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- Single nucleotide polymorphisms
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- single nucleotide polymorphisms
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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2018/02/24 16:24:23」(JST)
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ある生物種集団のゲノム塩基配列中に一塩基が変異した多様性が見られ、その変異が集団内で1%以上の頻度で見られる時、これを一塩基多型（いちえんき・たけい、SNP : Single Nucleotide Polymorphism）と呼ぶ。従って、対立遺伝子頻度がこれより低いときに使用するのは基本的に誤りで、そのような物は突然変異と呼ばれる（参照:多型）。ある一つの塩基が別の塩基に置換されて起きるため、一つのSNPには置換前と置換後の二種類の対立遺伝子しか見つからないことが多い。が、まれに3から4個の対立遺伝子があるSNPもある。複数形でSNPs（スニップスと発音）と呼ばれることもある。SNPの起源は中立進化説がいうように、種の分化後にランダムに発生したものだと考えられている。
SNPはSingle Nucleotide Poplymorphismの略とされているが、実際にこの用語が使用される場面では1塩基に限らず、2塩基から十数塩基程度の短い置換、挿入、欠失を含むデータを指している場合も多い。また、1%以上の頻度のものをSNPと呼ぶというルールも目安であり、現在では1%を閾値とする場合が多いが、5%が目安とされる場合もある。無作為抽出のサンプル数が少ない場合には、サンプリングをやりなおすと前回は1%以上であったSNPが1%以下になってしまうということもあり、厳密に1%という定義に意味があるわけではなく、commonに観察されることが期待される短い変異、程度の意味で使われることが多い[1]。
ヒトの染色体にはおよそ30億の塩基対があるが、その配列は個人間（相同染色体間）で異なっている。その量は1000塩基に1つ程度である。SNP をDNAマーカーとして利用すると遺伝的背景を調べることができる他、原因遺伝子のわかっている遺伝病については、将来的な危険率も診断することができる。また、SNP を利用した連鎖解析や関連解析によって疾患関連遺伝子の特定が行えると期待されている。 検出法としては古くは制限酵素断片長多型法（RFLP法）が用いられたが、操作が煩雑で長時間を要する上、SNP部位近辺の塩基配列によっては解析不可能な場合が多いなど、臨床検査の現場で使用するには問題の多いことが指摘されてきた。そこで近年では、より簡便で汎用性のある手法としてInvader法、TaqMan PCR法、一塩基伸長法、Pyrosequencing法、Exonuclease Cycling Assay法など種々の方法が開発されている。 アルコールに対する強さなどの遺伝的な要因は、主にアルデヒドデヒドロゲナーゼ遺伝子(ALDH2)の SNP に依存することが知られている。臨床での応用が期待される遺伝子のSNPも近年多く見出されており、多くの薬剤代謝に関与する酵素チトクロームP450（CYP）のファミリーや抗結核薬イソニアジドの代謝に関与するN-acetyltransferase 2 (NAT-2)、経口抗凝固剤ワーファリンの効果の強さに大きく影響するCYP2C9とVKORC1などがそれである。これらの遺伝子にその酵素活性を低下させるようなSNPがあると、薬剤の血中濃度が長時間に渡って高く保たれた結果、効果が強く発現したり、有毒な中間代謝産物が蓄積されたりすることがある。また、薬剤がうまく働くことのできないようなSNPがあると、投薬量を増やすなどの処置が必要となる。そこで、投薬前にこのような遺伝子のSNPを検査し、その遺伝子の型から判断して適切な薬剤の投薬量を決定するなどして、副作用を回避し、効率的な治療効果を得ようとする医療、すなわち、遺伝情報による患者個々の体質に応じたより適切な医療は「テーラーメイド医療」、「オーダメイド医療」、あるいは「個別化医療」と呼ばれており、これによって患者が無用の副作用によって苦しむことが減り、また、無用な副作用への対処や不適切な投薬を減らすことによって医療費削減への効果も期待できる。このように、SNPを利用した診断の実用化と普及が大いに期待されている。
DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (a C/T polymorphism).
