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PubMed:15951966 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-68 Sentence denotes Screening for exonic copy number mutations at MSH2 and MLH1 by MAPH.
T2 69-80 Sentence denotes BACKGROUND:
T3 81-284 Sentence denotes Exonic deletions in MSH2 and MLH1 are significant contributors to the mutation spectrum in HNPCC, and heterozygous changes in exon copy number are not detected by conventional mutation screening methods.
T4 285-290 Sentence denotes AIMS:
T5 291-467 Sentence denotes We aimed to develop methods for screening copy number changes in all the exons of the MLH1 and MSH2 genes using a single multiplex amplifiable probe hybridisation (MAPH) assay.
T6 468-476 Sentence denotes METHODS:
T7 477-703 Sentence denotes We developed a probe set consisting of probes from the 19 exons of MLH1 and 16 exons of MSH2, and 3 control probes, and applied it to screening for deletions and duplications using fluorescent detection of amplified fragments.
T8 704-712 Sentence denotes RESULTS:
T9 713-884 Sentence denotes We tested 73 DNA samples from controls and 50 from HNPCC patients in whom no point mutations had been found, and detected 10 copy number changes among the patient samples.
T10 885-1081 Sentence denotes A deletion of about 1.4 kb including exon 3 of MSH2 was confirmed by amplification of a junction fragment, and was shown to be the result of an unequal recombination between intronic Alu elements.
T11 1082-1182 Sentence denotes CONCLUSIONS: MAPH can detect exonic copy number changes in MLH1 and MSH2 in DNA from HNPCC patients.
T12 1183-1378 Sentence denotes Since finding an exonic deletion or duplication makes full sequence analysis unnecessary, it may be most cost-effective to pre-screen samples by MAPH or MLPA before screening for point mutations.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
1944 46-50 GeneOrGeneProduct denotes MSH2 NCBIGene:4436
1945 55-59 GeneOrGeneProduct denotes MLH1 NCBIGene:4292
1946 101-105 GeneOrGeneProduct denotes MSH2 NCBIGene:4436
1947 110-114 GeneOrGeneProduct denotes MLH1 NCBIGene:4292
1948 172-177 DiseaseOrPhenotypicFeature denotes HNPCC MESH:D003123
1949 377-381 GeneOrGeneProduct denotes MLH1 NCBIGene:4292
1950 386-390 GeneOrGeneProduct denotes MSH2 NCBIGene:4436
1951 544-548 GeneOrGeneProduct denotes MLH1 NCBIGene:4292
1952 565-569 GeneOrGeneProduct denotes MSH2 NCBIGene:4436
1953 764-769 DiseaseOrPhenotypicFeature denotes HNPCC MESH:D003123
1954 770-778 OrganismTaxon denotes patients NCBITaxon:9606
1955 868-875 OrganismTaxon denotes patient NCBITaxon:9606
1956 932-936 GeneOrGeneProduct denotes MSH2 NCBIGene:4436
1957 1141-1145 GeneOrGeneProduct denotes MLH1 NCBIGene:4292
1958 1150-1154 GeneOrGeneProduct denotes MSH2 NCBIGene:4436
1959 1167-1172 DiseaseOrPhenotypicFeature denotes HNPCC MESH:D003123
1960 1173-1181 OrganismTaxon denotes patients NCBITaxon:9606

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 57-64 SequenceVariant denotes H1 by M
T2 887-904 SequenceVariant denotes deletion of about

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 33-42 GeneOrGeneProduct denotes mutations
T2 46-50 GeneOrGeneProduct denotes MSH2
T3 55-59 GeneOrGeneProduct denotes MLH1
T4 101-105 GeneOrGeneProduct denotes MSH2
T5 110-114 GeneOrGeneProduct denotes MLH1
T6 151-159 GeneOrGeneProduct denotes mutation
T7 172-177 GeneOrGeneProduct denotes HNPCC
T8 257-265 GeneOrGeneProduct denotes mutation
T9 276-283 GeneOrGeneProduct denotes methods
T10 311-318 GeneOrGeneProduct denotes methods
T11 356-359 GeneOrGeneProduct denotes all
T12 377-381 GeneOrGeneProduct denotes MLH1
T13 386-390 GeneOrGeneProduct denotes MSH2
T14 468-475 GeneOrGeneProduct denotes METHODS
T15 544-548 GeneOrGeneProduct denotes MLH1
T16 565-569 GeneOrGeneProduct denotes MSH2
T17 571-576 GeneOrGeneProduct denotes and 3
T18 639-651 GeneOrGeneProduct denotes duplications
T19 716-722 GeneOrGeneProduct denotes tested
T20 764-769 GeneOrGeneProduct denotes HNPCC
T21 790-795 GeneOrGeneProduct denotes point
T22 796-805 GeneOrGeneProduct denotes mutations
T23 932-936 GeneOrGeneProduct denotes MSH2
T24 1037-1050 GeneOrGeneProduct denotes recombination
T25 1141-1145 GeneOrGeneProduct denotes MLH1
T26 1150-1154 GeneOrGeneProduct denotes MSH2
T27 1167-1172 GeneOrGeneProduct denotes HNPCC
T28 1189-1196 GeneOrGeneProduct denotes finding
T29 1219-1230 GeneOrGeneProduct denotes duplication
T30 1237-1241 GeneOrGeneProduct denotes full
T31 1288-1292 GeneOrGeneProduct denotes cost
T32 1336-1340 GeneOrGeneProduct denotes MLPA
T33 1362-1367 GeneOrGeneProduct denotes point
T34 1368-1377 GeneOrGeneProduct denotes mutations

