Variation data in VectorBase NIH/NIAID VectorBase site visit March 2015

Variation data types VectorBase captures both sequence and structural variations (stable chromosomal inversions in An. gambiae) The bulk of the data is sequence variants, primarily SNPs, based on high-throughput genomic re-sequencing of isolates. Data is formatted using VCF (Variant Call Format).

Variation data bridges between PopBio and genome browser (Ensembl) Variants are stored in a mySQL using the Ensembl RDB schema. Sample metdata is stored in the PopBio (Chado postgres). Large and complex data sets which depend on the accuracy of the genome assembly and parameterization of variant calling algorithms.

Summary of VectorBase variation datasets ( ) 1) Aedes aegypti contains the latest SNP chip data set from Powell et al, 2015 (PMID: ). 2) An. stephensi (Indian strain) was a new database distinct from the SDA-500 strain. 3) Four further variation datasets for An. farauti, An. merus, An. sinensis and An. melas are available and will be loaded after updates to the assemblies for these organisms.

Representation in Popbio Genomic (re)sequencing is an assay type in PopBio Sample metadata stored in PopBio and Biosamples databases MR4 colony sequencing (VBP )

Variant VectorBase

Querying and using variation VectorBase Browser tracks

Querying and using variation VectorBase Browser tracks Biomart datasets

Querying and using variation VectorBase Browser tracks Biomart datasets Sample metadata

Querying and using variation VectorBase Browser tracks Biomart datasets Sample metadata VEP tool (Variant Effect Predictor)

Internal VectorBase variation + PopBio dataflows. VCF ISA-TAB Sample + variation set ids Ensembl variation database PopBio Display of variant data in genomic context Display of detailed sample metadata, e.g. geodata

Use of Apache Solr to provide unified variation search across VectorBase site. VCF Ensembl variation database PopBio Display of variant data in genomic context Display of detailed sample metadata, e.g. geodata ISA-TAB

Identification and management of redundant variant records via MongoDB NoSQL db. Slide courtesy of Christoph Grabmüller – Ensembl Genomes 2014.

VectorBase interactions with external data sources relevant to variation studies. dbSNP EVA BioSamples Community Initial submission of variation data (multiple formats). VectorBase VCF format data Sample metadata (ontology compliant) Long term variation archive Ongoing curation of data either solely by community, or in collaboration with VectorBase

EVA - long term storage of variant data Processing of variation data for VectorBase species of dbSNP is too slow to be useful (>1 year) VectorBase accepts community variation data submissions and processes these rapidly (this involves active collaboration with submitters to convert submissions into suitable data formats and link entries to ontologies and other metadata tracking systems). Store submitted variation data as VCF files in the European Variation Archive long term ( ) EVA to broker submission of VCF data to dbSNP who can then resolve duplicate submissions and allocate persistent IDs which can be reincorporated into VectorBase variation records. VectorBase has submitted data for Anopheles coluzzii + Anopheles gambiae to EVA. The anopheles 16 genomes data will be submitted to the archive once remaining sample tracking issues have been resolved.

BioSample- sample metadata Joint EBI/NCBI database that stores submitter supplied data relating to samples used in other primary NCBI archives such as – SRA (Sequence Read Archive) – dbGaP (Genotypes and Phenotypes database) – GenBank VectorBase works with community members to ensure sample metadata is captured and tagged with appropriate ontology terms (e.g. “A Multipurpose High Throughput SNP Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti.” Evans et al PMID: ). Joint VectorBase/researcher submitters allow samples to be curated by the community.

Future plans Consolidation: Continue to broker and improve sample metadata submissions with BioSamples Work with EVA developers to pilot VCF brokerage with dbSNP Improve “Sample picker” interface New data: MalariaGen 1000 Anopheles project (AR2 data release) Individuals from 8 countries, min. 30 samples per population, est million variants Data queries: Increase use of SOLR to replace and augment BioMart functionality Use of other database solutions for specific queries (e.g. mongoDB)