外部リンク
- ゲノムの個人差とは―SNPをめぐる話
出典
- ^ István Albert (2016年12月7日), “The Biostar Handbook: A Beginner's Guide to Bioinformatics” (プレスリリース), https://read.biostarhandbook.com/
関連項目
- 偽遺伝子
- ジャンクDNA
- 熱中症
- インフルエンザ脳症
| この項目は、生物学に関連した書きかけの項目です。この項目を加筆・訂正などしてくださる協力者を求めています（プロジェクト:生命科学／Portal:生物学）。 |
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The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a C/A polymorphism)
A single-nucleotide polymorphism, often abbreviated to SNP (/snɪp/; plural /snɪps/), is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population (e.g. > 1%).[1]
For example, at a specific base position in the human genome, the C nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is an SNP at this specific position, and the two possible nucleotide variations – C or A – are said to be alleles for this position.
SNPs underlie differences in our susceptibility to disease; a wide range of human diseases, e.g. sickle-cell anemia, β-thalassemia and cystic fibrosis result from SNPs.[2][3][4] The severity of illness and the way our body responds to treatments are also manifestations of genetic variations. For example, a single-base mutation in the APOE (apolipoprotein E) gene is associated with a higher risk for Alzheimer's disease.[5]
A single-nucleotide variant (SNV) is a variation in a single nucleotide without any limitations of frequency and may arise in somatic cells. A somatic single-nucleotide variation (e.g., caused by cancer) may also be called a single-nucleotide alteration.
Contents
- 1 Types
- 2 Applications of SNPs
- 3 Frequency
- 3.1 Within a genome
- 3.2 Within a population
- 4 Importance
- 4.1 Biomedical research
- 4.2 Forensics
- 4.3 Pharmacogenetics
- 4.4 Disease
- 5 Examples
- 6 Databases
- 7 Nomenclature
- 8 SNP analysis
- 9 Programs for prediction of SNP effects
- 10 See also
- 11 Notes
- 12 References
- 13 External links
Types
| Types of SNPs |
|---|
|
Types of single-nucleotide polymorphism (SNPs)
Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions (regions between genes). SNPs within a coding sequence do not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code.
SNPs in the coding region are of two types: synonymous and nonsynonymous SNPs. Synonymous SNPs do not affect the protein sequence, while nonsynonymous SNPs change the amino acid sequence of protein. The nonsynonymous SNPs are of two types: missense and nonsense.
SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of noncoding RNA. Gene expression affected by this type of SNP is referred to as an eSNP (expression SNP) and may be upstream or downstream from the gene.
Applications of SNPs
- Association studies can determine whether a genetic variant is associated with a disease or trait.[6]
- A tag SNP is a representative single-nucleotide polymorphism (SNP's) in a region of the genome with high linkage disequilibrium (the non-random association of alleles at two or more loci). Tag SNPs are useful in whole-genome SNP association studies, in which hundreds of thousands of SNPs across the entire genome are genotyped.
- Haplotype mapping: sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs.
- Linkage disequilibrium (LD), a term used in population genetics, indicates non-random association of alleles at two or more loci, not necessarily on the same chromosome. It refers to the phenomenon that SNP allele or DNA sequence that are close together in the genome tend to be inherited together. LD is affected by two parameters: 1) The distance between the SNPs [the larger the distance, the lower the LD]. 2) Recombination rate [the lower the recombination rate, the higher the LD].[7]
Frequency
Within a genome
The genomic distribution of SNPs is not homogenous; SNPs occur in non-coding regions more frequently than in coding regions or, in general, where natural selection is acting and "fixing" the allele (eliminating other variants) of the SNP that constitutes the most favorable genetic adaptation.[8] Other factors, like genetic recombination and mutation rate, can also determine SNP density.[9]
SNP density can be predicted by the presence of microsatellites: AT microsatellites in particular are potent predictors of SNP density, with long (AT)(n) repeat tracts tending to be found in regions of significantly reduced SNP density and low GC content.[10]
Within a population
There are variations between human populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another. Within a population, SNPs can be assigned a minor allele frequency — the lowest allele frequency at a locus that is observed in a particular population. This is simply the lesser of the two allele frequencies for single-nucleotide polymorphisms.
