The genotype is the genetic constitution of a cell, an organism, or an individual (i.e. the specific allele makeup of the individual) usually with reference to a specific character under consideration. For instance, the human albino gene has two recessive alleles, recessive a and recessive a. It is a generally accepted theory that inherited genotype, transmitted epigenetic factors, and non-hereditary environmental variation contribute to the phenotype of an individual.
Non-hereditary DNA mutations are not classically understood as representing the individual's genotype. Hence, scientists and physicians sometimes talk for example about the (geno)type of a particular cancer, that is the genotype of the disease as distinct from the diseased.
One's genotype differs subtly from one's genomic sequence. A sequence is an absolute measure of base composition of an individual, or a representative of a species or group; a genotype typically implies a measurement of how an individual differs or is specialized within a group of individuals or a species. So typically, one refers to an individual's genotype with regard to a particular gene of interest and, in polyploid individuals, it refers to what combination of alleles the individual carries (see homozygous, heterozygous).
The distinction between genotype and phenotype is commonly experienced when studying family patterns for certain hereditary diseases or conditions, for example, haemophilia. Due to the diploidy of humans (and most animals), there are two alleles for any given gene. These alleles can be the same (homozygous) or different (heterozygous), depending on the individual (see zygote). With a dominant allele, the offspring is guaranteed to inherit the trait in question irrespective of the second allele.
With a recessive allele, the phenotype depends upon the other allele. In the case of haemophilia and similarly recessive diseases a heterozygous individual is a carrier. This person has a normal phenotype but runs a 50-50 risk of passing his or her abnormal gene on to offspring. A homozygous dominant individual has a normal phenotype and no risk of abnormal offspring. A homozygous recessive individual has an abnormal phenotype and is guaranteed to pass the abnormal gene onto offspring.
Inspired by the biological concept and usefulness of genotypes, computer science employs simulated phenotypes in genetic programming and evolutionary algorithms. Such techniques can help evolve mathematical solutions to certain types of otherwise difficult problems.
Genotyping is the process of elucidating the genotype of an individual with a biological assay. Also known as a genotypic assay, techniques include PCR, DNA fragment analysis, allele specific oligonucleotide (ASO) probes, DNA sequencing, and nucleic acid hybridization to DNA microarrays or beads. Several common genotyping techniques include restriction fragment length polymorphism (RFLP), terminal restriction fragment length polymorphism (t-RFLP), amplified fragment length polymorphism (AFLP), and multiplex ligation-dependent probe amplification (MLPA).
DNA fragment analysis can also be used to determine such disease causing genetics aberrations as microsatellite instability (MSI), trisomy or aneuploidy, and loss of heterozygosity (LOH). MSI and LOH in particular have been associated with cancer cell genotypes for colon, breast and cervical cancer.
The most common chromosomal aneuploidy is a trisomy of chromosome 21 which manifests itself as Down syndrome. Current technological limitations typically allow only a fraction of an individual’s genotype to be determined efficiently.