Navigation Links
New database to speed genetic discoveries
Date:3/18/2013

A new online database combining symptoms, family history and genetic sequencing information is speeding the search for diseases caused by a single rogue gene. As described in an article in the May issue of Human Mutation, the database, known as PhenoDB, enables any clinician to document cases of unusual genetic diseases for analysis by researchers at the Johns Hopkins University School of Medicine or the Baylor College of Medicine in Houston. If a review committee agrees that the patient may indeed have a previously unknown genetic disease, the patient and some of his or her family members may be offered free comprehensive genetic testing in an effort to identify the disease culprit.

"PhenoDB is much more useful than I even thought it would be," says Ada Hamosh, M.D., M.P.H., a professor in the McKusick-Nathans Institute of Genetic Medicine at the Johns Hopkins University School of Medicine. "Bringing all of this information together is crucial to figuring out what our genetic variations mean." The database is designed to capture a bevy of standardized information about phenotype, which Hamosh defines as "any characteristic of a person" symptoms, personal and family health history, appearance, etc.

Hamosh and others developed PhenoDB for the Baylor-Hopkins Center for Mendelian Genomics (BHCMG), a four-year initiative that, together with its counterparts at Yale University and the University of Washington, is charged with uncovering the genetic roots of every disorder caused by a single faulty gene. There are an estimated 3,000 inherited disorders that have been described phenotypically in scientific papers but whose genetic causes have not yet been pinpointed, Hamosh says, but since many single-gene disorders are extremely rare, she suspects that many more have not yet made it into the literature.

The Centers for Mendelian Genomics have a powerful tool at their disposal, known as whole-exome sequencing. Just a few years ago, Hamosh explains, a geneticist trying to diagnose the cause of an inherited disease would have made an educated guess based on the patient's signs and symptoms about which gene might be at fault, and ordered a test of that gene. If the test came back negative for a mutation, she would order a test of a different gene, and so on. But whole-exome sequencing, in which about 90% of a person's genes are sequenced at one time, has been growing steadily cheaper, and it is this tool that the Centers will use to capture genetic sequencing information (whole-genome sequencing is the next step, but it remains too expensive for many uses, Hamosh notes, as it includes all of a person's DNA, most of which contains no genes).

However, making sense of the deluge of data yielded by whole-exome sequencing presents its own challenges. "The average person has tens of thousands of variations from the standard genetic sequence," Hamosh explains, "and we don't know what most of those variations mean." To parse these variations, she says, "one of the things that needs to change is that the lab doing the testing needs to have the whole phenotype, from head to toe." Researchers will then be better equipped to figure out which variations may or may not be relevant to a patient's illness. Another advantage of the database is that it enables colleagues at distant locations such as Baylor and Johns Hopkins to securely access the information and collaborate. Hamosh notes that the database enables different users to be afforded different levels of access for example, a health provider will only be able to see the information he or she has entered and that information is deidentified to protect patient privacy. In addition, providers must have patients' consent to be included in PhenoDB.

PhenoDB would be useful for any research project that seeks to match genomic information with its phenotypic effects, Hamosh says, and with that in mind, the Baylor-Hopkins Center for Mendelian Genomics has made the PhenoDB software available for free download at http://phenodb.net. She predicts that similar tools will soon be incorporated into electronic health records as well, so that "doctors will have patients' genomic information at their fingertips and can combine that with information about health history, disease symptoms and social situation to practice truly individualized medicine."


'/>"/>

Contact: Shawna Williams
shawna@jhmi.edu
410-955-8236
Johns Hopkins Medicine
Source:Eurekalert

Related biology news :

1. CNIO researchers develop new databases for understanding the human genome
2. NREL updates solar radiation database
3. Privately owned genetic databases may hinder diagnosis and bar the way to the arrival of personalized medicine
4. Navigating the Patent Minefield of Embryonic Stem Cell Product Development; Free Kindle Fire Tablet and Research Database with Purchase
5. New databases harvest a rich bounty of information on crop plant metabolism
6. U-M Health and Retirement Study adds genetic data to NIH database
7. Research shows how Mallard dye fills need for speed
8. TAG Optics ultra-high speed variable focus TAG Lens 2.0 wins Prism Award
9. New marker of drug response may speed pace of lung cancer prevention trials
10. Total donates high-speed computer cluster to UH
11. High-speed video and artificial flowers shed light on mysteries of hummingbird-pollinated flowers
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:1/20/2016)... LONDON , Jan. 20, 2016 A ... positioned to directly benefit from the explosion in genomics ... from Howe Sound Research. A range of dynamic trends ... ...... - personalized medicine - pharmacogenomics - pathogen ... economies with large markets - greater understanding of the ...
(Date:1/20/2016)... SAN JOSE, Calif. , Jan. 20, 2016 ... leading developer of human interface solutions, today announced ... touch controller solution for wearables and small screen ... appliances such as printers. Supporting round and rectangular ... the S1423 offers excellent performance with moisture on ...
(Date:1/15/2016)... , Jan. 15, 2016 Recent publicized ... small to find new ways to ensure data security ... iOS and Android that ties ... biometrics, transforming it into a hardware authorization token. Customer ... swipe their fingerprint on their KodeKey enabled device to ...
Breaking Biology News(10 mins):
(Date:2/11/2016)... -- Wellcentive today announced it has been selected by FamilyCare ... community care organization (CCO) with more than 130,000 ... and care management solutions and services. Wellcentive,s capabilities ... managers, analysts and care managers while providing insight ... members. Oregon . ...
(Date:2/11/2016)... , Feb. 11, 2016  Dovetail Genomics™ LLC today ... beta program for a planned metagenomic genome assembly service. ... company,s metagenomic genome assembly method in a talk on ... Biology & Technology conference in Orlando, Fla. ... highly complex datasets is difficult. Using its proprietary ...
(Date:2/11/2016)... WASHINGTON , Feb. 11, 2016   BioInformant ... strategic report, "Stem Cell Research Products, Opportunities, Tools, and ... 2020. ... specialize in the stem cell industry, BioInformant has more ... of the stem cell market, by stem cell type. ...
(Date:2/11/2016)... ... February 11, 2016 , ... ... a new agreement with Bankok,Thailand-based Global Stem Cells Network (GSCN) to distribute exosome ... Latin American countries, including Mexico, Costa Rica, Dominican Republic, Colombia, Argentina, Nicaragua, Panama, ...
Breaking Biology Technology: