The InSiGHT Database: An Example LOVD System
The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) operates a database with an important function in medical genetics – the sharing of clinical and genetic variant data for genes associated with inherited colorectal cancer. The Leiden Open Variation Database (LOVD) technology used for this task has been updated to handle genomic data that is increasingly being generated, often for patients or individuals with diverse clinical phenotypes. The issue of variant interpretation is a high priority, and InSiGHT’s approach is detailed here, as well as other technical challenges and possible solutions.
KeywordsVariants Phenotypes Database Genomics Colorectal cancer
Glossary of Terms
Application Programming Interface, a technology to allow systems to communicate or share data with other systems, with or without human interaction.
Colon Cancer Family Registry http://www.coloncfr.org.
Global Alliance for Genomics and Health https://genomicsandhealth.org.
Human Genome Variation Society http://www.hgvs.org/.
Human Phenotype Ontology http://human-phenotype-ontology.github.io/.
Human Variome Project http://www.humanvariomeproject.org/.
A record in the database that could represent a patient with a disease or an otherwise healthy person.
International Society for Gastrointestinal Hereditary Tumours https://www.insight-group.org.
A specific database in operation. For example, InSiGHT operates its own instance of LOVD.
Leiden Open Variation Database www.lovd.nl.
The previous version of LOVD software.
The latest version of LOVD software, with genomic variant storage and other advanced features.
Locus-Specific Database, also referred to as gene/disease-specific database.
Leiden University Medical Center https://www.lumc.nl/.
Massively Parallel Sequencing, also known as NGS.
Online Mendelian Inheritance in Man https://www.omim.org/.
Prospective Lynch Syndrome Database http://www.lscarisk.org.
Variant Interpretation Committee.
Variant of Uncertain Significance.
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