Exome Sequencing Next “Big Thing” for Diagnosis

Exomes make up just 1.5% of human genome, yet this is where 85% of disease mutations exist

CEO SUMMARY: For disease diagnostics, exome sequencing is not yet routine, but geneticists are getting close. Using this technology, researchers read those parts of the human genome where about 85% of disease-causing mutations reside. By looking only at the regions that encode proteins—the workhorse machinery of the cell—researchers identify dis- ease causes much faster than with previous methods. The first diagnostic tests that utilize exome sequencing are starting to show up in the clinical market.

ONE EMERGING FIELD in genetic testing involves exome sequencing. One by one, clinical applications based on exome sequencing are appearing.

Think of exomes as a potentially elegant shortcut to a diagnostic answer. The exome of the human genome is estimated to comprise 1.5% of the total genome. Researchers and in vitro diagnostic test (IVD) developers recognize that, by focusing on this 1.5% of the entire human genome, they can use exome sequencing to extract useful diagnostic information with the least cost and a fast time-to-answer.

 Exome Sequencing Potential

At the Emory University School of Medicine and Sanford-Burnham Medical Research Institute in Atlanta, researchers say exomes are like an executive summary scan of a person’s entire genome. In February, these researchers published a case report in the American Journal of Human Genetics, showing how they combined a simple blood test with an exome scan to diagnose a type of severe metabolic disease.

There is plenty of excitement about the potential for exome sequencing. Researchers at Emory and Sanford-Burnham note that use of this type of sequencing to diagnose disease is not yet routine, but geneticists are getting close.

“It is estimated that most disease-causing mutations (around 85%) are found within the regions of the genome that encode proteins, the workhorse machinery of the cell,” stated Emory and Sanford-Burnham in a press release about exome sequencing. “Whole-exome sequencing reads only the parts of the human genome that encode proteins, leaving the other 99% of the genome unread.”

One lab company that is a first-mover in its use of exome-based genetic tests in clinical diagnostics is Ambry Genetics, based in Aliso Viejo, California. Ambry says it is the first CAP-accredited and CLIA-certified lab to provide researchers, physicians, and pathologists with exome sequencing services. The company believes its Clinical Diagnostic Exome (CDE) test is the first to deliver clinical results.

For Cancer Diagnostics, Clinical Tests Based On Exome Sequencing Soon To Be on Lab Menus

WITHIN 10 YEARS, exome sequencing could become an important component for physicians diagnosing and treating cancer patients. That’s the prediction of Jean Pierre Issa, M.D., an oncologist and researcher at Temple University in Philadelphia, Pennsylvania.

“Currently the gold standard for treating patients is sequencing one gene at a time using very accurate technology,” Issa said. “People are comfortable with this. We have been using this technology to make diagnostic or treatment decisions for many years.

“The question is: do we replace that with exome sequencing? Or, do we still apply the gold standard and use exome sequencing as a discovery tool to increase our chances of finding something?” asked Issa.

“Some form of next-generation sequencing or exome sequencing will be essential for managing patients with cancer,” he added. “Right now we are in the research phase and labs are struggling with whether this exome sequencing technology can be set up as a CLIA-approved test for managing patients or if it will remain as a research tool.

“For the degree of information clinicians get from exome sequencing, this technology has the potential to be a most cost effective technology,” noted Issa. “But the question is: do we need that depth of information to make decisions when treating patients? Do we want the whole genome or do we use exome sequencing to get 20 or 30 genes, giving us something much more focused to specific diseases? That battle will play out over a few years.

“If the technology to do the whole genome is cheap enough then everyone will do that,” he said. “But if it remains more expensive than doing 10 or 20 genes, then those technologies that do a more targeted approach will eventually win out.

“The next question is how reliable will this technology be,” Issa added. “That’s what I want to know for my patients. I may use exome sequencing as a first step and then use a different method to verify the results.

“That’s our institutional thinking right now,” he added. “I’m not convinced I can use exome sequencing with patients without validating the approach because there is no consensus yet on moving to the patient.”

