ClinVar: improvements to accessing data

ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools such as NCBI's E-utilities. The default view on the ClinVar website, the Variation page, was recently redesigned. The new layout includes several new sections that make it easier to find submitted data as well as summary data such as all diseases and citations reported for the variant. The new design also better represents more complex data such as haplotypes and genotypes, as well as variants that are in ClinVar as part of a haplotype or genotype but have no interpretation for the single variant. ClinVar's variant-centric XML had its production release in April 2019. The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file. ClinVar's search engine has been fine-tuned for improved retrieval of search results.

How the NIH Genetic Testing Registry and Medical Genetics Summaries can help oncologists adopt pharmacogenetics guidelines

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Background: Oncology is one of the few medical specialties where pharmacogenetic dosing is becoming a routine part of patient management. In the US, oncology drugs account for one-third of all drugs with pharmacogenetic data in their labeling. The NIH Genetic Testing Registry (GTR, www.ncbi.nlm.nih.gov/gtr ) is a freely available database of orderable genetic tests voluntarily provided by laboratories, and supports easy identification of both diagnostic and therapy-based tests. Medical Genetics Summaries (MGS, www.ncbi.nlm.nih.gov/books/NBK61999 ) presents actionable pharmacogenetic information by collating guidelines from authoritative professional (e.g. FDA, CPIC) and medical (e.g. ASCO) societies. MGS is regularly updated and can be found by searching PubMed. To increase oncologist adoption of pharmacogenetic recommendations, we analyzed the relationship between genetic tests in GTR and practice guidelines in MGS. Methods: The GTR database was queried to extract content, and we consulted the FDA Table of Pharmacogenomic Biomarkers in Drug Labeling. Results: Of the 90 oncology drugs that have pharmacogenetic information in their labeling, 29 drugs have at least one test for drug response in GTR. The oncology drugs most tested are mercaptopurine and irinotecan with 13 tests each, followed by thioguanine (12) and tamoxifen (9). For the remaining 61 drugs, only one drug (Pertuzumab) has a guideline, which is summarized in MGS. In total, MGS offers 10 summaries focused on oncology drugs. The 90 drug labels mention 49 distinct biomarkers (e.g. genes and variants). All 49 biomarkers can be interrogated using tests via the GTR. In total, GTR has approximately 3,500 tests for cancer diagnostics, 500 tests for cancer management, and 37 pharmacogenetic tests for cancer drugs. Conclusions: Searching for a genetic test in GTR by biomarker (100% coverage) is more efficient than by drug name (32% coverage) because of how laboratories describe their tests. Clinicians need to quickly find the best pharmacogenetic test and how tests are represented in the community affect the ability to search and find them. This presentation will show busy clinicians how to optimally use GTR and MGS. This work was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.

ClinVar: improving access to variant interpretations and supporting evidence

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.

ClinVar: public archive of interpretations of clinically relevant variants

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) at the National Center for Biotechnology Information (NCBI) is a freely available archive for interpretations of clinical significance of variants for reported conditions. The database includes germline and somatic variants of any size, type or genomic location. Interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, OMIM®, GeneReviews™, UniProt, expert panels and practice guidelines. In NCBI's Variation submission portal, submitters upload batch submissions or use the Submission Wizard for single submissions. Each submitted interpretation is assigned an accession number prefixed with SCV. ClinVar staff review validation reports with data types such as HGVS (Human Genome Variation Society) expressions; however, clinical significance is reported directly from submitters. Interpretations are aggregated by variant-condition combination and assigned an accession number prefixed with RCV. Clinical significance is calculated for the aggregate record, indicating consensus or conflict in the submitted interpretations. ClinVar uses data standards, such as HGVS nomenclature for variants and MedGen identifiers for conditions. The data are available on the web as variant-specific views; the entire data set can be downloaded via ftp. Programmatic access for ClinVar records is available through NCBI's E-utilities. Future development includes providing a variant-centric XML archive and a web page for details of SCV submissions.

The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency

The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information’s databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html).