PubMed:17003357 JSON TXT

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LitCoin-entities-OrganismTaxon-PD

{"project":"LitCoin-entities-OrganismTaxon-PD","denotations":[{"id":"T1","span":{"begin":1149,"end":1154},"obj":"OrganismTaxon"}],"attributes":[{"id":"A1","pred":"db_id","subj":"T1","obj":"NCBItxid:79338"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-sentences

{"project":"LitCoin-sentences","denotations":[{"id":"T1","span":{"begin":0,"end":66},"obj":"Sentence"},{"id":"T2","span":{"begin":67,"end":209},"obj":"Sentence"},{"id":"T3","span":{"begin":210,"end":367},"obj":"Sentence"},{"id":"T4","span":{"begin":368,"end":548},"obj":"Sentence"},{"id":"T5","span":{"begin":549,"end":676},"obj":"Sentence"},{"id":"T6","span":{"begin":677,"end":818},"obj":"Sentence"},{"id":"T7","span":{"begin":819,"end":979},"obj":"Sentence"},{"id":"T8","span":{"begin":980,"end":1169},"obj":"Sentence"},{"id":"T9","span":{"begin":1170,"end":1412},"obj":"Sentence"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-entities

LitCoin-SeqVar

{"project":"LitCoin-SeqVar","denotations":[{"id":"T1","span":{"begin":359,"end":364},"obj":"SequenceVariant"},{"id":"T2","span":{"begin":553,"end":558},"obj":"SequenceVariant"},{"id":"T3","span":{"begin":907,"end":912},"obj":"SequenceVariant"},{"id":"T4","span":{"begin":1216,"end":1221},"obj":"SequenceVariant"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-GeneOrGeneProduct-v0

{"project":"LitCoin-GeneOrGeneProduct-v0","denotations":[{"id":"T1","span":{"begin":12,"end":17},"obj":"GeneOrGeneProduct"},{"id":"T2","span":{"begin":34,"end":40},"obj":"GeneOrGeneProduct"},{"id":"T3","span":{"begin":57,"end":65},"obj":"GeneOrGeneProduct"},{"id":"T4","span":{"begin":92,"end":96},"obj":"GeneOrGeneProduct"},{"id":"T5","span":{"begin":124,"end":132},"obj":"GeneOrGeneProduct"},{"id":"T6","span":{"begin":150,"end":156},"obj":"GeneOrGeneProduct"},{"id":"T7","span":{"begin":191,"end":202},"obj":"GeneOrGeneProduct"},{"id":"T8","span":{"begin":250,"end":256},"obj":"GeneOrGeneProduct"},{"id":"T9","span":{"begin":267,"end":275},"obj":"GeneOrGeneProduct"},{"id":"T10","span":{"begin":284,"end":292},"obj":"GeneOrGeneProduct"},{"id":"T11","span":{"begin":421,"end":427},"obj":"GeneOrGeneProduct"},{"id":"T12","span":{"begin":439,"end":449},"obj":"GeneOrGeneProduct"},{"id":"T13","span":{"begin":482,"end":488},"obj":"GeneOrGeneProduct"},{"id":"T14","span":{"begin":517,"end":525},"obj":"GeneOrGeneProduct"},{"id":"T15","span":{"begin":536,"end":541},"obj":"GeneOrGeneProduct"},{"id":"T16","span":{"begin":542,"end":547},"obj":"GeneOrGeneProduct"},{"id":"T17","span":{"begin":648,"end":656},"obj":"GeneOrGeneProduct"},{"id":"T18","span":{"begin":731,"end":736},"obj":"GeneOrGeneProduct"},{"id":"T19","span":{"begin":768,"end":774},"obj":"GeneOrGeneProduct"},{"id":"T20","span":{"begin":798,"end":806},"obj":"GeneOrGeneProduct"},{"id":"T21","span":{"begin":854,"end":860},"obj":"GeneOrGeneProduct"},{"id":"T22","span":{"begin":892,"end":897},"obj":"GeneOrGeneProduct"},{"id":"T23","span":{"begin":916,"end":925},"obj":"GeneOrGeneProduct"},{"id":"T24","span":{"begin":936,"end":940},"obj":"GeneOrGeneProduct"},{"id":"T25","span":{"begin":955,"end":965},"obj":"GeneOrGeneProduct"},{"id":"T26","span":{"begin":992,"end":998},"obj":"GeneOrGeneProduct"},{"id":"T27","span":{"begin":999,"end":1010},"obj":"GeneOrGeneProduct"},{"id":"T28","span":{"begin":1097,"end":1101},"obj":"GeneOrGeneProduct"},{"id":"T29","span":{"begin":1102,"end":1110},"obj":"GeneOrGeneProduct"},{"id":"T30","span":{"begin":1122,"end":1126},"obj":"GeneOrGeneProduct"},{"id":"T31","span":{"begin":1238,"end":1243},"obj":"GeneOrGeneProduct"},{"id":"T32","span":{"begin":1268,"end":1276},"obj":"GeneOrGeneProduct"},{"id":"T33","span":{"begin":1284,"end":1290},"obj":"GeneOrGeneProduct"},{"id":"T34","span":{"begin":1361,"end":1367},"obj":"GeneOrGeneProduct"},{"id":"T35","span":{"begin":1398,"end":1406},"obj":"GeneOrGeneProduct"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-GeneOrGeneProduct-v2

