NCBI offers a variety of clinical genetic resources to help you research, diagnose, and treat diseases and conditions. You can quickly and easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website.
How and why should you use our resources? Consider the example below.
Your patient is a 58-year-old woman who has been diagnosed with Acute Coronary Syndrome, scheduled for an angioplasty, and she will need to take clopidogrel for at least three months. She mentions that her father died of a stroke while taking the drug and is concerned. You look into pharmacogenetic influences on clopidogrel response and use the results of your patient’s genetic test to determine if a change in the prescription is needed. Continue reading “Using NCBI Resources for Genotype-Based Medication Optimization”
Join us March 14-18 in Salt Lake City, Utah
We are excited to celebrate ClinVar’s 10th anniversary and look forward to seeing you in-person at the 2023 ACMG Annual Clinical Genetics Meeting, March 14-18, 2023, in Salt Lake City, Utah. We will participate in a variety of events and activities featuring our clinical and human genetic resources.
Check out NCBI’s schedule:
Continue reading “NCBI at ACMG 2023”
Join us October 25-29 in Los Angeles, CA
We are looking forward to seeing you in-person at the American Society of Human Genetics (ASHG) annual meeting, October 25-29, 2022, in Los Angeles, California.
We will present a variety of talks and posters featuring our clinical and human genetic resources, as well as genome products and tools. We are excited to introduce the NIH Comparative Genomics Resource (CGR), a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources to biomedical research. If you’re interested in providing feedback that will be used to help drive CGR forward, consider joining our round table discussion.
Check out NCBI’s schedule of activities and events:
Continue reading “Connect with NCBI at ASHG 2022”
Now it’s easier than ever to access all data in ClinVar for a variant or set of variants across all reported diseases. ClinVar’s new XML is organized by variant only (Variation ID), instead of the variant-disease pair. This reduces redundancy, for example in cases where a variant is related to several disease concepts, and makes the XML consistent with the ClinVar web pages. You can get ClinVarVariationRelease XML from the /xml/clinvar_variation/ directory on the ClinVar FTP site. New features in ClinVarVariationRelease XML shown in Figure 1 include:
- Explicit elements to distinguish between variants that were directly interpreted and “included” variants, those that were interpreted only as part of a Haplotype or Genotype. The clinical significance for included variants is indicated as “no interpretation for the single variant”.
- Explicit elements to distinguish records for simple allele, haplotypes, and genotypes
- The Replaces element that provides a history and indicates accessions that were merged into the current accession.
- A section that maps the submitted name or identifier for the interpreted condition to the corresponding name used in ClinVar and the MedGen Concept Identifier (CUI)
Figure 1. ClinVar variant-centric XML showing a variant record for a haplotype (VCV000236230) that comprises two included variations (SimpleAlleles) that are marked as “no interpretation for the single variant”. The record includes all the condition records (RCVList) with names and identifiers from MedGen, OMIM and other sources.
To learn more about how to use this data, read our documentation.
Tell us how ClinVar has helped you by writing to us at firstname.lastname@example.org.
If you’ve been searching in ClinVar, you might have noticed search improvements introduced in December that reliably connect you with information on your variant of interest. ClinVar has broadened its search capability to accept many different ways of expressing the same variation, including variation described on RefSeq transcripts and proteins. If your variant expression is not reported in ClinVar, we alert you to other variants at the same genomic location or link you to related information in other NCBI resources such as dbSNP, LitVar, and PubMed. ClinVar will also now interpret expressions that contain minor errors or warn you about improper syntax that it cannot interpret.
Figure 1. Improved search results in Clinvar showing mapping of an HGVS expression to the equivalent variant in ClinVar.
Here are some example queries that show the improved search results.
NM_001318787.1:c.2258G>A – an HGVS expression that is not in ClinVar, but ClinVar has an alternate expression for a variant (Figure 1).
NM_004958.3:c.7365C>A – a variant not in ClinVar, but another variant is at the same genomic location is in ClinVar.
NM_002113.2:c.19delG – a variant is not in ClinVar, but there is additional information for the variant in other databases.
We welcome your feedback on your search experience and any additional ideas on how to improve searching in ClinVar.
The ClinVar Team is happy to announce a new online form in the ClinVar Submission Portal, the Single SCV Update, which makes it easier for you to update a single record.
The new ClinVar Single SCV Update form showing the sections for editing the evaluation date, clinical significance, condition, and citations.
Continue reading “Update single records easily with ClinVar’s Single SCV Update”
MedGen is a free, comprehensive resource for one-stop access to essential information on phenotypic health topics related to medical genetics as collected from established high-quality sources. It integrates terminology from multiple primary ontologies (or nomenclatures) to facilitate standardization and more accurate results from search queries.
Some things you can do in MedGen:
Continue reading “MedGen: Your search engine for human medical genetics”