Importance
Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also critical for personalized medicine.[11]
Biomedical research
SNPs' greatest importance in biomedical research is for comparing regions of the genome between cohorts (such as with matched cohorts with and without a disease) in genome-wide association studies. SNPs have been used in genome-wide association studies as high-resolution markers in gene mapping related to diseases or normal traits. SNPs without an observable impact on the phenotype (so called silent mutations) are still useful as genetic markers in genome-wide association studies, because of their quantity and the stable inheritance over generations.[12]
Forensics
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SNPs were used initially for matching a forensic DNA sample to a suspect but it has been phased out with development of STR-based DNA fingerprinting techniques.[13] In the future SNPs may be used in forensics for some phenotypic clues like eye color, hair color, ethnicity etc. Kidd et al. have demonstrated that a panel of 19 SNPs can identify the ethnic group with good probability of match (Pm = 10^-7) in 40 population groups studied.[14] One example of how this might potentially be useful is in the area of artistic reconstruction of possible premortem appearances of skeletonized remains of unknown individuals. Although a facial reconstruction can be fairly accurate based strictly upon anthropological features, other data that might allow a more accurate representation include eye color, skin color, hair color, etc.
In a situation with a low amount of forensic sample or a degraded sample, SNP methods can be a good alternative to STR methods due to the abundance of potential markers, amenability to automation, and potential reduction of required fragment length to only 60-80 bp.[15] In the absence of a STR match in DNA profile database; different SNPs can be used to get clues regarding ethnicity, phenotype, lineage, and even identity.
Pharmacogenetics
Some SNPs are associated with the metabolism of different drugs.[16][17][18] The association of a wide range of human diseases like cancer, infectious diseases (AIDS, leprosy, hepatitis, etc.) autoimmune, neuropsychiatric and many other diseases with different SNPs can be made as relevant pharmacogenomic targets for drug therapy.[19]
Disease
A single SNP may cause a Mendelian disease, though for complex diseases, SNPs do not usually function individually, rather, they work in coordination with other SNPs to manifest a disease condition as has been seen in Osteoporosis.[20] One of the earliest successes in this field was finding a single base mutation in the non-coding region of the APOC3 (apolipoprotein C3 gene) that associated with higher risks of hypertriglyceridemia and atherosclerosis (see David J. Galton Lancet 1983 pp444-446).
All types of SNPs can have an observable phenotype or can result in disease:
- SNPs in non-coding regions can manifest in a higher risk of cancer,[21] and may affect mRNA structure and disease susceptibility.[22] Non-coding SNPs can also alter the level of expression of a gene, as an eQTL (expression quantitative trait locus).
- SNPs in coding regions:
- synonymous substitutions by definition do not result in a change of amino acid in the protein, but still can affect its function in other ways. An example would be a seemingly silent mutation in the multidrug resistance gene 1 (MDR1), which codes for a cellular membrane pump that expels drugs from the cell, can slow down translation and allow the peptide chain to fold into an unusual conformation, causing the mutant pump to be less functional (in MDR1 protein e.g. C1236T polymorphism changes a GGC codon to GGT at amino acid position 412 of the polypeptide (both encode glycine) and the C3435T polymorphism changes ATC to ATT at position 1145 (both encode isoleucine)).[23]
- nonsynonymous substitutions:
- missense – single change in the base results in change in amino acid of protein and its malfunction which leads to disease (e.g. c.1580G>T SNP in LMNA gene – position 1580 (nt) in the DNA sequence (CGT codon) causing the guanine to be replaced with the thymine, yielding CTT codon in the DNA sequence, results at the protein level in the replacement of the arginine by the leucine in the position 527,[24] at the phenotype level this manifests in overlapping mandibuloacral dysplasia and progeria syndrome)
- nonsense – point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product (e.g. Cystic fibrosis caused by the G542X mutation in the cystic fibrosis transmembrane conductance regulator gene).[25]
Examples
- rs6311 and rs6313 are SNPs in the Serotonin 5-HT2A receptor gene on human chromosome 13.[26]
- A SNP in the F5 gene causes Factor V Leiden thrombophilia.[27]
- rs3091244 is an example of a triallelic SNP in the CRP gene on human chromosome 1.[28]
- TAS2R38 codes for PTC tasting ability, and contains 6 annotated SNPs.[29]
- rs148649884 and rs138055828 in the FCN1 gene encoding M-ficolin crippled the ligand-binding capability of the recombinant M-ficolin.[30]
- An intronic SNP in DNA mismatch repair gene PMS2 (rs1059060, Ser775Asn) is associated with increased sperm DNA damage and risk of male infertility.[31]
Databases
As there are for genes, bioinformatics databases exist for SNPs.
