Genotyping
Genotypingis the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual'sDNAsequence usingbiological assaysand comparing it to another individual's sequence or a reference sequence. It reveals theallelesan individual has inherited from their parents.[1]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.
Techniques
[edit]Current methods of genotyping includerestriction fragment length polymorphismidentification (RFLPI) of genomic DNA,random amplified polymorphic detection(RAPD) of genomic DNA,amplified fragment length polymorphismdetection (AFLPD),polymerase chain reaction(PCR),DNA sequencing,allele specific oligonucleotide(ASO) probes, andhybridizationtoDNA microarraysor 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, such as with (epi)GBS (Genotyping by sequencing) orRADseq.New[2]mass-sequencing technologiespromise to provide whole-genome genotyping (orwhole genome sequencing) in the future.
Applications
[edit]Genotyping applies to a broad range of individuals, including microorganisms. For example,virusesandbacteriacan 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 asmolecular epidemiologyorforensicmicrobiology.
Human genotyping
[edit]Humans can also be genotyped. For example, when testing fatherhood or motherhood, scientists typically only need to examine 10 or 20 genomic regions (likesingle-nucleotide polymorphism(SNPs)), which represent a tiny fraction of the humangenome.
When genotypingtransgenicorganisms, a single genomic region may be all that needs to be examined to determine the genotype. A singlePCRassay is typically enough to genotype a transgenicmouse;the mouse is themammalianmodel of choice for much of medical research today.
Ethical concerns
[edit]The ethical concerns of genotyping humans have been a topic of discussion. The rise of genotyping technologies will make it possible toscreenlarge populations of people forgenetic diseasesand predispositions for disease.[3]The benefits of population wide genotyping have been contended by ethical concerns on consent and general benefit of wide span screening.[3]Genotyping identifiesmutationsthat increase susceptibility of a person to develop a disease, but disease development is not guaranteed in most cases, which can cause psychological damage.[4]Discriminationcan arise from various genetic markers identified by genotyping, such as athletic advantages or disadvantages in professional sports or risk of disease development later in life.[5][4]Much of the ethical concerns surrounding genotyping arise from information availability, as in who can access thegenotypeof an individual in various contexts.[4]
Tuberculosis
[edit]Genotyping is used in the medical field to identify and control the spread oftuberculosis(TB). Originally, genotyping was only used to confirm outbreaks of tuberculosis; but with the evolution of genotyping technology it is now able to do far more. Advances in genotyping technology led to the realization that many cases of tuberculosis, including infected individuals living in the same household, were not actually linked.[6]This caused the formation of universal genotyping in an attempt to understand transmission dynamics. Universal genotyping revealed complex transmission dynamics based on things like socio-epidemiological factors. This led to the use of polymerase chain reactions (PCR) which allowed for faster detection of tuberculosis. This rapid detection method is used to prevent TB.[6]The addition of whole genome sequencing (WGS) allowed for identification of strains of TB which could then be put in a chronological cluster map. These cluster maps show the origin of cases and the time in which those cases arose. This gives a much clearer picture of transmission dynamics and allows for better control and prevention of transmission. All of these different forms of genotyping are used together to detect TB, prevent its spread and trace the origin of infections. This has helped to reduce the number of TB cases.[6]
Agricultural Usage
[edit]Many types of genotyping are used inagriculture.One type that is used is genotyping by sequencing because it aids agriculture with crop breeding. For this purpose, single nucleotide polymorphisms (SNPs) are used as markers andRNA sequencingis used to look at gene expression in crops.[7]The knowledge gained from this type of genotyping allows for selective breeding of crops in ways which benefit agriculture. In the case of alfalfa, the cell wall was improved through selective breeding that was made possible by this type of genotyping.[7]These techniques have also resulted in the discovery of genes that provide resistance to diseases. A gene called Yr15 was discovered in wheat, which protects against a disease called yellow wheat rust. Selective breeding for the Yr15 gene then prevented yellow wheat rust, benefiting agriculture.[7]
See also
[edit]- Mendelian error– Error in the mendelian inheritance
- Quantitative trait locus– DNA locus associated with variation in a quantitative trait
- SNP genotyping– Measurement of genetic variations
References
[edit]- ^"Genotyping definition".NIH. 2011-09-21.Retrieved2011-09-21.
- ^"Genotyping at Illumina, Inc".Illumina. Archived fromthe originalon 2011-04-16.Retrieved2010-12-04.
- ^abHall, Alison Elizabeth (2013). "What ethical and legal principles should guide the genotyping of children as part of a personalised screening programme for common cancer?".Journal of Medical Ethics.
- ^abcMathaiyan, Jayanthi; Chandrasekaran, Adithan; Davis, Sanish (2013)."Ethics of genomic research".Perspectives in Clinical Research.4(1): 100–104.doi:10.4103/2229-3485.106405.ISSN2229-3485.PMC3601693.PMID23533991.
- ^Lippi, Giuseppe (2004)."Athletes Genotyping: Ethical and Legal Issues".International Journal of Sports Medicine.25(2): 159, author reply 160–1.doi:10.1055/s-2004-819956.PMID14986202.
- ^abcGarcía De Viedma, Darío; Pérez-Lago, Laura (2018-09-07). Baquero, Fernando; Bouza, Emilio; Gutiérrez-Fuentes, J.A.; Coque, Teresa M. (eds.)."The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis".Microbiology Spectrum.6(5).doi:10.1128/microbiolspec.MTBP-0002-2016.ISSN2165-0497.PMID30338753.S2CID53016602.
- ^abcScheben, Armin; Batley, Jacqueline; Edwards, David (2017)."Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application".Plant Biotechnology Journal.15(2): 149–161.doi:10.1111/pbi.12645.ISSN1467-7652.PMC5258866.PMID27696619.