To date, most expression quantitative trait loci (eQTL) studies, which investigate how genetic variants contribute to gene expression, have been performed in heterogeneous brain tissues rather than specific cell types. In this study, we performed an eQTL analysis using single-nuclei RNA sequencing from 192 individuals in eight brain cell types derived from the prefrontal cortex, temporal cortex and white matter. We identified 7,607 eGenes, a substantial fraction (46%, 3,537/7,607) of which show cell-type-specific effects, with strongest effects in microglia. Cell-type-level eQTLs affected more constrained genes and had larger effect sizes than tissue-level eQTLs. Integration of brain cell type eQTLs with genome-wide association studies (GWAS) revealed novel relationships between expression and disease risk for neuropsychiatric and neurodegenerative diseases. For most GWAS loci, a single gene co-localized in a single cell type, providing new clues into disease etiology. Our findings demonstrate substantial contrast in genetic regulation of gene expression among brain cell types and reveal potential mechanisms by which disease risk genes influence brain disorders.

BACKGROUND Baseline expression of FCRL5, a marker of naive and memory B cells, was shown to predict response to rituximab (RTX) in rheumatoid arthritis. This study investigated baseline expression of FCRL5 as a potential biomarker of clinical response to RTX in granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA).METHODS A previously validated quantitative PCR–based (qPCR-based) platform was used to assess FCRL5 expression in patients with GPA/MPA (RAVE trial, NCT00104299).RESULTS Baseline FCRL5 expression was significantly higher in patients achieving complete remission (CR) at 6, 12, and 18 months, independent of other clinical and serological variables, among those randomized to RTX but not cyclophosphamide-azathioprine (CYC/AZA). Patients with baseline FCRL5 expression ≥ 0.01 expression units (termed FCRL5hi) exhibited significantly higher CR rates at 6, 12, and 18 months as compared with FCRL5lo subjects (84% versus 57% [P = 0.016], 68% versus 40% [P = 0.02], and 68% versus 29% [P = 0.0009], respectively).CONCLUSION Our data taken together suggest that FCRL5 is a biomarker of B cell lineage associated with increased achievement and maintenance of complete remission among patients treated with RTX and warrant further investigation in a prospective manner.FUNDING The analysis for this study was funded by Genentech Inc.

In clinical trials, a placebo response refers to improvement in disease symptoms arising from the psychological effect of receiving a treatment rather than the actual treatment under investigation. Previous research has reported genomic variation associated with the likelihood of observing a placebo response, but these studies have been limited in scope and have not been validated. Here, we analyzed whole-genome sequencing data from 784 patients undergoing placebo treatment in Phase III Asthma or Rheumatoid Arthritis trials to assess the impact of previously reported variation on patient outcomes in the placebo arms and to identify novel variants associated with the placebo response. Contrary to expectations based on previous reports, we did not observe any statistically significant associations between genomic variants and placebo treatment outcome. Our findings suggest that the biological origin of the placebo response is complex and likely to be variable between disease areas.

Paola Bronson, Lennart Hammarström and colleagues report a genome-wide association study meta-analysis of selective IgA immunodeficiency in Europeans. They identify four new loci and a rare variant of a previously associated gene, IFIH1. Selective immunoglobulin A deficiency (IgAD) is the most common primary immunodeficiency in Europeans. Our genome-wide association study (GWAS) meta-analysis of 1,635 patients with IgAD and 4,852 controls identified four new significant (P < 5 × 10−8) loci and association with a rare IFIH1 variant (p.Ile923Val). Peak new variants (PVT1, P = 4.3 × 10−11; ATG13–AMBRA1, P = 6.7 × 10−10; AHI1, P = 8.4 × 10−10; CLEC16A, P = 1.4 × 10−9) overlapped with autoimmune markers (3/4) and correlated with 21 putative regulatory variants, including expression quantitative trait loci (eQTLs) for AHI1 and DEXI and DNase hypersensitivity sites in FOXP3+ regulatory T cells. Pathway analysis of the meta-analysis results showed striking association with the KEGG pathway for IgA production (pathway P < 0.0001), with 22 of the 30 annotated pathway genes containing at least one variant with P ≤ 0.05 in the IgAD meta-analysis. These data suggest that a complex network of genetic effects, including genes known to influence the biology of IgA production, contributes to IgAD.

