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PubMed:17683901 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-115 Sentence denotes An improved tetra-primer PCR approach for the detection of the FGFR3 G380R mutation responsible for achondroplasia.
T2 116-212 Sentence denotes Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500.
T3 213-397 Sentence denotes In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene.
T4 398-625 Sentence denotes We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation.
T5 626-752 Sentence denotes Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles.
T6 753-993 Sentence denotes The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP.
T7 994-1048 Sentence denotes We have observed complete concordance between methods.
T8 1049-1205 Sentence denotes Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
4319 63-68 GeneOrGeneProduct denotes FGFR3 NCBIGene:2261
4320 69-74 SequenceVariant denotes G380R DBSNP:rs28931614
4321 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia MESH:D000130
4322 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia MESH:D000130
4323 158-166 DiseaseOrPhenotypicFeature denotes dwarfism MESH:D004392
4324 273-330 SequenceVariant denotes G to A or G to C substitution at nucleotide position 1138 DBSNP:rs28931614
4325 332-339 SequenceVariant denotes p.G380R DBSNP:rs28931614
4326 348-383 GeneOrGeneProduct denotes fibroblast growth factor receptor 3 NCBIGene:2261
4327 385-390 GeneOrGeneProduct denotes FGFR3 NCBIGene:2261
4328 482-491 SequenceVariant denotes c.1138G>A DBSNP:rs28931614
4329 496-505 SequenceVariant denotes c.1138G>C DBSNP:rs28931614
4330 606-615 SequenceVariant denotes c.1138G>A DBSNP:rs28931614
4331 811-819 OrganismTaxon denotes patients NCBITaxon:9606
4332 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia MESH:D000130
4333 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia MESH:D000130
4334 962-971 SequenceVariant denotes c.1138G>A DBSNP:rs28931614
4335 1127-1132 GeneOrGeneProduct denotes FGFR3 NCBIGene:2261
4336 1133-1140 SequenceVariant denotes p.G380R DBSNP:rs28931614

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 69-74 SequenceVariant denotes G380R
T2 332-339 SequenceVariant denotes p.G380R
T3 482-491 SequenceVariant denotes c.1138G>A
T4 496-505 SequenceVariant denotes c.1138G>C
T5 606-615 SequenceVariant denotes c.1138G>A
T6 962-971 SequenceVariant denotes c.1138G>A
T7 1133-1140 SequenceVariant denotes p.G380R

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia 0007037
T2 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia 0007037
T3 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia 0007037
T4 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia 0007037
T5 1011-1019 DiseaseOrPhenotypicFeature denotes complete 0700063

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 12-17 GeneOrGeneProduct denotes tetra
T2 63-68 GeneOrGeneProduct denotes FGFR3
T3 75-83 GeneOrGeneProduct denotes mutation
T4 158-166 GeneOrGeneProduct denotes dwarfism
T5 191-204 GeneOrGeneProduct denotes approximately
T6 233-238 GeneOrGeneProduct denotes cases
T7 278-282 GeneOrGeneProduct denotes A or
T8 348-383 GeneOrGeneProduct denotes fibroblast growth factor receptor 3
T9 385-390 GeneOrGeneProduct denotes FGFR3
T10 435-439 GeneOrGeneProduct denotes tube
T11 440-445 GeneOrGeneProduct denotes tetra
T12 506-515 GeneOrGeneProduct denotes mutations
T13 616-624 GeneOrGeneProduct denotes mutation
T14 704-710 GeneOrGeneProduct denotes mutant
T15 718-722 GeneOrGeneProduct denotes in a
T16 772-778 GeneOrGeneProduct denotes tested
T17 929-943 GeneOrGeneProduct denotes determined the
T18 972-980 GeneOrGeneProduct denotes mutation
T19 988-992 GeneOrGeneProduct denotes RFLP
T20 1040-1047 GeneOrGeneProduct denotes methods
T21 1053-1058 GeneOrGeneProduct denotes tetra
T22 1094-1098 GeneOrGeneProduct denotes cost
T23 1116-1122 GeneOrGeneProduct denotes method
T24 1127-1132 GeneOrGeneProduct denotes FGFR3
T25 1173-1177 GeneOrGeneProduct denotes even
T26 1186-1190 GeneOrGeneProduct denotes tech

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 12-17 GeneOrGeneProduct denotes tetra
T2 63-68 GeneOrGeneProduct denotes FGFR3
T3 158-166 GeneOrGeneProduct denotes dwarfism
T4 348-383 GeneOrGeneProduct denotes fibroblast growth factor receptor 3
T5 385-390 GeneOrGeneProduct denotes FGFR3
T6 435-439 GeneOrGeneProduct denotes tube
T7 440-445 GeneOrGeneProduct denotes tetra
T8 704-710 GeneOrGeneProduct denotes mutant
T9 1053-1058 GeneOrGeneProduct denotes tetra
T10 1116-1122 GeneOrGeneProduct denotes method
T11 1127-1132 GeneOrGeneProduct denotes FGFR3
T12 1173-1177 GeneOrGeneProduct denotes even

