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PubMed:21219851 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-182 Sentence denotes A novel mutation screening system for Ehlers-Danlos Syndrome, vascular type by high-resolution melting curve analysis in combination with small amplicon genotyping using genomic DNA.
T2 183-331 Sentence denotes Ehlers-Danlos syndrome, vascular type (vEDS) (MIM #130050) is an autosomal dominant disorder caused by type III procollagen gene (COL3A1) mutations.
T3 332-459 Sentence denotes Most COL3A1 mutations are detected by using total RNA from patient-derived fibroblasts, which requires an invasive skin biopsy.
T4 460-674 Sentence denotes High-resolution melting curve analysis (hrMCA) has recently been developed as a post-PCR mutation scanning method which enables simple, rapid, cost-effective, and highly sensitive mutation screening of large genes.
T5 675-754 Sentence denotes We established a hrMCA method to screen for COL3A1 mutations using genomic DNA.
T6 755-887 Sentence denotes PCR primers pairs for COL3A1 (52 amplicons) were designed to cover all coding regions of the 52 exons, including the splicing sites.
T7 888-1000 Sentence denotes We used 15 DNA samples (8 validation samples and 7 samples of clinically suspected vEDS patients) in this study.
T8 1001-1100 Sentence denotes The eight known COL3A1 mutations in validation samples were all successfully detected by the hrMCA.
T9 1101-1297 Sentence denotes In addition, we identified five novel COL3A1 mutations, including one deletion (c.2187delA) and one nonsense mutation (c.2992C>T) that could not be determined by the conventional total RNA method.
T10 1298-1526 Sentence denotes Furthermore, we established a small amplicon genotyping (SAG) method for detecting three high frequency coding-region SNPs (rs1800255:G>A, rs1801184:T>C, and rs2271683:A>G) in COL3A1 to differentiate mutations before sequencing.
T11 1527-1666 Sentence denotes The use of hrMCA in combination with SAG from genomic DNA enables rapid detection of COL3A1 mutations with high efficiency and specificity.
T12 1667-1804 Sentence denotes A better understanding of the genotype-phenotype correlation in COL3A1 using this method will lead to improve in diagnosis and treatment.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 1355-1358 OrganismTaxon denotes SAG NCBItxid:59303
T2 1564-1567 OrganismTaxon denotes SAG NCBItxid:59303

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
8481 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type MESH:D004535
8482 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type MESH:D004535
8483 222-226 DiseaseOrPhenotypicFeature denotes vEDS MESH:D004535
8484 229-240 DiseaseOrPhenotypicFeature denotes MIM #130050 MESH:D004535
8485 248-275 DiseaseOrPhenotypicFeature denotes autosomal dominant disorder MESH:D030342
8486 286-306 GeneOrGeneProduct denotes type III procollagen NCBIGene:1281
8487 313-319 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8488 337-343 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8489 391-398 OrganismTaxon denotes patient NCBITaxon:9606
8490 719-725 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8491 777-783 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8492 971-975 DiseaseOrPhenotypicFeature denotes vEDS MESH:D004535
8493 976-984 OrganismTaxon denotes patients NCBITaxon:9606
8494 1017-1023 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8495 1139-1145 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8496 1181-1191 SequenceVariant denotes c.2187delA c|DEL|2187|A
8497 1220-1229 SequenceVariant denotes c.2992C>T c|SUB|C|2992|T
8498 1422-1431 SequenceVariant denotes rs1800255 DBSNP:rs1800255
8499 1432-1435 SequenceVariant denotes G>A DBSNP:rs1800255
8500 1437-1446 SequenceVariant denotes rs1801184 DBSNP:rs1801184
8501 1447-1450 SequenceVariant denotes T>C DBSNP:rs1801184
8502 1456-1465 SequenceVariant denotes rs2271683 DBSNP:rs2271683
8503 1466-1469 SequenceVariant denotes A>G DBSNP:rs2271683
8504 1474-1480 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8505 1612-1618 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281
8506 1731-1737 GeneOrGeneProduct denotes COL3A1 NCBIGene:1281

