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March 1, 2024

Database expedites diagnoses of rare diseases

By EVA PEKLE | March 28, 2013

As the field of genetics has burgeoned in the past decade with new gene analyzing technologies, it seems as though we are discovering new genes every day that are responsible for diseases like Alzheimer’s and schizophrenia. With the massive amount of genetic data studied each day, it has become difficult for various gene labs to collaborate and organize new genetic information in a coherent manner.

A new database has been developed to help with just that. It will not only categorize certain findings with other similar discoveries, but it will also expedite research for those working with rare genomes. The growing collection of data will facilitate researchers to find specific genes responsible for more than 3,000 rare disorders.

The new and free online database called PhenoDB has been developed by researchers from the Baylor-Hopkins Center for Mendelian Genomics. Along with researchers at Yale University and the University of Washington, Hopkins geneticists are working to find genes responsible for single-gene disorders, such as sickle cell anemia.

That seems to be a complicated  task to undertake as there are around 3,000 inherited disorders described in literature but which lacks genetic explanation. For instance, we have a basic understanding of the symptoms presented by schizophrenic patients, like hallucinations or delusions, but we are still trying to find which genes are responsible for it. Researchers will also have to account for the fact that many more single-gene disorders may not even be documented in scientific papers due to their rareness.

PhenoDB will include basic things such as symptoms, family history and genetic sequencing. However, it has been designed to collect more precise and specific data including photographs, CT scans, MRIs, and even videos. There is even the possibility to indicate whether each organ system is normal or not. If an abnormal answer appears, further information is obtained.

When a physician faces an unusual genetic disease, all the documented information about that patient is crucial for research at Hopkins and Baylor College of Medicine in Houston. For research, three different categories of genetic disorders were targeted: a known disease but with an unknown causal gene; genes situated at a different chromosomal position than the ones previously documented; and novel genes that have not been previously recorded in the Online Mendelian Inheritance in Man database.

This database presents unprecedented speeds at which researchers can identify genetic markers. Previously scientists made predictions to what genes were responsible for symptoms presented in a patient and order genetic testing individually. If the test came back negative certain mutations, another gene would need to be tested.

Fortunately, today, genetic data is collected from the affected patient using whole-exome sequencing. The exome is the portion of DNA that actually codes for proteins, and with this technique, 90 percent of a person’s coding gene are sequenced simultaneously. The robust approach has the potential to be clinically relevant in genetic diagnosis due to increasing understanding of mutations. Whole-exome sequencing turns out to be a cheaper alternative to the whole-genome sequencing.

The next step of the process is the actual analysis of the vast amount of information yielded from the whole-exome sequencing. The task is unfortunately not as simple as comparing a patient’s genetic sequence to some standard. For each person, there are tens of thousands variation from standard genomes. This is where having a complete physical and biological portrait is essential: it gives more accuracy to whether or not a variation is relevant to the disorder.

Another benefit of PhenoDB is that it enables researchers working on that project to securely access data at other locations. This ability to work remotely greatly aids collaboration between distant research labs. Different users can only access certain levels of information. For instance, your doctor would only be able to consult the information he entered about his patients. Everything is done to protect patient privacy, and the patient has to agree to have his information entered in the database.

With such powerful tools, it seems that soon enough it will be common for physician to have access to their patient’s genetic information. Therefore, it may become easy to combine this genetic information with presented disorders, effectively achieving truly individualized medicine.

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