Genetics 101: Utilization of patient DNA to assist the dental professional

The ease with which saliva can be collected by a dental hygienist or other dental professional is readily accepted by the patient population, and the benefits of saliva diagnosis are significant: It is painless, allows for early detection — and it is accurate.

In addition to what human DNA can tell us about a person’s genetic code, another kind of DNA test can be just as revealing. The presence of living organisms within the host medium, such as pathogenic bacteria, can be identified by the DNA of the bacteria. In fact, in screening for pathogens, saliva is a superior DNA specimen medium. This is because saliva consists of several bodily fluids, including gingival crevicular fluid, which has a composition similar to blood serum, and fluid released from the salivary glands.

The hereditary material of all multicellular organisms is the famous double helix of deoxyribonucleic acid (DNA) (see Fig. 1: DNA double helix), which contains all of our genes. DNA, in turn, is made up of four chemical bases, pairs of which form the “rungs” of the twisted, ladder-shaped DNA molecules. All genes are made up of stretches of these four bases, arranged in different ways and in different lengths. Genes are arranged, one after another, on structures called chromosomes (see Fig. 2: DNA molecule unwinding from a chromosome inside the nucleus of a cell). A chromosome contains a single, long DNA molecule, only a portion of which corresponds to a single gene. Humans have approximately 23,000 genes arranged on their chromosomes. A key enabler of the trend toward personalized medicine is the ability to harness DNA data through genetic sequencing. With an estimated 90 percent of prescription drugs working only about 50 percent of the time, prescribing doctors could use molecular diagnostics to test for specific genetic mutations that might cause one drug to be harmful, while another might be safe.[1]

All of us have a genome made up of DNA. DNA itself is made up of individual molecules, called nucleotides, which can come in four types designated by the letters A, G, T and C (see Fig. 3: DNA molecules are found inside the cell’s nucleus, tightly packed into chromosomes. Scientists use the term “double helix” to describe DNA’s winding, two-stranded chemical structure. Alternating sugar and phosphate groups form the helix’s two parallel strands, which run in opposite directions. Nitrogen bases on the two strands chemically pair together to form the interior, or the backbone of the helix. The base adenine {A} always pairs with thymine {T}, while guanine {G} always pairs with cytosine {C}). These nucleotide letters are connected together in long, linear sequences of DNA, spelling out genes and other important instructions along the way. Each of our chromosomes consists of such a sequence of DNA, millions of nucleotides in length. And because we have two copies of each chromosome — one from dad and one from mom, except for the X in males — we have two letters at each location in the genome (a “genotype”). If you compare the sequences of letters between two people, you’ll find that they are more than 99 percent identical. But there are places where the letters might be different. Some of these differences are large — chunks of letters are missing or duplicated — or they can be different at just a single letter location, for example an “AA” genotype in one person versus an ‘AC’ in another. These single-letter differences can be quite common, so to determine the individual’s genotype at hundreds of thousands of these variable sites, genetic testing companies typically identify these single nucleotide polymorphisms (SNPs).

Genomics provides a comprehensive view of the complete genetic makeup of an individual. The Human Genome Project (HGP) was the international, collaborative research program whose goal was the complete mapping and understanding of all the genes of human beings. All our genes together are known as our “genome.”

Sequence variations, as manifested by single nucleotide polymorphisms (SNPs), can provide insight into the basis for a large number of phenotypes. The phenotype is the outward appearance of the animal in all of its anatomical, physiological and behavioral characteristics as dictated by the genetic and environmental influences in its environment. In contradistinction, only inherited factors are taken into account in the genotype.[2]

DNA sequencing (see Fig. 4: Single nucleotide polymorphisms {SNPs} are a type of polymorphism involving variation of a single base pair. Scientists are studying how single nucleotide polymorphisms, or SNPs {pronounced ‘snips”}, in the human genome correlate with disease, drug response and other phenotypes) is a laboratory technique used to determine the exact sequence of bases (A, C, G, and T) in a DNA molecule. The DNA base sequence carries the information a cell needs to assemble protein and RNA molecules. RNA is part of a group of molecules known as the nucleic acids. DNA sequence information is important to scientists investigating the functions of genes (see Fig. 5: Installing a flow cell on an Illumina cluster station at the National Institutes of Health Intramural Sequencing Center in Rockville, Md.; and Fig. 5a: sequecer flow cell). The technology of DNA sequencing was made faster and less expensive as a part of the Human Genome Project. In the future, the ability to rapidly screen for SNPs will have a profound impact on a number of applications outside of medicine, including forensics in the law enforcement community (see Fig. 6: 456 Life Sciences Genomic Sequencer showing monitor with sequence data; and Fig. 7: Technician using hand pipette adding purified DNA to a sequencing reaction in a microtiter plate).

