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Technical challenges remain in genome sequencing


By Jaimy Lee
Posted: March 11, 2014 - 4:00 pm ET
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Even as clinical understanding of whole genome sequencing is improving and the costs of sequencing continue to drop, technical challenges remain, according to a study published today in the Journal of the American Medical Association.

The exploratory study looked at 12 healthy patients who underwent whole genome sequencing, the most comprehensive form of genetic testing.

A number of concerns with the genomic data that was gathered surfaced. Using whole genome sequencing was associated with incomplete coverage of inherited genes, researchers found. Other concerns include disagreement between the two technology platforms that were used as well as between clinicians' opinions about the clinical significance of potential risk variants.

“Our results suggest that although analytical validity of WGS is improving, technical challenges to sensitive and accurate assessment of individual genetic variation remain,” the authors wrote.

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Whole genome sequencing provides information about 95% of the patient's genome. Exome sequencing, which is less costly and more commonly used, details about 1% of a patient's genome.

The whole genome sequencing of one patient in the study led to the unanticipated identification of a BRCA gene, which means the patient is at higher risk for being diagnosed with hereditary breast and ovarian cancer. That patient underwent surgery to remove her ovaries and will also undergo increased cancer screenings as a result of the genetic findings.

Studies like this one “provide a glimpse of what is possible but demonstrate that much remains to be learned about previously assumed to be 'known' information as well as myriad 'known unknowns' and 'unknown unknowns' before truly successful widespread integration can occur,” Dr. William Gregory Feero wrote in an accompanying editorial.

For the patient at higher risk of breast and ovarian cancer, sequencing may improve her outcomes. For otherwise healthy patients, who have been provided with new but possibly uncertain genetic information, sequencing may lead to costly and potentially unnecessary secondary testing and referrals.

Primary-care physicians who reviewed the patients' genomic reports called for follow-up work-ups for some patients. The median estimated costs for such tests and referrals ranged between $351 and $776.

“There's a lot of discussion in the press currently about how inexpensive whole genome sequencing has become,” said Dr. Thomas Quertermous, chief of the cardiovascular medicine division at Stanford University in Palo Alto, Calif., and a co-author of the study. “It's staggering how quickly it has come down. The question is how we implement that technology in the clinical arena.”

Earlier this year Illumina, which markets genomic sequencing platforms, announced that its new HiSeq X Ten technology would sequence a human genome for a $1,000, an aspirational price that has long been cited as the point when whole genomic sequencing would become a mainstream part of clinical practice. Several years ago whole genome sequencing cost upwards of $100,000.

“Until very recently, the time, cost and technical expertise required to generate and analyze WGS data largely precluded serious consideration of its use outside of research settings,” Feero wrote. “This can no longer be assumed to be the case.”

What is challenging for clinicians is the time it can take to assess genetic variation for each patient, as well as the time needed to provide guidance to patients. “The amount of work that has to go into a single genome is quite significant,” Quertermous said.

Follow Jaimy Lee on Twitter: @MHjlee


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