Phenotypic prediction based on metabolomic data : lasso vs Bolasso, primary data vs wavelet transformation

International audienceUnderstanding the relations between various 'omics data (such as metabolomics or genomics data) and phenotypes of interest is one of the current major challenges in biology. This question can be addressed by trying to learn a way to predict the phenotype value from the omic from joint observations of the omic and of the phenotype. In this paper, we focus on the prediction of a phenotype related to the quality of the meat from metabolomic data. As metabolomic data are high dimensional data and as, conjointly, the number of observations is often restricted, model selection methods are a way both to obtain a relevant solution to the prediction problem but also to select the most important metabolomes related to the phenotype under study. During the past years, model selection has know a growing interest in the statistical community: the first - and also probably the most known - selection method has been introducted by \citep{Tibshirani:1996} under the name of LASSO. Several variants of this original approach has then been proposed such as, recently, a bootstraped LASSO, named BOLASSO, introduced in (Bach, 2009). The proposal of this paper is to combine a wavelet representation of the metabolome spectra (see (Mallat, 1999) and (Antonini, 1992) for a complete introduction to wavelets) with the BOLASSO approach. We compare this methodology to more classical methods using either the original spectra as predictors (instead of the wavelet representation) or the original LASSO to select the model. The following section deals with the methodological description of the approach whereas the next one details the experiments and results

Analysis of dietary pattern impact on weight status for personalised nutrition through on-line advice: the Food4Me Spanish cohort

Obesity prevalence is increasing. The management of this condition requires a detailed analysis of the global risk factors in order to develop personalised advice. This study is aimed to identify current dietary patterns and habits in Spanish population interested in personalised nutrition and investigate associations with weight status. Self-reported dietary and anthropometrical data from the Spanish participants in the Food4Me study, were used in a multidimensional exploratory analysis to define specific dietary profiles. Two opposing factors were obtained according to food groups’ intake: Factor 1 characterised by a more frequent consumption of traditionally considered unhealthy foods; and Factor 2, where the consumption of “Mediterranean diet” foods was prevalent. Factor 1 showed a direct relationship with BMI (β = 0.226; r2 = 0.259; p < 0.001), while the association with Factor 2 was inverse (β = −0.037; r2 = 0.230; p = 0.348). A total of four categories were defined (Prudent, Healthy, Western, and Compensatory) through classification of the sample in higher or lower adherence to each factor and combining the possibilities. Western and Compensatory dietary patterns, which were characterized by high-density foods consumption, showed positive associations with overweight prevalence. Further analysis showed that prevention of overweight must focus on limiting the intake of known deleterious foods rather than exclusively enhance healthy products

Capturing health and eating status through a nutritional perception screening questionnaire (NPSQ9) in a randomised internet-based personalised nutrition intervention : the Food4Me study

BACKGROUND: National guidelines emphasize healthy eating to promote wellbeing and prevention of non-communicable diseases. The perceived healthiness of food is determined by many factors affecting food intake. A positive perception of healthy eating has been shown to be associated with greater diet quality. Internet-based methodologies allow contact with large populations. Our present study aims to design and evaluate a short nutritional perception questionnaire, to be used as a screening tool for assessing nutritional status, and to predict an optimal level of personalisation in nutritional advice delivered via the Internet. METHODS: Data from all participants who were screened and then enrolled into the Food4Me proof-of-principle study (n = 2369) were used to determine the optimal items for inclusion in a novel screening tool, the Nutritional Perception Screening Questionnaire-9 (NPSQ9). Exploratory and confirmatory factor analyses were performed on anthropometric and biochemical data and on dietary indices acquired from participants who had completed the Food4Me dietary intervention (n = 1153). Baseline and intervention data were analysed using linear regression and linear mixed regression, respectively. RESULTS: A final model with 9 NPSQ items was validated against the dietary intervention data. NPSQ9 scores were inversely associated with BMI (β = -0.181, p < 0.001) and waist circumference (Β = -0.155, p < 0.001), and positively associated with total carotenoids (β = 0.198, p < 0.001), omega-3 fatty acid index (β = 0.155, p < 0.001), Healthy Eating Index (HEI) (β = 0.299, p < 0.001) and Mediterranean Diet Score (MDS) (β = 0. 279, p < 0.001). Findings from the longitudinal intervention study showed a greater reduction in BMI and improved dietary indices among participants with lower NPSQ9 scores. CONCLUSIONS: Healthy eating perceptions and dietary habits captured by the NPSQ9 score, based on nine questionnaire items, were associated with reduced body weight and improved diet quality. Likewise, participants with a lower score achieved greater health improvements than those with higher scores, in response to personalised advice, suggesting that NPSQ9 may be used for early evaluation of nutritional status and to tailor nutritional advice. TRIAL REGISTRATION: NCT01530139 .Peer reviewedFinal Published versio

