Glossary
From SNPedia
Note: for a more comprehensive glossary, visit NIH's Genetics Home Reference Glossary
Ancestry Informative Marker (AIM): AIMs are the subset of genetic markers that differ in allele frequencies across different populations of the world. Most variations are shared among populations, so for most loci the most common allele is the same in each population. AIMs may be used to categorize individuals into populations sharing similar markers and perhaps phenotypes (such as self-declared ethnicity).
Allele: Traditional definition: alternate forms of a gene, composed of one or more SNPs. More loosely: a SNP. For example, at a given position along a chromosome, most people might have the DNA base "A". A few might have an alternative sequence. Each defined type is an allele.
Biostatistics: The statistics involved in medical and epidemiological studies, which now includes many genomic studies. Medpage has an excellent Guide to Biostatistics.
Chromosome: The physical units of heredity; long linear strands of DNA. Humans normally have 46 chromosomes (23 inherited from Dad, 23 from Mom).
Compound heterozygote: When two different SNPs are carried by the paternal and maternal chromosomes for one gene; in other words, the maternally-inherited gene carries a variant SNP at one location, and the paternally-inherited gene carries a variant SNP at a different location.
Diplotype: What genotype is to allele, diplotype is to haplotype; a specific combination of two haplotypes.
Familial risk: The risk for individuals who's relatives have a disease compared to the risk for individuals who's relatives don't have the disease. It can vary depending on which relative(s) are specified. Occasionally also called 'recurrence risk'. Familial risk is typically higher for more common diseases (like breast cancer) compared to rare diseases.
Gene: An area along a chromosome typically encompassing the information necessary to encode one protein.
Genomics: The study of all the genetic material in a species taken as a whole (well, to the extent possible anyway).
Genome: All of the genetic material in a species. The human genome is approximately 3,300,000,000 base pairs in length and is distributed amongst 23 types of chromosomes (chromosome 1 through 22, in order of size, plus the X and Y chromosome that determine gender.)
Genome Wide Association Study: [PMID 18349094] guidelines
Genoset: A defined combination of alleles from 2 or more distinct SNPs.
Genotype: The two alleles inherited at a given SNP position, one inherited from Dad, one inherited from Mom. Example: rs16260(A;C) is how we indicate someone with a (A;C) genotype at SNP rs16260.
Genotype relative risk: The odds ratio of one specified genotype compared to another.
Haplotype: A specific combination of SNPs all occuring on the same chromosome (i.e. all occuring on the chromosome inherited from Dad, or, inherited from Mom). Human autosomal chromosomes normally come in pairs, and the combination in one individual of these two haplotypes is referred to as a diplotype.
Haplotype block: SNPs that are close enough to one another to be inherited together, ultimately indicating degrees of common ancestry. Haplotype blocks effectively define islands of lower meiotic recombination.
Heritability: The percentage of a trait estimated to be due to the variations you've inherited, as opposed to the contribution of non-genetic influences such as your environment or diet. For example, the heritability of bipolar disorder is estimated to be 70%, which means that genetic variations account for 70% of the overall odds of developing the disorder and non-genetic factors account for 30%.
Heterozygote: As opposed to a homozygote for a given SNP or allele, a heterozygote is a person who inherited different forms from Mom and Dad. Example: at the SNP position known as rs16260, a person who inherits a (C) and an (A) is a rs16260(A;C) heterozygote.
Homozygote: As opposed to a heterozygote for a given SNP or allele, a homozygote is a person who inherits the same form from Mom and Dad. Example: at the SNP position known as rs16260, a person who inherits a (C) from both parents is a rs16260(C;C) homozygote.
In/del: While many SNPs are swaps between the four DNA bases (A,C,G and T as abbreviated), extra DNA bases may be present (called "insertions"), or a few DNA bases may be missing ("deletions"). The term in/del refers to an insertion or deletion of this type.
Incidence: The number of newly diagnosed cases of a disease in a given population over a specified time period; for cancer, the annual incidence is usually specified as the number of (new) cases per 100,000 people.
Individual risk: The risk that you will contract a disease by a certain age, and one of the hardest numbers to estimate. A key factor in determining individual risk is the estimated penetrance of the disease susceptibility, which is just a way to say how much influence all the other factors (including all your other genes, and your lifestyle choices, etc) have compared to, say, one specific SNP, allele or genotype. Examples of genes with highly penetrant variations include the BRCA1 and CF genes.
Lifetime Risk: The risk of developing a given condition sometime during one's life. When calculated for a given population as a whole, it is known as average lifetime risk; in contrast to "your lifetime risk", which is calculated by applying relative risk or odds ratios based on your own genotype(s) to the average risk for your population. See also residual lifetime risk.
Locus (pl. loci): The name for a physical position on the genome. Can either refer to a large region such as a complete gene or a very specific region, like a particular base pair position.
Odds ratio (OR): The ratio of the odds within one group compared to the odds within another group. Although commonly reported for SNP associations with diseases, be wary of the tendency of the OR to overemphasize the effect of a SNP. This is particularly true in cases where the SNP in question is quite rare in both groups, and/or the group sizes themselves are rather small. See also Odds ratio in Wikipedia.
OMIM: OMIM is the Online Mendelian Inheritance in Man database, an online catalog of human genes and genetic disorders.
Phenotype: The traits or conditions you can see, measure, or diagnose, like eye color or breast cancer.
PMID: PubMed Identifier. A standard identifier for scientific articles, as indexed by the US National Library of Medicine.
Polymorphism: A sequence difference at a particular position. The alternative forms are called alleles.
Population attributable fraction: The percentage of cases of a disease in a given population that are theoretically explained by a certain genotype (or cause, such as exposure to a mutagen). To put it another way, this is how many occurences of a disease wouldn't occur if this genotype (or exposure) didn't exist. Example: by itself, even the most significant (SNP) genotype found so far for schizophrenia probably accounts for only 1-2% of schizophrenic diagnoses. Also known as the population attributable risk.
Relative Risk (RR): The ratio of the probability in one group compared to the probability in another group. Although reported less often in SNP studies than odds ratios, the RR is more intuitive (and generally lower). Note that at least one editor of a scientific journal [1] has indicated that when judging whether to publish a paper with a new finding they hope to see an RR of three or more. Note that many SNP publications cited here in SNPedia do not meet this criteria. For a more detailed explanation of RR, see Wikipedia's RR entry.
Residual Lifetime Risk: the risk of developing a given condition taking into account a person's age, in other words, given your age, the odds of developing a condition during the remainder of your lifetime. This is generally calculated as a population average, without taking into account your genotypes. Epidemiological tables often estimate residual lifetime risk in 1 year intervals, and they may also be calculated separately based on year of birth.
rs#: All this reflects is that the SNP in question has been officially registered and given an (rs) identifier by dbSNP, the largest public database of SNPs, maintained by the National Institutes of Health.
Single Nucleotide Polymorphism (SNP; pronounced snip): A precise position along a chromosome where the DNA of different people may vary. Generally two alternate alleles are found at a particular SNP. At least 2,000,000 SNPs are now known and there may be over 30,000,000 in the human genome. The SNPs that have medical or health consequences for you and your loved ones are the focus of SNPedia.
Wild-type: For a given SNP, allele, genotype or gene, the form that was either first discovered or is the most common is considered the reference against which all other forms are compared. This reference form is called the wild-type form.
