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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 allelic forms, dominant A and recessive a, and there are three possible genotypes- AA (homozygous dominant), Aa (heterozygous), and aa (homozygous recessive).
Non-hereditary DNA mutations are not classically understood as representing the individuals' genotype. Hence, scientists and doctors sometimes talk for example about the (geno)type of a particular cancer, that is the genotype of the disease as distinct from the diseased.
Genotype and genomic sequence
- Main article: Genome
One's genotype differs subtly from one's genomic sequence. A sequence is not 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).
Genotype and phenotype
- Main article: Phenotype
Any given gene will usually cause an observable change in an organism, known as the phenotype. The terms genotype and phenotype are distinct for at least two reasons:
- To distinguish the source of an observer's knowledge (one can know about genotype by observing DNA; one can know about phenotype by observing outward appearance of an organism).
- Genotype and phenotype are not always directly correlated. Some genes only express a given phenotype in certain environmental conditions. Conversely, some phenotypes could be the result of multiple genotypes. The genotype is commonly mixed up with the Phenotype which describes the end result of both the genetic and the environmental factors giving the observed expression (e.g. blue eyes, hair colour, or various hereditary diseases).
A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see Gregor Mendel). There are three available genotypes, PP (homozygous dominant), Pp (heterozygous), and pp (homozygous recessive). All three have different genotypes but the first two have the same phenotype (purple) as distinct from the third (white).
A more technical example to illustrate genotype is the single nucleotide polymorphism or SNP. A SNP occurs when corresponding sequences of DNA from different individuals differ at one DNA base, for example where the sequence AAGCCTA changes to AAGCTTA. This contains two alleles : C and T. SNPs typically have three genotypes, denoted generically AA Aa and aa. In the example above, the three genotypes would be CC, CT and TT. Other types of genetic marker, such as microsatellites, can have more than two alleles, and thus many different genotypes.
Genotype and Mendelian inheritance
- Main article: Mendelian inheritance
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.
Genotype and genetics
- Main article: Genetics
With careful experimental design, one can use statistical methods to correlate differences in the genotypes of populations with differences in their observed phenotype. These genetic association studies can be used to determine the genetic risk factors associated with a disease. They may even be able to differentiate between populations who may or may not respond favorably to a particular drug treatment. Such an approach is known as personalized medicine or pharmacogenetics.
Genotype and mathematics
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.
- Main article: Genotyping
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, ASO probes, sequencing, and nucleic acid hybridization to microarrays or beads. Several common genotyping techniques include Restriction Fragment Length Polymorphism (RFLP), Terminal Restriction Fragment Length Polymorphism (t-RFLP), Amplified Fragment Length Polymorphisms (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.
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