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Glossary

DNA

DNA (deoxyribonucleic acid) is the molecule that carries genetic information. It can be thought of as a blueprint for how to make and maintain all the cells and tissues of a living organism.

DNA is found in a compartment in the cell called the nucleus, where it is compacted forming structures called chromosomes. Humans have 23 pairs of chromosomes which contain all of our genes.

DNA is made up of repeating units of molecules called nucleotides. Nucleotides contain one of four nitrogenous bases: adenine (A), thymine (T), cytosine (C) and guanine (G). These bases come together in different orders within a DNA molecule to form the DNA sequence (e.g. ATGGCC). The order of the bases is read and copied into a related molecule called RNA. The instructions in RNA are then used to build proteins.

Proteins

Proteins are made up of amino acids. There are 20 different amino acids that come together in different orders to build unique proteins.

Proteins are the main workers in our cells. They perform important activities that allow our bodies to function properly. Proteins have different jobs such as helping to carry out chemical reactions, controlling the flow of molecules into and out of cells, acting as sensors to respond to changes in a cell and communicating with and between cells.

Some proteins move other molecules around and some serve as structural components within cells. They largely influence our physical traits and how our bodies function.

Genes

DNA contains an immense amount of information. Part of a DNA molecule might have instructions for eye colour, while another part might have instructions for regulating the immune system. These portions of DNA are called genes. Each gene directs the production of a specific RNA which can lead to the production of a specific protein that influences a trait. For example, genes that control eye colour have instructions for building proteins that affect the pigment in your eyes.

We inherit our genes from our parents. During fertilization, each person receives one copy of genes from their mother and one copy from their father. This means that we all have two copies of every gene. The interplay between the two gene products helps to determine what the resulting trait will be. This is why you may have your mother’s eyes but your father’s hair.

Genes have alternate forms or versions called alleles. For example, a gene for eye colour might have two alleles: brown and blue. Alleles are different forms of the same gene, so they are present at identical locations on both chromosomes.

A person’s genetic makeup is their genotype, whereas the visible characteristic is their phenotype. If both alleles are the same for a gene, the person is homozygous for that trait. A person who has two copies of the allele for blue eyes is homozygous for blue eyes and their phenotype is likely a blue eye colour. If the two alleles are different, the person is heterozygous for that trait. For example, a person who has one allele for brown eyes and one allele for blue eyes is heterozygous and, in this case, their phenotype is likely a brown eye colour. Many traits, such as eye colour, are influenced by more than one gene. In addition to genotype, environment also plays a role in affecting phenotype. For instance, the interaction between genotype and nutrition (environment) influences height (phenotype).

Along with our environment, genes influence many aspects of our lives, including our appearance, our predisposition to disease and how we respond to medications.

Genetic variation

Genetic variation occurs when there are changes to the DNA sequence, including:

A change of one nucleotide for another
Deletion, insertion or inversion of nucleotides
Translocation of a segment of DNA from one chromosome to another

Sometimes genetic variants are due to a change at a single nucleotide in the DNA sequence. For example, the sequence ATGCGA might be changed to ATGCGT. These variants are termed single nucleotide polymorphisms (SNPs). Certain SNPs can be inherited together. This collection of SNPs is called a haplotype. SNPs and haplotypes are useful to researchers because they sometimes correlate with drug response and disease risk.

Allele

Allele is an alternative form of a gene or DNA sequence. Variations in clinical traits and phenotypes are allelic if they arise from the same gene sequence or locus and nonallelic if they arise from different gene sequences of different loci.

Genotype

The specific set of two alleles inherited at a genetic locus.

Haplotype

The combination of linked marker alleles (may be polymorphisms or mutations) for a given region of DNA on a single chromosome.

Human Genome Project

Collective name for several projects begun in 1986 by the US Department of Energy (DOE) to create an ordered set of DNA segments from known chromosomal locations, develop new computational methods for analyzing genetic map and DNA sequence data, and develop new techniques and instruments for detecting and analyzing DNA. The joint national effort, led by DOE and the National Institutes of Health, was known as the Human Genome Project. The first draft of the human genome DNA sequence, produced by the efforts of the Human Genome Project, was completed in 2001. The Human Genome Project officially ended in April 2003.

Linkage disequilibrium (LD)

Refers to alleles at loci close enough together that they remain inherited together through many generations because their extreme close proximity makes recombination (crossing over) between them highly unlikely.

Locus (loci)

The physical site on a chromosome occupied by a particular gene or other identifiable DNA sequence characteristic.

Minor allele

The allele of a biallelic polymorphism that is less frequent in the study population. Minor allele frequency refers to the proportion of the less common of two alleles in a population (with two alleles carried by each person at each autosomal locus) ranging from less than 1% to less than 50%.

Nucleotide

The combination of a nitrogen-containing base, a 5-carbon sugar, and phosphate group forming the A, G, C, T of the sequence of DNA (DNA), for example.

Pharmacogenomics

Study of genes related to genetic controlled variation in drug responses.

Phenotype

The total observable nature of an individual, resulting from interaction of the genotype with the environment.

Polymerase chain reaction (PCR)

A procedure in which segments of DNA (including DNA copies of RNA) can be amplified using flanking oligonucleotides called primers and repeated cycles of replication by DNA polymerase.

Polymorphism

Difference in DNA sequence among individuals that may underlie differences in health. Genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkage analysis. The vast majority of DNA polymorphisms are benign and not associated with a detectable phenotype.

Single-nucleotide polymorphism (SNP)

DNA sequence variations that occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered. SNPs are the most abundant variant in the human genome and are the most common source of genetic variation, with more than 10 million SNPs present in the human genome, representing a density of one SNP for approximately every 100 bases.

Pharmacogenetic polymorphism

Genetic variants that alter the way an individual metabolizes or responds to a specific medication.

Pharmacokinetics

Pharmacokinetics refers to the movement of drugs into, through and out of the body. The type of response of an individual to a particular drug depends on the inherent pharmacological properties of the drug at its site of action. However, the speed of onset, the intensity and the duration of the response usually depend on parameters such as:

the rate and extent of uptake of the drug from its site of administration;
the rate and extent of distribution of the drug to different tissues, including the site of action;
the rate of elimination of the drug from the body.

Pharmacodynamics

Pharmacodynamics is defined as the response of the body to the drug. It refers to the relationship between drug concentration at the site of action and any resulting effects namely, the intensity and time course of the effect and adverse effects.

Pharmacodynamics is affected by receptor binding and sensitivity, post-receptor effects, and chemical interactions.

Pharmacogenomics Research

Pharmacogenomic research has been conducted all over the world for at least 50 years and it is still a quickly growing sector of science. The validity of evidence in this field can range from high to low level.

The importance of genes in both medication efficacy and toxicity risk is recognized by FDA (Food and Drug Administration), as well as other well respected scientific bodies. With certain medications, pharmacogenetic testing is actually mandatory.

The Clinical Pharmacogenetic Implementation Consortium (CPIC) and The Dutch Pharmacogenetics Working Group (DPWG) are two of the most highly regarded pharmacogenomic scientific institutions in the world. Both have begun issuing validation on the pharmacogenomic research can be utilized for human use.

Rx Report™ test reports only on drugs and phenotypes that have been validated by FDA, CPIC or DPWG. Pharmacogenomics is a dynamic science. More research is being conducted and will continue to be conducted over the next few years and beyond.

Personalized Prescribing Inc. updates and reports on any new validations by the above Institutions, including PharmGkb as soon as these validations are published. The PharmGkb is a pharmacogenomic knowledge resource that encompasses clinical information including clinical guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships.

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