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Executive Sequencing Project Highlights Complexity of Risk Prediction from Whole-Genome Data


By Monica Heger

A project intended to study the genetics of schizophrenia recently turned into a case study on how to return whole-genome sequence data to healthy individuals when a group of executives volunteered to be the controls in a sequencing study at the University of Texas Health Science Center.

Thomas Caskey, who led the project, said he was approached in the fall of 2010 by the Houston chapter of the Young Presidents' Organization, a network of CEOs and other corporate executives under the age of 45. The group requested an educational program on genomics with the option of sequencing interested members. The day-long program covered the technology, medical expectations, and ethical issues of participation in the schizophrenia sequencing study.

Since the business executives were to act as controls, the one requirement for participating was that members could not have schizophrenia or have any first-degree relatives with the disorder. Of the 150 members at the meeting, 81 volunteered for the study.

The university's institutional review board determined that the volunteers must have the option to receive medically relevant information or, if they chose, to not receive any information. None of the volunteers opted out of receiving the information.

Caskey and his team sequenced each of the 81 volunteers' exomes using Agilent SureSelect exome capture and Illumina sequencing. They also used Complete Genomics' whole-genome sequencing service for 13 individuals.

Caskey, who discussed the study in a presentation at last month's combined International Congress on Human Genomics/American Society of Human Genetics conference, said he spent about an hour with each executive explaining the results and what they meant in terms of disease risk for the volunteer as well as his or her children.

The information was also delivered as a written report that took into account personal medical history and three-generation pedigree analysis. The patients' physicians also received education on the reports.

Caskey said he has concluded from the experience that clinical sequencing is "absolutely ready for the prepared mind and the person who can handle risk and risk data."

However, he noted, there are still a number of kinks in the sequencing technology and in the available variant databases that make interpretation extremely challenging.

Wide Range of Risk

Sequencing was able to identify variants linked to a number of conditions, including recessive childhood disorders, cancer, Alzheimer's disease risk, cardiovascular disease, obesity, and diabetes.

For each individual, the number of medically relevant variants ranged from seven to as high as 31, Caskey said.

One female executive was found to be a carrier of the variant causing Fabry's disease, and also had a son affected with the disorder, while X-linked disease-causing variants were identified in two other female executives, who did not have any sons, and neither had a family history of the associated diseases.

One of the variants was for retinal pigmentosa while the other was for an immune deficiency disease. That information will be extremely important to the women, who were "sitting with a time bomb," as they make family-planning choices, Caskey said.

The sequencing also revealed a case of "classic hypercholesterolemia," which "shocked" Caskey because it had not been previously diagnosed. That person is now on statins and responding well, he added, so both he and his family will benefit from the sequencing results.

Additionally, he said, less straightforward information was identified such as variants increasing the risk of certain cancers. The sequencing identified two cancer risk alleles on one woman who, Caskey learned afterward, had had recurrent melanoma and breast cancer.

The study also found cancer risk alleles in healthy individuals. Returning the results in those cases was trickier, said Caskey, because the data had to be explained in such a way as to be informative while also emphasizing that a single risk allele does not mean cancer is inevitable.

In one case, exome sequencing elicited data that was difficult to interpret and Complete Genomics is now following it up with whole-genome sequencing. The individual was healthy with the exception of one episode of severe bleeding. He had a family history of Parkinson's disease and one of his siblings had a bleeding disorder. Exome sequencing identified two mutations in the PARK2 gene, which is associated with Parkinson's, and two mutations in SERPINA10, one of which is associated with venous thrombosis.

It was unclear, however, whether the two SERPINA10 mutations were on the same chromosome, leaving the volunteer with one normal copy of the gene, or whether there was one mutation on each chromosome, rendering both copies non-functional. The case illustrates the importance of also having haplotype information, Caskey said.

Finally, there was one case where the technology was just plain wrong, identifying a variant known to cause intellectual disability. "I asked [the CEO] if he was mentally retarded," Caskey said, and he replied "that no, he didn't think so, but his associates did."

Lessons Learned

Going forward, Caskey said his team will continue to follow up with the volunteers annually to "rerun the numbers." The pace of disease gene discovery is so fast that the "report I render today is not the same one it will be in October 2012," he said.

The study highlighted the potential challenges of returning results as whole-genome sequencing moves to the clinic, particularly when it comes to cancer risk, Caskey said. "When you identify a cancer risk association, you want to make sure they don't equate that to a cancer diagnosis."

Additionally, he said that his team found that the executives were more responsive when specific risk numbers were not given with the findings. For example, there are some mutations that confer a high risk of breast cancer, while others confer a low risk. Caskey said that his team did not distinguish between the two, but just told the individuals that there is a risk and what to do about it.

The experience also indicated that in order to implement whole-genome sequencing on a broader basis, it will be necessary to automate the informatics and generation of medical reports and to hire dedicated genetic counseling personnel. Caskey said that he spent about an hour with each patient, and while he did not feel like it was a burden, it was nonetheless time consuming.

Since sequencing the initial 81 executives, Caskey said he has received requests to offer sequencing to the Houston chapter's entire 450-member organization. In order to move forward with that, however, he would have to secure additional funding. The original study received grants from two Houston-based foundations.

Caskey said that his group has secured a grant from the Houston-based Cullen Foundation to launch a program that will educate physicians about genomic medicine and interpreting next-gen sequence data.

Going forward, it will be important to determine the medical value of whole-genome sequencing, which is expensive and not easy to understand, even among intelligent, highly motivated individuals. Nevertheless, "I see this as the future for disease prevention and risk reduction," Caskey said.

The project also illustrated the importance of the consent process in doing whole-genome sequencing studies, even for research purposes. "My objective is to discover genes associated with schizophrenia," said Caskey, adding that it was the IRB that decided that the controls should be able to receive information on a "need-to-know basis."

He added that different research protocols have different requirements for returning results, so having a more unified framework in place would be beneficial as next-gen sequencing studies become more common.

Technical Challenges

Caskey said that the study identified a number of technical challenges for whole-genome sequencing. For 13 of the 81 individuals, the team compared exome sequence data to Complete Genomics' whole-genome sequence data. The Complete Genomics data yielded more information than the exome capture and sequencing on Illumina, said Caskey.

While a good proportion of the called SNPs overlapped, many did not, and of those that were only called by exome sequencing on Illumina, "quite a number of them do not confirm," said Caskey. The exome sequencing also tended to yield systematic errors that were not present in the Complete Genomics data, he added.

And while the sequencing technology itself is not perfect, the bigger problem lies in the variant databases.

"You name how you can make a mistake in creating a database, and it's there," he said.

Because of this, he said, every time the researchers identified a result that appeared to be medically relevant, they would go back to the original paper to make sure the database annotation was correct and that its association with the disease was certain.

"We don't want to deliver information that is uncertain and will frighten [patients]," said Caskey. "We want it to be actionable."

Finally, basic research is still needed to improve functional annotation of genomic data. The "biological relevance of many nonsynonymous alleles is still uncertain," he said, which is a "major challenge" in deciding what results to return to the patient.

Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.

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