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Variant Report


The Variant Report provides information about sequence changes that have been significantly associated with a phenotypic effect on drug response. Each Variant Report, presented as a web page, has different blocks for Introduction, Pharmacogenomic Studies which describe the variant, Linkage Disequilibrium and References.

Please note: Variant Reports are only available for BKL subscribers who have licensed the PGMD module.

Variant Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.

Anatomy of a Variant Report

The structure of a Variant Report is described below. Detailed documentation for the individual BKL components is accessed from links in the menu on the left, at the top of this page.

  • Access help by clicking the help menu  help  and clicking the Locus report help link.

  • Navigate to the desired section of the report by opening the table of contents  toc

Points of navigation within the report are indicated by the following visual cues.

  • Links to additional reports within the BKL are presented as regular text links.

  • Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:  external link  .

  • Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:  expand content  .

Introduction Provides an overview of the physical properties of the variant.  
Variant summary
Provides a short free text description of the key information regarding a variant and its associated phenotypes. Links to the supporting studies are provided for access to further details. This field may not be available for all variants.
Overview of studies published
Provides a table with a more detailed overview of the individual studies described in the report than is provided by the Table of contents alone. For each study the following information is provided: the drug(s) that was the focus of the study, the disease(s) that was being treated as part of the study, the phenotype(s) measured by the study, special notation for phenotypes that are related to FDA recommendations, survival or drug response, whether the variant was studied by itself or as part of a haplotype and the PubMed ID of the reference from which the information was curated. Click the Study ID to jump further down the report and view the full details for the study. Click the drug and disease links to navigate to the Drug and Disease reports respectively.

Note that the FDA phenotype, Survival phenotype and Response phenotype columns can be sorted on by clicking the column header. This makes it possible, for large reports with many studies, to quickly zero in on the most important information.
Specifies the Ensembl gene or genes that a variant overlaps, linked to the corresponding Locus Report(s).
Nearby genes
If a site is intergenic, this field will contain the 4 nearest Ensembl genes (5' and 3' on the positive and negative strands, and a signed distance from each gene).
Variant type
Specifies the type of variation, including SNP, Insertion, Deletion, Indel, and VNTR. If a variant falls within more than one gene (e.g. on the positive and negative strands) more than one variation type may be listed.
Variant class
Specifies the class of variant, as predicted by snpEff, based on the "canonical" transcript. Values include missense, nonsense, synonymous, and frameshift; please refer to snpEff for the full vocabulary.
Specifies the genomic position of the variant, based on GRCh37 hg19 assembly using a 1-based coordinate system.
Reference allele
Specifies the allele found at this site, based on GRCh37 hg19 assembly.
Allele frequency
Specifies the frequency of identified alleles which have been calculated across multiple sources including the 1000 Genomes project, Ensembl, HapMap and more.
HGVS description
HGVS description of the variation as mentioned in dbSNP, or manually formatted based on HGVS nomenclature, or as mentioned in the literature.

Pharmacogenomic Studies Provides detailed information for studies which describe significant drug response effects for the variant, organized by the drug or drugs that were the focus of the study. The first section of each study provides general information about the study. The fields of information are described in the "Study Details" section below. The second section of each study is a table which provides details about each genotype - phenotype observation. The columns of the table are described in the "Genotype Details" section below. Only a subset of genotype details are selected for view by default. Use the Show/Hide columns option to customize the columns displayed. When you make a change in the selection of columns displayed, a cookie will be set in your and your column preference will be applied until you make a change to the column settings or clear your browser's cache. Note that some of the study details are repeated in the genotype details to make comparison of individual observations easier. Use the Show/Hide columns option to customize the columns displayed.  
Study Details
Describes the ethnicity of the cases using the MeSH vocabulary. When the case group includes individuals of more than one ethnic group, multiple terms will be listed.
Describes the age of the case group.
Describes the gender of individuals taken for the study.
Disease treated
Specifies the disease that was the focus of the study, linked to the corresponding Disease Report. If more than one disease is the focus of the study, multiple diseases will be listed.
Other drugs taken but not studied
Species any drugs that were taken by patients but were not the focus of the study, linked to the corresponding Drug Report.
Study design
Describes the study type.
Genetic model
Describes the genetic model used to analyze genotype-phenotype information from association studies.
Source used for genotyping
Describes the original source from which sample was genotyped.
Total sample size
Describes the total number of subjects in the study.
When a variant was studied as part of a haplotype, a link to the relevant Haplotype Report is provided. The additional variants that compose the haplotype are indicated. Navigate to the Haplotype Report to view the complete study details.
PubMed reference number, which specifies the source from which the information is captured.
Describes the dose, duration and the route of administration of drug used for the treatment in the case group.

Genotype Details
Describes the full allele/genotype that was implicated in the given phenotype.
Study group ID
A number unique within a particular study that is used to group one or more genotypes that were for a particular drug response. Each variation will belong to one or more groups. E.g. Variation G>C leads to three possible genotypes. G/G, G/C, and C/C, for a phenotype (e.g. Increased drug toxicity) leading to these three observations being grouped together with a unique group id. If these same 3 genotypes were also studied for another phenotype (e.g. Response rate), those records would be assigned a new group id.
Describes the impact of genetic variation on drug response.
Phenotype details
Describes the impact of genetic variation on drug response, typically detailing the fraction of subjects with the specified genetic profile that exhibited the given response, and further detail on that response that would be given in the Phenotype field.
Named variant
For star (*) alleles, genotypes are represented with gene names followed by allele description e.g. CYP2C9*1/CYP2C9*1.
Describes number of cases with a particular allele/genotype.
Describes number of controls with a particular allele/genotype.
Describes odds ratio, the odds that an individual with this genetic profile will actually exhibit this phenotype.
Describes the likelihood that an individual with this genetic profile will exhibit this phenotype versus the likelihood that someone who does not have this genetic profile will exhibit this phenotype.
Describes the confidence interval for the OR (95%) for a particular genotype.
p-value as specified for a particular genotype, as provided by the reference.
Describes the type of evidence that led to the finding.
A field describing the metabolizer status of the haplotype or diplotype. Typically only available for Named variations. Values are typically Slow Metabolizer, Poor Metabolizer, Intermediate Metabolizer, Moderate Metabolizer, Rapid Metabolizer, Extensive Metabolizer, Ultrarapid Metabolizer.
Hazard ratio
Typically given in case vs. control (drug vs. placebo) studies to indicate the difference in survival between the two groups.
Free text annotation which may include additional information about sample details, statistical tests, corrections used, etc.

Linkage Disequilibrium Provides a table of sites which are in linkage disequilibrium with the variant, based on data from HapMap.  
Describes the HapMap population that the LD scores apply to.
The absolute value of D′, determined by dividing D by its maximum possible value, given the allele frequencies at the two loci. The case of D′=1 is known as complete LD. Values of D′<1 indicate that the complete ancestral LD has been disrupted.
r2 is equal to D2 divided by the product of the allele frequencies at the two loci.

Identifiers Displays internal identifiers associated with the variant.  
BKL Accessions
Lists the identifier for the variant of the page.
External Identifiers
Displays hyperlinks to corresponding entries in external databases.

References Displays list of references cited in the Variant Report.  
This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [more ...] to view all references. View abstracts via webservice by additionally clicking the Show abstract button which appears.

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