Genotyping

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.[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
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 microarrays 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, such as with (epi)GBS (Genotyping by sequencing) or RADseq. New [2] mass-
sequencing technologies promise to provide whole-genome genotyping (or whole genome sequencing) in
the future.

Applications
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.

Human genotyping
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)), which
represent a tiny fraction of the human genome.

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 mammalian model of choice for much of medical research today.

Ethical concerns
The ethical concerns of genotyping humans have been a topic of discussion. The rise of genotyping
technologies will make it possible to screen large populations of people for genetic diseases and
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 identifies mutations that
increase susceptibility of a person to develop a disease, but disease development is not guaranteed in
most cases, which can cause psychological damage.[4] Discrimination can 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 the genotype of an individual in various contexts.[4]

Tuberculosis
Genotyping is used in the medical field to identify and control the spread of tuberculosis (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
Many types of genotyping are used in agriculture. 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 and RNA sequencing is 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
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
1. "Genotyping definition" ([Link] NIH. 2011-09-21.
Retrieved 2011-09-21.
 2. "Genotyping at Illumina, Inc" ([Link]
[Link]/applications/detail/snp_genotyping_and_cnv_analysis/whole_genome_genotyping_
and_copy_number_variation_analysis.ilmn). [Link]. Archived from the original (http://
[Link]/applications/detail/snp_genotyping_and_cnv_analysis/whole_genome_ge
notyping_and_copy_number_variation_analysis.ilmn) on 2011-04-16. Retrieved
2010-12-04.
3. Hall, 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.
4. Mathaiyan, Jayanthi; Chandrasekaran, Adithan; Davis, Sanish (2013). "Ethics of genomic
research" ([Link] Perspectives in Clinical
Research. 4 (1): 100–104. doi:10.4103/2229-3485.106405 ([Link]
-3485.106405). ISSN 2229-3485 ([Link]
PMC 3601693 ([Link] PMID 23533991
([Link]
5. Lippi, Giuseppe (2004). "Athletes Genotyping: Ethical and Legal Issues" ([Link]
[Link]/publication/7529881). International Journal of Sports Medicine. 25 (2): 159,
author reply 160–1. doi:10.1055/s-2004-819956 ([Link]
6). PMID 14986202 ([Link]
6. García 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" ([Link]
[Link]/doi/10.1128/[Link]-0002-2016). Microbiology Spectrum. 6 (5).
doi:10.1128/[Link]-0002-2016 ([Link]
BP-0002-2016). ISSN 2165-0497 ([Link]
PMID 30338753 ([Link] S2CID 53016602 ([Link]
[Link]/CorpusID:53016602).
7. Scheben, Armin; Batley, Jacqueline; Edwards, David (2017). "Genotyping-by-sequencing
approaches to characterize crop genomes: choosing the right tool for the right application"
([Link] Plant Biotechnology Journal. 15
(2): 149–161. doi:10.1111/pbi.12645 ([Link] ISSN 1467-
7652 ([Link] PMC 5258866 ([Link]
gov/pmc/articles/PMC5258866). PMID 27696619 ([Link]
9).

External links
International HapMap Project ([Link] Archived ([Link]
b/20140416084248/[Link] 2014-04-16 at the Wayback Machine
resources for genotyping microorganisms ([Link]

Retrieved from "[Link]