Individualized patient care and treatment

Periodontal disease

Genetic variations among individuals have a measurable influence on inflammation. Genetic influence is sufficient to make a difference in patients’ long-term wellness. Soft-tissue and bone-repair issues become increasingly important with an aging population, especially with that population’s routine acceptance of dental implants. Although periodontal diseases are initiated by bacteria that colonize the tooth surface and gingival sulcus, the host response is believed to play an essential role in the breakdown of connective tissue and bone, key features of the disease process.[3]

Salivary DNA testing helps dental professionals obtain precise evidence about periodontal genetic indicators. It enables more accurate and perhaps more effective treatment. The PST Genetic Susceptibility Test (Interleukin Genetics, Waltham, Mass.) assesses patients’ genetic risk of having periodontal disease and their genetic risk for progression. The PST brand name is derived from the abbreviation for “periodontitis susceptibility (or sensitivity) test.” OralDNA Labs, a Quest Diagnostics Company, is licensed to provide Interleukin’s periodontal and oral HPV salivary testing to dental practices.

Periodontal disease, similar to many other chronic inflammatory disorders, varies from one individual to another with its severity and progression dependent upon the interaction of genetic and behavioral risk factors. Interleukin’s PST testing provides a reliable way of assessing an individual’s genetic risk for periodontal disease, the most common cause of tooth loss. The PST Genetic Susceptibility Test is described as the first and only genetic test that analyzes two interleukin 1 (IL-1) genes for variations that identify an individual’s predisposition for over-expression of inflammation and risk for periodontal disease.[4]

DNA-based risk assessment testing is intended to identify common genetic variations that produce varying biochemical responses that are directly involved in the pathogenesis of a disease and are associated with adverse disease outcomes. Genetic variations that result in a biochemical imbalance and are associated with adverse clinical outcomes may provide further understanding as to why some people are more prone than others to developing serious chronic diseases and why some people respond to treatments for those diseases differently than others. By identifying these underlying biological mechanisms, preventive interventions can be targeted to help reinstate the biochemical balance that may help prolong health and wellness in these individuals.

Researchers have been studying SNPs (pronounced “snips”) and their impact on human health for many years now, and some links are well established. For example, a number of SNPs located in genes involved in the immune system have been associated with multiple autoimmune conditions such as rheumatoid arthritis and lupus. There are also many SNPs that have been associated with common cancers of the breast and prostate. But for the most part, the effect that each of these SNPs has on disease risk is small — usually modifying risk about 1-2 times compared with average.[5]

It is important to note that whenever the PST-positive genotype is present, it is associated with an increased susceptibility to periodontal disease and the overproduction of IL-1A, a cytokine that amplifies inflammation. The risk allele is T and is fairly common with a frequency rate of ~34 percent. The more Ts you have, the more IL-1A you’ll produce. Simply stated, when under attack by organisms, people with more Ts will have more gum inflammation. The IL-1 genetic influence on inflammation is strong enough to influence clinical outcomes. The results from genetic testing for periodontal disease will indicate whether or not your patient is positive and has an increased risk for more severe periodontal disease due to the genetic variations examined in that particular test. If patients have a PST-positive genotype they are at a three-to-seven-fold increased risk for severe periodontal disease. The PST composite genotype is based on the combination of the results for the IL-1A (+4845) and IL-1B (+3954) — the genetic address so to speak — that predisposes an individual to periodontal disease.[6]

Oral and throat cancer

If detected early, oral and throat cancers are almost always successfully treated. Unfortunately, many cases are advanced by the time they are diagnosed. Tobacco chewing or smoking, excessive alcohol consumption, prolonged sun exposure (to the lips) and human papillomavirus infection can all increase a person’s chances of developing oral or throat cancer. In the United States, one person in 99 will be diagnosed with the cancer during their lifetime.[1] One study compared 1,790 patients with 5,278 healthy controls from Europe and Latin America. The authors found that, compared with those with the CC genotype, subjects with either the CG or the GG genotype at rs1573496 had 0.7 times the odds of oral and throat (pharyngeal) cancer. The protective effect of having a G at this SNP was also seen for larynx cancer and esophageal cancer.[7,8]

Patient history and family history

DNA testing has become increasingly commonplace in the medical field to assist doctors in the early “pre-symptom” diagnosis of patients with a family history of diseases such as those affecting the lungs and heart, degenerative disorders (such as Parkinson’s), brain diseases (such as Alzheimer’s) and certain types of cancer. Now that salivary DNA testing is available to the dental profession, oral health, too, will benefit from the clinical and hereditary insights such test results can provide.[9] Prenatal testing has become commonplace to determine the risk of disease should both parents be carriers of a specific gene mutation. Considering the trend towards medical/dental collaboration, genetics will most certainly play a role in future patient care.