Methods for interpreting lists of affected genes obstained in a DNA microarray experiment

Background - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results - Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion - It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experimen

Cambios alimentarios y de estilo de vida como estrategia en la prevención del síndrome metabólico y la diabetes mellitus tipo 2: hitos y perspectivas

El elevado aporte calórico de la alimentación actual y el sedentarismo, son los principales causantes del notable incremento de la obesidad en nuestra sociedad. A su vez, esto conlleva un aumento de las patologías asociadas a ella, como pueden ser el síndrome metabólico y la diabetes tipo 2. En el presente trabajo, han sido revisados los estudios y programas más recientes y significativos en cuanto a su tamaño muestral y a su diversidad geográfica, poniendo de manifiesto que los cambios en la alimentación y en los estilos de vida, son un instrumento efectivo para combatir o retrasar la aparición de estas enfermedades. En este sentido, la prevención también es clave para evitar las graves consecuencias, relacionadas con la diabetes y el síndrome metabólico, que pueden afectar a la calidad de vida de la población.A high caloric intake in today’s nutrition and a sedentary lifestyle are the main causes of the notable increase in obesity in our society. In turn, this results in an increase in associated pathologies, such as metabolic syndrome and diabetes type 2. In the present work we review most recent studies and programs, which are significant due to their sample size and geographical diversity. It clearly shows that changes in alimentation and lifestyles are an effective instrument for combatting or delaying the onset of these diseases. In this sense, prevention is also key to avoiding serious consequences related to diabetes and metabolic syndrome, which can affect the life of the population

Personalized Nutrition Advice Reduces Intake of Discretionary Foods and Beverages: Findings From the Food4Me Randomized Controlled Trial

© 2021 American Society for Nutrition. Published by Elsevier Inc. This is an open access article distributed under the Creative Commons Attribution License, https://creativecommons.org/licenses/by-nc-nd/4.0/Objectives This study aimed to examine changes in intake of discretionary foods and beverages following a personalized nutrition intervention using two national classifications for discretionary foods. Methods Participants were recruited into a 6-month RCT across seven European countries (Food4Me) and were randomized to receive generalized dietary advice (Control) or one of three levels of personalized nutrition advice (based on dietary, phenotypic and genotypic information). Dietary intake from a FFQ was used to determine change between baseline and month 6 in (i) % energy, % contribution to total fat, SFA, total sugars and salt and (ii) contribution (%) made by sweets and snacks to intake of total fat, SFA, sugars and salt from discretionary foods and beverages, defined by Food Standards Scotland (FSS) and the Australian Dietary Guidelines (ADG). Results A total of 1270 adults (40.9 (SD 13.0) years; 57% female) completed the intervention. At month 6, percentage sugars from FSS discretionary items was lower in personalized nutrition vs control (19.0 ± 0.37 vs 21.1 ± 0.65; P = 0.005). Percentage energy (31.2 ± 0.59 vs 32.7 ± 0.59; P = 0.031), % total fat (31.5 ± 0.37 vs 33.3 ± 0.65; P = 0.021), SFA (36.0 ± 0.43 vs 37.8 ± 0.75; P = 0.034) and sugars (31.7 ± 0.44 vs 34.7 ± 0.78; P < 0.001) from ADG discretionary items were lower in personalized nutrition vs control. The % contribution of sugars from sweets and snacks was lower in personalized nutrition vs control (19.1 ± 0.36 vs 21.5 ± 0.63; P < 0.001). At 3 months, effects were consistent for ADG discretionary items, while there was no significant differences in personalized nutrition vs control for FSS discretionary items. Conclusions Compared with generalized dietary advice, personalized nutrition advice achieved greater reductions in intake of discretionary foods and beverages when the classification included all foods high in fat, added sugars and salt. Future personalized nutrition strategies may be used to target intake of discretionary foods and beverages. Funding Sources European Commission Food, Agriculture, Fisheries and Biotechnology Theme of the Seventh Framework Programme for Research and Technological Development [265494]. KML is supported by a NHMRC Emerging Leadership Fellowship (APP1173803).Peer reviewe

