Amplified fragment length homoplasy: in silico analysis for model and non-model species.

BACKGROUND: AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species. RESULTS: In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species. CONCLUSIONS: These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina.

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.

Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.

A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

The effect of climate on masting in the European larch and on its specific seed predators.

Masting is the intermittent production of large seed crops by a population of plants. Two main hypotheses have been proposed to explain masting. Variations in seed crop may result from stochastic climate factors (temperature, rainfall, etc.), and/or masting may be a plant evolutionary strategy to avoid specific seed predators. To determine the effect of climate on the annual pattern of cone production in the European larch (Larix decidua), we analyzed larch cone production from 1975 to 2005 at 20 sites in the French Alps, ranging from 1,300 to 2,100 m a.s.l. (on average 17 years per site were sampled). We examined the effects of mast seeding on the predation of larch cones by the dominant specific pre-dispersal seed predators, cone fly Strobilomyia spp. Larch cone production varied across the years and was spatially synchronized throughout the region. We constructed two models to explain seed production, one for sites at low (<1,800 m) and one for sites at high (> or =1,800 m) altitudes, using partial least squares (PLS) regressions to detect across a large number of climate indices (306) the factors which best explain cone production. Monthly indices were more accurate descriptors than 4-month period indices. The predation rate was lower in high cone production years that followed low production years, supporting the predator satiation hypothesis. However, variable cone production explained only a small part of predation rates (45 and 25% at low and high altitudes, respectively). Predation was also directly affected by climate conditions. PLS regressions taking into account both cone production and climate factors accounted for as much as 68 and 82% of the predation rate variation at low and high altitudes, respectively. This study contributes to a better understanding of how climate factors differently affect the members of an interacting community.

Cost-effectiveness analysis of gestational diabetes mellitus screening in France.

OBJECTIVE: To compare three strategies for gestational diabetes screening (i) screening of high-risk pregnant women with the 50 g oral glucose tolerance test (OGTT); (ii) screening of all pregnant women with the 50 g OGTT; (iii) screening of all pregnant women according to the 75 g OGTT. STUDY DESIGN: Cost-effectiveness analysis. The outcome measures, i.e. macrosomia, prematurity, perinatal mortality, hypertensive disorders rates were estimated from published studies and the costs from a prospective study involving 120 pregnant women. RESULTS: Compared to the first strategy, the cost to obtain one unit of additional effectiveness with the second screening strategy, was up to 1.1 times more expensive, and with the third strategy was up to 3.7 times more expensive. CONCLUSION: The costs per case prevented reflect a favourable cost-effectiveness ratio (CER) for screening of high-risk pregnant women by 50 g oral glucose test.

[Methodology of economic assessment: example in oncology]. / Méthodes d'évaluation médico-économique : applications à la cancérologie.

The increasing costs of care make it important to identify those strategies of greatest value from both an effectiveness and cost perspective. Economic analysis is characterized by a simultaneous consideration of alternatives costs and outcomes, and can provide useful data for managerial decision making. In this paper, methods of economic evaluations in general and in cancer in particular is reviewed. In cancer treatment, preventive, curative or palliative strategies can be concerned. Economic evaluation have become increasingly important in oncology because of the proliferation of expensive new treatments. Furthermore, considering quality of life effects is particularly important in oncology, where many treatments obtain modest improvements in response or survival. Quality of life measurements are also reviewed.

[Which medico-economic approaches must be taken to evaluate the impact of costly molecules in oncology? The model of Herceptin in the breast metastatic cancer]. / Quelles approches médico-économiques choisir pour l'évaluation de l'impact des molécules coûteuses en cancérologie ? Le modèle de l'Herceptin dans le cancer du sein métastatique.

In an era where health care expenditure control is a necessity, weighing a new treatment's cost against its added benefits is of crucial importance. These medico-economic analyses may be planned for the evaluation of new molecules in their daily use. Different methods may be used. The medico-economic evaluation of a drug can be performed with the use of clinical studies or modelization techniques. "Clinical studies" include the following methods: randomized trials, so-called "experimental", non-randomized studies, and observational studies. This classification follows a downward evolution of both the investigator's intervention power and the level of proof. Finally, modelization is becoming a commonly used tool. Randomized trials are the "gold standard" but the other, more pragmatic study types, providing a lesser degree of proof can complete the evaluation of a new molecule. One must find the best compromise between the study's objectives and the study type.

