Selective Phenotyping, Entropy Reduction, and the Mastermind game

<p>Abstract</p> <p>Background</p> <p>With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, <it>i</it>.<it>e</it>. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately.</p> <p>Results</p> <p>Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset.</p> <p>Conclusions</p> <p>Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping.</p

Impaired hepatic drug and steroid metabolism in congenital adrenal hyperplasia due to P450 oxidoreductase deficiency

Objective: Patients with congenital adrenal hyperplasia due to P450 oxidoreductase (POR) deficiency(ORD) present with disordered sex development and glucocorticoid deficiency. This is due to disruption of electron transfer from mutant POR to microsomal cytochrome P450 (CYP) enzymes that play a key role in glucocorticoid and sex steroid synthesis. POR also transfers electrons to all major drugmetabolizing CYP enzymes, including CYP3A4 that inactivates glucocorticoid and oestrogens. However, whether ORD results in impairment of in vivo drug metabolism has never been studied. Design:We studied an adult patient with ORD due to homozygous POR A287P, the most frequent POR mutation in Caucasians, and her clinically unaffected, heterozygous mother. The patient had received standard dose oestrogen replacement from 17 until 37 years of age when it was stopped after she developed breast cancer. Methods: Both subjects underwent in vivo cocktail phenotyping comprising the oral administration of caffeine, tolbutamide, omeprazole, dextromethorphan hydrobromide and midazolam to assess the five major drug-metabolizing CYP enzymes. We also performed genotyping for variant CYP alleles known to affect drug metabolism. Results: Though CYP enzyme genotyping predicted normal or high enzymatic activities in both subjects, in vivo assessment showed subnormal activities of CYP1A2, CYP2C9, CYP2D6 and CYP3A4 in the patient and of CYP1A2 and CYP2C9 in her mother. Conclusions: Our results provide in vivo evidence for an important role of POR in regulating drug metabolism and detoxification. In patients with ORD, in vivo assessment of drug-metabolizing activities with subsequent tailoring of drug therapy and steroid replacement should be considered

Age- and activity-related differences in the abundance of Myosin essential and regulatory light chains in human muscle

Traditional methods for phenotyping skeletal muscle (e.g., immunohistochemistry) are labor-intensive and ill-suited to multixplex analysis, i.e., assays must be performed in a series. Addressing these concerns represents a largely unmet research need but more comprehensive parallel analysis of myofibrillar proteins could advance knowledge regarding age- and activity-dependent changes in human muscle. We report a label-free, semi-automated and time efficient LC-MS proteomic workflow for phenotyping the myofibrillar proteome. Application of this workflow in old and young as well as trained and untrained human skeletal muscle yielded several novel observations that were subsequently verified by multiple reaction monitoring (MRM).We report novel data demonstrating that human ageing is associated with lesser myosin light chain 1 content and greater myosin light chain 3 content, consistent with an age-related reduction in type II muscle fibers. We also disambiguate conflicting data regarding myosin regulatory light chain, revealing that age-related changes in this protein more closely reflect physical activity status than ageing per se. This finding reinforces the need to control for physical activity levels when investigating the natural process of ageing. Taken together, our data confirm and extend knowledge regarding age- and activity-related phenotypes. In addition, the MRM transitions described here provide a methodological platform that can be fine-tuned to suite multiple research needs and thus advance myofibrillar phenotyping

