Human Variome Project Quality Assessment Criteria for Variation Databases

Abstract

Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved.

Variation Interpretation Predictors: Principles, Types, Performance, and Choice

“…The HVP has released quality assessment criteria to evaluate the quality of genetic variation databases and to stimulate database curators to make improvements where they are needed (http://www.humanvariomeproject.org/finish/19/255.html) [Vihinen et al., ]. Once the quality scheme is implemented, the quality information will allow users to check how reliable, up‐to‐date, and user‐friendly a certain database is.…”

A review of human genome project (HGP) from ethical perspectives

“…Apart from that, a new space in the field of anthropology has been introduced to identify the origins of humans, including their race, demography, genetic diseases and so on (Slatkin and Racimo, 2016;Parrington, 2015;Schiffels and Durbin, 2014;Richards and Hawley, 2010) and research on structure and function of human brain circuits (Green et al, 2015) for example the application of innovative technologies and tools to identify the brain cell types, its interconnected between different region and neurons in the brain by circuits and processing the brain signals and sensor in which has been conducted by The United States's Brain Research through Advancing Innovative Neurotechnologies (hereinafter referred to as "BRAIN"). Croce (2016) has listed five (5) advanced research on HGP namely International HAPMA Project, 1000 Genomes Project, DNA Fingerprinting, Forensic Analysis and Applied Genetic whereas Vihinen et al (2016) highlights on Human Variome Project with the defining goal is to collect all information on genetic variation that impedes human health. Similarly, 1000 Genomes Project is to produce an extensive and comprehensive catalog of human genetic variation that will support future medical research studies.…”

Clinical Interpretation of Genomic Variations

“…ClinVar is an interactive tool that can be divided into submitter, variation, phenotype, interpretation, and evidence. ClinVar represents the interpretation of a single allele, compound heterozygotes, haplotypes, and combinations of alleles in different genes [34,35]. …”