Where in the genome are significant single nucleotide polymorphisms from genome-wide association studies located?

Recent technological progress has permitted the efficient performance of genome-wide association studies (GWAS) to map genetic variants associated with common diseases. Here, we analyzed 2,893 single nucleotide polymorphisms (SNPs) that have been identified in 593 published GWAS as associated with a disease phenotype with respect to their genomic location. In absolute numbers, most significant SNPs are located in intergenic regions and introns. When compared to their representation on the chips, there is essentially overrepresentation of nonsynonymous coding SNPs (nsSNPs), synonymous coding SNPs, and SNPs in untranscribed regions upstream of genes among the disease associated SNPs. A Gene Ontology term analysis showed that genes putatively causing a phenotype often code for membrane associated proteins or signal transduction genes.     

Is transformation associated with an increased error frequency in mammalian cells?

Acute starvation of mammalian cells for amino acids results in translational errors that may be detected by two-dimensional polyacrylamide gel electrophoresis. Using this as an assay for error frequency in mammalian cells, we investigated the hypothesis that neoplastic transformation was associated with an increased error frequency which in turn leads to an increased mutation rate and a decreased efficiency of regulatory controls (phenomena of tumor progression). Although we found that transformation was not always associated with an increased level of mistranslation we showed that SV40 transformation increased the level of translational errors in all cell types tested.     

When should one adjust for measurement error in baseline variables in observational studies?

Previously, we showed that in randomised experiments, correction for measurement error in a baseline variable induces bias in the estimated treatment effect, and conversely that ignoring measurement error avoids bias. In observational studies, non-zero baseline covariate differences between treatment groups may be anticipated. Using a graphical approach, we argue intuitively that if baseline differences are large, failing to correct for measurement error leads to a biased estimate of the treatment effect. In contrast, correction eliminates bias if the true and observed baseline differences are equal. If this equality is not satisfied, the corrected estimator is also biased, but typically less so than the uncorrected estimator. Contrasting these findings, we conclude that there must be a threshold for the true baseline difference, above which correction is worthwhile. We derive expressions for the bias of the corrected and uncorrected estimators, as functions of the correlation of the baseline variable with the study outcome, its reliability, the true baseline difference, and the sample sizes. Comparison of these expressions defines a theoretical decision threshold about whether to correct for measurement error. The results show that correction is usually preferred in large studies, and also in small studies with moderate baseline differences. If the group sample sizes are very disparate, correction is less advantageous. If the equivalent balanced sample size is less than about 25 per group, one should correct for measurement error if the true baseline difference is expected to exceed 0.2-0.3 standard deviation units. These results are illustrated with data from a cohort study of atherosclerosis.     

Are there lessons from negative results in studies using video playback?

The use of video playback is a growing practice in animal behaviour. Studies that lead to unpredicted negative results are often considered failures and remain unpublished. In this article I review some of the published and unpublished studies that have led to negative results. Analysis of these studies suggests that no particular problem is responsible for more than a small number of negative results. I suggest further investigation of the potential causes of these negative results to assess their importance to the outcome of video playback experiments. Received: 31 January 2000 / Received in revised form: 27 March 2000 / Accepted: 28 March 2000     

Genome-wide association studies in plant pathosystems: success or failure?

Harnessing natural genetic variation is an established alternative to artificial genetic variation for investigating the molecular dialog between partners in plant pathosystems. Herein, we review the successes of genome-wide association studies (GWAS) in both plants and pathogens. While GWAS in plants confirmed that the genetic architecture of disease resistance is polygenic, dynamic during the infection kinetics, and dependent on the environment, GWAS shortened the time of identification of quantitative trait loci (QTLs) and revealed both complex epistatic networks and a genetic architecture dependent upon the geographical scale. A similar picture emerges from the few GWAS in pathogens. In addition, the ever-increasing number of functionally validated QTLs has revealed new molecular plant defense mechanisms and pathogenicity determinants. Finally, we propose recommendations to better decode the disease triangle.     

Positive and negative feedbacks in human population dynamics: future equilibrium or collapse?

The future number of people inhabiting the planet will influence the impact over natural ecosystems. In consequence, the growth of the human population represents one of the most important challenges for the near future. In this paper we used population dynamic theory to analyze human population growth. The results suggest that human population growth exhibited important fluctuations during the last 2000 years. In particular two different phases during the last 400 years can be distinguished, a positive relationship with population size implying positive feedback processes, followed by a negative relationship with population size – suggesting that negative feedback processes have been operating during the last 45 years. Our results support the view that ecological concepts derived from population ecology can be useful for understanding human dynamics. While cooperation at low densities in animal populations reminds us the Boserupian view that population growth induces economic development and higher standards of living, competition at high densities reconciles ecological theory with the original Malthusian view. We conclude that the present reduction in human per capita growth rates appears to be consequence of different limiting factors operating in combination around the globe in a similar manner, except in Africa where the factors operating appears to be very different. Humans may achieve a stable equilibrium population in the next century but the possibility of a population collapse caused by second‐order oscillations should be considered.     

