Kerstin Koch

Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource

Genome-wide association studies (GWAS) have identified over 300 regions associated with more than 70 common diseases. However, identifying causal genes within an associated region remains a major challenge. One approach to resolving causal genes is through the dissection of gene-phenotype correlations. Here we use polychromatic flow cytometry to show that differences in surface expression of the human interleukin-2 (IL-2) receptor alpha (IL2RA, or CD25) protein are restricted to particular immune cell types and correlate with several haplotypes in the IL2RA region that have previously been associated with two autoimmune diseases, type 1 diabetes (T1D) and multiple sclerosis. We confirm our strongest gene-phenotype correlation at the RNA level by allele-specific expression (ASE). We also define key parameters for the design and implementation of post-GWAS gene-phenotype investigations and demonstrate the usefulness of a large bioresource of genotype-selectable normal donors from whom fresh, primary cells can be analyzed.

Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function.

Within the healthy population, there is substantial, heritable, and interindividual variability in the platelet response. We explored whether a proportion of this variability could be accounted for by interindividual variation in gene expression. Through a correlative analysis of genome-wide platelet RNA expression data from 37 subjects representing the normal range of platelet responsiveness within a cohort of 500 subjects, we identified 63 genes in which transcript levels correlated with variation in the platelet response to adenosine diphosphate and/or the collagen-mimetic peptide, cross-linked collagen-related peptide. Many of these encode proteins with no reported function in platelets. An association study of 6 of the 63 genes in 4235 cases and 6379 controls showed a putative association with myocardial infarction for COMMD7 (COMM domain-containing protein 7) and a major deviation from the null hypo thesis for LRRFIP1 [leucine-rich repeat (in FLII) interacting protein 1]. Morpholino-based silencing in Danio rerio identified a modest role for commd7 and a significant effect for lrrfip1 as positive regulators of thrombus formation. Proteomic analysis of human platelet LRRFIP1-interacting proteins indicated that LRRFIP1 functions as a component of the platelet cytoskeleton, where it interacts with the actin-remodeling proteins Flightless-1 and Drebrin. Taken together, these data reveal novel proteins regulating the platelet response.

Genetic determinants of major blood lipids in Pakistanis compared with Europeans.

Background—Evidence is sparse about the genetic determinants of major lipids in Pakistanis. Methods and Results—Variants (n=45 000) across 2000 genes were assessed in 3200 Pakistanis and compared with 2450 Germans using the same gene array and similar lipid assays. We also did a meta-analysis of selected lipid-related variants in Europeans. Pakistani genetic architecture was distinct from that of several ethnic groups represented in international reference samples. Forty-one variants at 14 loci were significantly associated with levels of HDL-C, triglyceride, or LDL-C. The most significant lipid-related variants identified among Pakistanis corresponded to genes previously shown to be relevant to Europeans, such as CETP associated with HDL-C levels (rs711752; P<10−13), APOA5/ZNF259 (rs651821; P<10−13) and GCKR (rs1260326; P<10−13) with triglyceride levels; and CELSR2 variants with LDL-C levels (rs646776; P<10−9). For Pakistanis, these 41 variants explained 6.2%, 7.1%, and 0.9% of the variation in HDL-C, triglyceride, and LDL-C, respectively. Compared with Europeans, the allele frequency of rs662799 in APOA5 among Pakistanis was higher and its impact on triglyceride concentration was greater (P-value for difference <10−4). Conclusions—Several lipid-related genetic variants are common to Pakistanis and Europeans, though they explain only a modest proportion of population variation in lipid concentration. Allelic frequencies and effect sizes of lipid-related variants can differ between Pakistanis and Europeans.

P66 The UK Blood Service/Wellcome Trust Control Collection: a unique public resource of control samples for disease association studies

Disease association studies, designed to identify genetic risk factors for common diseases (e.g. obesity and diabetes), require large numbers of samples from both patients and controls. The existence of a common control cohort that can be used in all diseases would have significant benefits. The National Blood Service and Cambridge University, funded by a grant from the Wellcome Trust, have collected DNA, plasma and viable lymphocytes from approximately 3600 UK blood donors. These samples form the UK Blood Service/Wellcome Trust Control Collection (UK‐BS/WT‐CC). A training pack was developed for collection teams of the blood services involved. Following training of team staff, donors attending regional blood collection sessions over a 6‐month period from September 2005 to February 2006 were asked to consent. For isolation of viable lymphocytes an ACD anti‐coagulated blood aliquot was collected. Corresponding plasma and leukocyte filters for DNA isolation were provided by the blood services after the processing of the whole blood donation. The samples were assigned unique numeric identifiers and following sample processing a controlled anonymisation process was performed in which all identifiers linking the sample to the donor were destroyed. In addition, a number of biometric measurements (gender, BMI, height, weight, year of birth) were obtained from each donor at the time of sample collection. This anonymised collection represents a unique public resource of control samples collected from donors throughout the geographical regions of the UK. Currently, 1500 DNA samples are being genotyped on the Affymetrix GeneChip® Human Mapping 500K Array Set as part of the Wellcome Trust Case Control study (http://www.wtccc.org.uk). Here we give an overview of the sample collection and processing together with a description of the phenotypic data that characterise the collection. The UK‐BS/WT‐CC represents a unique resource that will be available to eligible users via an access committee. The UK‐BS/WT‐CC places the NHSBT at the forefront of ongoing disease association studies.