FINDbase: a worldwide database for genetic variation allele frequencies updated

Abstract

Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding.

Institutional Profile: Golden Helix Institute of Biomedical Research: Interdisciplinary Research and Educational Activities in Pharmacogenomics and Personalized Medicine

“…These activities have not only promoted the collection of genomic variation in the Hellenic population but have also encouraged new studies to document the genetic heterogeneity of the commonest genetic disorders in various parts of the country. These studies confirmed that the β-thalassemia mutation spectra indeed differ in different parts of Greece, compared to the frequencies calculated for the entire country [10, 11], further outlining the need to perform such investigations to better orientate molecular genetic testing services in various parts of the country. Also, board members of the HVP Hellenic node participate in nationwide studies to critically ascertain the general public’s awareness and healthcare professionals’ opinion on genetic and pharmacogenomic testing services in Greece [12–14].…”

“…To facilitate seamless access and retrieval of genomic data, the Golden Helix Institute of Biomedical Research has employed a Service Oriented Architecture (SOA) for its genomics databases [3, 10, 11]. Services have been designed to support both schematic recognition of data available as well as data retrieval using interoperability features.…”

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

“…Contrary to the previous FINDbase data content updates in 2010 (9) and 2013 (10), the recent (2014–2016) update did not only include data curation, update and correction, where necessary, but also extensive data enrichment in all three data modules.…”

Population-ethnic group specific genome variation allele frequency data: A querying and visualization journey

“…To this end, we are experimenting on various visualization techniques aiming to bridge the gap that is currently open by other related databases. Although the initial launch of the Frequency of Inherited Disorders database (FINDbase) included some basic data visualization functionality [10], the recently upgraded version does allow data querying to be coupled to data visualization [11]. In this work, we present the development and implementation of an interactive web-based data visualization and querying tool for FINDbase, which allows users to combine large groups of similar elements and identify hidden relationships between individual pieces of information.…”