PubMed:17000021 JSON TXT

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PubTator4TogoVar

{"project":"PubTator4TogoVar","denotations":[{"id":"17000021_0","span":{"begin":260,"end":265},"obj":"ProteinMutation"},{"id":"17000021_1","span":{"begin":934,"end":939},"obj":"ProteinMutation"},{"id":"17000021_2","span":{"begin":1549,"end":1572},"obj":"ProteinMutation"},{"id":"17000021_3","span":{"begin":1751,"end":1774},"obj":"ProteinMutation"}],"attributes":[{"id":"17000021_0_ProteinMutation","pred":"proteinmutation","subj":"17000021_0","obj":"rs2476601"},{"id":"17000021_1_ProteinMutation","pred":"proteinmutation","subj":"17000021_1","obj":"rs2476601"},{"id":"17000021_2_ProteinMutation","pred":"proteinmutation","subj":"17000021_2","obj":"rs2476601"},{"id":"17000021_3_ProteinMutation","pred":"proteinmutation","subj":"17000021_3","obj":"rs2476601"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}

TEST-DiseaseOrPhenotypicFeature

Test-SequenceVariant

{"project":"Test-SequenceVariant","denotations":[{"id":"T1","span":{"begin":251,"end":256},"obj":"SequenceVariant"},{"id":"T2","span":{"begin":260,"end":265},"obj":"SequenceVariant"},{"id":"T3","span":{"begin":381,"end":384},"obj":"SequenceVariant"},{"id":"T4","span":{"begin":789,"end":792},"obj":"SequenceVariant"},{"id":"T5","span":{"begin":823,"end":826},"obj":"SequenceVariant"},{"id":"T6","span":{"begin":900,"end":909},"obj":"SequenceVariant"},{"id":"T7","span":{"begin":919,"end":928},"obj":"SequenceVariant"},{"id":"T8","span":{"begin":934,"end":939},"obj":"SequenceVariant"},{"id":"T9","span":{"begin":966,"end":975},"obj":"SequenceVariant"},{"id":"T10","span":{"begin":1049,"end":1052},"obj":"SequenceVariant"},{"id":"T11","span":{"begin":1144,"end":1147},"obj":"SequenceVariant"},{"id":"T12","span":{"begin":1593,"end":1596},"obj":"SequenceVariant"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}

Test-GeneOrGeneProduct

{"project":"Test-GeneOrGeneProduct","denotations":[{"id":"T1","span":{"begin":81,"end":87},"obj":"GeneOrGeneProduct"},{"id":"T2","span":{"begin":113,"end":121},"obj":"GeneOrGeneProduct"},{"id":"T3","span":{"begin":191,"end":197},"obj":"GeneOrGeneProduct"},{"id":"T4","span":{"begin":390,"end":398},"obj":"GeneOrGeneProduct"},{"id":"T5","span":{"begin":712,"end":718},"obj":"GeneOrGeneProduct"},{"id":"T6","span":{"begin":1655,"end":1658},"obj":"GeneOrGeneProduct"},{"id":"T7","span":{"begin":2099,"end":2105},"obj":"GeneOrGeneProduct"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}

Test-merged-2

Test-merged

DisGeNET

{"project":"DisGeNET","denotations":[{"id":"T0","span":{"begin":712,"end":718},"obj":"gene:26191"},{"id":"T1","span":{"begin":789,"end":792},"obj":"disease:C0011854"},{"id":"T2","span":{"begin":712,"end":718},"obj":"gene:26191"},{"id":"T3","span":{"begin":802,"end":805},"obj":"disease:C3714757"},{"id":"T4","span":{"begin":712,"end":718},"obj":"gene:26191"},{"id":"T5","span":{"begin":802,"end":805},"obj":"disease:C3495559"},{"id":"T6","span":{"begin":712,"end":718},"obj":"gene:26191"},{"id":"T7","span":{"begin":823,"end":826},"obj":"disease:C0011854"}],"relations":[{"id":"R1","pred":"associated_with","subj":"T0","obj":"T1"},{"id":"R2","pred":"associated_with","subj":"T2","obj":"T3"},{"id":"R3","pred":"associated_with","subj":"T4","obj":"T5"},{"id":"R4","pred":"associated_with","subj":"T6","obj":"T7"}],"namespaces":[{"prefix":"gene","uri":"http://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"disease","uri":"http://purl.bioontology.org/ontology/MEDLINEPLUS/"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}

PubmedHPO

{"project":"PubmedHPO","denotations":[{"id":"T1","span":{"begin":333,"end":352},"obj":"HP_0002960"},{"id":"T2","span":{"begin":333,"end":343},"obj":"HP_0002960"},{"id":"T3","span":{"begin":410,"end":419},"obj":"HP_0001369"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}