Currently, there is an assortment of genetic tests available that could potentially be of interest to dental professionals, including these three available through the Inherent Health brand of genetic tests created by Interleukin Genetics:

• Heart Health Genetic Test identifies a person’s genetic predisposition to heart attack based on inflammation. The genetic analysis identifies individuals that have a lifelong tendency to overproduce certain chemicals in the body that lead to inflammation. Overproduction of these chemicals can start a chain reaction that ultimately may lead to a heart attack.
• Nutritional Needs Genetic Test identifies DNA variations in genes crucial to B-vitamin metabolism and the ability to manage oxidative stress. Individuals that show suboptimal results for the genes can be at increased risk for ineffective utilization of B-vitamins and potential for cell damage caused by oxidative stress.
• Bone Health Genetic Test identifies whether you are more likely to be susceptible to spine fractures and low bone mineral density associated with osteoporosis. Early intervention now can help prevent osteoporosis later. Preventative measures can reduce the risk of bone loss and fractures, which in the case of vertebral fractures leads to a hunched appearance.[10]

Genetic disorders specific to human dentition

Rare Disorders

Hypodontia is often familial and can also be associated with genetic disorders, such as ectodermal dysplasia or Down syndrome. Hypodontia can also been seen in people with cleft lip and palate. Possible causes can be genetic, hormonal, environmental or infectious. The Journal of the American Dental Association published preliminary data suggesting a statistical association between hypodontia of the permanent teeth and epithelial ovarian cancer (EOC). The study shows that women with EOC are 8.1 times more likely to have hypodontia than are women without EOC. The suggestion is that hypodontia can serve as a “marker” for potential risk of EOC in women.[10]

Amelogenesis imperfecta is a genetic condition that causes teeth to be abnormally small or discolored. Dentinogenesis imperfecta is a genetic disorder that interferes with normal tooth development. It affects approximately one in 6,000 to 8,000 people, according to the National Institutes of Health. There are three types of dentinogenesis imperfecta. Type I occurs in individuals who have another inherited disorder called osteogenesis imperfecta (causes brittle bones); whereas type II and type III occur in those without other genetic disorders. Some researchers believe types II and III are part of a single disorder along with another condition called dentin dysplasia type II, which primarily affects baby teeth more than adult teeth. General symptoms of dentinogenesis imperfecta include tooth discoloration (blue-gray or yellowish-brown), tooth translucency and weaker-than-normal teeth, which are prone to erosion, breakage and loss.

A rare chromosomal condition called 48,XXYY Syndrome affects one in 18,000 to 50,000 males. There is delayed appearance of primary and secondary teeth, crowded and/or misaligned teeth. Numerous cavities and thin tooth enamel also often accompany the disorder.

Hypohidrotic ectodermal dysplasia is an inherited condition affecting approximately one in 17,000 people worldwide. It causes abnormalities of the skin, nails, hair, sweat glands and teeth. Approximately 70 percent of carriers of the gene that causes the condition (those with only one, but not both, recessive mutated genes) display symptoms, including some missing or abnormal teeth, sparse hair and some sweat gland dysfunction.

Oculodentodigital dysplasia is an extremely rare genetic disease (with fewer than 1,000 people diagnosed worldwide) that affects the eyes, fingers and teeth. An autosomal dominant disorder, it develops when only one mutated gene is inherited from a parent.

Recombinant 8 Syndrome is a rare disease of unknown incidence primarily affecting an Hispanic population descending from the San Luis Valley of Colorado and Northern New Mexico. Inherited in an autosomal dominant pattern, Recombinant 8 Syndrome causes distinctive facial abnormalities, moderate to severe intellectual disability and heart and urinary tract problems. Abnormal teeth, an overgrowth of gums, small chin, thin upper lip and downturned mouth are all associated with the condition.[12]

Dental abnormalities seen in cleidocranial dysplasia may include delayed loss of the primary teeth; delayed appearance of the secondary teeth; unusually shaped, peg-like teeth; misalignment of the teeth and jaws (malocclusion); and extra teeth, sometimes accompanied by cysts in the gums.

Gingival Fibromatosis is a hereditary condition causing an overgrowth of the gum tissue; gingival fibromatosis is characterized by enlarged gum tissue and is associated with an overproduction of collagen.