- dbSNP is a SNP database from the National Center for Biotechnology Information (NCBI). As of 8 June 2015[update], dbSNP listed 149,735,377 SNPs in humans.[32][33]
- Kaviar[34] is a compendium of SNPs from multiple data sources including dbSNP.
- SNPedia is a wiki-style database supporting personal genome annotation, interpretation and analysis.
- The OMIM database describes the association between polymorphisms and diseases (e.g., gives diseases in text form)
- dbSAP – single amino-acid polymorphism database for protein variation detection[35]
- The Human Gene Mutation Database provides gene mutations causing or associated with human inherited diseases and functional SNPs
- The International HapMap Project, where researchers are identifying Tag SNP to be able to determine the collection of haplotypes present in each subject.
- GWAS Central allows users to visually interrogate the actual summary-level association data in one or more genome-wide association studies.
The International SNP Map working group mapped the sequence flanking each SNP by alignment to the genomic sequence of large-insert clones in Genebank. These alignments were converted to chromosomal coordinates that is shown in Table 1.[36]
| Chromosome | Length(bp) | All SNPs | TSC SNPs | ||
|---|---|---|---|---|---|
| Total SNPs | kb per SNP | Total SNPs | kb per SNP | ||
| 1 | 214,066,000 | 129,931 | 1.65 | 75,166 | 2.85 |
| 2 | 222,889,000 | 103,664 | 2.15 | 76,985 | 2.90 |
| 3 | 186,938,000 | 93,140 | 2.01 | 63,669 | 2.94 |
| 4 | 169,035,000 | 84,426 | 2.00 | 65,719 | 2.57 |
| 5 | 170,954,000 | 117,882 | 1.45 | 63,545 | 2.69 |
| 6 | 165,022,000 | 96,317 | 1.71 | 53,797 | 3.07 |
| 7 | 149,414,000 | 71,752 | 2.08 | 42,327 | 3.53 |
| 8 | 125,148,000 | 57,834 | 2.16 | 42,653 | 2.93 |
| 9 | 107,440,000 | 62,013 | 1.73 | 43,020 | 2.50 |
| 10 | 127,894,000 | 61,298 | 2.09 | 42,466 | 3.01 |
| 11 | 129,193,000 | 84,663 | 1.53 | 47,621 | 2.71 |
| 12 | 125,198,000 | 59,245 | 2.11 | 38,136 | 3.28 |
| 13 | 93,711,000 | 53,093 | 1.77 | 35,745 | 2.62 |
| 14 | 89,344,000 | 44,112 | 2.03 | 29,746 | 3.00 |
| 15 | 73,467,000 | 37,814 | 1.94 | 26,524 | 2.77 |
| 16 | 74,037,000 | 38,735 | 1.91 | 23,328 | 3.17 |
| 17 | 73,367,000 | 34,621 | 2.12 | 19,396 | 3.78 |
| 18 | 73,078,000 | 45,135 | 1.62 | 27,028 | 2.70 |
| 19 | 56,044,000 | 25,676 | 2.18 | 11,185 | 5.01 |
| 20 | 63,317,000 | 29,478 | 2.15 | 17,051 | 3.71 |
| 21 | 33,824,000 | 20,916 | 1.62 | 9,103 | 3.72 |
| 22 | 33,786,000 | 28,410 | 1.19 | 11,056 | 3.06 |
| X | 131,245,000 | 34,842 | 3.77 | 20,400 | 6.43 |
| Y | 21,753,000 | 4,193 | 5.19 | 1,784 | 12.19 |
| RefSeq | 15,696,674 | 14,534 | 1.08 | ||
| Totals | 2,710,164,000 | 1,419,190 | 1.91 | 887,450 | 3.05 |
Nomenclature
The nomenclature for SNPs can be confusing: several variations can exist for an individual SNP and consensus has not yet been achieved. One approach is to write SNPs with a prefix, period and "greater than" sign showing the wild-type and altered nucleotide or amino acid; for example, c.76A>T.[37][38][39] SNPs are frequently referred to by their dbSNP rs number, as in the examples above.