{"project":"LitCoin-GeneOrGeneProduct-v2","denotations":[{"id":"T1","span":{"begin":34,"end":40},"obj":"GeneOrGeneProduct"},{"id":"T2","span":{"begin":57,"end":65},"obj":"GeneOrGeneProduct"},{"id":"T3","span":{"begin":124,"end":132},"obj":"GeneOrGeneProduct"},{"id":"T4","span":{"begin":150,"end":156},"obj":"GeneOrGeneProduct"},{"id":"T5","span":{"begin":191,"end":202},"obj":"GeneOrGeneProduct"},{"id":"T6","span":{"begin":250,"end":256},"obj":"GeneOrGeneProduct"},{"id":"T7","span":{"begin":267,"end":275},"obj":"GeneOrGeneProduct"},{"id":"T8","span":{"begin":421,"end":427},"obj":"GeneOrGeneProduct"},{"id":"T9","span":{"begin":517,"end":525},"obj":"GeneOrGeneProduct"},{"id":"T10","span":{"begin":648,"end":656},"obj":"GeneOrGeneProduct"},{"id":"T11","span":{"begin":731,"end":736},"obj":"GeneOrGeneProduct"},{"id":"T12","span":{"begin":798,"end":806},"obj":"GeneOrGeneProduct"},{"id":"T13","span":{"begin":854,"end":860},"obj":"GeneOrGeneProduct"},{"id":"T14","span":{"begin":892,"end":897},"obj":"GeneOrGeneProduct"},{"id":"T15","span":{"begin":955,"end":965},"obj":"GeneOrGeneProduct"},{"id":"T16","span":{"begin":992,"end":998},"obj":"GeneOrGeneProduct"},{"id":"T17","span":{"begin":1097,"end":1101},"obj":"GeneOrGeneProduct"},{"id":"T18","span":{"begin":1238,"end":1243},"obj":"GeneOrGeneProduct"},{"id":"T19","span":{"begin":1268,"end":1276},"obj":"GeneOrGeneProduct"},{"id":"T20","span":{"begin":1284,"end":1290},"obj":"GeneOrGeneProduct"},{"id":"T21","span":{"begin":1361,"end":1367},"obj":"GeneOrGeneProduct"},{"id":"T22","span":{"begin":1398,"end":1406},"obj":"GeneOrGeneProduct"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-Disease-MeSH

