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:
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.
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.
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.
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.
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.
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
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.
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.