-
Journal of Clinical Immunology Oct 2022The International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) reports here the 2022 updated phenotypic...
The International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) reports here the 2022 updated phenotypic classification, which accompanies and complements the most-recent genotypic classification. This phenotypic classification is aimed for clinicians at the bedside and focuses on clinical features and laboratory phenotypes of specific IEI. In this classification, 485 IEI underlying phenotypes as diverse as infection, malignancy, allergy, auto-immunity and auto-inflammation are described, including 55 novel monogenic defects and 1 autoimmune phenocopy. Therefore, all 485 diseases of the genetic classification are presented in this paper in the form of colored tables with essential clinical or immunological phenotype entries.
Topics: Humans; Immunologic Deficiency Syndromes; Phenotype; Genotype; Hypersensitivity; Neoplasms
PubMed: 36198931
DOI: 10.1007/s10875-022-01352-z -
Respiratory Care Jul 2023COPD is a heterogeneous condition, the onset and trajectory of which is influenced not only by tobacco exposure but also an individual's genetics and the exposures they... (Review)
Review
COPD is a heterogeneous condition, the onset and trajectory of which is influenced not only by tobacco exposure but also an individual's genetics and the exposures they accumulate over their life course. In such a complex chronic disease, phenotyping individuals based on similar clinical or molecular characteristics can aid in guiding appropriate therapeutic management. Treatable traits, characteristics for which evidence exists for a specific favorable treatment response, are increasingly incorporated into COPD clinical guidelines. But the COPD phenotyping literature is evolving. Innovations in lung imaging and physiologic metrics, as well as omics technologies and biomarker science, are contributing to a better understanding of COPD heterogeneity. This review summarizes the evolution of COPD phenotyping, the current use of phenotyping to direct clinical care, and how innovations in clinical and molecular approaches to unraveling disease heterogeneity are refining our understanding of COPD phenotypes.
Topics: Humans; Pulmonary Disease, Chronic Obstructive; Lung; Biomarkers; Phenotype
PubMed: 37353326
DOI: 10.4187/respcare.11035 -
Pulmonology 2020Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous and multisystemic disease with progressive increasing morbidity and mortality. COPD is now widely... (Review)
Review
Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous and multisystemic disease with progressive increasing morbidity and mortality. COPD is now widely accepted as a heterogeneous condition with multiple phenotypes and endotypes. This review will discuss the old and new concepts for the different types of COPD phenotypes, as well as the inclusion of them in current guidelines. Phenotypical approach to COPD is having huge impact on everyday practice and changed nonpharmacological and pharmacological management of COPD in last decade. However, phenotypical approach is small step to precision medicine in COPD management in the absence of big, specific and well-designed COPD trials with exact identification of phenotypes for more personalization of the treatment of COPD.
Topics: Humans; Phenotype; Practice Guidelines as Topic; Precision Medicine; Pulmonary Disease, Chronic Obstructive
PubMed: 31740261
DOI: 10.1016/j.pulmoe.2019.10.006 -
Journal of Clinical Immunology Jan 2020Since 2013, the International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) has published an updated phenotypic...
Since 2013, the International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) has published an updated phenotypic classification of IEI, which accompanies and complements their genotypic classification into ten tables. This phenotypic classification is user-friendly and serves as a resource for clinicians at the bedside. There are now 430 single-gene IEI underlying phenotypes as diverse as infection, malignancy, allergy, autoimmunity, and autoinflammation. We herein report the 2019 phenotypic classification, including the 65 new conditions. The diagnostic algorithms are based on clinical and laboratory phenotypes for each of the ten broad categories of IEI.
Topics: Autoimmunity; Genotype; Hereditary Autoinflammatory Diseases; Humans; Hypersensitivity; Immunity; Immunologic Deficiency Syndromes; Phenotype
PubMed: 32048120
DOI: 10.1007/s10875-020-00758-x -
Plant Biotechnology Journal Jul 2020Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are... (Review)
Review
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
Topics: Breeding; Genome-Wide Association Study; Genomics; Genotype; Phenotype; Polymorphism, Single Nucleotide
PubMed: 32163658
DOI: 10.1111/pbi.13372 -
Trends in Ecology & Evolution Jan 2020Genetically identical individuals can be phenotypically variable, even in constant environmental conditions. The ubiquity of this phenomenon, known as 'intra-genotypic... (Review)
Review
Genetically identical individuals can be phenotypically variable, even in constant environmental conditions. The ubiquity of this phenomenon, known as 'intra-genotypic variability', is increasingly evident and the relevant mechanistic underpinnings are beginning to be understood. In parallel, theory has delineated a number of formal expectations for contexts in which such a feature would be adaptive. Here, we review empirical evidence across biological systems and theoretical expectations, including nonlinear averaging and bet hedging. We synthesize existing results to illustrate the dependence of selection outcomes both on trait characteristics, features of environmental variability, and species' demographic context. We conclude by discussing ways to bridge the gap between empirical evidence of intra-genotypic variability, studies demonstrating its genetic component, and evidence that it is adaptive.
