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Additional file 1: Supplemental Figure 1. Scatter plots of purified classical and non-classical monocytes. PBMCs = peripheral blood mononuclear cells, percentages in the gates for classical and non-classical monocytes indicate the purity of populations purified. Supplemental Figure 2. Quantile ��� quantile plot showing eQTL associations with SLE risk loci. A) Classical monocytes; B) Non-classical monocytes. A very early deviation of the observed from the expected P value for eQTL associations suggested high type I error, which we found to relate to within-person correlations and distributional properties of the single cell data as described in the paper. eQTL associations that remained significant after using the approaches described in the Methods to correct for the distributional properties of the data are highlighted in orange for classical and magenta for non-classical monocytes. Supplemental Figure 3. On/off pattern of IRF1 gene expression in monocytes from a single cell RNA sequencing study examining patients with multiple myeloma. X-axis shows individual patients and the Y-axis shows gene expression values for the IRF1 transcript. Each plotted dot represents the expression level for IRF1 in one cell. Bars show the median, error bars show the interquartile range. Data from public database as reported in Haradhvala, N.J., et al., Cancer Research, 2019.

This is the peer reviewed version of the following article: Hinks, A., Marion, M.C., Cobb, J., Comeau, M.E., Sudman, M., Ainsworth, H.C., ... Prahalad, S. (2018). Brief Report: The Genetic Profile of Rheumatoid Factor? Positive Polyarticular Juvenile Idiopathic Arthritis Resembles That of Adult Rheumatoid Arthritis. Arthritis & Rheumatology, 70(6), 957-962, which has been published in final form at https://doi.org/10.1002/art.40443. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Objective: Juvenile idiopathic arthritis (JIA) comprises 7 heterogeneous categories of chronic childhood arthritides. Approximately 5% of children with JIA have rheumatoid factor (RF)–positive arthritis, which phenotypically resembles adult rheumatoid arthritis (RA). Our objective was to compare and contrast the genetics of RF‐positive polyarticular JIA with those of RA and selected other JIA categories, to more fully understand the pathophysiologic relationships of inflammatory arthropathies. Methods: Patients with RF‐positive polyarticular JIA (n = 340) and controls (n = 14,412) were genotyped using the Immunochip array. Single‐nucleotide polymorphisms were tested for association using a logistic regression model adjusting for admixture proportions. We calculated weighted genetic risk scores (wGRS) of reported RA and JIA risk loci, and we compared the ability of these wGRS to predict RF‐positive polyarticular JIA. Results: As expected, the HLA region was strongly associated with RF‐positive polyarticular JIA (P = 5.51 × 10−31). Nineteen of 44 RA risk loci and 6 of 27 oligoarticular/RF‐negative polyarticular JIA risk loci were associated with RF‐positive polyarticular JIA (P < 0.05). The RA wGRS predicted RF‐positive polyarticular JIA (area under the curve [AUC] 0.71) better than did the oligoarticular/RF‐negative polyarticular JIA wGRS (AUC 0.59). The genetic profile of patients with RF‐positive polyarticular JIA was more similar to that of RA patients with age at onset 16–29 years than to that of RA patients with age at onset ≥70 years. Conclusion: RF‐positive polyarticular JIA is genetically more similar to adult RA than to the most common JIA categories and thus appears to be a childhood‐onset presentation of autoantibody‐positive RA. These findings suggest common disease mechanisms, which could lead to novel therapeutic targets and shared treatment strategies.

Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (∼50% of these regions have multiple independent associations); these include 24 novel SLE regions (P