Treatment of metastatic breast cancer: a large observational study on adherence to French prescribing guidelines and financial cost of the anti-HER2 antibody trastuzumab.

OBJECTIVE: This observational study aimed at analyzing adherence to prescribing guidelines of anti-HER2 monoclonal antibody trastuzumab treatment for metastatic breast cancer. Efficacy and costs were also evaluated. METHODS: The adherence to the trastuzumab treatment plan was analyzed according to both the French postlicensing guidelines published in 2001 and clinical guidelines from the regional cancer network in a cohort of 131 consecutive patients. RESULTS: The level of appropriateness to the molecular target was very high (92% of the patients showed a positive HER2 status, defined as HER2 3+ confirmed by immunohistochemistry or 2+ confirmed by fluorescent in situ hybridization). The treatment plan was made according to the French postlicensing guidelines in 41 patients (31.3%) and to the regional clinical guidelines for 109 patients (83.2%). The main reason for the difference was the type of molecules authorized for combination to trastuzumab. The median overall survival of the studied population was 18.6 months and the median progression-free survival rate was 7.7 months. Up to death or end of the study, the overall cost for the treatment of breast cancer with trastuzumab per patient and per year was 47,832 euro. CONCLUSION: This quite low adherence of clinicians to the French postlicensing guidelines is in contrast with the high level of adherence to the regional clinical guidelines. The reason is that the latter are less rigid about previously received treatments and enlarge the potential associated cytotoxics to vinorelbine. This supports the French National Cancer Institute decision to get expert clinicians involved together with the French agency for sanitary security of health products and the high health authority in a common elaboration of guidelines.

Specific information about the WHO guidelines for gestational diabetes screening improves clinical practices.

RATIONALE, AIMS AND OBJECTIVE: To evaluate the impact of specific information on World Health Organization (WHO) guidelines for gestational diabetes mellitus (GDM) screening on clinical practices and to estimate its acceptance by women. METHODS: A non-randomized interventional study, comparing two periods, that is, before (period I) and after (period II) the implementation of the WHO guidelines during year 2000 in three obstetrical units, using reminders, meetings and pre-printed prescription sheets. Women were interviewed on GDM screening acceptance. RESULTS: A total of 333 pregnant women were included in period I and 345 in period II. The proportion of women who were screened significantly increased between period I and period II (0.9% in period I, 59.1% in period II, P < 10(-3)). The screening test was realized in accordance with guidelines for 80% of women in period II. The acceptability of the test by women was estimated at 98%. Furthermore, 90% of them would accept to be screened again during another pregnancy. DISCUSSION: Specific information about WHO screening guidelines improves doctor practices. Moreover, the high rate of acceptance by women is an argument to promote more widespread WHO screening for GDM during pregnancy.

Use of the monoclonal antibody anti-HER2 trastuzumab in the treatment of metastatic breast cancer: a cost-effectiveness analysis.

BACKGROUND: This open controlled prospective study aimed at evaluating the medical and economical impact of first line chemotherapy for metastatic breast cancer (MBC). PATIENTS AND METHODS: Two groups of HER +++ MBC patients were compared: 26 were treated by a combination of trastuzumab and paclitaxel in 4 "prescriber" centers (group A) and 19 patients were treated by any chemotherapy without addition of trastuzumab, in 6 control centers (group B). The cost of chemotherapy and related hospitalizations was taken into account during the first 8 cycles. RESULTS: Forty-five patients, mean age 51 years have been included. The objective response rate was significantly higher in group A (42% vs. 6%, P = 0.036). The median overall survival was 17 months longer in the group A (29 vs. 12 months). The median progression free survival rate was 12.2 months longer in the group A (19 vs. 7 months). The 1-year survival rate was 85% in the group A and 47% in the group B. The mean overall care cost was 33.271 euro per patient in group A versus 11.191 euro per patient in group B. The additional cost per saved year of life expressed as the incremental cost-effectiveness ratio is 15.370 euro 2002. CONCLUSION: The related additional cost seems affordable for an European health care system and justifies the recommendation for its use in the subpopulation overexpressing HER2.