Analysis of binary traits: testing association in the presence of linkage

Most methods for testing association in the presence of linkage, using family-based studies, have been developed for continuous traits. FBAT (family-based association tests) is one of few methods appropriate for discrete outcomes. In this article we describe a new test of association in the presence of linkage for binary traits. We use a gamma random effects model in which association and linkage are modelled as fixed effects and random effects, respectively. We have compared the gamma random effects model to an FBAT and a generalized estimating equation-based alternative, using two regions in the Genetic Analysis Workshop 14 simulated data. One of these regions contained haplotypes associated with disease, and the other did not.     

HLA-A confers an HLA-DRB1 independent influence on the risk of multiple sclerosis

A recent high-density linkage screen confirmed that the HLA complex contains the strongest genetic factor for the risk of multiple sclerosis (MS). In parallel, a linkage disequilibrium analysis using 650 single nucleotide polymorphisms (SNP) markers of the HLA complex mapped the entire genetic effect to the HLA-DR-DQ subregion, reflected by the well-established risk haplotype HLA-DRB1*15,DQB1*06. Contrary to this, in a cohort of 1,084 MS patients and 1,347 controls, we show that the HLA-A gene confers an HLA-DRB1 independent influence on the risk of MS (P = 8.4x10(-10)). This supports the opposing view, that genes in the HLA class I region indeed exert an additional influence on the risk of MS, and confirms that the class I allele HLA-A*02 is negatively associated with the risk of MS (OR = 0.63, P = 7x10(-12)) not explained by linkage disequilibrium with class II. The combination of HLA-A and HLA-DRB1 alleles, as represented by HLA-A*02 and HLA-DRB1*15, was found to influence the risk of MS 23-fold. These findings imply complex autoimmune mechanisms involving both the regulatory and the effector arms of the immune system in the triggering of MS.     

Effects of anticoagulants and storage conditions on clinical oxylipid levels in human plasma

Metabolomics and lipidomics are of fundamental importance to personalized healthcare. Particularly the analysis of bioactive lipids is of relevance to a better understanding of various diseases. Within clinical routines, blood derived samples are widely used for diagnostic and research purposes. Hence, standardized and validated procedures for blood collection and storage are mandatory, in order to guarantee sample integrity and relevant study outcomes. We here investigated different plasma storage conditions and their effect on plasma fatty acid and oxylipid levels. Our data clearly indicate the importance of storage conditions for plasma lipidomic analysis. Storage at very low temperature (?80?°C) and the addition of methanol directly after sampling are the most important measures to avoid ex vivo synthesis of oxylipids. Furthermore, we identified critical analytes being affected under certain storage conditions. Finally, we carried out chiral analysis and found possible residual enzymatic activity to be one of the contributors to the ex vivo formation of oxylipids even at ?20?°C.     

Egg production and hatching success in the calanoid copepods Calanus helgolandicus and Calanus finmarchicus in the North Sea from March to September 2001

Spatial and seasonal egg production rates (E_r) and egg hatchingsuccess in the copepods Calanus finmarchicus and Calanus helgolandicuswere measured in the North Sea from March to September. Foodavailability was monitored by chlorophyll and protist concentrationsand three size fractions of seston fatty acids. Seasonal andspatial distribution and production differed between the species.Calanus finmarchicus was found only offshore of the 50-m isobath,with decreasing E_r (37–28 eggs female^–1 day^–1)from March to July. Calanus helgolandicus had two abundancepeaks, in spring and autumn, with a low in May during whichtime the highest E_r were observed (38 eggs female^–1 day^–1).At other times, E_r in C. helgolandicus remained lower than inC. finmarchicus (     

Refinement of the dominant optic atrophy locus (OPA1) to a 1.4-cM interval on chromosome 3q28-3q29, within a 3-Mb YAC contig

Dominant optic atrophy, type Kjer, is an autosomal dominant eye disease that is characterized by progressive optic atrophy with onset in early childhood, decrease of visual acuity, colour vision defects and centrocecal scotoma. By examination of 5 Danish families and the use of polymorphic markers, we have refined the localization of the OPA1 locus and assigned it to a 1.4-cM interval on chromosome 3q28-3q29, between markers D3S3669 and D3S3562. This localizes the gene on a 3-Mb YAC contig covering the disease locus. We have also located a possible candidate gene HRY to this contig. Received: 1 April 1996 / Revised: 8 August 1996