{"project":"LitCoin-Disease-MeSH","denotations":[{"id":"T1","span":{"begin":50,"end":65},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T2","span":{"begin":117,"end":132},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T3","span":{"begin":260,"end":275},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T4","span":{"begin":510,"end":525},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T5","span":{"begin":641,"end":656},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T6","span":{"begin":791,"end":806},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T7","span":{"begin":1261,"end":1276},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T8","span":{"begin":1391,"end":1406},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A6","pred":"originalLabel","subj":"T6","obj":"D003922"},{"id":"A1","pred":"originalLabel","subj":"T1","obj":"D003922"},{"id":"A4","pred":"originalLabel","subj":"T4","obj":"D003922"},{"id":"A3","pred":"originalLabel","subj":"T3","obj":"D003922"},{"id":"A8","pred":"originalLabel","subj":"T8","obj":"D003922"},{"id":"A2","pred":"originalLabel","subj":"T2","obj":"D003922"},{"id":"A5","pred":"originalLabel","subj":"T5","obj":"D003922"},{"id":"A7","pred":"originalLabel","subj":"T7","obj":"D003922"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-GeneOrGeneProduct-v3

{"project":"LitCoin-GeneOrGeneProduct-v3","denotations":[{"id":"T1","span":{"begin":34,"end":40},"obj":"GeneOrGeneProduct"},{"id":"T2","span":{"begin":150,"end":156},"obj":"GeneOrGeneProduct"},{"id":"T3","span":{"begin":191,"end":202},"obj":"GeneOrGeneProduct"},{"id":"T4","span":{"begin":250,"end":256},"obj":"GeneOrGeneProduct"},{"id":"T5","span":{"begin":421,"end":427},"obj":"GeneOrGeneProduct"},{"id":"T6","span":{"begin":854,"end":860},"obj":"GeneOrGeneProduct"},{"id":"T7","span":{"begin":992,"end":998},"obj":"GeneOrGeneProduct"},{"id":"T8","span":{"begin":1284,"end":1290},"obj":"GeneOrGeneProduct"},{"id":"T9","span":{"begin":1361,"end":1367},"obj":"GeneOrGeneProduct"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin_Mondo_095

{"project":"LitCoin_Mondo_095","denotations":[{"id":"T1","span":{"begin":50,"end":65},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T2","span":{"begin":117,"end":132},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T3","span":{"begin":204,"end":207},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T4","span":{"begin":260,"end":275},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T5","span":{"begin":510,"end":525},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T6","span":{"begin":641,"end":656},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T7","span":{"begin":791,"end":806},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T8","span":{"begin":1261,"end":1276},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T9","span":{"begin":1391,"end":1406},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A4","pred":"mondo_id","subj":"T4","obj":"0005147"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"0024551"},{"id":"A6","pred":"mondo_id","subj":"T6","obj":"0005147"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"0005147"},{"id":"A1","pred":"mondo_id","subj":"T1","obj":"0005147"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"0005147"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"0005147"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"0005147"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"0005147"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-MeSH-Disease-2

{"project":"LitCoin-MeSH-Disease-2","denotations":[{"id":"T1","span":{"begin":50,"end":65},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T2","span":{"begin":117,"end":132},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T3","span":{"begin":260,"end":275},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T4","span":{"begin":510,"end":525},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T5","span":{"begin":641,"end":656},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T6","span":{"begin":791,"end":806},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T7","span":{"begin":1261,"end":1276},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T8","span":{"begin":1391,"end":1406},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A2","pred":"ID:","subj":"T2","obj":"D003922"},{"id":"A8","pred":"ID:","subj":"T8","obj":"D003922"},{"id":"A7","pred":"ID:","subj":"T7","obj":"D003922"},{"id":"A3","pred":"ID:","subj":"T3","obj":"D003922"},{"id":"A1","pred":"ID:","subj":"T1","obj":"D003922"},{"id":"A5","pred":"ID:","subj":"T5","obj":"D003922"},{"id":"A4","pred":"ID:","subj":"T4","obj":"D003922"},{"id":"A6","pred":"ID:","subj":"T6","obj":"D003922"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-MONDO_bioort2019

