Each simple allele in the set is described in the path //ReferenceClinVarAssertion/MeasureSet/Measure. The path //ReferenceClinVarAssertion/MeasureSet contains all the metadata ClinVar has accumulated about any haplotype. Released on the first Thursday of the month. Thus, for single nucleotide variants not in repeat regions, the location based on VCF or HGVS will match on nucleotide position, but for insertions, duplications, and deletions in repeat regions, the different conventions of left justification (VCF) and right justification (HGVS) will make it appear that the definitions of the locations of the alleles are inconsistent among the files. Please note, however, that the convention for reporting location in the XML (SequenceLocation element) and tab-delimited files is consistent with HGVS expression, while the location in the VCF meets the VCF standard. Most of these records are old, and ClinVar is continuing to remove these gaps.Īll reports of the location of a variant are currently based on offset 1. Submissions accepted from non-OMIM sources without having validated the sequence definition.A frequent example of these would be reports of exon loss, without evidence of genomic deletion or single nucleotide changes affecting splice junctions. Variants originally defined based on analyses of cDNAs, without evidence of the genomic basis of the sequence change.ClinVar does not have the resources to research all of these to define the molecular basis of the report, but staff does continue to try to reduce the number of gaps. ClinVar processes allelic variant records on behalf of OMIM, and until recently, most allelic variant records did not contain a computable sequence definition of the allele.There are several causes of this, ranked below in decreasing order of frequency. Some of the records in ClinVar report alleles that have not been mapped to genomic coordinates. The most detailed comprehensive file is the full release ( ), but for a tabular comprehensive subset of data, also lists alleles and their placements on GRCh37 and GRCh38. There are multiple files that maintain information defining simple and complex alleles. variant instead of variant-phenotype assessment).ĭefinition of simple and complex alleles represented in ClinVar Not all of the data in the ObservedIn elements from each ClinVarAssertion/SCV are aggregated into the ReferenceClinVarAssertion/RCV, so the XML path //ClinVarAssertion//ObservedIn should be used to extract all submitted evidence.ĬlinVar also reports data in other formats and with different organizing principles ( e. The evidence is represented in //ObservedIn elements. The data received from the submitter (ClinVarAssertion) has a versioned accession starting with SCV, and packages the data as submitted (usually after transformation from a spreadsheet to XML). The ReferenceClinVarAssertion has a versioned accession starting with RCV. These files are retained until the next monthly release.Įach record (ClinVarSet element) in the full release contains one ReferenceClinVarAssertion element, which is based on the aggregation of data received by ClinVar (ClinVarAssertion element) and data added by NCBI’s processing, such as rs#, equivalent HGVS expressions, identifiers for disorders, allele frequencies, etc. These records represent aggregation of data by variant and interpreted phenotype combinations.Ĭomplete extractions are also reported week, usually Monday, in the path. The complete extraction of data in ClinVar is reported the first Thursday of each month as. ClinVar archives each submission (the accession beginning with SCV), aggregates data by variant/phenotype pairs and accessions that relationship (RCV), adds information such as database identifiers and locations on multiple assemblies (RCV only) and also aggregates data by simple alleles or complex alleles (VariationID). Thus ClinVar maintains standardized information about variants, diagnostic terms, phenotypic measures, methods of data acquisition, methods of data assessment, and evidence supporting the existence of the variant-phenotype relationship based on family studies, analyses of populations, or functional assays. The unit of record accessioned by ClinVar is the assessment made by the submitter about the relationship between variants and phenotypes, with supporting evidence. Phenotypic details about individuals assessed.Evidence about individuals or families assessed.Current assessment of alleles based on the name of the trait.Current assessment of alleles independent of name of the trait.Definition of genotypes represented in ClinVar. Definition of simple and complex alleles represented in ClinVar.Guide to using files from the ftp site or accessed via e-utilities Use cases
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