DisGeNET5_variant_disease

DisGeNET5_gene_disease

{"project":"DisGeNET5_gene_disease","denotations":[{"id":"17000021-0#81#87#gene26191","span":{"begin":81,"end":87},"obj":"gene26191"},{"id":"17000021-0#81#87#gene26191","span":{"begin":81,"end":87},"obj":"gene26191"},{"id":"17000021-0#113#142#diseaseC3495559","span":{"begin":113,"end":142},"obj":"diseaseC3495559"},{"id":"17000021-0#113#142#diseaseC3714757","span":{"begin":113,"end":142},"obj":"diseaseC3714757"},{"id":"17000021-0#93#108#diseaseC0011854","span":{"begin":93,"end":108},"obj":"diseaseC0011854"},{"id":"17000021-9#197#203#gene26191","span":{"begin":2099,"end":2105},"obj":"gene26191"},{"id":"17000021-9#241#253#diseaseC0004364","span":{"begin":2143,"end":2155},"obj":"diseaseC0004364"}],"relations":[{"id":"81#87#gene26191113#142#diseaseC3495559","pred":"associated_with","subj":"17000021-0#81#87#gene26191","obj":"17000021-0#113#142#diseaseC3495559"},{"id":"81#87#gene26191113#142#diseaseC3714757","pred":"associated_with","subj":"17000021-0#81#87#gene26191","obj":"17000021-0#113#142#diseaseC3714757"},{"id":"81#87#gene2619193#108#diseaseC0011854","pred":"associated_with","subj":"17000021-0#81#87#gene26191","obj":"17000021-0#93#108#diseaseC0011854"},{"id":"81#87#gene26191113#142#diseaseC3495559","pred":"associated_with","subj":"17000021-0#81#87#gene26191","obj":"17000021-0#113#142#diseaseC3495559"},{"id":"81#87#gene26191113#142#diseaseC3714757","pred":"associated_with","subj":"17000021-0#81#87#gene26191","obj":"17000021-0#113#142#diseaseC3714757"},{"id":"81#87#gene2619193#108#diseaseC0011854","pred":"associated_with","subj":"17000021-0#81#87#gene26191","obj":"17000021-0#93#108#diseaseC0011854"},{"id":"197#203#gene26191241#253#diseaseC0004364","pred":"associated_with","subj":"17000021-9#197#203#gene26191","obj":"17000021-9#241#253#diseaseC0004364"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}

tmVarCorpus

{"project":"tmVarCorpus","denotations":[{"id":"T1","span":{"begin":27,"end":36},"obj":"DNAMutation:c|SUB|G|-1123|C"},{"id":"T2","span":{"begin":40,"end":49},"obj":"DNAMutation:c|SUB|A|+2740|G"},{"id":"T3","span":{"begin":250,"end":258},"obj":"DNAMutation:c|SUB|C|+1858|T"},{"id":"T4","span":{"begin":260,"end":265},"obj":"ProteinMutation:p|SUB|R|620|W"},{"id":"T5","span":{"begin":900,"end":909},"obj":"SNP:rs2488457"},{"id":"T6","span":{"begin":919,"end":928},"obj":"SNP:rs2476601"},{"id":"T7","span":{"begin":934,"end":939},"obj":"ProteinMutation:p|SUB|R|620|W"},{"id":"T8","span":{"begin":966,"end":975},"obj":"SNP:rs1217412"}],"text":"No independent role of the -1123 G\u003eC and+2740 A\u003eG variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.\nINTRODUCTION: The PTPN22 is a negative regulator of the T cell response. Its +1858C\u003eT (R620W) polymorphism has been shown to associate with a risk for multiple autoimmune diseases, including type 1 diabetes (T1D) and juvenile idiopathic arthritis (JIA). The minor (susceptibility) allele is absent in Asian populations, but a recent study suggested an independent involvement of another polymorphism located within the promoter -1123 nucleotides relative to the translational start site.\nAIMS: We aimed to analyse the association of three PTPN22 polymorphisms in two distinct Caucasian populations, the Czechs (with T1D and with JIA) and Azeri (with T1D).\nMETHODS: The single nucleotide polymorphisms (SNP) at positions -1123 (rs2488457), +1858 (rs2476601, the R620W substitution), and +2740 (rs1217412) were genotyped using TaqMan assays in 372 subjects with childhood-onset T1D, 130 subjects with JIA, and 400 control subjects of Czech origin, and in 160 subjects with T1D and 271 healthy controls of Azeri origin.\nRESULTS: In the Czechs, all three SNPs were in a tight linkage disequlibrium, while in the Azeri, the linkage disequlibrium was limited to between the promoter and 3'-UTR polymorphism, D'(-1123, +2740)=0.99, r(2)=0.72. Haplotype reconstruction via the expectation-maximization algorithm showed in both populations that only the haplotype containing the minor (W) allele at codon 620 was associated with T1D (OR=2.26, 95% CI 1.68-3.02 in Czechs, OR=14.8, 95% CI 2.0-651 in Azeri) or JIA (OR=2.43, 95% CI 1.66-3.56 in Czechs). The haplotypes having the wild-type (R) allele at codon 620 and minor alleles at -1123 and/or +2740 were neutral as to the risk of autoimmune conditions in both populations.\nCONCLUSIONS: In two different Caucasian populations, the Czechs and the Azeri, no independent contribution can be detected either of the -1123 promoter SNP or the +2740 3'-UTR SNP, and only the minor allele at PTPN22 codon 620 contributes to the risk of autoimmunity."}