ClinVar’s new XML aggregated by Variation ID


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)

ClinVarXML_markupFigure 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 clinvar@ncbi.nlm.nih.gov.

NCBI at the ACMG meeting in Seattle next week (April 2-6, 2019)


In about a week, NCBI staff will join GeneReviews® on their home turf, Seattle, at the Annual Clinical Genetics Meeting hosted by the American College of Medical Genetics and Genomics (ACMG). While there we will have an exhibit booth (#531) where you can meet our staff, get answers to your questions, and pick-up informative handouts on our various resources for clinical practice.

Also, be sure to visit our two posters on Friday, April 5 from 10:30 AM to 12 PM.

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MedGen: Your search engine for human medical genetics


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:

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NCBI presents resources for genetic counselors at NSGC 2018


Today, November 8, National Society of Genetic Counselors (NSGC) celebrates the second annual Genetic Counselor Awareness Day. At NCBI, we’ve been working hard to provide and improve resources, such as MedGen, Genetic Testing Registry (GTR), ClinVar, and Medical Genetics Summaries (MGS), to help genetic counselors.

Next week, NCBI staff will be at the NSGC 2018 conference in Atlanta, GA. While there, you can chat in person with us at booth #700 to learn about our medical genetics resources and pick up helpful material. We’d also love to hear any other questions or feedback to help support you.

To stay up-to-date about NCBI staff at NSGC 2018 follow us on Twitter at @NCBI_Clinical ‏and @NCBI. For more information about other NCBI presentations at NSGC, check the Conferences and Presentations page.

Discover GTR at AMP 2018 (Nov 1-3)


Starting this Thursday, November 1st, NCBI staff from projects like ClinVar, GTR, MedGen, Medical Genetics Summaries and OSIRIS will be ready to hear your feedback at the Association for Molecular Pathology (AMP) 2018 Annual Meeting & Expo in San Antonio, Texas. Come to booth #1810 and tell us how to make our resources better for you or ask questions about how to participate and use these resources!

Staff will also present on their current work at AMP 2018. We will present our analyses of current GTR tests and discuss how GTR data aims to reflect the current genetic testing landscape.

Below is a sneak peek on two different presentations to learn about “The NIH Genetic Testing Registry (GTR): Test Methodologies as a Sensor of the Precision Medicine Environment”:

  • Poster TT046 – Friday, November 2 from 2:30 – 3:30 PM
  • Technical Topics Platform Presentation – Saturday, November 3 from 7:45 – 8:00 AM

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NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources


As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.

This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!

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October 10 Webinar: Using NCBI Medical Genetics Resources: MedGen, ClinVar, GTR


Next Wednesday, October 10, 2018,  NCBI staff will show you how to use the NCBI resources MedGen, ClinVar, and GTR to locate records for a specified list of symptoms or clinical features, explore specific disease-causing variants, see the review status of the clinical significance for a genetic variant, and find tests relevant to a clinical feature, gene or disease. You will also learn which resource works best for different types of searches.

Date and time: Wed, Oct 10, 2018 12:00 PM – 12:45 PM EDT

Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more


Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.

NCBI Minute: Getting the Most out of Web BLAST Tabular Format

The NCBI web BLAST service has several useful download formats, including tabular formats. All formats allow you to easily save your BLAST results for processing, editing, and annotating.

This video will show you how to use basic Unix tools and EDirect to expand and enhance your tabular saved BLAST results. You will also see learn how to add useful information like taxonomy and sequence titles.

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May 2 webinar: Using NCBI’s MedGen in Clinical Practice


Join us next Wednesday, May 2, 2018, 12:00 PM – 12:30 PM EDT for a webinar on MedGen, NCBI’s portal to clinical genetics. We’ll show you how to find information in MedGen on genetic phenotypes, clinical features of disorders, and more. You’ll also learn how to retrieve actionable information such as practice guidelines for a condition and get a list of available genetic tests in GTR, and how to easily access resources like GeneReviews, OMIM and ClinicalTrials.gov, the Genetic and Rare Diseases Information Center, and Medline Plus.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

ClinVar Allele-Based Summaries Now Available for FTP Download


ClinVar, NCBI’s archive of submitted associations between alleles in the human genome and diseases or phenotypes, is now producing XML files that aggregate all submitted disease/phenotype information by variant (or set of variants) for public release via FTP bulk download. The new product, called ClinVarVariationRelease, is currently in beta release and will move to full release in early September 2017.

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