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Cheek Swab SNP Panels Offer Nutrigenomic Guidance: Are They Ready to Be Served?

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In a near future envisioned by pharmacogenomics, doctors will be able to easily test their patients for groups of SNPs associated with various diseases, then, depending on the results, prescribe drugs or life-style changes accordingly.

This future is already here — sort of — in the form of two SNP panels being offered as a service to clinicians in the US. This service, entitled Integrative Genomics, is being offered by Integrative Therapeutics, a privately owned Wilson-ville, Oregon-based nutritional supplement maker, in collaboration with GeneLink, a Hawthorne, NY supplier of oligos and other genomic reagents.

These SNP tests, which can be run on a sample taken with a mouth swab and run an average of $350 for each panel, include a basic panel that looks for 12 different SNPs and a “cardio SNP” panel with 26 SNPS associated with heart health. The company is coming out with an immune panel looking at SNPs that involve oxidative stress and detoxification pathways for substances that are known to cause DNA damage.

But Integrative Therapeutics explicitly states that the panel is not a diagnostic test. “It doesn’t predict any disease.” said Cheryl Myers, the company’s director of Information and Development. “It looks at pathways in the body that can perform efficiently or inefficiently and if those pathways are performing inefficiently, all of the things we look for are actionable, which means there’s something you can do to make them work more efficiently.”

Myers said the SNPs in the Integrative Genomics panels include only those that have been “assessed in peer-reviewed published studies to show less than favorable outcomes associated with a disadvantageous” allele.

As an example of “actionable SNPs,” Myers cited those on the cardio panel that are on the genes for homocysteine metabolism (MTHFR_c677T-U8, MTHFR_ A1298C-U9, MTR_A2756G_U2, and MTRR_lle22Met-U5). “Homocysteine levels that are higher or unmanageable are associated with adverse cardiac outcomes,” she said. “It doesn’t predict disease, but by knowing that your body needs some help handling homocysteine, then the next conclusion is that by handling the homocysteine better [you] will have improved cardiac health.” One simple way to help the body handle homocysteine better is to take higher doses of the B vitamins than people who handle homocysteine well, she said.

This “nutrigenomics” feature fits with the company’s main product line — it’s nutritional supplements. Integrative Therapeutics’ sales team is currently marketing the test to its established client base for its nutritional supplement products, including MDs, naturopaths, nurse practitioners, and clinical nutritionists.

The company has had to educate these clinicians about the panels and how they can be used —not as a diagnostic test but in conjunction with other clinical factors, Myers said. So far, the company said the service is catching on.

“There are thousands of healthcare providers across the U.S. using Integrative Genomics,” said Lauren Abel, an outside spokesperson for the company.

This emerging nutrigenomic medicine, however, is not without its critics. “We don’t have enough information right now, enough linkages between nutrients and specific genes to tell someone, based on 30 SNPs in 30 genes, that they should have more vitamin B or less Vitamin C,” said Jim Kaput, of the section of cellular and molecular biology at UC Davis.

Kaput believes that there needs to be more research before such SNP panels are put into clinical practice. Currently, he serves as CFO of NutraGenomics, a Chicago-based company that performs contract research to identify genes whose expression is regulated by diet as well as genotype (and which could be a competitor to Integrative Genomics one day.) Kaput and his research collaborators have also obtained IRB approval for a study in which they are trying to link various genes whose expression can be regulated by diet to chronic diseases, he said.

Companies like Integrative Genomics that look at one SNP for a handful of SNPS “are forgetting that they are just taking the last gene in the pathway,” Kaput said. Instead, he said thinks that scientists — not just in nutrigenomics but in pharmacogenomics as well — need to look at all of the steps of the pathway affected.

The basic Integrative Genomics panel includes 12 SNPs associated with bone mineral density, detoxification, blood pressure; lipid metabolism; oxidative stress; skin & connective tissue; and vascular integrity (see table, p. 6).

The cardio panel includes:

  • three groups of SNPs for blood lipid metabolism (CETP G-971A and C-629A, LPL_HindIII, and ABOP_ Arg3611Glu, Gin4154Lys, and Xbal)
  • eight SNP families for vascular integrity (hTNFalpha_U6, MTHFR C677T-U8 and A1298C-U9, MTR A2756G-U2, MTRR lle22Met U5, PON1 Arg192Gln-U3, NOS3 Glu298Asp-U11, SELE A561C-U8, IL6 G-174CU7)
  • four SNP groups for healthy blood pressure (ADD1 Gly460Trp-U4, AGT Met235Thr-U9 and Thr174Met-U1, CYP11B2-C344T-U4, GNB3 C825T-U8), and
  • six groups of SNPs for blood circulation (F2-G20210A-U9, F5 Arg506Gln-U1, F7 Arg353Gln-U2, PAI1 4G/5G-U6, GP1BA-Thr145Met-U7, ITGB3 L33P-U4).

—MMJ

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