SNP analysis
SNPs are usually biallelic and thus easily assayed.[40] Analytical methods to discover novel SNPs and detect known SNPs include:
- DNA sequencing;[41]
- capillary electrophoresis;[42]
- mass spectrometry;[43]
- single-strand conformation polymorphism (SSCP);[44]
- single-base extension;
- electrochemical analysis;
- denaturating HPLC and gel electrophoresis;
- restriction fragment length polymorphism;
- hybridization analysis;
Programs for prediction of SNP effects
An important group of SNPs are those that corresponds to missense mutations causing amino acid change on protein level. Point mutation of particular residue can have different effect on protein function (from no effect to complete disruption its function). Usually, change in amino acids with similar size and physico-chemical properties (e.g. substitution from leucine to valine) has mild effect, and opposite. Similarly, if SNP disrupts secondary structure elements (e.g. substitution to proline in alpha helix region) such mutation usually may affect whole protein structure and function. Using those simple and many other machine learning derived rules a group of programs for the prediction of SNP effect was developed:
- SIFT
- SNAP2
- SuSPect
- PolyPhen-2
- PredictSNP
- MutationTaster: official website
- Variant Effect Predictor from the Ensembl project
See also
- Affymetrix
- HapMap
- Illumina
- International HapMap Project
- Short tandem repeat (STR)
- Single-base extension
- SNP array
- SNP genotyping
- SNPedia
- Snpstr
- SNV calling from NGS data
- Tag SNP
- TaqMan
- Variome
Notes
- ^ "single-nucleotide polymorphism / SNP | Learn Science at Scitable". www.nature.com. Retrieved 2015-11-13.
- ^ Ingram, V. M. (13 October 1956). "A specific chemical difference between the globins of normal human and sickle-cell anaemia haemoglobin". Nature. 178 (4537): 792–794. doi:10.1038/178792a0. PMID 13369537.
- ^ Chang, J. C.; Kan, Y. W. (June 1979). "Beta 0 thalassemia, a nonsense mutation in man". Proceedings of the National Academy of Sciences of the United States of America. 76 (6): 2886–2889. doi:10.1073/pnas.76.6.2886. PMC 383714 . PMID 88735.
- ^ Hamosh, A.; King, T. M.; Rosenstein, B. J.; Corey, M.; Levison, H.; Durie, P.; Tsui, L. C.; McIntosh, I.; Keston, M.; Brock, D. J.; Macek, M.; Zemková, D.; Krásničanová, H.; Vávrová, V.; Macek, M.; Golder, N.; Schwarz, M. J.; Super, M.; Watson, E. K.; Williams, C.; Bush, A.; O'Mahoney, S. M.; Humphries, P.; Dearce, M. A.; Reis, A.; Bürger, J.; Stuhrmann, M.; Schmidtke, J.; Wulbrand, U.; Dörk, T. (August 1992). "Cystic fibrosis patients bearing both the common missense mutation Gly----Asp at codon 551 and the delta F508 mutation are clinically indistinguishable from delta F508 homozygotes, except for decreased risk of meconium ileus". American Journal of Human Genetics. 51 (2): 245–250. PMC 1682672 . PMID 1379413.
- ^ Wolf, A. B.; Caselli, R. J.; Reiman, E. M.; Valla, J. (April 2013). "APOE and neuroenergetics: An emerging paradigm in Alzheimer's disease". Neurobiology of Aging. 34 (4): 1007–17. doi:10.1016/j.neurobiolaging.2012.10.011. PMID 23159550.
- ^ http://genome.cshlp.org/content/14/5/908.full
- ^ Gupta, P.K.; Roy, J.K.; Prasad, M. (25 February 2001). "Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants". Current Science. 80 (4): 524–535.
- ^ Barreiro L. B.; Laval G.; Quach H.; Patin E.; Quintana-Murci L. (March 2008). "Natural selection has driven population differentiation in modern humans". Nature Genetics. 40 (3): 340–345. doi:10.1038/ng.78. PMID 18246066.
- ^ Nachman, Michael W. (September 2001). "Single-nucleotide polymorphisms and recombination rate in humans". Trends in Genetics. 17 (9): 481–485. doi:10.1016/S0168-9525(01)02409-X. PMID 11525814.
- ^ M. A. Varela; W. Amos (March 2010). "Heterogeneous distribution of SNPs in the human genome: Microsatellites as predictors of nucleotide diversity and divergence". Genomics. 95 (3): 151–159. doi:10.1016/j.ygeno.2009.12.003. PMID 20026267.
