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Leiden Open Variation Database for Diagnostics — LOVD+
Analysis of whole-exome data using LOVD
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LOVD+ — Leiden Open Variation Database for Diagnostics
The LOVD-team has developed a version of LOVD for diagnostic application, coined LOVD+.
LOVD+ has been developed to facilitate analysis of NGS data, i.e. large numbers of variants derived from gene panel and whole exome sequencing data, using configurable analyses.
LOVD+ is built on top of LOVD3 and comes with a user-friendly environment familiar to LOVD users.
LOVD+ is developed and actively used by collaborating teams from the Leiden University Medical Center (Netherlands) and the Melbourne Genomics Health Alliance (Australia).
Currently, over 10 institutes world-wide use LOVD+ for analyzing their gene panels or whole exome data.
LOVD+ is open source, released under the GPL license, and is under active development.
Workflow
This is how LOVD+ fits in the workflow of your diagnostic lab, to find clinically relevant and potentially causative variants.
- Your patient comes into your clinic and is assessed. Since the cause of the disease is not known, the patient's DNA sample is sent to be sequenced.
- The patient's DNA is sequenced, pre-analyzed (alignment, variant calling, annotation using tools like Ensemble's Variant Effect Predictor is performed) and optionally, pre-filtered (sequencing quality, variant frequencies, etc).
- The annotated variant data is loaded into LOVD+ and analyzed; potentially causative variants are selected, labeled and classified. You can use the pre-built analysis workflows (e.g., to find de novo variants or X-linked recessive variants), remove any filters in these workflows, or create your own analysis workflow. Variants of interest can be marked in various ways and exported to your LIMS system, if needed.
- If needed, the variant(s) selected to be confirmed are validated in the lab by, e.g., Sanger sequencing.
- Validated potentially causative variants are reported back.
Benefits of LOVD+
| Whole exome sequencing data analysis in seconds |
Fully configurable gene panels with full editing history which can be linked to the patient's disease |
Customize and adjust the way your variants are displayed |
| Clear overview of available analyses and each filter step |
Submit selected variants for automated validation by PCR and Sanger sequencing |
Complete workflow including closing analyses to be curated by senior staff members |
Interested?
If you're interested in trying out LOVD+, please contact us.
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