Eliminating the Long, Cumbersome and Costly Diagnosis of Genetic Diseases – HIT Consultant

Posted: July 1, 2020 at 12:44 pm

Christine Stanley, Ph.D., Chief Director of Clinical Genomics at Variantyx

The answer to questions about human disease can be found in our genes. The difficulty in the past has been the testing process, a sort of trial and error approach of drilling down into the multitude of variants that can be found within the genes, variants that when analyzed in tandem with detailed clinical histories can actually tell the story and lead to a faster diagnosis.

Human beings carry around 20,000 genes and, of those, approximately 5,000 are somewhat understood, and those genes can be associated with several diseases and each disease can be associated with dozens of clinical symptoms or more. It was believed that five percent or less of the human population carry variants involved in genetic diseases. But a recent study in the Annals of Internal Medicine, now suggests the number of people with variants linked to genetic diseases is closer to 20 percent. Many other factors may determine whether an individual actually develops a disorder, but these numbers suggest the acceptance of a new approach that provides the most useful diagnostic data from a single test thats easier on the patients and families and provides the shortest time to a diagnosis and the best chance at implementing treatments.

Here is an important reason. Parents with children suspected of having a genetic disease routinely face a diagnostic odyssey that typically lasts five to seven years and entails seeing an average of seven different physicians. Its an odyssey that comes with an average cost of diagnosis reaching $21,099, more than seven times the cost of a single whole-genome sequencing test.

Historically, genetic testing has been really disjointed. Tests that were developed 10 to 15 years ago are still being run today by laboratories. These tests target extremely specific areas for an exceedingly small number of changes that cause a certain disease. It is like looking under a lamp post. And an individual, who is suspected of having the disease, will be tested for one particular variant or a small number of variants. It is an approach that is lacking in quick, definitive, and accurate results. Unless the tested area accounted for the majority of the disease-causing variants, it then forces the ordering of more tests to try to find other causes of the disease, either within that same gene or within other genes. This is happening sequentially, so the patient keeps receiving negative results, and then additional tests are ordered and the merry-go-round can continue for years. It cost families financially and emotionally. Delaying the time to diagnosis can also close the effective treatment window in cases where early treatment is important for a good prognosis.

Ordering a single whole-genome sequencing (WGS) test right off the bat replaces almost all of those long, cumbersome, and costly processes. It all but eliminates having to endure multiple genetic tests because a patient needs only one sample and one turnaround time for the greatest chance to arrive at the correct diagnosis. More importantly, if the test results were negative and then a new gene associated with the patients disease is reported the next day, and that patient has a variant in that gene, a clinician can make that connection by reanalyzing the data rather than by bringing the patient back in for a new sample. In that way, genomic testing has really revolutionized the entire genetic testing industry by providing a comprehensive analysis with the shortest time to diagnosis.

Whole-genome sequencing does not require the mechanical step of isolating genes first. It enables the identification of different types of variants that labs do not typically see when one isolates genes. It also enables the use of sophisticated algorithms applied via software to allow for the ranking of variants in a way that pulls variants that are known to cause the disease to the top of the list for examination. Variants can also be ranked by looking at the severity of the effect of the variant on genes that most closely match the patients clinical symptoms. Those results are parsed based on the known inheritance patterns of these genes. Patients can be looked at through both of those lenses at the same timethe severity of the changes that are identified, and the changes that match with the clinical symptoms of the patient.

Whole-genome testing will soon become the first line of defense, rather than a last resort for families or individuals seeking clarity on genetic diseases because of its ability to incorporate sophisticated bioinformatics and data interpretation. It is a faster route for the proper diagnosis and treatment for both early-onset diseases like epilepsy and intellectual disabilities, as well as late-onset disorders like ataxia and ALS. It can be used to diagnose almost any genetic disorder spanning such areas as neurology, endocrinology, nephrology, hearing and vision loss, blood disorders like thalassemia, muscular dystrophy, etc. While insurance reimbursement can be challenging today, the insurance payers will come around, as they have always done in the past, because this test saves time, money, and supports better outcomes for patients.

About Christine Stanley, Ph.D.

Christine Stanley, Ph.D., is the Chief Director of Clinical Genomics for Variantyx, a provider of highly specialized genetic testing to clinicians and their patients. Christine is responsible for overseeing clinical genomic interpretations and regulatory compliance for the clinical laboratory.

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Eliminating the Long, Cumbersome and Costly Diagnosis of Genetic Diseases - HIT Consultant

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