Whole Genome Association Study of Systemic Lupus Erythematosus

The goal of this collaborative study was to identify new genetic risk factors for Systemic Lupus Erythematosus (SLE). To do this

we conducted a genome-wide scan by combining the resources and expertise from a number of SLE researchers to establish a large

sample set comprising 1311 SLE cases and 3340 controls. The SLE case samples were genotyped from the following collections: 338

subjects from the Autoimmune Biomarkers Collaborative Network (ABCoN), an NIH/NIAMS funded repository, 141 subjects from the

Multiple Autoimmune Disease Genetics Consortium (MADGC), 613 subjects from the University of California San Francisco (UCSF) Lupus

Genetics, and 335 subjects from the University of Pittsburgh Medical Center (UPMC), plus 8 samples collected at The Feinstein

Institute for Medical Research.

A total of 3583 control samples were examined in the association analyses. As part of this project, 1861 control samples were

selected and then genotyped from the New York Cancer Project (NYCP), based on self-described ethnicity, gender and age.

In addition, genotype data from 1722 control samples (all self-described North Americans of European descent) were obtained from

the publicly available iControlDB database (http://www.illumina.com/pages.ilmn?ID=231).

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A total of 1311 SLE case and 1783 control DNA samples (all North Americans of European descent) were genotyped for over 500,000 single nucleotide polymorphisms. Genotypes from 1557 additional controls were obtained from public data repositories. Control samples from the NYCP (N=1861) were genotyped on the IlluminaHumanHap550 Genotyping BeadChip at The Feinstein Institute. 1465 samples (464 cases, 1001 controls) were genotyped on the HumanHap550v1 chip and 1875 samples (1015 cases, 860 controls) were genotyped on the HumanHap550v3 chip.CASES

All subjects (fulfillment of four or more of the 1997 American College of Rheumatology (ACR) defined criteria was confirmed

in all cases by medical record review (94%) or through written documentation of criteria by treating rheumatologists (6%).

CONTROLS

The controls are from the New York Cancer Project (NYCP).

These subjects were voluntarily consented for broad use of medical research with de-identified data and samples. The self-reported

data include demographics, personal and family medical history, lifestyle, etc. NYCP participants also donated approximately 50

milliliters of blood, which is stored in the NYCP Biorepository at the North Shore Long Island Jewish Research Institute.

All NYCP control data generated from this study were deposited in the iControlDB database.]]>