IMPORTANCE:The present study identified potential genetic modifiers that may delay or accelerate age at onset of familial Alzheimer disease (AD) by examining age at onset in PSEN1 mutation carrier families, and further investigation of these modifiers may provide insight into the pathobiology of AD and potential therapeutic measures.OBJECTIVE:To identify genetic variants that modify age at onset of AD.DESIGN, SETTING, AND PARTICIPANTS:Using a subset of Caribbean Hispanic families that carry the PSEN1 p.G206A mutation, we performed a 2-stage genome study. The mutation carrier families from an ongoing genetic study served as a discovery set, and the cohort of those with LOAD served as a confirmation set. To identify candidate loci, we performed linkage analysis using 5 p.G206A carrier families (n = 56), and we also performed whole-exome association analysis using 31 p.G206A carriers from 26 families. To confirm the genetic modifiers identified from the p.G206A carrier families, we analyzed the GWAS data for 2888 elderly individuals with LOAD. All study participants were Caribbean Hispanics.MAIN OUTCOMES AND MEASURES:Age at onset of AD.RESULTS:Linkage analysis of AD identified the strongest linkage support at 4q35 (LOD [logarithm of odds] score, 3.69), and the GWAS of age at onset identified variants on 1p13.1, 2q13, 4q25, and 17p11. In the confirmation stage, genewise analysis identified SNX25, PDLIM3, and 3 SH3 domain genes (SORBS2, SH3RF3, and NPHP1) to be significantly associated with LOAD. Subsequent allelic association analysis confirmed SNX25, PDLIM3, and SORBS2 as genetic modifiers of age at onset of EOAD and LOAD and provided modest support for SH3RF3 and NPHP1.CONCLUSIONS AND RELEVANCE:Our 2-stage analysis revealed that SNX25, PDLIM3, and SORBS2 may serve as genetic modifiers of age at onset in both EOAD and LOAD.

Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein- coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2x10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6x10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, P-omnibus = 6x10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P-omnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.

Mutations in UNC5C are identified in individuals with late-onset Alzheimer's disease and increase susceptibility of neurons to cell death. We have identified a rare coding mutation, T835M (rs137875858), in the UNC5C netrin receptor gene that segregated with disease in an autosomal dominant pattern in two families enriched for late-onset Alzheimer's disease and that was associated with disease across four large case-control cohorts (odds ratio = 2.15, Pmeta = 0.0095). T835M alters a conserved residue in the hinge region of UNC5C, and in vitro studies demonstrate that this mutation leads to increased cell death in human HEK293T cells and in rodent neurons. Furthermore, neurons expressing T835M UNC5C are more susceptible to cell death from multiple neurotoxic stimuli, including β-amyloid (Aβ), glutamate and staurosporine. On the basis of these data and the enriched hippocampal expression of UNC5C in the adult nervous system, we propose that one possible mechanism in which T835M UNC5C contributes to the risk of Alzheimer's disease is by increasing susceptibility to neuronal cell death, particularly in vulnerable regions of the Alzheimer's disease brain.

TREM and TREM-like receptors are a structurally similar protein family encoded by genes clustered on chromosome 6p21.11. Recent studies have identified a rare coding variant (p.R47H) in TREM2 that confers a high risk for Alzheimer's disease (AD). In addition, common single nucleotide polymorphisms in this genomic region are associated with cerebrospinal fluid biomarkers for AD and a common intergenic variant found near the TREML2 gene has been identified to be protective for AD. However, little is known about the functional variant underlying the latter association or its relationship with the p.R47H. Here, we report comprehensive analyses using whole-exome sequencing data, cerebrospinal fluid biomarker analyses, meta-analyses (16,254 cases and 20,052 controls) and cell-based functional studies to support the role of the TREML2 coding missense variant p.S144G (rs3747742) as a potential driver of the meta-analysis AD-associated genome-wide association studies signal. Additionally, we demonstrate that the protective role of TREML2 in AD is independent of the role of TREM2 gene as a risk factor for AD.

