Tag: ClinVar

New ClinVar graphical display

New ClinVar graphical display

Maps clinically significant variants by gene and position!

ClinVar is a freely accessible, public archive of reports of the relationships between human variations and phenotypes, with supporting evidence at NLM/NCBI. To help you access your variants of interest quickly, ClinVar is introducing an all-new visualization tool in the search results. This graphical display provides an overview of variants when you search by gene or genomic region (Figures 1 and 2). You can only get the graphical display with gene or genomic region searches. For other types of searches, you will see the table only.

Gene search display

The display for a gene search highlights small variants within the gene. Large structural variants are also marked as a single dot in the middle of the variation. The interactive display shows the placement of variants on the gene and their clinical significance and allows you to zoom in or pan right / left and limit results to variants in a chosen gene. Figure 1 shows the graphical display as it appears at the top of the search results for the desmoglein 2 (DSG2) gene and how to filter and navigate to variants of interest (Search ClinVar: DSG2[gene]).

Figure 1 (A-D). Graphical display views in ClinVar for variants in DSG2, a gene with many known pathogenic variants

A. Graphical view showing all variants for the DSG2 gene

B. You can zoom in by mousing over the 8th exon in the gene diagram, which activates a pop-up menu that allows you to re-display only this region by following the link (red box).

C. Refreshed result for the 8th exon of DSG2 showing a number of variants including pathogenic, benign, and ones with conflicting interpretations of pathogenicity. You can select the filters on the left-hand side of the ClinVar result to limit to variants with characteristics of interest, for example Conflicting Interpretations of pathogenicity.

D. Variants in exon 8 of DSG2 filtered for conflicting interpretations of pathogenicity. You can retrieve individual variants by mousing over the graphic to activate the pop-up menu and following the link (red box).

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NCBI ALFA Project at Bio-IT World 2022 Hackathon

NCBI ALFA Project at Bio-IT World 2022 Hackathon

Announcing the Allele Frequency Aggregator (ALFA) Project as part of the Bio-IT World 2022 Hackathon: Visualization of NCBI ALFA Variants

Join NCBI at the Bio-IT World 2022 Hackathon on May 4-5, 2022 to learn about and work with data from our ALFA project! The primary goal of this hackathon project is to develop a novel tool, app, or approach to explore and visualize NCBI ALFA variants and allele frequency for 12 different human populations. We aspire to create a new helpful variant interpretation resource for the clinical and research communities.

We hope to see you there! More information and registration hereContinue reading “NCBI ALFA Project at Bio-IT World 2022 Hackathon”

Using NCBI resources to research, detect, and treat genetic phenotypes

Using NCBI resources to research, detect, and treat genetic phenotypes

Clinical Genetics Information at Your Fingertips

NCBI offers a portfolio of medical genetics resources to help you research, diagnose, and treat diseases and conditions. You can easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website. We also encourage you to join our community of thousands of submitters and share your germline and/or somatic data to advance discovery and optimize clinical care. 

How and why should you use our resources? Consider the example below. 

Your patient is a 40-year-old mother of two presenting with changes in bathroom habits, bleeding, and belly pain. She has a medical history of colonic polyps. Her family history reveals that her maternal grandmother, mother and uncle had several forms of cancers including colon, breast, and endometrium. 

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Ten reasons to submit to ClinVar

Wondering why 2,100 submitters from 83 countries have deposited more than 1.9 million records of their latest variation information in ClinVar? Curious about why genetic counselors, physicians, researchers, and so many others enthusiastically use data for nearly 1.2 million unique variants in ClinVar? Thinking about becoming part of this global community and sharing your knowledge to further science and make an impact on patient health? Well, we thought we should help you along by making the case for why everyone should submit to ClinVar.

#1: Every deposit can help a patient

The healthcare community relies on the standardized view offered by ClinVar variant reports, which include interpretations of clinical significance in relation to Mendelian disease, cancer and pharmacogenetics; an aggregated view of interpretations highlighting those in consensus, conflict or reviewed by expert panel; and detailed views of submitter data, including supporting evidence for the interpretation such as phenotype, assertion criteria and references.

