Knowing your genetic profile:
Better, faster technology expected soon, info specialist says
In a little more than a decade, genetic sequencing has evolved from a lengthy, expensive process to one that rapidly is becoming commonplace.
Advances in genetic sequencing increasingly are making personalized medicine accessible to the masses, said Health Sciences Library System molecular biology information specialist Carrie Iwema in a recent HSLS Lunch With a Librarian presentation, “Personal Genomics, Personalized Medicine and You.”
Genetic sequencing technologies have developed rapidly and the so-called “thousand dollar genome” — a term that has become a buzzword in personalized medicine circles — looms on the horizon.
“It was in 1995 … the first genome of a free-living organism, Haemophilus influenzae, was sequenced,” Iwema said. “Five years after that, the draft sequence of the human genome was released, and that took over 13 years and $2.7 billion to do.”
Three years later, a complete human reference genome was completed.
In 2007, the first individual diploid genome — of Cellomics entrepreneur Craig Venter — was published. “This genome sequence, compared to 2000, was ‘only’ $1 million and took only one month to do. It was quite an improvement although still quite expensive,” she said. “Three years after that, in 2010, we finally moved away from the wealthy white male genomes and added Korean-Asian and African-American genomes, again with a decrease in both time and money — $24,000 in about 15 days,” she said.
Decreasing costs and desktop-sized NGS (next-generation sequencing) machines are bringing genetic sequencing ever closer to the consumer.
“Now it’s projected by 2014, the big race is going on for what they’re calling the thousand-dollar genome. And that’ll take about 15 minutes to do. That’s what the projection is right now,” Iwema said.
She noted that in 2001 the cost of sequencing a genome was $100 million, but by last January it had dropped to $10,000. “At that rate, it’s going to reach $1,000 or less per genome, making it more affordable for everybody.”
Personal genome sequencing
When it comes to genomic sequencing, the focus has turned to the individual. “Personal genome sequencing is an analysis of your specific genes looking for the differences and mutations — it’s essentially like that large Human Genome Project, but specific to you,” Iwema said.
Such testing identifies single nucleotide polymorphisms, or SNPs, which are a variation of just one nucleotide in a person’s DNA. “As simple as it may seem, a lot of times it’s just that one nucleotide that can make a difference” in whether a person has a certain characteristic or is more likely to get a certain disease, she said.
Today, the Personal Genome Project (www.personalgenomes.org), led by Harvard researchers, is seeking 100,000 participants who will have their genomes sequenced and made public.
The National Institutes of Health also is collecting individual genetic sequences in genome-wide association studies that aim to gather information to compare variations across a large population.
Direct-to-consumer tests already are on the market. Some companies, such as 23andMe and deCODEme, are consumer-oriented, allowing customers to order tests and receive results directly. Others — Navigenics or Pathway Genomics, for instance, work through physicians.
For as little as $99, an individual can order a genetic test kit and return a saliva sample for analysis. “The company puts your sample on a chip and reports back to you,” Iwema said. “It’s important to point out, for most of these, you’re not getting your full sequence done.”
The reports contain information on a person’s gender, ancestry, physical traits and other details such as whether they carry genetic variations that are associated with certain diseases or conditions.
Exactly how many people are buying DTC tests is unclear, although Iwema noted that one report estimated 20,000-30,000 such scans were done in 2009.
Why get tested?
What makes people interested in their genetic information? Perhaps they are curious about their ancestry or merely are interested in new technologies and in sharing information. Or they may be concerned about diseases in their genetic background, particularly if they are concerned for the potential effect on their offspring.
Most reasons fall into four basic categories, Iwema said.
• Predictive testing, which seeks to determine whether a person is at risk for any particular diseases;
• Diagnostic testing, which searches for a genetic basis for a disease a person has;
• Carrier testing, which provides information on whether a person has a genetic condition that could be passed on to his or her children, and
• Prenatal testing, which examines the genetic profile of a fetus.
Knowing the details of your genetic sequence can be helpful, Iwema said. It can serve to predict the probability for disease and enable people to take preventive measures. It also can enable doctors to tailor personalized drug therapies based on what is known about how people with different genetic variants may respond to a particular medication.