Background/Aims: Genome-wide association (GWA) studies have reported susceptible regions in the human genome for many common diseases and traits; however, these loci only explain a minority of trait heritability. To boost the power of a GWA study, substantial research endeavors have been focused on integrating other available genomic information in the analysis. Advances in high through-put technologies have generated a wealth of genomic data and made combining SNP and gene expression data become feasible. Results: In this paper, we propose a novel procedure to incorporate gene expression information into GWA analysis. This procedure utilizes weights constructed by gene expression measurements to adjust p values from a GWA analysis. Results from simulation analyses indicate that the proposed procedures may achieve substantial power gains, while controlling family-wise type I error rates at the nominal level. To demonstrate the implementation of our proposed approach, we apply the weight adjustment procedure to a GWA study on serum interferon-regulated chemokine levels in systemic lupus erythematosus patients. The study results can provide valuable insights for the functional interpretation of GWA signals. Availability: The R source code for implementing the proposed weighting procedure is available at http://www.biostat.umn.edu/∼yho/research.html.

A founder mutation G206A in PSEN1 was reported in Caribbean Hispanic families with early onset Alzheimer's disease (EOAD). The age at onset (AAO) of Alzheimer's disease (AD) in carriers of this mutation varied widely (range: 22-77). However, neither the APOE-ε4 allele nor environmental factors explained the differences in onset among mutation carriers. To identify genetic factors that may modify AAO, we conducted a 2-stage genomic study of EOAD, and then examined those genes in Caribbean Hispanics with late onset AD (LOAD). Three sets of Caribbean Hispanics with familial AD were investigated. First, 5 multiplex EOAD families that carry the G206A-PSEN1 mutation were examined using linkage analysis. Second, 31 individuals who carry the G206A-PSEN1 mutation were investigated using exome sequencing. Lastly, two LOAD GWAS sets of Caribbean Hispanics were used to determine whether the same genes influence AAO. Genome wide linkage analysis of AD identified the strongest linkage support for rs13478 at 4q35.1 (LOD=3.69). We then examined the exome data under the linkage peak. An effect allele of rs13130022 in SORBS2 was associated with delay in AAO by ∼11 years. In the remaining exome, the strongest signal for AAO was observed at rs906815 in NPHP1 at 2q13 (P=4.51E-6), and homozygous carriers of the rare allele had the onset ∼21 years earlier than carriers of the common allele. In addition, an effect variant rs6542814 in SH3RF3, flanking NPHP1, was associated with a delay in AAO by ∼9 years. In addition, these genes -- SORBS2, SHR3RF3 and NPHP1 -- were associated with AAO in individuals with LOAD (p=3.8E-6, p=2.7E-11, p=5.5E-5, respectively). However, the differences in AAO in individuals with LOAD were much smaller than those observed in EOAD. We report that variants in a family of SH3 domain genes, SORBS2, SH3RF3 and NPHP1 may modify AAO of AD in Caribbean Hispanic carriers of the G206A variant. Further, these genes may play a role in AAO of LOAD. Given the related nature of these genes they are attractive therapeutic targets for further investigation.

Much of the heritability of late-onset Alzheimer's disease (LOAD) remains unaccounted for, despite progress from genome-wide association studies. The overall contribution of rare variants to the risk of LOAD remains to be determined and, to date, few rare variants in LOAD have been identified and functionally characterized. We performed exome and whole-genome sequencing in multiplex AD family, in which we previously discarded mutation in APP, PSEN1 and 2. We identified a rare variant that segregates in families with LOAD, is associated with disease in large case/control studies, and leads to increased neuronal cell death. A missense variant in UNC5C segregated with disease in a large pedigree with autosomal dominant inheritance of LOAD. To confirm the association, we screened a collection of families enriched for LOAD and identified additional families where the variant segregates with disease. The variant was also enriched in large collections of LOAD cases compared to controls (metaP = 0.006, OR = 2.15). The variant alters an evolutionarily conserved residue in the hinge region of UNC5C and leads to increased cell death in vitro. These studies identified a novel pathway in AD pathogenesis and suggest that a strategy that combines pedigree analysis with case/control studies will be valuable in the identification of rare variants in complex disease.

We identified the G206A mutation in PSEN1 in 2001, and observed that this mutation was highly penetrant, but it was associated with a wide range of age at onset. Carriers of the mutation ranged as much as 20+ years in age at onset. The observed variation in age at onset was explained by neither APOE-ε4 nor known environmental risk factors (e.g., levels of education). To identify variants that influence age at onset of AD, we investigated five families that had familial EOAD and carried the G206A variant in PSEN1. We performed a linkage analysis to identify candidate regions that may harbour variants, and then conducted a joint linkage and association analysis with additional 543 unaffected Hispanics as controls. We then performed whole exome sequencing (WES) on a subset of individuals to identify genetic variants that are associated with variable age at onset. Multiple regression was used to assess mean age at onset by genotype. The linkage analysis revealed that 2p25 and 4q35 had LOD scores>3, and additional loci elsewhere in the genome had suggestive linkage. For nine top linkage signals, we performed a joint linkage and association analysis to ensure that there exist candidate variants that are associated with AD under the linkage peaks. Subsequently, we selected 27 individuals from the same set of families and performed exome sequencing to identify variants that are associated with variable age at onset. This analysis identified multiple loci – specifically, 1p13.1, 2q13, 4q25, 17p11 – that were significant at p

