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While individual genetic tests could have been performed for each of the medical conditions in these cases, the cost of genome sequencing is dropping so quickly that it will soon be cheaper to sequence the whole genome rather than various parts. Quake, who published his own genome sequence, without interpretation, in 2009, can now go back to his genome anytime a new publication describes the possible implications of one of his variations.

In the Lancet paper, Quake and his collaborators undertook a comprehensive analysis of his genome. The researchers focused on variants that had been linked to risk of disease in previous studies, and those thought to play a role in a patient’s response to drugs. Beginning with an average risk for a particular disease of someone of Quake’s age and background, they added or subtracted risk using the genetic information. “That’s the most challenging thing, there is no accepted method for how to do that,” says Ashley. “We tried to prioritize what would be the most important thing to discuss with a doctor.”

Highlighting just how difficult it is to analyze a genome, Quake points out that it took just a few weeks to sequence his genome, which was published in a scientific paper with three authors. Analyzing the genome for its clinical relevance took a year, and the resulting paper has 20 authors.

The rare variant that led Quake to Ashley’s office in the first place provides an illustrative example of the state of genome interpretation. The variant is located in a gene that is well-known to be linked to sudden death. But it turns out that Quake’s particular variation is fairly common and present in some healthy people. Combining that knowledge with the results of screening tests–all perfectly normal–led the team to conclude it isn’t dangerous. The team also found a completely new variant in that gene, which they haven’t yet been able to interpret. “At the moment our tools are relatively limited,” says Ashley.

In addition, researchers found variants in other genes linked to cardiomyopathy, a disease that weakens and enlarges the heart, which may help explain a history of sudden death in the family. “Maybe I could have guessed it based on family history,” says Quake. “But it’s one thing to know there is a family history and another to know I had the allele. That sent me to a cardiologist.”

Quake says he hasn’t listened to all the medical advice derived from his genome. While he learned that he has a higher-than-average genetic risk for other types of heart disease, he found via the traditional way that physicians use to calculate risk–which doesn’t include genetic information–that he’s just under the threshold for statin use. Ashley felt the genetic risk factors were enough to put him over the line and suggested he start taking the drugs. “I haven’t followed that yet,” says Quake. “I’m still thinking about it.”

If Quake does start taking the drugs, his genome suggests he will respond to them and is unlikely to suffer one of the drug’s more serious side effects, muscle pain.

Some experts are already concerned that widespread genetic testing will lead to unnecessary medical follow-ups, driving high medical costs even higher. But Quake hopes that genome sequencing will ultimately lower costs. “I think this will provide a way to ration health care so that people at risk can get [screening tests] more frequently and those who aren’t get it less frequently,” he says.

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Credit: Stanford University School of Medicine

Tagged: Biomedicine, genome, sequencing, personalized medicine, genetic variation, Stephen Quake

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