Influence of genotyping error in linkage mapping for complex traits – an analytic study

<p>Abstract</p> <p>Background</p> <p>Despite the current trend towards large epidemiological studies of unrelated individuals, linkage studies in families are still thoroughly being utilized as tools for disease gene mapping. The use of the single-nucleotide-polymorphisms (SNP) array technology in genotyping of family data has the potential to provide more informative linkage data. Nevertheless, SNP array data are not immune to genotyping error which, as has been suggested in the past, could dramatically affect the evidence for linkage especially in selective designs such as affected sib pair (ASP) designs. The influence of genotyping error on selective designs for continuous traits has not been assessed yet.</p> <p>Results</p> <p>We use the identity-by-descent (IBD) regression-based paradigm for linkage testing to analytically quantify the effect of simple genotyping error models under specific selection schemes for sibling pairs. We show, for example, that in extremely concordant (EC) designs, genotyping error leads to decreased power whereas it leads to increased type I error in extremely discordant (ED) designs. Perhaps surprisingly, the effect of genotyping error on inference is most severe in designs where selection is least extreme. We suggest a genomic control for genotyping errors via a simple modification of the intercept in the regression for linkage.</p> <p>Conclusion</p> <p>This study extends earlier findings: genotyping error can substantially affect type I error and power in selective designs for continuous traits. Designs involving both EC and ED sib pairs are fairly immune to genotyping error. When those designs are not feasible the simple genomic control strategy that we suggest offers the potential to deliver more robust inference, especially if genotyping is carried out by SNP array technology.</p

IL6 and CRP haplotypes are associated with COPD risk and systemic inflammation: a case-control study

<p>Abstract</p> <p>Background</p> <p>Elevated circulating levels of C-reactive protein (CRP), interleukin (IL)-6 and fibrinogen (FG) have been repeatedly associated with many adverse outcomes in patients with chronic obstructive pulmonary disease (COPD). To date, it remains unclear whether and to what extent systemic inflammation is primary or secondary in the pathogenesis of COPD.</p> <p>The aim of this study was to examine the association between haplotypes of <it>CRP</it>, <it>IL6 </it>and <it>FGB </it>genes, systemic inflammation, COPD risk and COPD-related phenotypes (respiratory impairment, exercise capacity and body composition).</p> <p>Methods</p> <p>Eighteen SNPs in three genes, representing optimal haplotype-tagging sets, were genotyped in 355 COPD patients and 195 healthy smokers. Plasma levels of CRP, IL-6 and FG were measured in the total study group. Differences in haplotype distributions were tested using the global and haplotype-specific statistics.</p> <p>Results</p> <p>Raised plasma levels of CRP, IL-6 and fibrinogen were demonstrated in COPD patients. However, COPD population was very heterogeneous: about 40% of patients had no evidence of systemic inflammation (CRP < 3 mg/uL or no inflammatory markers in their top quartile). Global test for haplotype effect indicated association of <it>CRP </it>gene and CRP plasma levels (P = 0.0004) and <it>IL6 </it>gene and COPD (P = 0.003). Subsequent analysis has shown that <it>IL6 </it>haplotype H2, associated with an increased COPD risk (p = 0.004, OR = 4.82; 1.64 to 4.18), was also associated with very low CRP levels (p = 0.0005). None of the genes were associated with COPD-related phenotypes.</p> <p>Conclusion</p> <p>Our findings suggest that common genetic variation in <it>CRP </it>and <it>IL6 </it>genes may contribute to heterogeneity of COPD population associated with systemic inflammation.</p

Translational studies in the complex role of neurotransmitter systems in anxiety and anxiety disorders

Discovery of innovative anxiolytics is severely hampering. Existing anxiolytics are developed decades ago and are still the therapeutics of choice. Moreover, lack of new drug targets forecasts a severe jeopardy in the future treatment of the huge population of CNS-diseased patients. We simply lack the knowledge on what is wrong in brains of anxious people (normal and diseased). Translational research, based on interacting clinical and preclinical research, is extremely urgent. In this endeavor, genetic and genomic approaches are part of the spectrum of contributing factors. We focus on three druggable targets: serotonin transporter, 5-HT1A, and GABAA receptors. It is still uncertain whether and how these targets are involved in normal and diseased anxiety processes. For serotonergic anxiolytics, the slow onset of action points to indirect effects leading to plasticity changes in brain systems leading to reduced anxiety. For GABAA benzodiazepine drugs, acute anxiolytic effects are found indicating primary mechanisms directly influencing anxiety processes. Close translational collaboration between fundamental academic and discovery research will lead to badly needed breakthroughs in the search for new anxiolytics.</p

Utility of whole-genome sequence data for across-breed genomic prediction

Background: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. Methods: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands. BovineHD genotypes for all bulls were imputed to WGS using Beagle4 and Minimac2. Genomic prediction across the three populations was performed with ASReml4, with each population used as single reference and as single validation sets. In addition to the 50k, HD and WGS, markers that were significantly associated with stature in a large meta-GWAS analysis were selected and used for prediction, resulting in 10 prediction scenarios. Furthermore, we estimated the proportion of genetic variance captured by markers in each scenario. Results: Across breeds, 50k, HD and WGS markers resulted in very low accuracies of prediction ranging from − 0.04 to 0.13. Accuracies were higher in scenarios with pre-selected markers from a meta-GWAS. For example, using only the 133 most significant markers in 133 QTL regions from the meta-GWAS yielded accuracies ranging from 0.08 to 0.23, while 23,125 markers with a − log10(p) higher than 7 resulted in accuracies of up 0.35. Using WGS data did not significantly improve the proportion of genetic variance captured across breeds compared to scenarios with few but pre-selected markers. Conclusions: Our results demonstrated that the accuracy of across-breed GP can be improved by using markers that are pre-selected from WGS based on their potential causal effect. We also showed that simply increasing the number of markers up to the WGS level does not increase the accuracy of across-breed prediction, even when markers that are expected to have a causal effect are included

Polymorphisms in genes controlling inflammation and tissue repair in rheumatoid arthritis: a case control study.