A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as r

Several rare genetic variants cause early-onset Alzheimer's disease(EOAD), including mutations in amyloid-β precursor protein (APP), presenilin-1 (PSN1), and presenilin-2 (PSN2). However, these variants account for less than 5% of all AD cases. The overall contribution of rare variants to the risk of late-onset Alzheimer's disease (LOAD) is unknown and, to date, few rare variants in LOAD have been identified and functionally characterized. To elucidate novel risk variants, we performed linkage analysis and whole genome sequencing in a large pedigree with apparent dominant inheritance of LOAD and identified a candidate rare variant in the Netrin receptor UNC5C (rs137875858). This variant segregates with disease in two families enriched for LOAD and shows association with LOAD in four independent case/control cohorts. The consequence of this variant is a single amino acid change from a highly conserved threonine residue, T835, to a methionine. T835M is located in the hinge region of UNC5C just upstream of the death domain, which may affect protein structure and death domain access. UNC5C plays a role in axonal guidance during development and is highly expressed in the adult hippocampus and cerebellum. To characterize the functional role of T835M in LOAD, we expressed T835M in 293T cells and found that overexpression of this variant leads to growth defects caused by enhanced apoptosis. Moreover, T835M-expressing hippocampal neurons showed increased vulnerability when treated with Aβ, suggesting that neurons in T835M-carriers are more susceptible to cell death in the presence of amyloid. These studies implicate an important role for UNC5C in regulating neuronal cell death, and identify a novel pathway that may contribute to Alzheimer's disease pathogenesis.

The discovery that type I interferon (IFN)-inducible genes were strongly upregulated in peripheral blood in SLE over a decade ago sparked interest in understanding the relationship between type I IFN and SLE. Genome-wide association studies provide strong genetic evidence that type I IFNs are important for SLE risk. Of 47 genetic variants associated with SLE, over half (27/47,57%) can be linked to type I IFN production or signaling. The recent identification of single gene mutations for disorders that share features with SLE - Aicardi-Goutieres syndrome, chilblain lupus, and spondyloenchondrodysplasia - provide additional support for the hypothesis that type I IFNs are central drivers of SLE pathogenesis. These insights provide significant focus for efforts to tackle SLE therapeutically.

Selective IgA deficiency (IgAD; serum IgA<0.07 g/l) is the most common form of human primary immune deficiency, affecting approximately 1∶600 individuals in populations of Northern European ancestry. The polygenic nature of IgAD is underscored by the recent identification of several new risk genes in a genome-wide association study. Among the characterized susceptibility loci, the association with specific HLA haplotypes represents the major genetic risk factor for IgAD. Despite the robust association, the nature and location of the causal variants in the HLA region remains unknown. To better characterize the association signal in this region, we performed a high-density SNP mapping of the HLA locus and imputed the genotypes of common HLA-B, -DRB1, and -DQB1 alleles in a combined sample of 772 IgAD patients and 1,976 matched controls from 3 independent European populations. We confirmed the complex nature of the association with the HLA locus, which is the result of multiple effects spanning the entire HLA region. The primary association signal mapped to the HLA-DQB1*02 allele in the HLA Class II region (combined P = 7.69×10(-57); OR = 2.80) resulting from the combined independent effects of the HLA-B*0801-DRB1*0301-DQB1*02 and -DRB1*0701-DQB1*02 haplotypes, while additional secondary signals were associated with the DRB1*0102 (combined P = 5.86×10(-17); OR = 4.28) and the DRB1*1501 (combined P = 2.24×10(-35); OR = 0.13) alleles. Despite the strong population-specific frequencies of HLA alleles, we found a remarkable conservation of these effects regardless of the ethnic background, which supports the use of large multi-ethnic populations to characterize shared genetic association signals in the HLA region. We also provide evidence for the location of association signals within the specific extended haplotypes, which will guide future sequencing studies aimed at characterizing the precise functional variants contributing to disease pathogenesis.