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type 0017314
T2 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type 0017314
T3 183-205 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome 0020066

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 1181-1191 SequenceVariant denotes c.2187delA
T2 1220-1229 SequenceVariant denotes c.2992C>T
T3 1422-1431 SequenceVariant denotes rs1800255
T4 1437-1446 SequenceVariant denotes rs1801184
T5 1456-1465 SequenceVariant denotes rs2271683

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 2-7 GeneOrGeneProduct denotes novel
T2 8-16 GeneOrGeneProduct denotes mutation
T3 52-60 GeneOrGeneProduct denotes Syndrome
T4 79-83 GeneOrGeneProduct denotes high
T5 95-102 GeneOrGeneProduct denotes melting
T6 103-108 GeneOrGeneProduct denotes curve
T7 138-143 GeneOrGeneProduct denotes small
T8 197-205 GeneOrGeneProduct denotes syndrome
T9 291-294 GeneOrGeneProduct denotes III
T10 295-306 GeneOrGeneProduct denotes procollagen
T11 313-319 GeneOrGeneProduct denotes COL3A1
T12 321-330 GeneOrGeneProduct denotes mutations
T13 337-343 GeneOrGeneProduct denotes COL3A1
T14 344-353 GeneOrGeneProduct denotes mutations
T15 376-381 GeneOrGeneProduct denotes total
T16 447-451 GeneOrGeneProduct denotes skin
T17 460-464 GeneOrGeneProduct denotes High
T18 476-483 GeneOrGeneProduct denotes melting
T19 484-489 GeneOrGeneProduct denotes curve
T20 540-544 GeneOrGeneProduct denotes post
T21 549-557 GeneOrGeneProduct denotes mutation
T22 567-573 GeneOrGeneProduct denotes method
T23 580-587 GeneOrGeneProduct denotes enables
T24 588-594 GeneOrGeneProduct denotes simple
T25 603-607 GeneOrGeneProduct denotes cost
T26 623-629 GeneOrGeneProduct denotes highly
T27 640-648 GeneOrGeneProduct denotes mutation
T28 662-667 GeneOrGeneProduct denotes large
T29 698-704 GeneOrGeneProduct denotes method
T30 719-725 GeneOrGeneProduct denotes COL3A1
T31 726-735 GeneOrGeneProduct denotes mutations
T32 767-772 GeneOrGeneProduct denotes pairs
T33 777-783 GeneOrGeneProduct denotes COL3A1
T34 822-825 GeneOrGeneProduct denotes all
T35 872-880 GeneOrGeneProduct denotes splicing
T36 1017-1023 GeneOrGeneProduct denotes COL3A1
T37 1024-1033 GeneOrGeneProduct denotes mutations
T38 1061-1064 GeneOrGeneProduct denotes all
T39 1133-1138 GeneOrGeneProduct denotes novel
T40 1139-1145 GeneOrGeneProduct denotes COL3A1
T41 1146-1155 GeneOrGeneProduct denotes mutations
T42 1210-1218 GeneOrGeneProduct denotes mutation
T43 1246-1259 GeneOrGeneProduct denotes be determined
T44 1280-1285 GeneOrGeneProduct denotes total
T45 1290-1296 GeneOrGeneProduct denotes method
T46 1328-1333 GeneOrGeneProduct denotes small
T47 1355-1358 GeneOrGeneProduct denotes SAG
T48 1360-1366 GeneOrGeneProduct denotes method
T49 1387-1391 GeneOrGeneProduct denotes high
T50 1392-1401 GeneOrGeneProduct denotes frequency
T51 1474-1480 GeneOrGeneProduct denotes COL3A1
T52 1498-1507 GeneOrGeneProduct denotes mutations
T53 1564-1567 GeneOrGeneProduct denotes SAG
T54 1585-1592 GeneOrGeneProduct denotes enables
T55 1612-1618 GeneOrGeneProduct denotes COL3A1
T56 1619-1628 GeneOrGeneProduct denotes mutations
T57 1634-1638 GeneOrGeneProduct denotes high
T58 1731-1737 GeneOrGeneProduct denotes COL3A1
T59 1749-1755 GeneOrGeneProduct denotes method

