Genotype

A genotype is the genetic makeup (set of genes) of an individual organism or cell. The expression of this genetic information is known as the phenotype, which is the total of observable characteritics of the individual, including anatomical, physiological, biochemical, and behavioral (Mayr 2001). The phenotypic traits expressed by an individual essentially results from interaction of the inherited genotype and the environment, with the genotype determining the potential and limitations of that phenotype. There may also any influence from epigenetic factors, those changes in genome function that do not alter the nucleotide sequence within the DNA.

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 individuals' genotype. Hence, scientists and doctors sometimes talk for example about the (geno)type of a particular cancer, thus separating the disease from the diseased. While codons for different amino acids may change in a random mutation (changing the sequence coding a gene), this doesn't necessarily alter the phenotype.

Genotype and genomic sequence

Main article: Genome

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).

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:

1. 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).
2. 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 refers to the physical appearance

An 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, hemophilia. Sometimes people who do not have hemophilia can have children with the disease, because the parents each "carried" hemophilia genes in their body, even though these genes have no effect on the parents' health. The parents in this case are called carriers. Healthy people who are not carriers and healthy people who are carriers of the hemophilia gene have the same outer appearance (i.e. they do not have the disease), therefore they are said to have the same phenotype. However, the carriers have the gene and the other healthy people do not (they have different genotypes).

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

Main articles: Genetic programming and evolutionary algorithm

Inspired by the biological concept and usefulness of genotypes, computer science employs simulated genotypes in genetic programming and evolutionary algorithms. Such techniques can help evolve mathematical solutions to certain types of otherwise difficult problems.

Determining Genotype

Main article: Genotyping

Genotyping is the process of ellucidating the genotype of an individual with a biological assay. Also known as a genotypic assay, techniques include PCR, DNA Fragment Analysis, sequencing, and hybridization to microarrays or beads. Several common genotyping techniques include Restriction Fragment Length Polymorphism (RFLP), Terminal Restriction Fragment Length Polymorphism (t-RFLP)[1], Amplified Fragment Length Polymorphisms (AFLP)[2], and Multiplex Ligation-dependent Probe Amplification (MLPA)[3]. DNA fragment analysis can also be used to determine such disease causing genetics abberations as Microsatellite Instability (MSI)[4], Trisomy [5] or Aneuploidy, and Loss of Heterozygosity (LOH)[6]. 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.

References

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