Replication has become the gold standard for assessing statistical results from genome-wide association studies. Unfortunately this replication requirement may cause real genetic effects to be missed. A real result can fail to replicate for numerous reasons including inadequate sample size or variability in phenotype definitions across independent samples. In genome-wide association studies the allele frequencies of polymorphisms may differ due to sampling error or population differences. We hypothesize that some statistically significant independent genetic effects may fail to replicate in an independent dataset when allele frequencies differ and the functional polymorphism interacts with one or more other functional polymorphisms. To test this hypothesis, we designed a simulation study in which case-control status was determined by two interacting polymorphisms with heritabilities ranging from 0.025 to 0.4 with replication sample sizes ranging from 400 to 1600 individuals. We show that the power to replicate the statistically significant independent main effect of one polymorphism can drop dramatically with a change of allele frequency of less than 0.1 at a second interacting polymorphism. We also show that differences in allele frequency can result in a reversal of allelic effects where a protective allele becomes a risk factor in replication studies. These results suggest that failure to replicate an independent genetic effect may provide important clues about the complexity of the underlying genetic architecture. We recommend that polymorphisms that fail to replicate be checked for interactions with other polymorphisms, particularly when samples are collected from groups with distinct ethnic backgrounds or different geographic regions.

Background: Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be the result of single points of failure but instead likely arise from the joint failure of two or more interacting components. The hope in genome-wide screens is that these points of failure can be linked to single nucleotide polymorphisms (SNPs) which confer disease susceptibility. Detecting interacting variants that lead to disease in the absence of singlegene effects is difficult however, and methods to exhaustively analyze sets of these variants for interactions are combinatorial in nature thus making them computationally infeasible. Efficient algorithms which can detect interacting SNPs are needed. ReliefF is one such promising algorithm, although it has low success rate for noisy datasets when the interaction effect is small. ReliefF has been paired with an iterative approach, Tuned ReliefF (TuRF), which improves the estimation of weights in noisy data but does not fundamentally change the underlying ReliefF algorithm. To improve the sensitivity of studies using these methods to detect small effects we introduce Spatially Uniform ReliefF (SURF).

Mutations in the tumor suppressor BRCA1 predispose women to breast and ovarian cancers. The mechanism underlying the tissuespecific nature of BRCA1's tumor suppression is obscure. We previously showed that the antioxidant pathway regulated by the transcription factor NRF2 is defective in BRCA1-deficient cells. Reactivation of NRF2 through silencing of its negative regulator KEAP1 permitted the survival of BRCA1-null cells. Here we show that estrogen (E2) increases the expression of NRF2-dependent antioxidant genes in various E2-responsive cell types. Like NRF2 accumulation triggered by oxidative stress, E2-induced NRF2 accumulation depends on phosphatidylinositol 3-kinase-AKT activation. Pretreatment of mammary epithelial cells (MECs) with the phosphatidylinositol 3-kinase inhibitor BKM120 abolishes the capacity of E2 to increase NRF2 protein and transcriptional activity. In vivo the survival defect of BRCA1-deficient MECs is rescued by the rise in E2 levels associated with pregnancy. Furthermore, exogenous E2 administration stimulates the growth of BRCA1-deficient mammary tumors in the fat pads of male mice. Our work elucidates the basis of the tissue specificity of BRCA1-related tumor predisposition, and explains why oophorectomy significantly reduces breast cancer risk and recurrence in women carrying BRCA1 mutations.breast cancer | reactive oxygen species | hormones | PTEN B RCA1 mutations promote tumor formation almost exclusively in hormone-responsive tissues such as breast and ovary (1). It has been proposed that the steroid hormone estrogen (E2) increases the survival of BRCA1-deficient cells in these tissues, favoring tumorigenesis (2). However, why BRCA1-mutated breast and ovarian epithelial cells have a survival advantage remains unclear.E2 regulates cell differentiation, growth, and survival in a broad range of human tissues. The most abundant and potent E2 circulating in the body is 17β-estradiol. In its classical mechanism of action, E2 diffuses into the cells and binds to two nuclear E2 receptors (ERs), ERα and ERβ, which act as transcription factors and influence gene expression (3). Nonclassical mechanisms involve E2 binding to plasma membrane-associated ER proteins. An example of the latter is the phosphatidylinositol 3-kinase (PI3K) that is known to mediate E2-induced cell survival and proliferation (4). In female mice, E2 administration activates PI3K in ovarian granulosa cells (5). In vitro, E2 treatment of ER + MCF7 human breast cancer cells stimulates the serine/threonine-protein kinase, AKT, and leads to increased glucose uptake (6) and cell cycle progression (7). E2-induced AKT activation is also involved in axonal growth and neuronal morphogenesis (8). PI3K-AKT activation in response to growth factors potentiates ERα transcriptional activity (9, 10), suggesting positive cross-talk between E2 and the PI3K-AKT pathway. Clinical studies in ER + breast cancer patients have shown that PI3K-AKT activation underlies acquired resistance to anti-E2 or tamoxifen treatment (11). Indeed, clinicians...

Inflammatory bowel disease (IBD) pathogenesis is associated with dysregulated CD4 + Th cell responses, with intestinal homeostasis depending on the balance between IL-17-producing Th17 and Foxp3 + Tregs. Differentiation of naive T cells into Th17 and Treg subsets is associated with specific gene expression profiles; however, the contribution of epigenetic mechanisms to controlling Th17 and Treg differentiation remains unclear. Using a murine T cell transfer model of colitis, we found that T cell-intrinsic expression of the histone lysine methyltransferase G9A was required for development of pathogenic T cells and intestinal inflammation. G9A-mediated dimethylation of histone H3 lysine 9 (H3K9me2) restricted Th17 and Treg differentiation in vitro and in vivo. H3K9me2 was found at high levels in naive Th cells and was lost following Th cell activation. Loss of G9A in naive T cells was associated with increased chromatin accessibility and heightened sensitivity to TGF-β1. Pharmacological inhibition of G9A methyltransferase activity in WT T cells promoted Th17 and Treg differentiation. Our data indicate that G9A-dependent H3K9me2 is a homeostatic epigenetic checkpoint that regulates Th17 and Treg responses by limiting chromatin accessibility and TGF-β1 responsiveness, suggesting G9A as a therapeutic target for treating intestinal inflammation. IntroductionThe inflammatory bowel diseases (IBDs) are a group of chronic intestinal inflammatory diseases that include ulcerative colitis (UC) and Crohn disease (CD). IBD is thought to occur as a result of a complex interplay between host genetics and environmental factors leading to a dysregulated intestinal immune response (1). A recent meta-analysis of existing genome-wide association studies identified over 160 loci associated with both UC and CD (2). Gene ontology (GO) analysis of these IBD loci showed that the terms "regulation of cytokine production" and "T cell activation" were significantly enriched (2), suggesting that dysregulated production of cytokines by activated T cells is a critical factor in the development of IBD. Thus, a better understanding of the molecular mechanisms that regulate T cell activation and function may provide novel pathways to target therapeutically.A pathogenic role for CD4 + Th cells in intestinal inflammation has been clearly shown in a murine T cell transfer model of IBD. Adoptive transfer of highly purified naive CD4 + CD25 -CD45RB hi Th cells into immunodeficient Rag1 -/-mice results in the development of chronic intestinal inflammation, leading to weight loss and death (3,4). Disease pathology of Th cell transfer colitis shares many similarities with human IBD, including transmural inflammation,

These data indicate that gene-gene interactions impact MTX efficacy and tolerability in rheumatoid arthritis.