Contains fulltext : 97228.pdf (publisher's version ) (Open Access)BACKGROUND: Various cytokines and inflammatory mediators are known to be involved in the pathogenesis of rheumatoid arthritis (RA). We hypothesized that polymorphisms in selected inflammatory response and tissue repair genes contribute to the susceptibility to and severity of RA. METHODS: Polymorphisms in TNFA, IL1B, IL4, IL6, IL8, IL10, PAI1, NOS2a, C1INH, PARP, TLR2 and TLR4 were genotyped in 376 Caucasian RA patients and 463 healthy Caucasian controls using single base extension. Genotype distributions in patients were compared with those in controls. In addition, the association of polymorphisms with the need for anti-TNF-alpha treatment as a marker of RA severity was assessed. RESULTS: The IL8 781 CC genotype was associated with early onset of disease. The TNFA -238 G/A polymorphism was differentially distributed between RA patients and controls, but only when not corrected for age and gender. None of the polymorphisms was associated with disease severity. CONCLUSIONS: We here report an association between IL8 781 C/T polymorphism and age of onset of RA. Our findings indicate that there might be a role for variations in genes involved in the immune response and in tissue repair in RA pathogenesis. Nevertheless, additional larger genomic and functional studies are required to further define their role in RA

Assessment of global phase uncertainty in case-control studies

<p>Abstract</p> <p>Background</p> <p>In haplotype-based candidate gene studies a problem is that the genotype data are unphased, which results in haplotype ambiguity. The <inline-formula><graphic file="1471-2156-10-54-i1.gif"/></inline-formula> measure <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> quantifies haplotype predictability from genotype data. It is computed for each individual haplotype, and for a measure of global relative efficiency a minimum <inline-formula><graphic file="1471-2156-10-54-i1.gif"/></inline-formula> value is suggested. Alternatively, we developed methods directly based on the information content of haplotype frequency estimates to obtain global relative efficiency measures: <inline-formula><graphic file="1471-2156-10-54-i2.gif"/></inline-formula> and <inline-formula><graphic file="1471-2156-10-54-i3.gif"/></inline-formula> based on A- and D-optimality, respectively. All three methods are designed for single populations; they can be applied in cases only, controls only or the whole data. Therefore they are not necessarily optimal for haplotype testing in case-control studies.</p> <p>Results</p> <p>A new global relative efficiency measure <inline-formula><graphic file="1471-2156-10-54-i4.gif"/></inline-formula> was derived to maximize power of a simple test statistic that compares haplotype frequencies in cases and controls. Application to real data showed that our proposed method <inline-formula><graphic file="1471-2156-10-54-i4.gif"/></inline-formula> gave a clear and summarizing measure for the case-control study conducted. Additionally this measure might be used for selection of individuals, who have the highest potential for improving power by resolving phase ambiguity.</p> <p>Conclusion</p> <p>Instead of using relative efficiency measure for cases only, controls only or their combined data, we link uncertainty measure to case-control studies directly. Hence, our global efficiency measure might be useful to assess whether data are informative or have enough power for estimation of a specific haplotype risk.</p

Restoration of salt marshes in the Netherlands

The conquest of land from the sea has been a long tradition in the Netherlands. When salt marshes were high enough, they were embanked when it was economically feasible, and transformed into intensively exploited agricultural land. This resulted in the transformation of halophytic communities to glycophytic communities. Often as an alternative, a low levee, a summerdike was built, which greatly reduced the flooding frequency of the landward summerpolder, hence creating a sedimentation deficit therein. Such summerpolders now cover 1200 ha in the Netherlands, 2100 ha in NW-Germany and small areas in England. Due to continuous embankments, the present salt-marsh area is relatively small with respect to the tidal basins. Discussions have been started how to increase the salt-marsh area. Two options will be discussed, firstly de-embankment of summerpolders and maintenance of the protective seawall, secondly increase of the effects of saline seepage behind the seawall by top soil removal. Both options include the restoration of salt-marsh communities (target communities) in intensively agriculturally exploited sites that have been salt marshes before. From the few examples abroad and experiments it is discussed (1) to which extent the sedimentation deficit in summerpolders could be compensated for, (2) if the soil seed bank is likely to contribute to re-establishment of salt-marsh communities, (3) if the dispersal of propagules of halophytic plants will be possible by hydrochory when the summerdike is breached, (4) to what extent is dispersal by endozoochory through waterfowl important in case re-establishment in a saline seepage area behind the seawall without open connection to the sea is envisaged. Two case studies of de-embanked summerpolders in the Netherlands revealed that the sedimentation deficit can be counteracted by rapid sedimentation, provided enough transport is possible from the foreshore. Dispersal by incoming tidal water from the nearby salt-marsh source area into the target area is possible for many salt-marsh plant species. The rate of success seems to depend on the relative position of source area and target area. A case study in a saline seepage area after top soil removal in the Netherlands, showed that the number of viable seeds dispersed by droppings from waterfowl is limited. Hence the possibilities for restoration of inland halophytic plant communities seem much lower than after de-embankment of summerpolders