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 46-50 GeneOrGeneProduct denotes MSH2
T2 55-59 GeneOrGeneProduct denotes MLH1
T3 101-105 GeneOrGeneProduct denotes MSH2
T4 110-114 GeneOrGeneProduct denotes MLH1
T5 172-177 GeneOrGeneProduct denotes HNPCC
T6 377-381 GeneOrGeneProduct denotes MLH1
T7 386-390 GeneOrGeneProduct denotes MSH2
T8 544-548 GeneOrGeneProduct denotes MLH1
T9 565-569 GeneOrGeneProduct denotes MSH2
T10 764-769 GeneOrGeneProduct denotes HNPCC
T11 932-936 GeneOrGeneProduct denotes MSH2
T12 1037-1050 GeneOrGeneProduct denotes recombination
T13 1141-1145 GeneOrGeneProduct denotes MLH1
T14 1150-1154 GeneOrGeneProduct denotes MSH2
T15 1167-1172 GeneOrGeneProduct denotes HNPCC

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 172-177 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T2 764-769 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T3 1167-1172 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 46-50 GeneOrGeneProduct denotes MSH2
T2 55-59 GeneOrGeneProduct denotes MLH1
T3 101-105 GeneOrGeneProduct denotes MSH2
T4 110-114 GeneOrGeneProduct denotes MLH1
T5 377-381 GeneOrGeneProduct denotes MLH1
T6 386-390 GeneOrGeneProduct denotes MSH2
T7 544-548 GeneOrGeneProduct denotes MLH1
T8 565-569 GeneOrGeneProduct denotes MSH2
T9 932-936 GeneOrGeneProduct denotes MSH2
T10 1141-1145 GeneOrGeneProduct denotes MLH1
T11 1150-1154 GeneOrGeneProduct denotes MSH2

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 172-177 DiseaseOrPhenotypicFeature denotes HNPCC 0018630
T2 764-769 DiseaseOrPhenotypicFeature denotes HNPCC 0018630
T3 1100-1103 DiseaseOrPhenotypicFeature denotes can 0012833
T4 1167-1172 DiseaseOrPhenotypicFeature denotes HNPCC 0018630

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 172-177 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T2 764-769 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T3 1167-1172 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 172-177 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T2 764-769 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T3 1167-1172 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 770-778 OrganismTaxon denotes patients
T2 868-875 OrganismTaxon denotes patient
T3 1173-1181 OrganismTaxon denotes patients

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label
T11 1150-1154 GeneOrGeneProduct denotes MSH2
T10 1141-1145 GeneOrGeneProduct denotes MLH1
T9 932-936 GeneOrGeneProduct denotes MSH2
T8 565-569 GeneOrGeneProduct denotes MSH2
T7 544-548 GeneOrGeneProduct denotes MLH1
T6 386-390 GeneOrGeneProduct denotes MSH2
T5 377-381 GeneOrGeneProduct denotes MLH1
T4 110-114 GeneOrGeneProduct denotes MLH1
T3 101-105 GeneOrGeneProduct denotes MSH2
T2 55-59 GeneOrGeneProduct denotes MLH1
T1 46-50 GeneOrGeneProduct denotes MSH2
T3928 1167-1172 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T91820 764-769 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T45079 172-177 DiseaseOrPhenotypicFeature denotes HNPCC DISEASE
T32182 1173-1181 OrganismTaxon denotes patients
T15786 868-875 OrganismTaxon denotes patient
T86915 770-778 OrganismTaxon denotes patients
T25583 887-904 SequenceVariant denotes deletion of about
T96994 57-64 SequenceVariant denotes H1 by M

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
15951966-6#55#59#gene4436 1150-1154 gene4436 denotes MSH2
15951966-6#72#77#diseaseC1333990 1167-1172 diseaseC1333990 denotes HNPCC
55#59#gene443672#77#diseaseC1333990 15951966-6#55#59#gene4436 15951966-6#72#77#diseaseC1333990 associated_with MSH2,HNPCC

DisGeNET

Id Subject Object Predicate Lexical cue
T0 386-390 gene:4436 denotes MSH2
T1 764-769 disease:C1333990 denotes HNPCC
R1 T0 T1 associated_with MSH2,HNPCC