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 2-7 GeneOrGeneProduct denotes novel
T2 52-60 GeneOrGeneProduct denotes Syndrome
T3 79-83 GeneOrGeneProduct denotes high
T4 138-143 GeneOrGeneProduct denotes small
T5 197-205 GeneOrGeneProduct denotes syndrome
T6 295-306 GeneOrGeneProduct denotes procollagen
T7 313-319 GeneOrGeneProduct denotes COL3A1
T8 337-343 GeneOrGeneProduct denotes COL3A1
T9 540-544 GeneOrGeneProduct denotes post
T10 567-573 GeneOrGeneProduct denotes method
T11 662-667 GeneOrGeneProduct denotes large
T12 698-704 GeneOrGeneProduct denotes method
T13 719-725 GeneOrGeneProduct denotes COL3A1
T14 777-783 GeneOrGeneProduct denotes COL3A1
T15 1017-1023 GeneOrGeneProduct denotes COL3A1
T16 1133-1138 GeneOrGeneProduct denotes novel
T17 1139-1145 GeneOrGeneProduct denotes COL3A1
T18 1290-1296 GeneOrGeneProduct denotes method
T19 1328-1333 GeneOrGeneProduct denotes small
T20 1355-1358 GeneOrGeneProduct denotes SAG
T21 1360-1366 GeneOrGeneProduct denotes method
T22 1387-1391 GeneOrGeneProduct denotes high
T23 1392-1401 GeneOrGeneProduct denotes frequency
T24 1474-1480 GeneOrGeneProduct denotes COL3A1
T25 1564-1567 GeneOrGeneProduct denotes SAG
T26 1612-1618 GeneOrGeneProduct denotes COL3A1
T27 1634-1638 GeneOrGeneProduct denotes high
T28 1731-1737 GeneOrGeneProduct denotes COL3A1
T29 1749-1755 GeneOrGeneProduct denotes method

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type D004535
T2 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type D004535
T3 248-275 DiseaseOrPhenotypicFeature denotes autosomal dominant disorder DISEASE

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 295-306 GeneOrGeneProduct denotes procollagen
T2 313-319 GeneOrGeneProduct denotes COL3A1
T3 337-343 GeneOrGeneProduct denotes COL3A1
T4 719-725 GeneOrGeneProduct denotes COL3A1
T5 777-783 GeneOrGeneProduct denotes COL3A1
T6 1017-1023 GeneOrGeneProduct denotes COL3A1
T7 1139-1145 GeneOrGeneProduct denotes COL3A1
T8 1355-1358 GeneOrGeneProduct denotes SAG
T9 1474-1480 GeneOrGeneProduct denotes COL3A1
T10 1564-1567 GeneOrGeneProduct denotes SAG
T11 1612-1618 GeneOrGeneProduct denotes COL3A1
T12 1731-1737 GeneOrGeneProduct denotes COL3A1

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type 0017314|0007524
T3 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type 0017314|0007524
T5 222-226 DiseaseOrPhenotypicFeature denotes vEDS 0017314
T6 447-451 DiseaseOrPhenotypicFeature denotes skin 0002531
T7 630-639 DiseaseOrPhenotypicFeature denotes sensitive 0000605
T8 971-975 DiseaseOrPhenotypicFeature denotes vEDS 0017314