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ClinVar annotations now available in NCBI Genome Browsers

Do you need to know which of the many NCBI dbSNP variants annotated near your region of interest are likely to be functionally or clinically significant? Figure it out with the track labelled  ‘ClinVar variants with precise endpoints’, available on sequence display viewers at NCBI, including the Genome Data Viewer (GDV) and Variation Viewer!

This track shows variation annotation, including single nucleotide variants and other short variants (e.g. insertions, deletions, etc.) in the NCBI ClinVar database and provides pathogenicity and other metadata. The ClinVar track is displayed next to the default NCBI and Ensembl gene annotation tracks and other NCBI-provided dbSNP and RNA-seq expression tracks.

screenshot of Genome Data Viewer with 'ClinVar variants' track displayed
Figure 1. GDV showing ‘ClinVar variants with precise endpoints’ track next to NCBI human gene annotation. Tracks are color coded for quick and easy interpretation. Legend is also provided.

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NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel!

Introducing GaPTools for dbGaP Submitters

This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.

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Automate your workflow with the ClinVar Submission API

ClinVar and our scientific and patient-care community rely on your submissions. With our new Application Programming Interface (API) for submissions, we’ve made it even easier for you to provide us with your most up-to-date classification of variants. The new RESTful API allows you to automate your submission workflow so that you can submit new records and update existing records faster. Setting up your account to use the API requires three one-time activities:

ClinVar Submission API Setup

 

 

 

 

 

 

Click on each of the steps in order to set up your account to use the API!

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ClinVar Reaches One Million Variants!

A counter ticks up to 1,000,000. Text reads "Celebrating 1,000,000 variants in ClinVar"

ClinVar has become a go-to resource for the clinical genetics community.  You have come to ClinVar to look for the reported clinical significance of human genetic variants that you’ve identified in clinical testing or through your research.  You have researched the supporting evidence and publications to the benefit of the health and genetic science community .  You have surveyed all available variants within a gene to understand the spectrum of variation for that gene and to curate gene-disease relationships.

We know how critical this information is to you on a daily basis.

We keep ClinVar free and publicly available and work closely with our submitters to add more variants and supporting information, so that you can continue to benefit from this reliable information at your fingertips.

Today, we are proud to announce that ClinVar has passed the milestone of one million variants in our database. Continue reading “ClinVar Reaches One Million Variants!”

NCBI RefSeq and Ensembl/GENCODE taking MANE mainstream with v0.92!

NCBI and EBI have been hard at work on our joint MANE collaborationproviding a set of representative transcripts for human protein-coding genes that are identically annotated in the NCBI RefSeq and Ensembl/GENCODE annotation sets and exactly match the GRCh38 reference assembly. We’re pleased to announce MANE v0.92, now covering 16,865 genes or ~88% of known human protein-coding genes.

In particular, we’ve focused on clinically relevant genes and MANE Select now includes 99% of genes with high gene-disease validity. This release also includes 43 extra transcripts labeled “MANE Plus Clinical” that we’ve chosen to aid in clinical reporting, for example, when there are additional pathogenic variants not covered in the MANE Select transcript. While it’s critical to consider other alternatively-spliced transcripts for variant interpretation or functional analyses, the MANE Select and MANE Plus Clinical transcripts provide a common foundation for clinical reporting, and other analyses that benefit from using just one well-supported transcript or protein per gene.

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New Automated Validation in ClinVar Submission

You, as a submitter, are the beating heart of ClinVar. Your contributions helps thousands of genetic counselors and clinicians, as well as their patients and patients’ family members. We have added validation to the online file submissions portal, so that you submitters have more control over how to deal with errors in your submitted files.

You now have two options when submitting data. You can submit any data that passes validation and receive a report of the data that failed. The failed data can be reviewed and resubmitted when it’s convenient for you.

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