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T2 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia D000130
T3 158-166 DiseaseOrPhenotypicFeature denotes dwarfism D004392
T4 244-251 DiseaseOrPhenotypicFeature denotes disease D004194
T5 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T6 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia D000130

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 63-68 GeneOrGeneProduct denotes FGFR3
T2 158-166 GeneOrGeneProduct denotes dwarfism
T3 348-383 GeneOrGeneProduct denotes fibroblast growth factor receptor 3
T4 385-390 GeneOrGeneProduct denotes FGFR3
T5 1127-1132 GeneOrGeneProduct denotes FGFR3

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia 0007037
T2 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia 0007037
T3 418-427 DiseaseOrPhenotypicFeature denotes sensitive 0000605
T4 520-523 DiseaseOrPhenotypicFeature denotes can 0012833
T5 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia 0007037
T6 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia 0007037
T7 1079-1088 DiseaseOrPhenotypicFeature denotes sensitive 0000605

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T2 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia D000130
T3 158-166 DiseaseOrPhenotypicFeature denotes dwarfism D004392
T4 244-251 DiseaseOrPhenotypicFeature denotes disease D004194
T5 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T6 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia D000130

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T2 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia D000130
T3 158-166 DiseaseOrPhenotypicFeature denotes dwarfism D004392
T4 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T5 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia D000130

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 811-819 OrganismTaxon denotes patients

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label
T5 1127-1132 GeneOrGeneProduct denotes FGFR3
T4 385-390 GeneOrGeneProduct denotes FGFR3
T3 348-383 GeneOrGeneProduct denotes fibroblast growth factor receptor 3
T2 158-166 GeneOrGeneProduct denotes dwarfism
T1 63-68 GeneOrGeneProduct denotes FGFR3
T52596 883-897 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T99429 825-839 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T87795 158-166 DiseaseOrPhenotypicFeature denotes dwarfism D004392
T72387 116-130 DiseaseOrPhenotypicFeature denotes Achondroplasia D000130
T49846 100-114 DiseaseOrPhenotypicFeature denotes achondroplasia D000130
T38869 811-819 OrganismTaxon denotes patients
T7 1133-1140 SequenceVariant denotes p.G380R
T6 962-971 SequenceVariant denotes c.1138G>A
T78114 606-615 SequenceVariant denotes c.1138G>A
T14500 496-505 SequenceVariant denotes c.1138G>C
T93333 482-491 SequenceVariant denotes c.1138G>A
T27184 332-339 SequenceVariant denotes p.G380R
T43152 69-74 SequenceVariant denotes G380R

DisGeNET

Id Subject Object Predicate Lexical cue
T0 63-68 gene:2261 denotes FGFR3
T1 100-114 disease:C0001080 denotes achondroplasia
R1 T0 T1 associated_with FGFR3,achondroplasia

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 158-166 HP_0003510 denotes dwarfism
T1 158-166 HP_0003510 denotes dwarfism

DisGeNET5_variant_disease

Id Subject Object Predicate Lexical cue
17683901-0#69#74#geners28931614 69-74 geners28931614 denotes G380R
17683901-0#100#114#diseaseC0001080 100-114 diseaseC0001080 denotes achondroplasia
69#74#geners28931614100#114#diseaseC0001080 17683901-0#69#74#geners28931614 17683901-0#100#114#diseaseC0001080 associated_with G380R,achondroplasia

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
17683901-0#63#68#gene2261 63-68 gene2261 denotes FGFR3
17683901-0#100#114#diseaseC0001080 100-114 diseaseC0001080 denotes achondroplasia
63#68#gene2261100#114#diseaseC0001080 17683901-0#63#68#gene2261 17683901-0#100#114#diseaseC0001080 associated_with FGFR3,achondroplasia

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 69-74 ProteinMutation:p|SUB|G|380|R denotes G380R
T2 332-339 ProteinMutation:p|SUB|G|380|R denotes p.G380R
T3 482-491 DNAMutation:c|SUB|G|1138|A denotes c.1138G>A
T4 496-505 DNAMutation:c|SUB|G|1138|C denotes c.1138G>C
T5 606-615 DNAMutation:c|SUB|G|1138|A denotes c.1138G>A
T6 962-971 DNAMutation:c|SUB|G|1138|A denotes c.1138G>A
T7 1133-1140 ProteinMutation:p|SUB|G|380|R denotes p.G380R