Supernumerary teeth are extra permanent teeth that may or may not erupt. Many are abnormally shaped and can appear anywhere in the mouth. The most common supernumerary teeth are mesiodens, small teeth with a cone-shaped crown and a short root located between the maxillary central incisors. Supernumerary teeth also are common in the upper molar area (distomolars or fourth molars). While other factors are also thought to contribute, heredity is believed to play a role in the development of supernumerary teeth, because they are more common in relatives of affected children than among the general population. Multiple supernumerary teeth are rare in people with no other associated diseases or syndromes. Conditions frequently associated with a higher incidence of supernumerary teeth include cleft lip/palate, cleidocranial dysplasia (a genetic disorder affecting bone and teeth development) and Gardner syndrome (inherited disorder leading to colon cancer).[13]

In one major study, researches examined 462 individuals of central European ancestry born with cleft lip (some also had cleft palate). The researchers also genotyped 954 people born without either condition. Having one A at rs987525 increased the odds of cleft lip with or without cleft palate by 2.6 times. Having an A at both copies of the SNP increased the odds 6.1 times. The study’s authors estimate that 41 percent of the cases of these birth defects in this population were attributable to the SNP.[14]

Ehlers-Danlos Syndrome with severe early-onset periodontal disease (EDS-VIII) is a distinct, heterogeneous disorder with one predisposition gene at chromosome 12p13. It can be difficult diagnosis, requiring the expertise of a medical geneticist.

Conclusion

Knowing about your individual ancestry can teach you not only about your family’s cultural heritage, but perhaps also, your personal risk for disease. Typical DNA reports from saliva testing will list your propensity for specific diseases, but can also bring you the peace of mind that you are not a carrier for some others. Test results may include information on how genetics influence your sensitivity to a drug, a drug’s risk of potential side effects or a drug’s general effectiveness.

We are entering an age of personalized medicine. Family traits such as eye color or hair color are what people generally think of when they hear the word “genes.” But some other characteristics, such as the ability to taste bitterness in broccoli, having wet ear wax or detecting a distinct odor in one’s urine after eating asparagus are a surprise to most!

In the future, advances in DNA testing will be assisting us to customize patient treatment by using a scientific rather than a subjective approach. The pathogenesis of periodontitis, the patient’s unique nutritional needs or overall disease resistance could be traced back to their inherent genetic makeup. Research and testing is being done on the utilization of portable rapid PCR detection devices for law enforcement at crime scenes. With technological breakthroughs, could a portable device be coming soon to assist us chairside in the dental office? From the simple canker sore to life-threatening diseases, genetics offers us the potential for vast insights. More knowledge means more informed decisions for the patient, and more effective treatment planning from the dental professional.

Terms

Allele — An allele (see Fig. 8: Though the term “allele” was originally used to describe variation among genes, it now also refers to variation among non-coding DNA sequences) is one of two or more versions of a gene. An individual inherits two alleles for each gene, one from each parent. If the two alleles are the same, the individual is homozygous for that gene. If the alleles are different, the individual is heterozygous.

Autosome — An autosome is a chromosome that is not an allosome — i.e., not a sex chromosome.

Chromosome Packaged — DNA and protein in cells. Human beings have 23 pairs of chromosomes. One-half of each pair is inherited from a parent.

Cytokine — A protein or peptide that is outside the cell and serves as a communication signal to cells. Examples are interleukins, interferons, and tumor necrosis factors that facilitate the inflammatory response.

DNA (deoxyribonucleic acid) — The molecule inside the nucleus or core of each of the body’s trillions of cells, that carries genetic instructions for making living organisms. DNA is made up of sequences, or what is referred to as your genetic code. Each gene is the code or recipe for a single protein.

Gene — The basic physical unit of inheritance. A functional segment of DNA located in a specific region on a chromosome that directs the formation of a protein.

Genetic counseling — A short-term educational counseling process for persons and families who have an inherited disease or who are at risk for such a disease. Genetic counseling provides persons with information about their condition and helps them make informed decisions.

Genome — The sum total of all the genetic information in an organism; its instruction book — the blueprint that directs the development and functioning of human beings and other organisms.

Heterozygote/heterozygous — Possessing two different copies of a particular gene, e.g., two different alleles, one inherited from each parent; a heterozygous person is also called a carrier.

Locus/loci — Actual physical position of a gene or marker on a chromosome, a kind of genetic street address. The plural of locus is loci.

Mutation — A change in a DNA sequence. Mutations are often harmful, causing irreversible diseases. However, some mutations may not have an effect on living organisms, while others confer beneficial effects.

Nutritional genomics — A field of study focused on optimizing an individual’s genetic potential through understanding how genetic variations (SNPs) influence molecular pathways and define nutritional needs. Conversely, the field is focused on the influence of nutrition and lifestyle on the molecular expression of genetic variations.

PCR — The polymerase chain reaction (PCR) is a biochemical technology in molecular biology used to exponentially replicate a single or a few copies of a piece of DNA, generating thousands to millions of copies of a particular DNA sequence.[15]

(Note: A complete list of reerences is available from the publisher.)