Topics: Biological Evolution; Genotype; Humans; Phenotype; Selection, Genetic
PubMed: 31519463
DOI: 10.1016/j.tree.2019.08.005 -
Current Topics in Developmental Biology 2021Genetic assimilation and genetic accommodation are mechanisms by which novel phenotypes are produced and become established in a population. Novel characters may be... (Review)
Review
Genetic assimilation and genetic accommodation are mechanisms by which novel phenotypes are produced and become established in a population. Novel characters may be fixed and canalized so they are insensitive to environmental variation, or can be plastic and adaptively responsive to environmental variation. In this review we explore the various theories that have been proposed to explain the developmental origin and evolution of novel phenotypes and the mechanisms by which canalization and phenotypic plasticity evolve. These theories and models range from conceptual to mathematical and have taken different views of how genes and environment contribute to the development and evolution of the properties of phenotypes. We will argue that a deeper and more nuanced understanding of genetic accommodation requires a recognition that phenotypes are not static entities but are dynamic system properties with no fixed deterministic relationship between genotype and phenotype. We suggest a mechanistic systems-view of development that allows one to incorporate both genes and environment in a common model, and that enables both quantitative analysis and visualization of the evolution of canalization and phenotypic plasticity.
Topics: Adaptation, Physiological; Animals; Biological Evolution; Drosophila; Epigenesis, Genetic; Gene-Environment Interaction; Genetic Techniques; Models, Genetic; Mutation; Phenotype; Plants; Signal Transduction
PubMed: 33602492
DOI: 10.1016/bs.ctdb.2020.11.006 -
Current Opinion in Chemical Biology Dec 2021A cell's phenotype is the culmination of several cellular processes through a complex network of molecular interactions that ultimately result in a unique morphological... (Review)
Review
A cell's phenotype is the culmination of several cellular processes through a complex network of molecular interactions that ultimately result in a unique morphological signature. Visual cell phenotyping is the characterization and quantification of these observable cellular traits in images. Recently, cellular phenotyping has undergone a massive overhaul in terms of scale, resolution, and throughput, which is attributable to advances across electronic, optical, and chemical technologies for imaging cells. Coupled with the rapid acceleration of deep learning-based computational tools, these advances have opened up new avenues for innovation across a wide variety of high-throughput cell biology applications. Here, we review applications wherein deep learning is powering the recognition, profiling, and prediction of visual phenotypes to answer important biological questions. As the complexity and scale of imaging assays increase, deep learning offers computational solutions to elucidate the details of previously unexplored cellular phenotypes.
Topics: Deep Learning; Diagnostic Imaging; Phenotype
PubMed: 34023800
DOI: 10.1016/j.cbpa.2021.04.001 -
Trends in Plant Science Feb 2022Optical sensors and sensing-based phenotyping techniques have become mainstream approaches in high-throughput phenotyping for improving trait selection and genetic gains... (Review)
Review
Optical sensors and sensing-based phenotyping techniques have become mainstream approaches in high-throughput phenotyping for improving trait selection and genetic gains in crops. We review recent progress and contemporary applications of optical sensing-based phenotyping (OSP) techniques in cereal crops and highlight optical sensing principles for spectral response and sensor specifications. Further, we group phenotypic traits determined by OSP into four categories - morphological, biochemical, physiological, and performance traits - and illustrate appropriate sensors for each extraction. In addition to the current status, we discuss the challenges of OSP and provide possible solutions. We propose that optical sensing-based traits need to be explored further, and that standardization of the language of phenotyping and worldwide collaboration between phenotyping researchers and other fields need to be established.
Topics: Crops, Agricultural; Edible Grain; Phenotype
PubMed: 34417079
DOI: 10.1016/j.tplants.2021.07.015 -
Clinical and Experimental Dermatology Apr 2021Vascular malformations (VMs) are caused by localized defects of vascular development. Most VMs are due to sporadic, postzygotic mutations, while some are the result of... (Review)
Review
Vascular malformations (VMs) are caused by localized defects of vascular development. Most VMs are due to sporadic, postzygotic mutations, while some are the result of autosomal dominant germline mutations. Genotype-phenotype correlation is influenced by many factors. Individual genes can induce different phenotypes (pleiotropy), and similar phenotypes can be due to different genes/mutations (redundancy). The phenotypic spectrum of somatic mutations is wide, and depends on variant allele frequency, timing during embryogenesis, cell type(s) involved and type of mutation. The phenotype of germline mutations is determined by penetrance and expressivity, and is influenced by epigenetic factors (DNA methylation, histone modification) or 'second-hit' somatic mutations. Except for disorders with pathognomonic phenotypes such as Proteus syndrome or a characteristic constellation of symptoms such as CLOVES [congenital lipomatous (fatty) overgrowth, vascular malformations, epidermal naevi and scoliosis/skeletal/spinal anomalies] or PIK3CA-related overgrowth spectrum syndrome, differential diagnosis of VM is therefore difficult. It will be greatly facilitated with increasing analytic sensitivity of sequencing techniques such as next-generation sequencing. High-sensitivity molecular techniques are a prerequisite for targeted pharmacotherapy, i.e. selective therapeutic inhibition of activating mutations underlying VM, which has shown promising results in preliminary studies.
Topics: Epigenesis, Genetic; Genes, Dominant; Genotype; Germ-Line Mutation; Humans; Mutation; Penetrance; Phenotype; Vascular Malformations
PubMed: 33368487
DOI: 10.1111/ced.14513