Roger James

The Human Phenotype Ontology in 2017

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

DNA-Mediated Gene Transfer into Mammalian Cells

In many situations it is very convenient to express a gene in a variety of different cell types, other than those from which it was derived. This could be useful in a number of areas such as the study of the regulation of gene expression and the biological function of gene products. There are a number of methods available (outlined below) to transfer both cloned and uncloned genes. Unfortunately, there is no method suitable for all situations and one must choose a particular method to suit the genetic material being used, the type of study to be undertaken and, most importantly, the cell type under study. Suggestions for suitable usage are made in each section. The calcium phosphate precipitation method1 is the one most widely used because it is suitable for most forms of DNA and is technically very simple to perform. Consequently, this method is described in most detail. Other methods which require sophisticated apparatus (such as microinjection) or great expertise (such as viral transformation) are described in less detail, but give essential references for those whose needs are suited to these methods.