Time to renal disease and end-stage renal disease in

PROFILE: a multiethnic lupus cohort. PLoS Med. 3, e396 (2006).

S10. Kelley, J. et al. Variation in the relative copy number of the TLR7 gene in

patients with systemic lupus erythematosus and healthy control subjects.

Arthritis Rheum. 56, 3375-3378, 2007.

S11.. Gaffney, P.M. et al. A genome-wide search for susceptibility genes in

human systemic lupus erythematosus sib-pair families. Proc. Natl. Acad. Sci.

U S A. 8, 14875-14879 (1998).

S12. Wu, H. et al. Association of a common complement receptor 2 haplotype

with increased risk of SLE. Proc. Natl. Acad. Sci. 104, 3961-3966 (2007).

S13. Russell, A.I. et al. Polymorphism at the C-reactive protein locus influences

gene expression and predisposes to systemic lupus erythematosus. Hum.

Mol. Genet. 13, 137-147 (2004).

S14. Power, C. Elliott, J. Cohort profile: 1958 British birth cohort (National Child

Development Study). Int. J. Epidemiol. 35, 34-41 (2006).

S15 . http://www.illumina.com/pages.ilmn?ID=231

S16. De Bakker, P.I. et al. A high-resolution HLA and SNP haplotype map for

disease association studies in the extended human MHC. Nat. Genet. 38,

1166-1172 (2006).