HGVbase

HGVbase provides a curated database of human genomic variation focused on single nucleotide polymorphisms (SNPs) and disease-associated mutations to support studies of genetic variation, disease associations, and pharmacogenomics.

Key Features:

• Comprehensive Data Coverage: Contains records of neutral polymorphisms and disease-linked mutations across the human genome.
• Query Capabilities: Supports queries by sequence similarity, keywords, and genome coordinates.
• Multiple Data Formats: Offers data downloads in XML, Fasta, SRS, SQL, and tagged-text file formats.
• Contextual Sequence Information: Presents each variant with surrounding sequence context and links to neighboring human genes and affected features.
• Population Allele Frequencies: Includes population allele frequency data where available.
• Data Integrity and Consistency: Employs semi-automated data checking to ensure internal consistency and correct common source errors.
• Automated Annotation: Uses fully automated annotation tools to uniquely map variants to the draft genome sequence and reference positions in EMBL/GenBank files.
• Genotyping Assays and Functional Predictions: Provides genotyping assay information and functional prediction data to support experimental validation and interpretation.
• Haplotype and Genotype Data: Captures haplotype and genotype information within extended data structures.
• Collaborative Clinical Variant Curation: Participates with BiSC and HUGO-MDI in establishing a central repository for clinical mutations and associated disease phenotypes.

Scientific Applications:

• Disease Genetics: Enables identification and comparison of variants implicated in common and Mendelian diseases.
• Pharmacogenomics: Supports analysis of genetic variants affecting drug response.
• Population Genetics: Facilitates studies of allele frequency distribution across populations.
• Genotype–Phenotype Correlation: Serves as a resource for linking clinical phenotypes to curated variant records.
• Experimental Design and Validation: Provides genotyping assays and functional predictions to inform experimental validation of variants.

Methodology:

Semi-automated data checking and fully automated annotation are used to ensure internal consistency, uniquely map variants to the draft genome sequence, and reference positions in EMBL/GenBank files.