Pharmacogenomics, which is based on how one’s genotype influences how the body reacts to various medications, can help doctors prescribe the right medicines and dosages, leading to the development of better medications and perhaps lower overall health care costs.
What then?
“What do you do with the information once you have it?” Iwema asked.
Having a single nucleotide polymorphism associated with a disease typically doesn’t mean that a person will get that disease, only that there is an association, although some genetic markers, such as for Huntingdon’s disease, show a very strong correlation between the SNP mutation and the disease.
Individuals who have received results can choose to discuss them with their doctor or a genetic counselor at the testing firm, or can take the do-it-yourself route. “You can take it into your own hands,” she said, cautioning, “That doesn’t mean you can analyze it any better, but it gives you control.”
Armed with test results, individuals can have their genetic data file analyzed at www.snpedia.com and in a few minutes receive details on what certain SNPs may mean. In addition to gender, ethnic background and associated medical conditions, the tool also can reveal other interesting details about traits associated with particular genetic variations.
Challenges
While knowing one’s genetic profile has benefits, the tests sometimes can reveal problematic information: What if you discover your father isn’t your father, for instance?
Will knowing about an increased risk of disease raise insurance worries?
What about other effects on family members?
“If I find I’m a carrier of some disease, that means my parents have it — do we tell them?” Iwema asked. “What if they don’t want to know?”
Similarly, should your children be tested as well? What about potential kids? Is fetal testing something to consider? And what do you do if you find something amiss?
Concerns about privacy and who should have access to the results are another challenge, she said. One study found that doctors, spouses and researchers ranked high on respondents’ list of people they felt could be trusted with their genetic information. Respondents were less comfortable with police having the information and even more wary of allowing health insurers and employers to have the information, Iwema said.
The Genetic Information Nondiscrimination Act, passed in 2008, provides some protection by prohibiting employers or health insurers from discriminating based on a person’s genetic information.
Controversy
“There are some issues, as you might think, with offering medical information to the general public,” Iwema said, noting that controversy over genetic testing has surfaced in several recent situations.
A pair of California universities brought the issue home to college campuses last summer.
UC-Berkeley truncated its plan to offer incoming students testing for three genetic variants as part of a program on personalized medicine after state officials raised legal concerns. However, Stanford medical school allowed students the option of using their own genetic data obtained through a kit in a genomics and personalized medicine elective.
“This is already moving into our colleges, for better or for worse,” Iwema said.
More broadly, a deal that would have put Pathway Genomics direct-to-consumer tests on Walgreen’s pharmacy shelves was put on hold after the Food and Drug Administration took note.
The FDA launched a molecular and clinical genetics panel to examine the potential risks and benefits of direct-to-consumer tests that make medical claims. Consumer protection concerns over ensuring scientific validity of the tests and correct interpretation of results remain. A public comment period on the issue closed May 2.
“There’s probably going to be some kind of regulation associated with these, but the public has a right to their own personal information. That’s where the main conflict is,” Iwema said.
On the positive side, direct-to-consumer testing has benefited the public good, Iwema noted. The direct-to-consumer firm 23andMe has been comparing its own database with other studies and advancing scientific knowledge in the process.
“There’s some skepticism about some of the things they found in certain papers. They’re actually pushing science forward as well — they’re not just collecting. The whole idea is to make this information public, so they’re using it to see what’s out there and add to it.”
—Kimberly K. Barlow
Want more information?
Workshop materials from Carrie Iwema’s April 28 presentation are available on the Health Sciences Library System (HSLS) site by selecting “Personal Genomics, Personalized Medicine and You” at www.hsls.pitt.edu/molbio/tutorials.
For additional information on genetic sequencing and personalized medicine, Iwema suggested “The $1,000 Genome: The Revolution in DNA Sequencing and the New Era of Personalized Medicine.” The book, by Kevin Davies, is available through HSLS.
Iwema also recommended several web sites:
• Genomes Unzipped
• Genomics Law Report
• National Human Genome Research Institute
• Personal Genetics Education Project
http://genepath.med.harvard.edu/WuLab/pgEd/
• Personal Genome Project
• Personalized Medicine Coalition
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