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Wikipedia

Genotyping

February 16, 2024

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 edit

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 edit

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 edit

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 edit

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 edit

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 edit

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 edit

References edit

  1. ^ "Genotyping definition". NIH. 2011-09-21. Retrieved 2011-09-21.
  2. ^ . Illumina.com. Archived from the original on 2011-04-16. Retrieved 2010-12-04.
  3. ^ a b 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. ^ a b c Mathaiyan, Jayanthi; Chandrasekaran, Adithan; Davis, Sanish (2013). "Ethics of genomic research". Perspectives in Clinical Research. 4 (1): 100–104. doi:10.4103/2229-3485.106405. ISSN 2229-3485. PMC 3601693. PMID 23533991.
  5. ^ 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. PMID 14986202.
  6. ^ a b c 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". Microbiology Spectrum. 6 (5). doi:10.1128/microbiolspec.MTBP-0002-2016. ISSN 2165-0497. PMID 30338753. S2CID 53016602.
  7. ^ a b c Scheben, 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. ISSN 1467-7652. PMC 5258866. PMID 27696619.

External links edit

  • International HapMap Project 2014-04-16 at the Wayback Machine
  • resources for genotyping microorganisms

February 16, 2024
genotyping, process, determining, differences, genetic, make, genotype, individual, examining, individual, sequence, using, biological, assays, comparing, another, individual, sequence, reference, sequence, reveals, alleles, individual, inherited, from, their,. 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 Contents 1 Techniques 2 Applications 2 1 Human genotyping 2 1 1 Ethical concerns 2 1 2 Tuberculosis 2 2 Agricultural Usage 3 See also 4 References 5 External linksTechniques editCurrent 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 editGenotyping 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 edit 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 edit 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 edit 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 edit 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 editMendelian error Error in the mendelian inheritance Quantitative trait locus DNA locus associated with variation in a quantitative trait SNP genotyping Measurement of genetic variationsReferences edit Genotyping definition NIH 2011 09 21 Retrieved 2011 09 21 Genotyping at Illumina Inc Illumina com Archived from the original on 2011 04 16 Retrieved 2010 12 04 a b 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 a b c Mathaiyan Jayanthi Chandrasekaran Adithan Davis Sanish 2013 Ethics of genomic research Perspectives in Clinical Research 4 1 100 104 doi 10 4103 2229 3485 106405 ISSN 2229 3485 PMC 3601693 PMID 23533991 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 PMID 14986202 a b c Garcia De Viedma Dario Perez Lago Laura 2018 09 07 Baquero Fernando Bouza Emilio Gutierrez 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 ISSN 2165 0497 PMID 30338753 S2CID 53016602 a b c Scheben 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 ISSN 1467 7652 PMC 5258866 PMID 27696619 External links editInternational HapMap Project Archived 2014 04 16 at the Wayback Machine resources for genotyping microorganisms Retrieved from https en wikipedia org w index php title Genotyping amp oldid 1188137343, wikipedia, wiki, book, books, library,

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