Tag Archives: medical genomics

Video Tip of the Week: New Genetic Testing Registry (GTR) Resource


Late last month the National Center for Biotechnology Information, or NCBI, released a new resource containing information on genetic tests. The resource’s name is the Genetic Testing Registry (GTR), and according to its homepage, the GTR:

” provides a central location for voluntary submission of genetic test information by providers. The scope includes the test’s purpose, methodology, validity, evidence of the test’s usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.”

I’m always interested in checking out new resources from NCBI, especially when it is my turn to do a weekly tip. Initially I figured that I would check out the GTR and post a video on how to use it – but the NCBI beat me to that. You can see their YouTube tips (there are two) by clicking the link on their homepage & learn some search tips, etc. [Note, the two videos continued to loop for me & I needed to stop them after viewing them once].

But the question that I came up with is, “What will the GTR provide me with that I am not already getting from other clinical resources that I use, and that OpenHelix trains on?” I try to address that question in my video by doing the same search, for “Cystic fibrosis”, at five different clinically-related resources, and discussing what each offers and specializes in doing. Of course, in a five minute video I can’t be comprehensive – either for resources or what they cover – but I think it will give you enough of a taste for you to appreciate what the GTR offers you, or to continue the comparison on your own.

The resources that I visit in the tip movie are: the GTR, GeneTests, the Genetic Home Reference (GHR), OMIM, and Orphanet. At each resource I do a basic search for the the disease “Cystic fibrosis” and show the initial results display that resulted. I don’t have time to compare the detailed reports available at each, but lower on the post I link to a reference on the resource (if available), as well as the landing page for OpenHelix training materials on the resource – since we have a tutorial on many of these resources. I also include direct links to each resource.

I’d suggest that you read the NIH News article on the GTR release for some background on the GTR. I won’t cover everything here, but there are a couple of paragraphs that I want to point your attention to. The first explains the relationship between GeneTests and GTR, and says:

“GTR is built upon data pulled from the laboratory directory of GeneTests, a pioneering NIH-funded resource that will be phased out over the coming year. GTR is designed to contain more detailed information than its predecessor, as well as to encompass a much broader range of testing approaches, such as complex tests for genetic variations associated with common diseases and with differing responses to drugs. GeneReviews, which is the section of GeneTests that contains peer-reviewed, clinical descriptions of more than 500 conditions, is also now available through GTR.”

It seems to be another case where it was deemed easier to start a new resource (GTR) than to try and revamp an old resource (GeneTests) to handle the amazing influx of new data. Often resources aren’t retired as soon as expected, due to user feedback, but it is important to note that GTR seems to be in place to eventually replace GeneTests. I assume the GeneReviews will still be edited by & copyright to the University of Washington, Seattle, but I don’t have a reference for that. The similar transition occurred for OMIM, which was hosted at NCBI for years but now has a new URL at Johns Hopkins (watch for our new tutorial on OMIM, which is currently in the works).

The second paragraph that I found particularly interesting was the one on what the GTR contains, and will contain. It states:

“In addition to basic facts, GTR will offer detailed information on analytic validity, which assesses how accurately and reliably the test measures the genetic target; clinical validity, which assesses how consistently and accurately the test detects or predicts the outcome of interest; and information relating to the test’s clinical utility, or how likely the test is to improve patient outcomes.”

I didn’t immediately find mention of who will provide the validity or utility information in the GTR documentation, which is currently under construction. It is clear that much of the content of the database will be “voluntarily submitted by test providers”, and it is stated that “NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading.”, but I also saw that experts will input on GTR’s content regularly, as can be read here. The GTR team is also very interested in receiving input on the resource, which can be submitted through the GTR feedback form. 

Quick Links:

The Genetic Testing Registry (GTR) – http://www.ncbi.nlm.nih.gov/gtr/

GTR YouTube Tips from NCBI – http://www.youtube.com/playlist?list=PL1C4A2AFF811F6F0B

GeneTests – http://www.ncbi.nlm.nih.gov/sites/GeneTests/?db=GeneTests

GeneTests Introductory Tutorial by OpenHelix* – http://bit.ly/genetests

Genetic Home Reference (GHR) – http://ghr.nlm.nih.gov/

GHR Introductory Tutorial by OpenHelix* – http://bit.ly/geneticshomeref

Online Mendelian Inheritance in Man (OMIM) – http://www.omim.org/

OMIM Introductory Tutorial by OpenHelix – (coming soon, currently being updated)

Orphanet – http://www.orpha.net/

form.

*OpenHelix tutorials for these resources available for individual purchase or through a subscription

Available References:

For GeneTests (free from PMC)Pagon RA (2006). GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94 (3), 343-8 PMID: 16888670

For GHR (free from PMC)Mitchell JA, Fomous C, & Fun J (2006). Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94 (3), 336-42 PMID: 16888669

For OMIM (open access article)Amberger, J., Bocchini, C., & Hamosh, A. (2011). A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) Human Mutation, 32 (5), 564-567 DOI: 10.1002/humu.21466

For Orphanet (full access requires subscription) - Aymé, S., & Schmidtke, J. (2007). Networking for rare diseases: a necessity for Europe Bundesgesundheitsblatt – Gesundheitsforschung – Gesundheitsschutz, 50 (12), 1477-1483 DOI: 10.1007/s00103-007-0381-9

Video Tip of the Week: The New Database of Genomic Variants – DGV2 (edited)


In today’s tip I will briefly introduce you to the beta version of the updated DGV resource. The Database of Genomic Variants, or DGV, was created in 2004 at a time early in the understanding of human structural variation, or SV, which is defined by DGV as genomic variation larger than 50bp. DGV has historically provided public access to SV data in humans who are non-diseased. In the past it both accepted direct data submissions on SV and also provided high quality curation and analysis of the data such that it was appropriate for use in biomedical studies.

