Clinical Annotation Reference Templates: a resource for consistent variant annotation

Annotating the impact of a variant on a gene is a vital component of genetic medicine and genetic research. Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available. The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome. The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM. Often the transcripts used to annotate gene variation are not provided, impeding interoperability and consistency. Here we introduce the concept of the Clinical Annotation Reference Template (CART). CARTs are analogous to the reference genome; they provide a universal standard template so reference genomic coordinates are consistently annotated at the protein level. Naturally, there are many situations where annotations using a specific transcript, or multiple transcripts are useful. The aim of the CARTs is not to impede this practice. Rather, the CART annotation serves as an anchor to ensure interoperability between different annotation systems and variant frequency accuracy. Annotations using other explicitly-named transcripts should also be provided, wherever useful. We have integrated transcript data to generate CARTs for over 18,000 genes, for both GRCh37 and GRCh38, based on the associated NM and ENST identified through the CART selection process. Each CART has a unique ID and can be used individually or as a stable set of templates; CART37A for GRCh37 and CART38A for GRCh38. We have made the CARTs available on the UCSC browser and in different file formats on the Open Science Framework: https://osf.io/tcvbq/. We have also made the CARTtools software we used to generate the CARTs available on GitHub. We hope the CARTs will be useful in helping to drive transparent, stable, consistent, interoperable variant annotation.

Implications of Web 2.0 Technology on Healthcare

Now that the health and medical sector is slowly but surely beginning to embrace Web 2.0 technologies and tactics such as social networking, blogging, and sharing health information, such usage may become an everyday occurrence. This new trend is emerging under the Health 2.0 umbrella where it has important effects on the future of medicine. This chapter introduces some important Health 2.0 concepts and discusses their advantages for health care and medical practice. In addition, this chapter provides a case study for building a Semantic Blog for Gene Annotation and Searching (GAS) among social network users. The GAS Blog enables users to syndicate and aggregate gene case studies via the RSS protocol, annotate gene case studies with the ability to add new tags (folksonomy), and search for/navigate gene case studies among a group or cross-groups based on FOAF, GO, and SCORM metadata. The GAS Blog is built upon an open source toolkit (WordPress) and further programmed via PHP. The GAS Blog is found to be very effective for annotation and navigation when compared with the traditional gene annotation and navigation systems, as well as with traditional search engines such as XPath.