Single nucleotide polymorphism: Difference between revisions

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A '''single nucleotide polymorphism''' (SNP) is a potential genetic mutation that occurs in a single spot in the human genome.<ref>{{Cite web|url=https://ghr.nlm.nih.gov/primer/genomicresearch/snp|title=What are single nucleotide polymorphisms (SNPs)?|last=Genetics Home Reference|first=|authorlink=|last2=|first2=|authorlink2=|date=|website=Genetics Home Reference|language=en|archive-url=|archive-date=|dead-url=|access-date=2019-10-03}}</ref>  A single spot in the human genome is represented physically by a particular nucleotide base-pair in the DNA, such as cytosine-guanine or adenine-thymine.  For example, 60% of the general population may have a cytosine-guanine base pair at a particular location in their DNA, but 40% of the population may have a adenine-thymine base pair at that location instead.  SNP's are often represented by an "rs" number, such as "rs53576".<ref>{{Cite web|url=https://www.snpedia.com/index.php/Rs53576|title=rs53576 - SNPedia|website=www.snpedia.com|access-date=2019-10-06}}</ref>
A '''single nucleotide polymorphism''' (SNP) is a potential genetic mutation that occurs in a single spot in the human genome.<ref>{{Cite web|url=https://ghr.nlm.nih.gov/primer/genomicresearch/snp|title=What are single nucleotide polymorphisms (SNPs)?|last=Genetics Home Reference|first=|authorlink=|last2=|first2=|authorlink2=|date=|website=Genetics Home Reference|language=en|archive-url=|archive-date=|dead-url=|access-date=2019-10-03}}</ref>  A single spot in the human genome is represented physically by a particular nucleotide base-pair in the DNA, such as cytosine-guanine or adenine-thymine.  For example, 60% of the general population may have a cytosine-guanine base pair at a particular location in their DNA, but 40% of the population may have a adenine-thymine base pair at that location instead.  SNP's are often represented by an "rs" number, such as "rs53576".<ref>{{Cite web|url=https://www.snpedia.com/index.php/Rs53576|title=rs53576 - SNPedia|website=www.snpedia.com|access-date=2019-10-06}}</ref>
== Autoimmune ==
A 2020 study found two autoimmune-related SNPs associated with ME/CFS patients with an infectious onset.<ref>{{Cite journal|last=Steiner|first=Sophie|last2=Becker|first2=Sonya C.|last3=Hartwig|first3=Jelka|last4=Sotzny|first4=Franziska|last5=Lorenz|first5=Sebastian|last6=Bauer|first6=Sandra|last7=Löbel|first7=Madlen|last8=Stittrich|first8=Anna B.|last9=Grabowski|first9=Patricia|date=2020|title=Autoimmunity-Related Risk Variants in PTPN22 and CTLA4 Are Associated With ME/CFS With Infectious Onset|url=https://www.frontiersin.org/articles/10.3389/fimmu.2020.00578/full|journal=Frontiers in Immunology|language=English|volume=11|doi=10.3389/fimmu.2020.00578|issn=1664-3224}}</ref>
'''PTPN22 rs2476601''' aka R620W or C1858T (OR 1.63, CI 1.04–2.55, p = 0.016) - ''PTPNN22 (Tyrosine phosphatase non-receptor type 22)''
'''CTLA4 rs3087243''' (OR 1.53, CI 1.17–2.03, p = 0.001) - ''CTLA4 (Cytotoxic T-lymphocyte-associated protein 4)''
PTPN22 rs2476601 has been found in multiple autoimmune diseases including Hashimoto's thyroiditis, psoriasis, and Type I diabetes.<ref>{{Cite journal|last=Lee|first=Hye-Soon|last2=Kang|first2=Jungoo|last3=Yang|first3=Seiwon|last4=Kim|first4=Dukhee|last5=Park|first5=Yongsoo|date=2011-11|title=Susceptibility influence of a PTPN22 haplotype with thyroid autoimmunity in Koreans|url=https://pubmed.ncbi.nlm.nih.gov/22069277/|journal=Diabetes/Metabolism Research and Reviews|volume=27|issue=8|pages=878–882|doi=10.1002/dmrr.1265|issn=1520-7560|pmid=22069277}}</ref><ref>{{Cite journal|last=Chen|first=Yu-Fu|last2=Chang|first2=Jeffrey S.|date=2012-08|title=PTPN22 C1858T and the risk of psoriasis: a meta-analysis|url=https://pubmed.ncbi.nlm.nih.gov/22544573/|journal=Molecular Biology Reports|volume=39|issue=8|pages=7861–7870|doi=10.1007/s11033-012-1630-z|issn=1573-4978|pmid=22544573}}</ref><ref>{{Cite journal|last=Steck|first=AK|last2=Baschal|first2=EE|last3=Jasinski|first3=JM|last4=Boehm|first4=BO|last5=Bottini|first5=N|last6=Concannon|first6=P|last7=Julier|first7=C|last8=Morahan|first8=G|last9=Noble|first9=JA|date=2009-12|title=rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805459/|journal=Genes and immunity|volume=10|issue=Suppl 1|pages=S21–S26|doi=10.1038/gene.2009.87|issn=1466-4879|pmc=2805459|pmid=19956096}}</ref>