Guide for Current Nutrigenetic, Nutrigenomic, and Nutriepigenetic Approaches for Precision Nutrition Involving the Prevention and Management of Chronic Diseases Associated with Obesity

Chronic diseases, including obesity, are major causes of morbidity and mortality in most countries. The adverse impacts of obesity and associated comorbidities on health remain a major concern due to the lack of effective interventions for prevention and management. Precision nutrition is an emerging therapeutic approach that takes into account an individual's genetic and epigenetic information, as well as age, gender, or particular physiopathological status. Advances in genomic sciences are contributing to a better understanding of the role of genetic variants and epigenetic signatures as well as gene expression patterns in the development of diverse chronic conditions, and how they may modify therapeutic responses. This knowledge has led to the search for genetic and epigenetic biomarkers to predict the risk of developing chronic diseases and personalizing their prevention and treatment. Additionally, original nutritional interventions based on nutrients and bioactive dietary compounds that can modify epigenetic marks and gene expression have been implemented. Although caution must be exercised, these scientific insights are paving the way for the design of innovative strategies for the control of chronic diseases accompanying obesity. This document provides a number of examples of the huge potential of understanding nutrigenetic, nutrigenomic, and nutriepigenetic roles in precision nutrition

The effect of the apolipoprotein E genotype on response to personalized dietary advice intervention: findings from the Food4Me randomized controlled trial

Background: The apolipoprotein E (APOE) risk allele (ɛ4) is associated with higher total cholesterol (TC), amplified response to saturated fatty acid (SFA) reduction, and increased cardiovascular disease. Although knowledge of gene risk may enhance dietary change, it is unclear whether ɛ4 carriers would benefit from gene-based personalized nutrition (PN). Objectives: The aims of this study were to 1) investigate interactions between APOE genotype and habitual dietary fat intake and modulations of fat intake on metabolic outcomes; 2) determine whether gene-based PN results in greater dietary change than do standard dietary advice (level 0) and nongene-based PN (levels 1–2); and 3) assess the impact of knowledge of APOE risk (risk: E4+, nonrisk: E4−) on dietary change after gene-based PN (level 3). Design: Individuals (n = 1466) recruited into the Food4Me pan-European PN dietary intervention study were randomly assigned to 4 treatment arms and genotyped for APOE (rs429358 and rs7412). Diet and dried blood spot TC and ω-3 (n–3) index were determined at baseline and after a 6-mo intervention. Data were analyzed with the use of adjusted general linear models. Results: Significantly higher TC concentrations were observed in E4+ participants than in E4− (P < 0.05). Although there were no significant differences in APOE response to gene-based PN (E4+ compared with E4−), both groups had a greater reduction in SFA (percentage of total energy) intake than at level 0 (mean ± SD: E4+, −0.72% ± 0.35% compared with −1.95% ± 0.45%, P = 0.035; E4−, −0.31% ± 0.20% compared with −1.68% ± 0.35%, P = 0.029). Gene-based PN was associated with a smaller reduction in SFA intake than in nongene-based PN (level 2) for E4− participants (−1.68% ± 0.35% compared with −2.56% ± 0.27%, P = 0.025). Conclusions: The APOE ɛ4 allele was associated with higher TC. Although gene-based PN targeted to APOE was more effective in reducing SFA intake than standard dietary advice, there was no difference between APOE “risk” and “nonrisk” groups. Furthermore, disclosure of APOE nonrisk may have weakened dietary response to PN