High-density genotyping: an overkill for QTL mapping? Lessons learned from a case study in maize and simulations

High-density genotyping is extensively exploited in genome-wide association mapping studies and genomic selection in maize. By contrast, linkage mapping studies were until now mostly based on low-density genetic maps and theoretical results suggested this to be sufficient. This raises the question, if an increase in marker density would be an overkill for linkage mapping in biparental populations, or if important QTL mapping parameters would benefit from it. In this study, we addressed this question using experimental data and a simulation based on linkage maps with marker densities of 1, 2, and 5 cM. QTL mapping was performed for six diverse traits in a biparental population with 204 doubled haploid maize lines and in a simulation study with varying QTL effects and closely linked QTL for different population sizes. Our results showed that high-density maps neither improved the QTL detection power nor the predictive power for the proportion of explained genotypic variance. By contrast, the precision of QTL localization, the precision of effect estimates of detected QTL, especially for small and medium sized QTL, as well as the power to resolve closely linked QTL profited from an increase in marker density from 5 to 1 cM. In conclusion, the higher costs for high-density genotyping are compensated for by more precise estimates of parameters relevant for knowledge-based breeding, thus making an increase in marker density for linkage mapping attractive.     

The Göttingen minipig for assessment of retinoid efficacy in the skin: comparison of results from topically treated animals with results from organ-cultured skin

Göttingen minipigs were treated topically for 6 d with a novel retinoid (MDI 301) at concentrations ranging from 0.3% to 30% in cream vehicle. Treatment of the minipigs did not adversely affect their health (hematological and necropsy parameters) or produce changes in the skin suggestive of retinoid-induced skin irritation. After killing the animals, skin samples from each treatment site were excised and maintained in organ culture for 6 d. In addition, untreated skin was also maintained in organ culture and treated with MDI 301 (0.1–5 μg/ml). After 3 d, the culture supernatants were collected and analyzed for levels of collagen type I and for matrix metalloproteinases (MMPs). Both skin samples treated in vivo and skin samples exposed to MDI 301 in culture demonstrated increased collagen production. Only slight changes in levels of MMP-2 (gelatinase A) or MMP-9 (gelatinase B) were seen. After 6 d, the organ-cultured skin was fixed in formalin and prepared for histology. The organ-cultured skin was compared to skin that was fixed at killing after in vivo treatment. Epidermal hyperplasia was quantified at various MDI 301 concentrations. In vivo and in vitro treatments showed similar results—although the thickness was not substantially changed on average, there were focal areas of hyperplasia at higher retinoid concentrations. Taken together, these data suggest that MDI 301 enhances collagen production in minipig skin, without irritation. Furthermore, these studies suggest that minipig skin exposed to the retinoid in organ culture is equally predictive as topically treated skin. The in vitro organ culture approach may provide a cost-effective alternative model to that of the intact animal for skin retinoid testing.     

Triphalangeal thumb in association with split hand/foot: A phenotypic marker for SHFM3?

BACKGROUND: At least five distinct loci have been implicated in split hand foot malformation (SHFM). Establishing genotype/phenotype correlations at the chromosomal level may elucidate responsible developmental genes and improve patient management. In our analysis of previously published genetically mapped SHFM cases, preaxial hand involvement was a significant discriminating variable, most commonly seen at the SHFM3 locus (OMIM 600095) at 10q24. Of the 47 SHFM3 patients analyzed, 15 (31.9%) had triphalangeal thumb (TPT), a limb finding not reported at any other locus. METHODS: The association of TPT/split foot, in particular, prompted us to review the literature for similar cases. RESULTS: We ascertained a number of unmapped familial and sporadic cases with TPT/split foot, including a group of patients with triphalangeal thumb-brachyectrodactyly syndrome. Certain trends were similar in both SHFM3 and these unmapped literature cases. With respect to gender, 7/12 (58%) of mapped SHFM3 cases with TPT/split foot were male whereas 5/12 (42%) were female, compared with 22/50 (44%) males and 28/50 (56%) females among unmapped cases (P=0.3715). Individuals in both groups usually had bilateral involvement, with 67 and 60% showing bilateral TPT among mapped and literature cases, respectively (P=0.6714). Bilateral involvement of the feet was even more striking (83% of SHFM3 patients and 96% of literature cases; P=0.0808). CONCLUSIONS: Patients with TPT/split foot may in fact represent SHFM3 cases and should be evaluated for genomic rearrangements at 10q24. TPT may be identified only by radiographic analysis, emphasizing the importance of imaging these patients and their family members.     

A study of French centenarians: are ACE and APOE associated with longevity?

Association study is the method of choice to identify genes involved in complex processes that result from the interaction of environmental and genetic factors. However, because of biases that increase the risk of false positive reports, preliminary positive conclusions have to be reproduced on other populations to be validated as firm conclusions. In 1994, certain alleles of two genes, APOE (Apolipoprotein E) and ACE (angiotensin converting enzyme), were reported to be more frequent in French centenarians, suggesting an association with such a complex polyfactorial process as longevity. Enlargement of the French centenarian cohort allows a new assessment of this hypothesis on 563 centenarians. In contrast to APOE, the ACE association was not confirmed. Retrospective analysis of the initial study revealed discrepancies that may in part explain this observation. Risk of reporting false positive associations is discussed and recommendations to set up a rigorous experimental design are proposed.