Genotyping
Encyclopedia
Genotyping is the process of determining differences in the genetic make-up (genotype
) of an individual by examining the individual's DNA
sequence using biological assays
and comparing it to another individual's sequence or a reference sequence. It reveals the alleles
an individual has inherited from their parents . Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.
Current methods of genotyping include restriction fragment length polymorphism
identification (RFLPI) of genomic DNA, random amplified polymorphic detection
(RAPD) of genomic DNA, amplified fragment length polymorphism
detection (AFLPD), polymerase chain reaction
(PCR), DNA sequencing
, allele specific oligonucleotide
(ASO) probes, and hybridization
to DNA microarray
s or beads. Genotyping is important in research of genes and gene variants associated with disease. Due to current technological limitations, almost all genotyping is partial. That is, only a small fraction of an individual’s genotype is determined. New mass-sequencing technologies promise to provide whole-genome genotyping (or whole genome sequencing) in the future.
Genotyping applies to a broad range of individuals, including microorganisms. For example, viruses and bacteria
can be genotyped. Genotyping in this context may help in controlling the spreading of pathogens, by tracing the origin of outbreaks. This area is often referred to as molecular epidemiology
or forensic microbiology
.
Humans can also be genotyped. For example, when testing fatherhood or motherhood, scientists typically only need to examine 10 or 20 genomic regions (like single-nucleotide polymorphism (SNPs)). That is a tiny fraction of the human genome
, which consists of three billion or so nucleotide
s.
When genotyping transgenic organisms, a single genomic region may be all that needs to be examined to determine the genotype. A single PCR assay is typically enough to genotype a transgenic mouse
; the mouse is the mammal
ian model of choice for much of medical research today.
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...
) of an individual by examining the individual's DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
sequence using biological assays
Bioassay
Bioassay , or biological standardization is a type of scientific experiment. Bioassays are typically conducted to measure the effects of a substance on a living organism and are essential in the development of new drugs and in monitoring environmental pollutants...
and comparing it to another individual's sequence or a reference sequence. It reveals the alleles
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
an individual has inherited from their parents . Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.
Current methods of genotyping include restriction fragment length polymorphism
Restriction fragment length polymorphism
In molecular biology, restriction fragment length polymorphism, or RFLP , is a technique that exploits variations in homologous DNA sequences. It refers to a difference between samples of homologous DNA molecules that come from differing locations of restriction enzyme sites, and to a related...
identification (RFLPI) of genomic DNA, random amplified polymorphic detection
RAPD
RAPD stands for random amplification of polymorphic DNA. It is a type of PCR reaction, but the segments of DNA that are amplified are random. The scientist performing RAPD creates several arbitrary, short primers , then proceeds with the PCR using a large template of genomic DNA, hoping that...
(RAPD) of genomic DNA, amplified fragment length polymorphism
Amplified fragment length polymorphism
Amplified Fragment Length Polymorphism PCR is a PCR-based tool used in genetics research, DNA fingerprinting, and in the practice of genetic engineering. Developed in the early 1990s by Keygene, AFLP uses restriction enzymes to digest genomic DNA, followed by ligation of adaptors to the sticky...
detection (AFLPD), polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
(PCR), DNA sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
, allele specific oligonucleotide
Allele specific oligonucleotide
An allele-specific oligonucleotide is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay...
(ASO) probes, and hybridization
Sequencing by Hybridization
Sequencing by Hybridization is a class of methods for determining the order in which nucleotides occur on a strand of DNA. Typically used for looking for small changes relative to a known DNA sequence....
to DNA microarray
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
s or beads. Genotyping is important in research of genes and gene variants associated with disease. Due to current technological limitations, almost all genotyping is partial. That is, only a small fraction of an individual’s genotype is determined. New mass-sequencing technologies promise to provide whole-genome genotyping (or whole genome sequencing) in the future.
Genotyping applies to a broad range of individuals, including microorganisms. For example, viruses and bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
can be genotyped. Genotyping in this context may help in controlling the spreading of pathogens, by tracing the origin of outbreaks. This area is often referred to as molecular epidemiology
Molecular epidemiology
Molecular epidemiology is a branch of medical science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of disease within families and across populations. This field has emerged from...
or forensic microbiology
Microbiology
Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
.
Humans can also be genotyped. For example, when testing fatherhood or motherhood, scientists typically only need to examine 10 or 20 genomic regions (like single-nucleotide polymorphism (SNPs)). That is a tiny fraction of the human genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, which consists of three billion or so nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s.
When genotyping transgenic organisms, a single genomic region may be all that needs to be examined to determine the genotype. A single PCR assay is typically enough to genotype a transgenic mouse
Mouse
A mouse is a small mammal belonging to the order of rodents. The best known mouse species is the common house mouse . It is also a popular pet. In some places, certain kinds of field mice are also common. This rodent is eaten by large birds such as hawks and eagles...
; the mouse is the mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
ian model of choice for much of medical research today.
See also
- Mendelian errorMendelian errorA Mendelian error in the genetic analysis of a species, describes an allele in an individual which could not have been received from either of its biological parents by Mendelian inheritance. Inheritance is defined by a set of related individuals who have the same or similar phenotypes for a locus...
- Quantitative trait locusQuantitative trait locusQuantitative traits refer to phenotypes that vary in degree and can be attributed to polygenic effects, i.e., product of two or more genes, and their environment. Quantitative trait loci are stretches of DNA containing or linked to the genes that underlie a quantitative trait...
- SNP genotypingSNP genotypingSNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms between members of a species. It is a form of genotyping, which is the measurement of more general genetic variation. SNPs are one of the most common types of genetic variation...
External links
- Delaware Valley Personalized Medicine Project Uses genotyping to make medicine personal
- Mouse Genotype Affordable high quality mouse genotyping service
- Rat Genotype Affordable high quality rat genotyping service
- Gene Typer High throughput PCR mouse genotyping service
- International HapMap Project
- UCLA Genotyping Core
- resources for genotyping microorganisms