Elizabeth Chao, M.D., the Director of Translational Medicine for Ambry Genetics, agreed. “The accuracy of next-generation sequencing far exceeds that of traditional methodologies,” she said.

“Next-generation sequencing is still new to clinical diagnostics and clinical exome sequencing even more so,” she continued. “So today, we still confirm all positive exome results by Sanger sequencing (the gold standard) prior to reporting the results, thereby eliminating the need for the clinician to arrange or order any validation studies.

“With experience—both in our lab and in the field—the need for this additional validation step will no longer be necessary,” concluded Chao. “That is the point when massive parallel sequencing will become the new standard.”

Ambry says its CDE test can be used to identify genes for rare diseases or for complex cases when the diagnosis is unclear. The assay has also been used in pharmacogenomics research.

Earlier this year, Ambry used its CDE test to identify rare genetic conditions in four individuals whose health problems had previously eluded diagnosis. “Right now, we apply the CDE test to cases where conventional genetic testing has failed,” said Elizabeth Chao, M.D., Ambry’s Director of Translational Medicine.

Ambry’s Clinical Diagnostic Exome costs $7,900. The company says that major national health insurers will often cover the cost of this testing. Current turnaround time for a CDE test is 8 to 16 weeks.

“All of about 20,000 human genes are included as part of the test, with coverage for over 300,000 exons,” said Chao. “Our minimum specifications guarantee that 90% of that 51 megabases of DNA sequence will be covered at adequate depth to reliably detect a heterozygosis variant. In actuality, our coverage typically far exceeds that.”

Moving into Clinical Practice

Wenqi Zeng, Ph.D., Ambry’s Director of Clinical Genomics, points out that exome sequencing has significant clinical advantages. “We’re now finding the cause of the disease much faster because we are able to look into the patient’s blueprint,” she said. “This is essentially a human genome project for an individual patient.”

The announcements by Ambry and Emory show that exome sequencing— which was first offered commercially for clinical diagnosis last year—is entering medical practice. Researchers at Emory Genetics Laboratory say that exome sequencing can be a cheaper, faster, and more efficient way to read the parts of the genome believed to be the most significant for diagnosing disease. The Emory lab is preparing to offer exome sequencing as a clinical diagnostic service.

Baylor College of Medicine (BCM) in Houston, Texas, launched whole exome sequencing (WES) for clinical diagnosis in October 2011. That makes it one of the first labs to offer WES for clinical diagnosis. So far, BCM has received nearly 100 samples for WES from patients with constitutional disease, such as those with intellectual disabilities, neurological disorders, and congenital anomalies of unknown cause.

Next-Gen Sequencing

BCM’s new Cancer Genetics Laboratory (CGL) offers next-generation sequencing for a panel of key cancer genes that include many clinically actionable mutations. “We use this technology because of its high sensitivity, fast turnaround time, and low cost,” said CGL Lab Director Marilyn M. Li, M.D.

“A physician who has a patient with colon cancer or breast cancer needs to know how to treat that patient right away,” she added. “Each cancer is time sensitive and a stat case. Having the ability to use next-gen and exome sequencing technologies to deliver a faster and more accurate diagnosis to the physician can mean the patient gets the right drug in time to save that patient’s life.

“However, mutation detection using next-gen panel sequencing is limited to the genes/mutations targeted,” Li said. “It would be ideal to use both targeted panel sequencing that offers high sensitivity and fast turnaround time and whole exome or whole genome sequencing that provides a more comprehensive landscape of the cancer genome. The need for cancer WES is obvious and BCM will launch cancer WES soon and offer both a next-gen panel and WES to cancer patients.”

Ambry’s Chao agreed that faster time- to-answer is a major benefit of the newest gene sequencing technologies. “Until very recently, sequencing large amounts of DNA was both time and cost-prohibitive,” she commented. “Next-generation sequencing technology has changed that. It has made large gene testing panels— including more than 20,000 genes in exome testing—a reality.

Tapping the Potential

“Now, the potential for exome sequencing is enormous,” she added. “We anticipate a time when superior analytic validity, decreased costs, and rapid turn-around time will make exome sequencing the test of choice in genetics.”

 

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