- ^ Carlson, Bruce (15 June 2008). "SNPs — A Shortcut to Personalized Medicine". Genetic Engineering & Biotechnology News. Mary Ann Liebert, Inc. 28 (12). Retrieved 2008-07-06.
(subtitle) Medical applications are where the market's growth is expected
- ^ Thomas, P. E.; Klinger, R.; Furlong, L. I.; Hofmann-Apitius, M.; Friedrich, C. M. (2011). "Challenges in the association of human single-nucleotide polymorphism mentions with unique database identifiers". BMC Bioinformatics. 12: S4. doi:10.1186/1471-2105-12-S4-S4. PMC 3194196 . PMID 21992066.
- ^ Butler, John M. (2010). Fundamentals of forensic DNA typing. Burlington, MA: Elsevier/Academic Press. ISBN 9780080961767.
- ^ Kidd, KK; Pakstis, AJ; Speed, WC; Grigorenko, EL; Kajuna, SL; Karoma, NJ; Kungulilo, S; Kim, JJ; Lu, RB; Odunsi, A; Okonofua, F; Parnas, J; Schulz, LO; Zhukova, OV; Kidd, JR (1 December 2006). "Developing a SNP panel for forensic identification of individuals". Forensic Science International. 164 (1): 20–32. doi:10.1016/j.forsciint.2005.11.017. PMID 16360294.
- ^ Budowle, B; van Daal, A (April 2008). "Forensically relevant SNP classes". BioTechniques. 44 (5): 603–8, 610. doi:10.2144/000112806. PMID 18474034.
- ^ Goldstein, J. A. (2001). "Clinical relevance of genetic polymorphisms in the human CYP2C subfamily". British Journal of Clinical Pharmacology. 52 (4): 349–355. doi:10.1046/j.0306-5251.2001.01499.x. PMC 2014584 . PMID 11678778.
- ^ Lee, C. R. (July–August 2004). "CYP2C9 genotype as a predictor of drug disposition in humans". Methods and findings in experimental and clinical pharmacology. 26 (6): 463–472. PMID 15349140.
- ^ Yanase, K.; Tsukahara, S.; Mitsuhashi, J.; Sugimoto, Y. (8 March 2006). "Functional SNPs of the breast cancer resistance protein ‐ therapeutic effects and inhibitor development". Cancer Letters. 234 (1): 73–80. doi:10.1016/j.canlet.2005.04.039. PMID 16303243.
- ^ Fareed, M.; Afzal, M. (April 2013). "Single-nucleotide polymorphism in genome-wide association of human population: A tool for broad spectrum service". Egyptian Journal of Medical Human Genetics. 14 (2): 123–134. doi:10.1016/j.ejmhg.2012.08.001.
- ^ Singh, Monica; Singh, Puneetpal; Juneja, Pawan Kumar; Singh, Surinder; Kaur, Taranpal (2010). "SNP–SNP interactions within APOE gene influence plasma lipids in postmenopausal osteoporosis". Rheumatology International. 31 (3): 421–3. doi:10.1007/s00296-010-1449-7. PMID 20340021.
- ^ Li, G.; Pan, T.One of the earliest successes in this field was finding a single base mutation in the non-coding region of the APOC3 (apolipoprotein C3 gene) that associated with higher risks of hypertriglyceridemia and atherosclerosis (see David J Galton Lancet 1983 pp444-446).; Guo, D.; Li, L. C. (2014). "Regulatory Variants and Disease: The E-Cadherin -160C/A SNP as an Example". Mol Biol Int. 2014: 967565. doi:10.1155/2014/967565. PMC 4167656 . PMID 25276428.
- ^ Lu, Yi-Fan; Mauger, David M.; Goldstein, David B.; Urban, Thomas J.; Weeks, Kevin M.; Bradrick, Shelton S. (4 November 2015). "IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance". Scientific Reports. 5: 16037. doi:10.1038/srep16037. PMC 4631997 . PMID 26531896.
- ^ Kimchi-Sarfaty, C.; Oh, JM.; Kim, IW.; Sauna, ZE.; Calcagno, AM.; Ambudkar, SV.; Gottesman, MM. (Jan 2007). "A "silent" polymorphism in the MDR1 gene changes substrate specificity". Science. 315 (5811): 525–8. doi:10.1126/science.1135308. PMID 17185560.