Exploratory QTL analyses of some pepper physiological traits in two environments

behind phenotypic differences and led to selection of genotypes having favourable traits. Continuous monitoring of environmental conditions has also become an accessible option. Rather than single trait evaluation, we would prefer smarter approaches capable of evaluating multiple, often correlated and time dependent traits simultaneously as a function of genes (QTLs) and environmental inputs, where we would The use of molecular breeding techniques has increased insight into the genetics like to include intermediate genomic information as well. In this paper, an exploratory QTL analysis over two environments was undertaken using available genetic and phenotypic data from segregating recombinant inbred lines (RIL) of pepper (Capsicum annuum). We focused on vegetative traits, e.g. stem length, speed of stem development, number of internodes etc. We seek to improve the estimation of allelic values of these traits under the two environments and determine possible QTL x E interaction. Almost identical QTLs are detected for each trait under the two environments but with varying LOD scores. No clear evidence was found for presence of QTL by environment interactions, despite differences in phenotypes and in magnitude of QTLs expression. Within the EU project SPICY (Voorrips et al., 2010 this issue), a larger number of environments will be studied and more advanced statistical analysis tools will be considered. The correlation between the traits will also be modelled. The identification of markers for the important QTL (Nicolaï et al., 2010 this issue) will improve the speed and accuracy of genomic prediction of these complex phenotype

Why dried blood spots are an ideal tool for CYP1A2 phenotyping

Background and Objective: Dried blood spot (DBS) sampling has gained wide interest in bioanalysis during the last decade and has already been successfully applied in pharmacokinetic and phenotyping studies. However, all of the available phenotyping studies used small datasets and did not include a systematic evaluation of DBS-specific parameters. The latter is important since several of these factors still challenge the breakthrough of DBS in routine practice. In this study, caffeine and paraxanthine are determined in capillary DBS, venous DBS, whole blood and plasma for cytochrome P450 (CYP) 1A2 phenotyping. The aim of this study was to explore the usefulness of DBS as a tool for CYP1A2 phenotyping. Methods: A CYP1A2 phenotyping study was conducted in 73 healthy volunteers who received a 150 mg oral dose of caffeine. Six hours post-administration, caffeine and paraxanthine concentrations and paraxanthine:caffeine molar concentration ratios, i.e., the actual CYP1A2 phenotyping indices, were determined in capillary DBS (obtained by non-volumetric application, direct from the fingertip), venous DBS, whole blood, and plasma. Furthermore, the impact of DBS-specific parameters, including hematocrit, volume spotted, and punch location, was evaluated. Results: Concentrations of caffeine and paraxanthine in capillary DBS were, respectively, on average 12.7 and 13.8 % lower than those in venous DBS and 31.5 and 33.1 % lower than those in plasma. While these differences were statistically significant (p = 0.053). This ratio also alleviated the impact of hematocrit and volume spotted. Conclusions: Using the largest DBS-based phenotyping study to date, we have demonstrated that CYP1A2 phenotyping in capillary DBS is a valid and convenient alternative for the classical plasma-based approach. Additionally, we have provided an objective basis as to why DBS are an ideal tool for CYP1A2 phenotyping

ARIGAN: Synthetic Arabidopsis Plants using Generative Adversarial Network

In recent years, there has been an increasing interest in image-based plant phenotyping, applying state-of-the-art machine learning approaches to tackle challenging problems, such as leaf segmentation (a multi-instance problem) and counting. Most of these algorithms need labelled data to learn a model for the task at hand. Despite the recent release of a few plant phenotyping datasets, large annotated plant image datasets for the purpose of training deep learning algorithms are lacking. One common approach to alleviate the lack of training data is dataset augmentation. Herein, we propose an alternative solution to dataset augmentation for plant phenotyping, creating artificial images of plants using generative neural networks. We propose the Arabidopsis Rosette Image Generator (through) Adversarial Network: a deep convolutional network that is able to generate synthetic rosette-shaped plants, inspired by DCGAN (a recent adversarial network model using convolutional layers). Specifically, we trained the network using A1, A2, and A4 of the CVPPP 2017 LCC dataset, containing Arabidopsis Thaliana plants. We show that our model is able to generate realistic 128x128 colour images of plants. We train our network conditioning on leaf count, such that it is possible to generate plants with a given number of leaves suitable, among others, for training regression based models. We propose a new Ax dataset of artificial plants images, obtained by our ARIGAN. We evaluate this new dataset using a state-of-the-art leaf counting algorithm, showing that the testing error is reduced when Ax is used as part of the training data.Comment: 8 pages, 6 figures, 1 table, ICCV CVPPP Workshop 201