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type D004535
T2 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type D004535
T3 222-226 DiseaseOrPhenotypicFeature denotes vEDS DISEASE
T4 229-240 DiseaseOrPhenotypicFeature denotes MIM #130050 DISEASE
T5 248-275 DiseaseOrPhenotypicFeature denotes autosomal dominant disorder DISEASE
T6 971-975 DiseaseOrPhenotypicFeature denotes vEDS DISEASE

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type D004535
T2 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type D004535
T3 222-226 DiseaseOrPhenotypicFeature denotes vEDS DISEASE
T4 229-240 DiseaseOrPhenotypicFeature denotes MIM #130050 DISEASE
T5 248-275 DiseaseOrPhenotypicFeature denotes autosomal dominant disorder DISEASE
T6 971-975 DiseaseOrPhenotypicFeature denotes vEDS DISEASE

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 391-398 OrganismTaxon denotes patient
T2 976-984 OrganismTaxon denotes patients

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 1355-1358 ChemicalEntity denotes SAG http://purl.obolibrary.org/obo/CHEBI_138438
T2 1564-1567 ChemicalEntity denotes SAG http://purl.obolibrary.org/obo/CHEBI_138438
T3 1761-1765 ChemicalEntity denotes lead D007854

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T3 1761-1765 ChemicalEntity denotes lead D007854
T2 1564-1567 ChemicalEntity denotes SAG http://purl.obolibrary.org/obo/CHEBI_138438
T1 1355-1358 ChemicalEntity denotes SAG http://purl.obolibrary.org/obo/CHEBI_138438
T12 1731-1737 GeneOrGeneProduct denotes COL3A1
T11 1612-1618 GeneOrGeneProduct denotes COL3A1
T10 1564-1567 GeneOrGeneProduct denotes SAG
T9 1474-1480 GeneOrGeneProduct denotes COL3A1
T8 1355-1358 GeneOrGeneProduct denotes SAG
T7 1139-1145 GeneOrGeneProduct denotes COL3A1
T6 1017-1023 GeneOrGeneProduct denotes COL3A1
T5 777-783 GeneOrGeneProduct denotes COL3A1
T4 719-725 GeneOrGeneProduct denotes COL3A1
T27668 337-343 GeneOrGeneProduct denotes COL3A1
T55142 313-319 GeneOrGeneProduct denotes COL3A1
T57369 295-306 GeneOrGeneProduct denotes procollagen
T93608 971-975 DiseaseOrPhenotypicFeature denotes vEDS DISEASE
T32104 248-275 DiseaseOrPhenotypicFeature denotes autosomal dominant disorder DISEASE
T35010 229-240 DiseaseOrPhenotypicFeature denotes MIM #130050 DISEASE
T37080 222-226 DiseaseOrPhenotypicFeature denotes vEDS DISEASE
T64173 183-220 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos syndrome, vascular type D004535
T70985 38-75 DiseaseOrPhenotypicFeature denotes Ehlers-Danlos Syndrome, vascular type D004535
T65371 976-984 OrganismTaxon denotes patients
T3696 391-398 OrganismTaxon denotes patient
T71565 1456-1465 SequenceVariant denotes rs2271683
T83194 1437-1446 SequenceVariant denotes rs1801184
T55173 1422-1431 SequenceVariant denotes rs1800255
T13559 1220-1229 SequenceVariant denotes c.2992C>T
T99805 1181-1191 SequenceVariant denotes c.2187delA

DisGeNET

Id Subject Object Predicate Lexical cue
T0 313-319 gene:1281 denotes COL3A1
T1 183-220 disease:C0268338 denotes Ehlers-Danlos syndrome, vascular type
T2 313-319 gene:1281 denotes COL3A1
T3 222-226 disease:C0268338 denotes vEDS
R1 T0 T1 associated_with COL3A1,"Ehlers-Danlos syndrome, vascular type"
R2 T2 T3 associated_with COL3A1,vEDS

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 248-266 HP_0000006 denotes autosomal dominant