- ^ Al-Haggar M; Madej-Pilarczyk A; Kozlowski L; Bujnicki JM; Yahia S; Abdel-Hadi D; Shams A; Ahmad N; Hamed S; Puzianowska-Kuznicka M (2012). "A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome". Eur J Hum Genet. 20 (11): 1134–40. doi:10.1038/ejhg.2012.77. PMC 3476705 . PMID 22549407.
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References
- Nature Reviews Glossary
- Human Genome Project Information — SNP Fact Sheet
External links
| Wikimedia Commons has media related to Single-nucleotide polymorphism. |
- NCBI resources – Introduction to SNPs from NCBI
- The SNP Consortium LTD – SNP search
- NCBI dbSNP database – "a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms"
- HGMD – the Human Gene Mutation Database, includes rare mutations and functional SNPs
- GWAS Central – a central database of summary-level genetic association findings
- 1000 Genomes Project – A Deep Catalog of Human Genetic Variation
- WatCut – an online tool for the design of SNP-RFLP assays
- SNPStats – SNPStats, a web tool for analysis of genetic association studies
- Restriction HomePage – a set of tools for DNA restriction and SNP detection, including design of mutagenic primers
- American Association for Cancer Research Cancer Concepts Factsheet on SNPs
- PharmGKB – The Pharmacogenetics and Pharmacogenomics Knowledge Base, a resource for SNPs associated with drug response and disease outcomes.
- GEN-SNiP – Online tool that identifies polymorphisms in test DNA sequences.
- Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat
- HGNC Guidelines for Human Gene Nomenclature
- SNP effect predictor with galaxy integration
- Open SNP – a portal for sharing own SNP test results
- dbSAP – SNP database for protein variation detection
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UpToDate Contents
全文を閲覧するには購読必要です。 To read the full text you will need to subscribe.
- 1. 遺伝的変異の概要 overview of genetic variation
- 2. 遺伝性疾患の基本原則 basic principles of genetic disease
- 3. 遺伝関連研究：原理および応用 genetic association studies principles and applications
- 4. 鎌状細胞貧血における臨床的ばらつき clinical variability in sickle cell anemia
- 5. オーダーメイド医療 personalized medicine
English Journal
- Natural variation in folate levels among tomato (Solanum lycopersicum) accessions.
- Upadhyaya P1, Tyagi K2, Sarma S3, Tamboli V4, Sreelakshmi Y5, Sharma R6.
- Food chemistry.Food Chem.2017 Feb 15;217:610-9. doi: 10.1016/j.foodchem.2016.09.031. Epub 2016 Sep 7.
- Folate content was estimated in tomato (Solanum lycopersicum) accessions using microbiological assay (MA) and by LC-MS. The MA revealed that in red-ripe fruits folate levels ranged from 4 to 60μg/100g fresh weight. The LC-MS estimation of red-ripe fruits detected three folate forms, 5-CH3-THF, 5-CH
- PMID 27664678
- PMID 27380623
- Association of functional genetic variation in PP2A with prefrontal working memory processing.
- Rampino A1, Di Carlo P2, Fazio L2, Ursini G3, Pergola G2, De Virgilio C4, Gadaleta G4, Giordano GM5, Bertolino A1, Blasi G6.
- Behavioural brain research.Behav Brain Res.2017 Jan 1;316:125-130. doi: 10.1016/j.bbr.2016.08.054. Epub 2016 Aug 31.
- Variation in prefrontal dopaminergic signaling mediated by D2 receptor has been implicated in cognitive phenotypes of schizophrenia, including working memory. Molecular cascades downstream of D2 receptor include a cAMP-dependent- and a cAMP-independent-pathway. Protein-Phosphatase-2A (PP2A) is a key
- PMID 27591184
Related Links
- 「SNPs」とは - Single Nucleotide Polymorphisms（一塩基多型）の略。 SNPsは、個人間における遺伝子の違いを意味する。 ヒトの場合、各人が持っているゲノム（DNA）は、それぞれ約0.1％ずつ異なっている。
- 知恵蔵2015 - SNPの用語解説 - 一塩基多型のこと。スニップと読む。複数形はスニップス(SNPs)。ヒトのゲノムDNAの約30億個の塩基の並びは、全ての人間で同じではない。標準的な塩基配列と比べると、一塩基だけが違って多様性(多型)が ...
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