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Making Sense of SNPs

Small genetic variations can have a big influence on your health — and affect your nutritional needs, too.

snps

April had suffered two devastating miscarriages in less than two years. Otherwise in good health, she insisted on a complete medical workup at a major hospital. The doctors could find nothing wrong with her, so they deemed her miscarriages an unlucky mystery.

“My husband and I stopped trying to get pregnant at that point,” says April, who asked that her real name not be used. “One doctor said we should just think about it as ‘a swing and a miss.’ But we couldn’t face another loss like that.”

Several years later, dealing with a different health concern, April had a comprehensive exam with an integrative physician who recommended both a nutritional screening and a genetic panel that examined her DNA.

The panel revealed two variations in a gene that’s responsible for methylenetetrahydrofolate reductase (MTHFR), a vitamin-dependent enzyme.

The type of gene variation April has is called a single nucleotide polymorphism, or SNP (pronounced “snip”). People with a SNP on the MTHFR gene aren’t able to process certain B vitamins and folate properly, and can suffer a number of health issues as a result.

“I learned that the SNP I carried has been linked to neural-tube defects in fetuses that can lead to miscarriages,” says April, whose labs confirmed significant B-vitamin deficiencies.

April also learned that MTHFR SNPs are surprisingly common — half of us carry at least one variant on the MTHFR gene.

People with this SNP are often advised to increase their intake of B-rich foods and to take activated (methylated) forms of B12 and folate rather than standard supplements.

April now takes these supplements daily in addition to eating a nutrient-rich diet. Since starting the regimen, she says she’s noticed a marked improvement in her mood, energy, and clarity of mind.

Sadly, the information about her SNP came too late to support a successful pregnancy. “It’s such a shame I didn’t know this back then,” says April, now 48. “It could have changed the outcomes of those pregnancies, and I might be a mom now.”

What’s in Our Genes?

Existing cells within our bodies divide to make new cells, copying our DNA structure along the way. Frequently, though, blips occur in which a single nucleotide — a building block of DNA — is substituted with another during the copying process. The resulting variations are SNPs.

SNPs are passed down from parents to children, and these small variations can have big impacts. With an estimated 10 million SNPs in the human genome, these variants account for roughly 90 percent of human genetic variation.

(Though the terms are often used interchangeably, even by scientists, SNPs are not the same as mutations. Both SNPs and mutations involve some alteration of basic genetic code, but SNP variations are present in at least 1 percent of a given population while mutations are much rarer.)

Though most SNPs have no discernible health effects, some can increase the likelihood of certain diseases and can affect the way a person metabolizes nutrients or responds to drugs, viruses, bacteria, and environmental toxins.

Scientists have identified several health-affecting SNPs present in small but significant subsets of the population. For example, some variations (including SNPs and mutations) that affect the BRCA1 and BRCA2 genes are linked to breast and ovarian cancer. SNPs in the apolipoprotein E (ApoE) gene are often associated with cardiovascular conditions and Alzheimer’s disease. MTHFR SNPs have been linked with depression, addiction, miscarriage, and Parkinson’s disease. (For details on these SNPs, see “SNPs and Nutrition,” below.)

Connecting SNPs and Diet

The identification of April’s SNPs — and her nutrition-centric solution — represents an emerging understanding of the unique ways each of us responds to our environment, including how our genetic makeup influences our individual nutrition and lifestyle needs.

The science of nutrition has historically been focused on preventing and treating diseases caused by a deficiency of vitamins and minerals. But the alarming rise of diet-related disease has triggered the study of nutrient-related interactions at the gene, protein, and metabolic levels.

The new field of nutrigenomics explores the ways individual genetic variations can affect a person’s response to nutrients. Research in this area is illuminating how SNPs can make a difference in everyday health and function.

“Every generation is the source of a few more SNPs in our genome, but many of those SNPs have remained silent for years,” explains José Ordovás, PhD, director of nutrition and genomics at the USDA Human Nutrition Research Center on Aging at Tufts University.

“Modern-day stressors — from foods, toxins, and lifestyle — have ‘turned on’ the negative effects of some of those SNPs that were asymptomatic in the past and are now found to be predisposing us to disease in the current environment.”

Personalized Nutrition

Our growing understanding of genetic variety casts even greater doubts on the appropriateness of one-size-fits-all recommended daily allowances (RDAs) — the average amount of nutrients declared necessary for maintenance of good health by the Food and Nutrition Board of the Institute of Medicine of the National Academies.

“As we begin to understand nutri-genomics and study SNPs, what we recognize is that the differences from one person to another may be much greater than previously thought,” says Jeffrey Bland, PhD, author of The Disease Delusion and founder and president of the Personalized Lifestyle Medicine Institute, a nonprofit organization for patient-activated healthcare.

“What’s adequate for some would be nutrient deficient for others,” he says. “Our needs are based on our unique genetics, so the idea of one recommended level of nutrition is becoming outdated.”

Ordovás believes that RDAs are a good starting point for most individuals, but he agrees that the approach has limits. “It’s very difficult to account for all the particular needs of each individual, considering the different environments to which we are exposed and the different stages of life we’re in,” he says. “We need to consider the individual heterogeneity of genetic variation and move toward more personalized nutrition.”