Allie

Id Subject Object Predicate Lexical cue
SS1_21219851_3_0 460-498 expanded denotes High-resolution melting curve analysis
SS2_21219851_3_0 500-505 abbr denotes hrMCA
SS1_21219851_9_0 1328-1353 expanded denotes small amplicon genotyping
SS2_21219851_9_0 1355-1358 abbr denotes SAG
AE1_21219851_3_0 SS1_21219851_3_0 SS2_21219851_3_0 abbreviatedTo High-resolution melting curve analysis,hrMCA
AE1_21219851_9_0 SS1_21219851_9_0 SS2_21219851_9_0 abbreviatedTo small amplicon genotyping,SAG

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
21219851-1#130#136#gene1281 313-319 gene1281 denotes COL3A1
21219851-1#0#37#diseaseC0268338 183-220 diseaseC0268338 denotes Ehlers-Danlos syndrome, vascular type
21219851-1#39#43#diseaseC0268338 222-226 diseaseC0268338 denotes vEDS
130#136#gene12810#37#diseaseC0268338 21219851-1#130#136#gene1281 21219851-1#0#37#diseaseC0268338 associated_with COL3A1,"Ehlers-Danlos syndrome, vascular type"
130#136#gene128139#43#diseaseC0268338 21219851-1#130#136#gene1281 21219851-1#39#43#diseaseC0268338 associated_with COL3A1,vEDS

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 1181-1191 DNAMutation:c|DEL|2187|A denotes c.2187delA
T2 1220-1229 DNAMutation:c|SUB|C|2992|T denotes c.2992C>T
T3 1422-1431 SNP:rs1800255 denotes rs1800255
T4 1432-1435 DNAMutation:|SUB|G||A denotes G>A
T5 1437-1446 SNP:rs1801184 denotes rs1801184
T6 1447-1450 DNAMutation:|SUB|T||C denotes T>C
T7 1456-1465 SNP:rs2271683 denotes rs2271683
T8 1466-1469 DNAMutation:|SUB|A||G denotes A>G

PubTator4TogoVar

Id Subject Object Predicate Lexical cue resolved_to
41 1422-1431 SNP denotes rs1800255 tmVar:rs1800255;VariantGroup:0;CorrespondingGene:1281;RS#:1800255;CorrespondingSpecies:9606
43 1437-1446 SNP denotes rs1801184 tmVar:rs1801184;VariantGroup:2;CorrespondingGene:1281;RS#:1801184;CorrespondingSpecies:9606
45 1456-1465 SNP denotes rs2271683 tmVar:rs2271683;VariantGroup:1;CorrespondingGene:1281;RS#:2271683;CorrespondingSpecies:9606

PubTatorOnTogoVar

Id Subject Object Predicate Lexical cue resolved_to
41 1422-1431 SNP denotes rs1800255 tmVar:rs1800255;VariantGroup:0;CorrespondingGene:1281;RS#:1800255;CorrespondingSpecies:9606
43 1437-1446 SNP denotes rs1801184 tmVar:rs1801184;VariantGroup:2;CorrespondingGene:1281;RS#:1801184;CorrespondingSpecies:9606
45 1456-1465 SNP denotes rs2271683 tmVar:rs2271683;VariantGroup:1;CorrespondingGene:1281;RS#:2271683;CorrespondingSpecies:9606
T1 1422-1431 SNP denotes rs1800255 tmVar:rs1800255;VariantGroup:0;CorrespondingGene:1281;RS#:1800255;CorrespondingSpecies:9606
T2 1437-1446 SNP denotes rs1801184 tmVar:rs1801184;VariantGroup:2;CorrespondingGene:1281;RS#:1801184;CorrespondingSpecies:9606
T3 1456-1465 SNP denotes rs2271683 tmVar:rs2271683;VariantGroup:1;CorrespondingGene:1281;RS#:2271683;CorrespondingSpecies:9606