Whole Genome Typing
“We are still in the very early days of whole genome typing,” said Greg Lennon, cofounder, SNPedia (www.snpedia.com). “There are still significant scientific limitations to our ability to derive actionable knowledge from this data. Even though chips can characterize thousands or millions of SNPs, very few of the SNPs—less than 2,000—are known today to have medical significance.”
SNPedia originated as a free online forum for sharing information about SNPs and their disease associations. The user-driven format, analogous to Wikipedia, enables researchers to directly input and edit data. The SNPedia website provides cross-references between SNPs originating from different methods and possesses substantial information about SNPs not represented on either of the leading chip platforms.
“As we accumulate information about individual SNPs, we foresee that it will be easier and easier to find common associations between them and thus to predict their cumulative effects,” continues Dr. Lennon.
“SNPedia creates a bridge between individual research and global forums. We hope that our virtual meeting space will bring together experts in different clinical areas who can start building disease models based on curated collections of SNP information from around the world.” SNPedia provides the infrastructure for accumulation of knowledge that could eventually transform clinical practices.
Although it is generally agreed that little actionable information can be derived from the human genotyping today, companies focused on clinical diagnostics frequently visit SNPedia. As the direct-to-consumer genomic profiling continues to grow, average consumers will be able to form SNPedia forums around common genetic variations. Comparison of individual genotypes could help to subdivide the patients currently grouped under the same disease umbrella, to stratify populations based on their response to medications, or to aid those lacking family history.
“No matter how valuable this information potentially is, without an appropriate regulatory framework consumers are at risk of receiving data of dubious quality, of misinterpretation of the results, or of being misled by unproven claims or benefits,” cautioned Gail Javitt, J.D., Genetics and Public Policy Center Johns Hopkins University (www.dnapolicy.org).
“What’s missing is an independent external evaluation of analytical and clinical validity of genetic tests,” said Javitt. Errors in genetic testing can have tragic consequences; the errors could multiply in cases of diagnostics based on assaying multiple individual SNPs. Genetic testing laboratories are not required to participate in externally administered proficiency testing programs. Therefore, consumers must rely on each lab’s self-assessment for information on consistency and reliability of their services.
In 2006, after years of protracted regulation development, the Centers for Medicare and Medicaid Services, vested with overseeing the quality of clinical laboratories, inexplicably rejected the implementation of CLIA to strengthen the standards for genetic testing. The renewed hope for enhancements to CLIA may come from the recently posted draft report titled “U.S. System of Oversight of Genetic Testing”. The report was prepared by the Secretary’s Advisory Committee on Genetics, Health, and Society, and it contains a comprehensive map of the steps, structures, and regulatory policies needed to oversee genetic and genomic tests.
“Another issue for DTC genetic testing is interpretation of genetic information,” continued Javitt. “Few patients have access to genetic expertise, especially for complex multifactorial conditions. In the absence of qualified genetic counselors a patient would have difficulties determining if the information provided by testing was supported by available evidence.”
While the American public overwhelmingly supports a law forbidding genetic discrimination by health insurers and employers, the Genetic Information Non-discrimination Act is stalled in the Senate. This delay means that the uncertainty surrounding genetic discrimination continues, and may negatively impact businesses like Navigenics.
“We are yet to see how the general public will react to personalized diagnostics based on global knowledge about the genome.” Uncertainty regarding how tests are regulated and whether privacy of the information is protected could further impede the future of personalized genetic medicine,” concluded Javitt.