{"project":"LitCoin-MONDO_bioort2019","denotations":[{"id":"T1","span":{"begin":50,"end":65},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T2","span":{"begin":117,"end":132},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T3","span":{"begin":260,"end":275},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T4","span":{"begin":510,"end":525},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T5","span":{"begin":641,"end":656},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T6","span":{"begin":791,"end":806},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T7","span":{"begin":1261,"end":1276},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T8","span":{"begin":1391,"end":1406},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A6","pred":"#label","subj":"T6","obj":"D003922"},{"id":"A4","pred":"#label","subj":"T4","obj":"D003922"},{"id":"A8","pred":"#label","subj":"T8","obj":"D003922"},{"id":"A1","pred":"#label","subj":"T1","obj":"D003922"},{"id":"A3","pred":"#label","subj":"T3","obj":"D003922"},{"id":"A7","pred":"#label","subj":"T7","obj":"D003922"},{"id":"A5","pred":"#label","subj":"T5","obj":"D003922"},{"id":"A2","pred":"#label","subj":"T2","obj":"D003922"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-Chemical-MeSH-CHEBI

{"project":"LitCoin-Chemical-MeSH-CHEBI","denotations":[{"id":"T1","span":{"begin":191,"end":202},"obj":"ChemicalEntity"}],"attributes":[{"id":"A1","pred":"ID:","subj":"T1","obj":"D010744"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

LitCoin-training-merged

{"project":"LitCoin-training-merged","denotations":[{"id":"T1","span":{"begin":191,"end":202},"obj":"ChemicalEntity"},{"id":"T9","span":{"begin":1361,"end":1367},"obj":"GeneOrGeneProduct"},{"id":"T8","span":{"begin":1284,"end":1290},"obj":"GeneOrGeneProduct"},{"id":"T7","span":{"begin":992,"end":998},"obj":"GeneOrGeneProduct"},{"id":"T6","span":{"begin":854,"end":860},"obj":"GeneOrGeneProduct"},{"id":"T5","span":{"begin":421,"end":427},"obj":"GeneOrGeneProduct"},{"id":"T4","span":{"begin":250,"end":256},"obj":"GeneOrGeneProduct"},{"id":"T3","span":{"begin":191,"end":202},"obj":"GeneOrGeneProduct"},{"id":"T2","span":{"begin":150,"end":156},"obj":"GeneOrGeneProduct"},{"id":"T4228","span":{"begin":34,"end":40},"obj":"GeneOrGeneProduct"},{"id":"T22725","span":{"begin":1391,"end":1406},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T6692","span":{"begin":1261,"end":1276},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T88422","span":{"begin":791,"end":806},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T20962","span":{"begin":641,"end":656},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T3469","span":{"begin":510,"end":525},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T61453","span":{"begin":260,"end":275},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T13626","span":{"begin":117,"end":132},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T22291","span":{"begin":50,"end":65},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T67104","span":{"begin":1216,"end":1221},"obj":"SequenceVariant"},{"id":"T34458","span":{"begin":907,"end":912},"obj":"SequenceVariant"},{"id":"T29946","span":{"begin":553,"end":558},"obj":"SequenceVariant"},{"id":"T22904","span":{"begin":359,"end":364},"obj":"SequenceVariant"}],"attributes":[{"id":"A1","pred":"ID:","subj":"T1","obj":"D010744"},{"id":"A8","pred":"#label","subj":"T22725","obj":"D003922"},{"id":"A7","pred":"#label","subj":"T6692","obj":"D003922"},{"id":"A6","pred":"#label","subj":"T88422","obj":"D003922"},{"id":"A5","pred":"#label","subj":"T20962","obj":"D003922"},{"id":"A4","pred":"#label","subj":"T3469","obj":"D003922"},{"id":"A3","pred":"#label","subj":"T61453","obj":"D003922"},{"id":"A2","pred":"#label","subj":"T13626","obj":"D003922"},{"id":"A71273","pred":"#label","subj":"T22291","obj":"D003922"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