We’ve had an introductory tutorial on using DGV for years, and we’ve posted on changes at DGV in the past, so we were quite interested to read in their recent newsletter that there is a newly updated beta version of the DGV resource. The increase in SV data being generated by many large-scale sequencing projects as well as individual labs, has made it difficult for the DGV to continue to collect SV data, to provide a stable and comprehensive data archive AND to manually curate it at the level they have in the past. Therefore the DGV team is now partnering with DGVa at EBI and dbVar at NCBI. DGVa and dbVar will accept SV data submissions, and will function as public data archives (PDA) and, according to the publication sited below, DGVa and dbVar will:

 “...provide stable and traceable identifiers and allow for a single point of access for data collections, facilitating download and meta-analysis across studies.

DGV will no longer accept data submissions, but will instead use accessioned SV data from the archives and focus on providing the scientific community and public at-large with a subset of the data. Again quoting from the paper referenced below:

The main role of DGV going forward will be to curate and visualize selected studies to facilitate interpretation of SV data, including implementing the highest-level quality standards required by the clinical and diagnostic communities.

The original DGV resource is still available while comments are collected on the updated beta site. For more information on the updated DGV I suggest you check out this documentation from the DGV team: From their FAQ – “What is the data model used for DGV2?” and from a link in their top navigation area – “DGV Beta User Tutorial“. Be sure to check out the new displays & data that’s available, and most importantly to send your comments & suggestions to the group so that they can design a resource best suited for your needs.

Quick Links:

Original Database of Genomic Variants: http://projects.tcag.ca/variation/

New beta version of the Updated DGV: http://dgvbeta.tcag.ca/dgv/app/home

Introductory OpenHelix on Original DGV: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=88

DGV Beta User Tutorial from DGV: http://dgvbeta.tcag.ca/dgv/docs/20111019-DGV_Beta_User_Tutorial.pdf

Reference:
Church, D., Lappalainen, I., Sneddon, T., Hinton, J., Maguire, M., Lopez, J., Garner, J., Paschall, J., DiCuccio, M., Yaschenko, E., Scherer, S., Feuk, L., & Flicek, P. (2010). Public data archives for genomic structural variation Nature Genetics, 42 (10), 813-814 DOI: 10.1038/ng1010-813
(Free access from PubMed Central here)

Edit, March 5, 2012 – I wanted to add a clarification that we recieved through our contact link. I am pasting it in full, with permission from Margie:

“Hi Jennifer
We at TCAG think you did a great job on your video blog of the New Database of Genomic Variants.
I wanted to make a correction to one of your statements: “The increase in SV data (…) at the level they have in the past.”
We, the DGV team, have built a system that CAN handle the new volumes and types of SV data now being published, and we are able to curate all of these data. The reason we partnered with DGVa and dbVar was primarily to provide stable, “universal” accessions for SV data. We also work with DGVa and dbVar to define standard terminology, data types, and data exchange formats.
I just wanted to make sure it was clear that we are fully capable to handle the SV data being published now. Our reason for partnership was to foster standardized data and open data sharing across systems.
Thanks again for your blog post!
Margie Manker”

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the Week: Genome Variation Tour II

The last tip of the week I did was Genome Variation Tour I where we started our journey following one SNP in an individual’s genome through various databases to see what we can find out about that variation. In that tip we started out by looking at a SNP in the CYP4F2 gene in the UCSC Genome Browser and followed it to dbSNP. Today’s tip will continue our journey to OMIM to see what information we can find there. We’ll find this variation is clinically associated with Warfarin dosage effects and specifically this individual’s C/T heterozygosity indicates an intermediate dosage for effectiveness if indeed he ever needed this drug.  In some ways, your guess is as good as mine as to what we will find and what avenues we will be taking in the next few tips I’ll be doing. I’m am discovering information as I go along too. I can tell you though that the next installment of the genome variation tour will take us to PubMed, and a few not particularly well known but gem databases perhaps and probably back to the UCSC Genome Browser to expand our look at the interactions of several variations in this individuals genome.

Tip of the Week: Genomic Variation Tour I

Today’s tip of the week is actually the first in a series of tips I will be doing over the next couple months. The recent paper in Lancet did a clinical assessment of an individual genome. In doing so, the researchers used various genomic resources do ascertain and interpret the data. We have a free tutorial on NIEHS SNPs that walks through some of these resources, but I thought it might be useful to follow one specific nucleotide variation through a lot more genomic databases to show the user what data is available and how to access it. Each tip I do over the next couples months (not every week, I do tips every 2-3 weeks) will follow a specific SNP through the databases. In this case, rs108622 in the CYP4F2 gene (cytochrome P450, family 4). These tips aren’t for the genome jockey’s and SNP surfers among us, they are more an introductory tour of what’s out there. They will be useful for those just starting to look at genomic variations, medical practitioners, clinicians or those just curious what is available. Today’s tip will start with the UCSC Genome Browser, find the variation and follow it through to dbSNP. Next tip will look closer at the dbSNP information and then follow the trail to OMIM and GeneTests. In later tips we’ll take the variation to another 4-6 different databases and genomic variation resources from HapMap and others. In the posts themselves I’ll link to even other variation databases. There is a plethora of them.