Tag Archives: genetic testing

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/


*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

Regulating DNA (tests)

I’ve mentioned before that personal genomics seemed to have hit a tipping point. Some of the evidence of that seems to be that the FDA and other regulatory agencies have taken a heightened interest in mass-market gene and genomics tests.

That is going to be the next step in our progress towards personal genomics and medicine, and one that if done right will make this part of our history a successful one. To that end, the Genomics Law Report has an interesting post: “Transparency First: A Proposal for DTC Genetic Testing Regulation.” His argument, make the registry mandatory, make transparency mandatory, is a good start.

There is also a debate going on (which I’m going to be a fence-sitter on for now) on whether the FDA should be governing these ‘Direct to Consumer’ tests. Decisiontree says no:

The controversy seems to have stirred the FDA to assert its authority – and that of physicians – over any and all medical metrics. As readers of The Decision Tree know, I have little patience for the argument that we need doctors as gatekeepers of our genetic information. This isn’t a drug, and this isn’t a device – it’s information about ourselves, as ordinary as our hair color or our waist size or our blood pressure – all things that we can measure and consider without a doctor’s permission.

Gene Sherpa says they got it all wrong:

This is not about getting access to your data.

Fine, you want a whole genome, go get it!

The FDA is not asking should people be able to go out and buy this. It is asking several other questions.

1. Is Interpretation of biometric data considered medicine?

2. Is DTCG analyzing biometric data and intending to give an interpretation of that data which indicates a disease a person has?

3. Should we regulate a system which has not given indication of their quality control if they are indeed intending to provide medical diagnosis?

4. Are these methods of obtaining human samples to derive biometric data for the intent of analyzing and providing information about disease considered medical devices?

All three are interesting and informative reads. Just thought I’d point them out. (hat tip on those last to to Daily Scan).

Friday SNPpets

We are going to try a new Friday feature. 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. We are going to start posting them in a Friday feature of a list of snippets of information we call “SNPpets” :D (cute, huh?). So without further ado…

Tugging at the public’s heart strings-and wallets!

kids runningAfter the mad rush of the holiday season, I found a little time to catch up on reading, and stumbled across an astounding article in the NYtimes: New Genetic Test Asks Which Sport a Child was Born to Play, by Juliet Macur.

A company called ATLAS (Athletic Talent Laboratory Analysis System) is offering a genetic test for kids which they claim will determine if your child is likely to be a super-athlete.  Furthermore, they say it can tell you what type of a super-athlete your child may become, i.e., a sprinter or a weightlifter, so that you can begin preparations and training sessions for your child as early as one year old.

This test is based on genotyping for an isoform of the muscle protein actinin, ACTN3.

Actinins are an important family of actin-binding proteins.

Well, since I am a mom of a seven year old and a scientist that has spent more than fifteen years doing basic muscle research, this really caught my attention. My first thoughts were that this was morally appalling and scientifically impossible. All that I had learned and studied about muscle had led me to believe that muscles just don’t work that way.

No doubt that the actinins are crucial to muscle function, but I thought that one muscle protein couldn’t do all of that. My off-the-cuff guess would be that at least 200 genes would contribute to such traits, and probably half would encode non-muscle proteins (genes related to drive, metabolism and many other factors would seem likely to be involved equally here). I wondered if I had missed some major development in the muscle field while enjoying motherhood, Continue reading

Genetic testing for Annie? Nah.

annie_day2.jpgWell, finally, on Sunday, I broke down. I’ve been wanting another cat for some time. My last 19-year-old passed about a year ago now. But for several external reasons the timing wasn’t right and I wasn’t ready.

But one more story about the shelters getting filled up with pets as a result of the economic crisis just pushed me over the edge.

Economic crisis has animal shelters crammed with dogs and cats

….When the economy tanks and expenses rise, people take a hard look at what they can live without, often making painful cuts.

When they lose their houses to foreclosure, they often have to downsize and do without things they love….

So I went over to the Animal Rescue League and fell for a cream puff. And as she’s a calico I get to tell the X-inactivation story (which I already have, twice now). Her shelter name is Annie. By the next morning she was all set for belly rubs and copious purring. I think we have a fit.

I’ve always been happy with mutt-style pets. I have no illusions to pedigree for myself or for my pets. But I’m dying to know what she is. I suspect she is half Maine Coon based on her phenotype and behavior. At the shelter I laughed when they said she eats “with company” in the health review. Turns out that is Maine Coon behavior.

I’m nearly convinced–and now a little daunted by how big she might get. But I began to wonder about testing…Lo and behold it is out there. Norwegian forest cats testing for a number of possible mutations. Hypertrophic Cardiomyopathy in Maine Coons. Parentage testing. Blood type. I stumbled upon the Canine Inherited Disease Database in this little exercise.

I probably won’t. But I admit I’m curious. It will suffice to look around the GBrowse installation for the cat at NCI. It is called Garfield. I swear:

Genome Annotation Resource Fields—GARFIELD: A Genome Browser for Felis catus. 2007. Joan U. Pontius, and Stephen J. O’Brien. Journal of Heredity 2007 98(5):386-389; doi:10.1093/jhered/esm055.

EDIT: BTW, Animal Planet has a new show called Cats 101, and this upcoming Saturday they are supposed to include Maine Coons according to my Tivo listing.

Oversight Report on Genetic Testing

sacghs_report.jpgWell, as soon as the President signs the GINA legislation, we will be in a new era in genomics in the US–as far as I’m concerned. There were plenty of things I would not have participated in before, from specific aberrant gene testing, to research projects, to having a personal genome done. And I would have advised my family against it as well, since their test results could ripple though the family. But now those things are back on the table. I’m not saying I will do it, actually. But that the possibility is there now and I had written it all off before.

But we aren’t done yet. We need to brace ourselves for a widened era of personal and consumer testing. The Secretary’s Advisory Committee on Genetics, Health, and Society (SACGHS) was charged with creating a study:

U.S. System of Oversight of Genetic Testing: A Response to the Charge of the Secretary of Health and Human Services (pdf–large pdf–almost 300 pages).

I have just learned about its recent completion, and quite honestly, have not read the whole thing. But one section jumped right out at me:

To meet the educational needs of health professionals, public health workers, patients, and consumers, HHS should support efforts to identify education or training deficiencies in each of these groups and support research and development of effective clinical decision support systems. In addition, FDA should prepare a guidance document articulating the scope of its regulation of clinical decision support systems.

We have got to get people trained up to understand genomics. We’d be happy to help :)