The InSiGHT Database: An Example LOVD System

  • John Paul Plazzer
  • Johan den Dunnen
  • Finlay Macrae
Chapter

Abstract

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.

Keywords

Variants Phenotypes Database Genomics Colorectal cancer 

Notes

Glossary of Terms

API

Application Programming Interface, a technology to allow systems to communicate or share data with other systems, with or without human interaction.

CCFR

Colon Cancer Family Registry http://www.coloncfr.org.

GA4GH

Global Alliance for Genomics and Health https://genomicsandhealth.org.

HGNC

HUGO Gene Nomenclature Committee http://www.genenames.org/. HUGO is the HUman Genome Organisation http://www.hugo-international.org/.

HGVS

Human Genome Variation Society http://www.hgvs.org/.

HPO
HVP
Individual

A record in the database that could represent a patient with a disease or an otherwise healthy person.

InSiGHT

International Society for Gastrointestinal Hereditary Tumours https://www.insight-group.org.

Instance

A specific database in operation. For example, InSiGHT operates its own instance of LOVD.

LOVD

Leiden Open Variation Database www.lovd.nl.

LOVDv2

The previous version of LOVD software.

LOVDv3

The latest version of LOVD software, with genomic variant storage and other advanced features.

LSDB

Locus-Specific Database, also referred to as gene/disease-specific database.

LUMC

Leiden University Medical Center https://www.lumc.nl/.

MPS

Massively Parallel Sequencing, also known as NGS.

NGS

Next-Generation Sequencing.

OMIM

Online Mendelian Inheritance in Man https://www.omim.org/.

PLSD

Prospective Lynch Syndrome Database http://www.lscarisk.org.

VIC

Variant Interpretation Committee.

VUS

Variant of Uncertain Significance.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • John Paul Plazzer
    • 1
  • Johan den Dunnen
    • 2
  • Finlay Macrae
    • 1
    • 3
  1. 1.Colorectal Medicine & GeneticsThe Royal Melbourne HospitalMelbourneAustralia
  2. 2.Human Genetics & Clinical GeneticsLeiden University Medical CenterLeidenthe Netherlands
  3. 3.Department of MedicineThe University of MelbourneMelbourneAustralia

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