Systemic lupus erythematosus (SLE) is a genetically complex disease with heterogeneous clinical manifestations. Recent studies have greatly expanded the number of established SLE risk alleles, but the distribution of multiple risk alleles in cases versus controls and their relationship to subphenotypes have not been studied. We studied 22 SLE susceptibility polymorphisms with previous genome-wide evidence of association (p < 5 x 10⁻¹²⁸) in 1919 SLE cases from 9 independent Caucasian SLE case series and 4813 independent controls. The mean number of risk alleles in cases was 15.1 (SD 3.1) while the mean in controls was 13.1 (SD 2.8), with trend p = 4 x 10⁻⁸. We defined a genetic risk score (GRS) for SLE as the number of risk alleles with each weighted by the SLE risk odds ratio (OR). The OR for high-low GRS tertiles, adjusted for intra-European ancestry, sex, and parent study, was 4.4 (95% CI 3.8-5.1). We studied associations of individual SNPs and the GRS with clinical manifestations for the cases: age at diagnosis, the 11 American College of Rheumatology classification criteria, and double-stranded DNA antibody (anti-dsDNA) production. Six subphenotypes were significantly associated with the GRS, most notably anti-dsDNA (OR(high-low) = 2.36, p = 9e-9), the immunologic criterion (OR(high-low) = 2.23, p = 3e-7), and age at diagnosis (OR(high-low) = 1.45, p = 0.0060). Finally, we developed a subphenotype-specific GRS (sub-GRS) for each phenotype with more power to detect cumulative genetic associations. The sub-GRS was more strongly associated than any single SNP effect for 5 subphenotypes (the above plus hematologic disorder and oral ulcers), while single loci are more significantly associated with renal disease (HLA-DRB1, OR = 1.37, 95% CI 1.14-1.64) and arthritis (ITGAM, OR = 0.72, 95% CI 0.59-0.88). We did not observe significant associations for other subphenotypes, for individual loci or the sub-GRS. Thus our analysis categorizes SLE subphenotypes into three groups: those having cumulative, single, and no known genetic association with respect to the currently established SLE risk loci.

Backgroundand objectives Lupus nephritis (LN) is a cause of significant morbidity and mortality and occurs in 15–50% of patients with SLE. Proliferative nephritis is most severe and 10% of LN patients develop end stage renal disease (ESRD). Several susceptibility genes for SLE have been identified where an association with LN has been shown for SNPs in STAT4 and ITGAM. The aim of this investigation was to analyse the genetic data from a previous study1 for association with LN, in particular proliferative nephritis and ESRD. Materials and methods The authors included 567 Swedish Caucasian patients with SLE and 512 matched controls. All samples had been genotyped on a custom array 12K chip1. A total of 195 (34.4%) patients had a history of LN. Renal biopsies were available from 153 patients where 92 (60.1%) showed a proliferative nephritis. During follow-up (median 14 years, range 0–46), 11.1% reached ESRD. Case-control association analyses were performed for patients with LN, proliferative nephritis, ESRD and for comparison all SLE patients, versus controls. Results The authors detected strong signals of association between SNPs in STAT4 (OR 2.2, 95% CI 1.7 to 2.8), IRF5 (OR 2.0, 95% CI 1.5 to 2.7) and a marker for HLA-DR3 (OR 1.95, 95% CI 1.4 to 2.6), in the analysis of LN patients versus controls (all p<0.0001). In addition, six genes showed an association with LN with OR 1.5-2.2, p<0.001 (PMS2, TNIP1, CARD11, ITGAM, BLK and IRAK1). When analysing only the patients with proliferative nephritis versus controls the OR for association increased for STAT4, IRF5 and BLK to 2.4, 2.2 and 1.7 respectively (all p<0.01). For patients in ESRD the OR for STAT4, IRF5 and BLK increased further to 2.9, 3.1 and 2.1 whereas the OR for association with the HLA-DR3 marker was decreased to 1.7. The association between the risk alleles in IRF5, STAT4 and BLK and LN phenotypes was stronger than the association to SLE per se. Conclusions Risk alleles in STAT4, IRF5 and BLK are associated with an increased risk for LN. The association with proliferative nephritis was particularly strong and the risk of developing ESRD was even more striking. On the contrary, the HLA-DR3 marker did not display a strong association with LN. The authors conclude that variations in genes in immunological pathways predispose to LN severity and renal outcome.