Sharing and analyzing clinical NGS data using LOVD 3€¦ · Sharing and analyzing clinical NGS data using LOVD 3.0 LOVD - Leiden Open Variation Database Locus-Speci c (mutation)

Sharing and analyzing clinicalNGS data using LOVD 3.0


DTL Focus meeting: ‘NGS Data Sharing & Repository’

Leiden University Medical Center Ivo F.A.C. Fokkema February 3rd , 2014 Slide 01/11


LOVD - Leiden Open Variation Database

• Locus-Specific (mutation) Database (LSDB)• Gene- or disease-centered database of sequence variants• LOVD 3.0 also allows inter-genic variants (NGS)

• Open Source, free, web-based, can be used locally

• In use since 2003, first released in January 2004

• Within few years became the most popular LSDB software

• 50% of genes in LSDBs worldwide is LOVD (2009)• 98% of genes in LSDBs worldwide is LOVD (Jan 2014)

• 620K fully annotated variants in registered LOVDs (70%)



Why are LSDBs needed?

• Need for finding curated data about a found variant

• Sources where to get variant information• HGMD

• (Partially) paid resource• First report only (frequency unknown)• Only variants reported as pathogenic

• dbSNP• Mixed bag of everything• Not all variants are actually confirmed• Not clear if functional consequences have been reported

• LSDBs• All variants, all reports• Curated by expert



Some LOVD key advantages (1)

• Direct online submission

• Advanced searching

• Curator chooses which data to store (custom columns)

• Link with Mutalyzer to check variant correctness

• Application Programming Interface (API)• Software can discover information in LOVDs• Create views in genome browsers• Global search interface

• Accessed 2.2M times in 2012• Accessed 5.2M times in 2013



Some LOVD key advantages (2)New in LOVD 3.0

• Describe variants on more than one transcript

• VCF file import• Find affected transcripts (Mutalyzer)• Create gene entries automatically (HGNC)

• Reference sequences (Mutalyzer/NCBI/EBI)

• Map position on transcript(s) (Mutalyzer)• Predict RNA & protein change (Mutalyzer)

• SeattleSeq annotated file import• Variants with effect on transcripts and many annotations

• Search variant on other LOVDs



Still under construction

• Add data licenses• Let data owner decide if data is redistributable, and under

which terms• Use Creative Commons license schema• Modify API, make accepting license mandatory

• Allow LOVDs to fetch variant frequencies from data sets• Exome Variant Server, 1000 Genomes, GoNL, ...• Or use DVD?


Analyzing clinical NGS data with LOVD (1)



• New analysis platform based on LOVD 3.0

• Developed for clinical genetics department in Leiden

• Exome sequencing on patients with rare diseases

• VCF run through internally developed pipeline for annotations• Tab delimited file with variants of affected child• SeattleSeq annotations (conservation, effect prediction)• Fields for coverage information, score for variant in parent

• Filters implemented to find the causative variant

• Variants can be scored by user and flagged for confirmation




• All analyses first filter on gene panel

• De novo variants, not previously reported• Not found in dbSNP, 1000 Genomes, GoNL, EVS; Not present

in mother or father

• X-linked recessive variants (male patients)• Chromosome X; Not present in father; Not homozygous in

mother

• Recessive variants• Homozygous or compound heterozygous in patient; Not

homozygous in parents


Analyzing NGS data with LOVD (4)




Acknowledgements

• LOVD 3.0 development• Ivar Lugtenburg• Jerry Hoogenboom

• LOVD team• Johan den Dunnen• Peter Taschner• Julia Lopez Hernandez

www.LOVD.nl

• Mutalyzer• Jeroen Laros• Martijn Vermaat

www.Mutalyzer.nl


Varda: A platform for sharing NGS variantsin medical research and diagnostics

Martijn Vermaat

Department of Human Genetics

Leiden University Medical Center

Varda

Platform for sharing variant frequencies

Central human genomic variant database

• Focussed on frequencies, not individuals

• Only accessible to collaborators

• Using is sharing

Goal

• Share variants found in sequencing experiments

• Find functionally relevant variants

DTL Focus Meeting 1/7 Monday, 3 February 2014

Varda

Technical details

• Annotate by sharing

• Store coverage information to determine reference calls

• Pooling without loss of information

• Encrypted connection with authentication

• REST API• Command line client for pipelines• web client for people


Platform overview


Data model

Sample anonymity

Guaranteed by

• No browsing

• Only disclose database-wide variant frequencies

• No individual genotypes


Data model

Sample anonymity

Guaranteed by

• No browsing

• Only disclose database-wide variant frequencies

• No individual genotypes

Additionally, samples can be pooled

• Merge variants from multiple samples

• Before uploading to the server

• Without loss of functionality


Data model: coverage profiles


Current and future work

Conclusions

We propose a shared variant database to facilitate in filteringobserved variants with high frequency in the population

Application: Shared variant database for Dutch medical researchcenters, coordinated by NBIC BioAssist. (trac.nbic.nl/dvd)

Application: Variant frequency database for LUMC clinicaldiagnostics NGS pipeline.

github.com/martijnvermaat/varda


Questions?

Acknowledgements:

Jeroen LarosMichiel van Galen

Ivo FokkemaPeter Taschner

Johan den Dunnen

Leon Mei (LUMC, NBIC)David van Enckevort (NBIC)

Pieter Neerincx (UMCG)Morris Swertz (UMCG)


Documents

Sharing and analyzing clinical NGS data using LOVD 3€¦ · Sharing and analyzing clinical NGS data using LOVD 3.0 LOVD - Leiden Open Variation Database Locus-Speci c (mutation)