== Learn more ==
== Learn more ==

Revision as of 02:23, December 26, 2020

A single nucleotide polymorphism (SNP) is a potential genetic mutation that occurs in a single spot in the human genome.[1] A single spot in the human genome is represented physically by a particular nucleotide base-pair in the DNA, such as cytosine-guanine or adenine-thymine. For example, 60% of the general population may have a cytosine-guanine base pair at a particular location in their DNA, but 40% of the population may have a adenine-thymine base pair at that location instead. SNP's are often represented by an "rs" number, such as "rs53576".[2]

Autoimmune[edit | edit source]

A 2020 study found two autoimmune-related SNPs associated with ME/CFS patients with an infectious onset.[3]

PTPN22 rs2476601 aka R620W or C1858T (OR 1.63, CI 1.04–2.55, p = 0.016) - PTPNN22 (Tyrosine phosphatase non-receptor type 22)

CTLA4 rs3087243 (OR 1.53, CI 1.17–2.03, p = 0.001) - CTLA4 (Cytotoxic T-lymphocyte-associated protein 4)

PTPN22 rs2476601 has been found in multiple autoimmune diseases including Hashimoto's thyroiditis, psoriasis, and Type I diabetes.[4][5][6]

Learn more[edit | edit source]

References[edit | edit source]

  1. Genetics Home Reference. "What are single nucleotide polymorphisms (SNPs)?". Genetics Home Reference. Retrieved October 3, 2019. Cite has empty unknown parameter: |dead-url= (help)
  2. "rs53576 - SNPedia". www.snpedia.com. Retrieved October 6, 2019.
  3. Steiner, Sophie; Becker, Sonya C.; Hartwig, Jelka; Sotzny, Franziska; Lorenz, Sebastian; Bauer, Sandra; Löbel, Madlen; Stittrich, Anna B.; Grabowski, Patricia (2020). "Autoimmunity-Related Risk Variants in PTPN22 and CTLA4 Are Associated With ME/CFS With Infectious Onset". Frontiers in Immunology. 11. doi:10.3389/fimmu.2020.00578. ISSN 1664-3224.
  4. Lee, Hye-Soon; Kang, Jungoo; Yang, Seiwon; Kim, Dukhee; Park, Yongsoo (2011-11). "Susceptibility influence of a PTPN22 haplotype with thyroid autoimmunity in Koreans". Diabetes/Metabolism Research and Reviews. 27 (8): 878–882. doi:10.1002/dmrr.1265. ISSN 1520-7560. PMID 22069277. Check date values in: |date= (help)
  5. Chen, Yu-Fu; Chang, Jeffrey S. (2012-08). "PTPN22 C1858T and the risk of psoriasis: a meta-analysis". Molecular Biology Reports. 39 (8): 7861–7870. doi:10.1007/s11033-012-1630-z. ISSN 1573-4978. PMID 22544573. Check date values in: |date= (help)
  6. Steck, AK; Baschal, EE; Jasinski, JM; Boehm, BO; Bottini, N; Concannon, P; Julier, C; Morahan, G; Noble, JA (2009-12). "rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype". Genes and immunity. 10 (Suppl 1): S21–S26. doi:10.1038/gene.2009.87. ISSN 1466-4879. PMC 2805459. PMID 19956096. Check date values in: |date= (help)