SNP Action Plans

Of course, no one’s overall health is determined solely by his or her genetics.

“It’s important to remember that each of us carries more than 3 million SNPs, and most of those genetic variants are really quite common,” says Stephan J. Sanders, PhD, assistant professor and genetic researcher at the University of California, San Francisco.

He points out that most common disorders or chronic conditions, such as obesity or heart disease, do not have a single specific genetic cause. Rare is the gene — and SNP — that operates in isolation.

“When it comes to complex disorders, it’s not a simple case where one gene causes one disorder,” Sanders says. He likens our DNA to a computer program that interacts with our cells and with the environment. This “program” allows each cell to perform in the correct way in the correct situation.

“It’s a continuous flow of information back and forth. If you change one component, you’ll change many aspects of what that program might do.”

Indeed, it appears that we can, in some cases, repair or reverse the negative impact of a SNP through carefully targeted lifestyle and nutritional solutions.

“Genetics might load the gun, but environment can pull the trigger,” says P. Michael Stone, MD, MS, IFMPC, a family physician in Ashland, Ore., and a faculty member at the Institute for Functional Medicine.

Focusing your eating to support your unique genetic makeup — and account for its potential weaknesses — can be one way to set the safety on that gun, he explains.

“We know that, for virtually any condition, there can be improvement with nutritional intervention. And if we know more about a person’s SNPs, there is often a specific and detailed list of nutrients and foods that can markedly improve the trajectory to health.”

Stone says patients often arrive at his clinic with the results from their nutrigenomic testing panels in hand, asking for help with what to do next.

“To create effective action plans, we look not just at their genetics but also at their lifestyle, including nutrition, sleep, relaxation, and resilience,” he says. Stone has developed what he calls a therapeutic alliance with in-clinic nutritionists to help with diet change and education.

“My job is the view from the stethoscope, and their job is the view from the fork; together we support the patient in his or her healthy nutrition and lifestyle changes.”

A New Genetic Understanding

The study of genetics and its role in human health is vast and, despite exciting discoveries over the past decade or so, still in its infancy.

“Here at the intersection of genetic testing and biomarker testing, we’re on the verge of an incredible transformation,” says Bland.

Sanders agrees that there is a positive message behind this ability to receive personal genetic information, but cautions us to remember that SNP information is just one part of our overall health and nutrition picture.

“The field of genetics is experiencing transformative levels of change all the time, but our current genetic testing methods are still limited in providing truly useful information to individuals about their own specific risks for common disease,” Sanders says.

Even so, Stone is a vocal proponent of the positive lifestyle changes that can be made as a result of genetic testing. “The importance of knowing your SNPs lies in learning how to act on the information, adjusting your diet and lifestyle to your individual needs,” he says. “Knowing more about your SNPs can help you make choices to promote overall health.”

WEB EXTRA!

Nutrigenomics Glossary

Allele: A variant form of a gene located along a chromosome.

Bases: Compounds that help make up the DNA code: adenine (A), cytosine (C), guanine (G), and thymine (T). The human genome contains 3.2 billion base pairs, and an average-size gene has about 3,000 of these pairs.

Biomarker: A biologic feature used to measure the presence or progress of disease or the effects of treatment.

Chromosome: A long, linear strand of DNA; humans normally have 46 chromosomes (23 inherited from each biological parent).

DNA: Molecules inside cells that carry genetic information.

Epigenetics: Study of how genetic traits can change and be inherited.

Gene: Made up of DNA, the basic physical and functional unit of heredity.

Gene expression: Process by which information from a gene is used in the synthesis of a functional gene product, such as a protein.

Genome: The entire set of genetic information across all 23 chromosome pairs, including all genes.

Genotype: Each person’s unique arrangement of genes.

Haplotype: A set of DNA variations, or polymorphisms, that tend to be inherited together. A haplotype can refer to a combination of alleles or to a set of SNPs found on the same chromosome.

Nucleotide: The building block of DNA, consisting of a nitrogenous base (adenine (A), cytosine (C), guanine (G), or thymine (T)), a phosphate group, and a sugar. The way they are arranged on the DNA molecule determines which proteins will be coded by them. Each nucleotide on a chromosome is matched to a nucleotide on the opposite side of the DNA spiral.

Nutrigenomics: The study of the role of nutrients and bioactive food compounds in gene expression.

Nutrigenetics: The study of the effects of genetic variation on dietary response.

Orthomolecular medicine: Based on the theory that illness can be treated, and health maximized, by creating the optimal molecular environment for the cells of the body through the introduction of natural substances.

Personalized nutrition: An application of nutrigenomics that helps tailor dietary recommendations to a person’s DNA.

Phenotype: The combination of observable characteristics or traits and the products of behavior.

SNP (Single nucleotide polymorphism): The most common form of genetic variation, these changes in DNA happen when one single nucleotide is replaced with another, potentially contributing to disease or affecting reactions to bacteria, viruses, nutrients, drugs, and environmental factors.

Julie Kendrick is a science writer based in Minneapolis

Illustration by Stuart Bradford

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