DisGeNET

{"project":"DisGeNET","denotations":[{"id":"T0","span":{"begin":34,"end":40},"obj":"gene:26191"},{"id":"T1","span":{"begin":50,"end":65},"obj":"disease:C0011854"},{"id":"T2","span":{"begin":150,"end":156},"obj":"gene:26191"},{"id":"T3","span":{"begin":117,"end":132},"obj":"disease:C0011854"},{"id":"T4","span":{"begin":250,"end":256},"obj":"gene:26191"},{"id":"T5","span":{"begin":260,"end":275},"obj":"disease:C0011854"},{"id":"T6","span":{"begin":421,"end":427},"obj":"gene:26191"},{"id":"T7","span":{"begin":510,"end":525},"obj":"disease:C0011854"},{"id":"T8","span":{"begin":1284,"end":1290},"obj":"gene:26191"},{"id":"T9","span":{"begin":1261,"end":1276},"obj":"disease:C0011854"},{"id":"T10","span":{"begin":1284,"end":1290},"obj":"gene:26191"},{"id":"T11","span":{"begin":1391,"end":1406},"obj":"disease:C0011854"},{"id":"T12","span":{"begin":1361,"end":1367},"obj":"gene:26191"},{"id":"T13","span":{"begin":1261,"end":1276},"obj":"disease:C0011854"},{"id":"T14","span":{"begin":1361,"end":1367},"obj":"gene:26191"},{"id":"T15","span":{"begin":1391,"end":1406},"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"},{"id":"R5","pred":"associated_with","subj":"T8","obj":"T9"},{"id":"R6","pred":"associated_with","subj":"T10","obj":"T11"},{"id":"R7","pred":"associated_with","subj":"T12","obj":"T13"},{"id":"R8","pred":"associated_with","subj":"T14","obj":"T15"}],"namespaces":[{"prefix":"gene","uri":"http://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"disease","uri":"http://purl.bioontology.org/ontology/MEDLINEPLUS/"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

DisGeNET5_variant_disease

{"project":"DisGeNET5_variant_disease","denotations":[{"id":"17003357-8#46#53#geners2476601","span":{"begin":1216,"end":1223},"obj":"geners2476601"},{"id":"17003357-8#91#106#diseaseC0011854","span":{"begin":1261,"end":1276},"obj":"diseaseC0011854"},{"id":"17003357-8#221#236#diseaseC0011854","span":{"begin":1391,"end":1406},"obj":"diseaseC0011854"}],"relations":[{"id":"46#53#geners247660191#106#diseaseC0011854","pred":"associated_with","subj":"17003357-8#46#53#geners2476601","obj":"17003357-8#91#106#diseaseC0011854"},{"id":"46#53#geners2476601221#236#diseaseC0011854","pred":"associated_with","subj":"17003357-8#46#53#geners2476601","obj":"17003357-8#221#236#diseaseC0011854"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

DisGeNET5_gene_disease

{"project":"DisGeNET5_gene_disease","denotations":[{"id":"17003357-0#34#40#gene26191","span":{"begin":808,"end":860},"obj":"gene26191"},{"id":"17003357-0#50#65#diseaseC0011854","span":{"begin":970,"end":1276},"obj":"diseaseC0011854"}],"relations":[{"id":"34#40#gene2619150#65#diseaseC0011854","pred":"associated_with","subj":"17003357-0#34#40#gene26191","obj":"17003357-0#50#65#diseaseC0011854"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}

tmVarCorpus

{"project":"tmVarCorpus","denotations":[{"id":"T1","span":{"begin":359,"end":366},"obj":"DNAMutation:|SUB|C|1858|T"},{"id":"T2","span":{"begin":907,"end":914},"obj":"DNAMutation:|SUB|G|2250|C"},{"id":"T3","span":{"begin":1216,"end":1223},"obj":"DNAMutation:|SUB|C|1858|T"}],"text":"A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.\nA recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P \u003c 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk."}