Modeling of PTPN22 and HLA-DRB1 susceptibility to rheumatoid arthritis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-12-18

AUTHORS

France Gagnon, David Hajage, Sabine Plancoulaine, Sophie Tezenas du Montcel

ABSTRACT

In the present paper, we used the North American Rheumatoid Arthritis Consortium data provided for Genetic Analysis Workshop 15 Problem 2 to: 1) estimate the penetrances of PTPN22 and HLA-DRB1 and, 2) test the selected model of PTPN22 conditional on the rheumatoid factor status. To achieve these aims, we used the marker association segregation chi-square method, fitting simultaneously both genotype frequency and identical by descent distributions in a sample of 3690 White individuals from 604 nuclear families. A co-dominant model fitted the rs2476601 (R620W) single-nucleotide polymorphism (SNP) of the PTPN22 gene well, whereas a lack of fit for all models was observed for the HLA-DRB1 locus. Testing genetic models of rheumatoid arthritis that include the PTPN22 SNP in addition to the HLA-DRB1 locus did not affect the results, nor did subgroup analysis of PTPN22 conditional on the rheumatoid factor status. In conclusion, PTPN22 R620W SNP is a risk factor for rheumatoid arthritis. The genetic architecture of the HLA-DRB1 locus is highly complex, and more elaborate modeling of this locus is required. More... »

PAGES

s14

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1753-6561-1-s1-s14

DOI

http://dx.doi.org/10.1186/1753-6561-1-s1-s14

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1003406240

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18466483


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Public Health Sciences, Faculty of Medicine, University of Toronto, 155 College Street, M5T 3M7, Toronto, Ontario, Canada", 
          "id": "http://www.grid.ac/institutes/grid.17063.33", 
          "name": [
            "Department of Public Health Sciences, Faculty of Medicine, University of Toronto, 155 College Street, M5T 3M7, Toronto, Ontario, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gagnon", 
        "givenName": "France", 
        "id": "sg:person.01021200231.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021200231.89"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Universit\u00e9 Pierre et Marie Curie-Paris 6, EA3974 Mod\u00e9lisation en Recherche Clinique, F-75013, Paris, France", 
          "id": "http://www.grid.ac/institutes/grid.462844.8", 
          "name": [
            "Universit\u00e9 Pierre et Marie Curie-Paris 6, EA3974 Mod\u00e9lisation en Recherche Clinique, F-75013, Paris, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hajage", 
        "givenName": "David", 
        "id": "sg:person.0625635603.54", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0625635603.54"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratoire de G\u00e9n\u00e9tique Humaine des Maladies Infectieuses, Facult\u00e9 de M\u00e9decine Ren\u00e9 Descartes, Universit\u00e9 de Paris Ren\u00e9 Descartes, site Necker, F-75015, Paris, France", 
          "id": "http://www.grid.ac/institutes/grid.463939.2", 
          "name": [
            "INSERM, U550, F-75015, Paris, France", 
            "Laboratoire de G\u00e9n\u00e9tique Humaine des Maladies Infectieuses, Facult\u00e9 de M\u00e9decine Ren\u00e9 Descartes, Universit\u00e9 de Paris Ren\u00e9 Descartes, site Necker, F-75015, Paris, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Plancoulaine", 
        "givenName": "Sabine", 
        "id": "sg:person.0725733235.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0725733235.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "D\u00e9partement de Sant\u00e9 Publique, Unit\u00e9 de Biostatistique et Information M\u00e9dicale, AP-HP, Groupe Hospitalier Piti\u00e9-Salp\u00e9tri\u00e8re, F-75013, Paris, France", 
          "id": "http://www.grid.ac/institutes/grid.411439.a", 
          "name": [
            "Universit\u00e9 Pierre et Marie Curie-Paris 6, EA3974 Mod\u00e9lisation en Recherche Clinique, F-75013, Paris, France", 
            "D\u00e9partement de Sant\u00e9 Publique, Unit\u00e9 de Biostatistique et Information M\u00e9dicale, AP-HP, Groupe Hospitalier Piti\u00e9-Salp\u00e9tri\u00e8re, F-75013, Paris, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tezenas du Montcel", 
        "givenName": "Sophie", 
        "id": "sg:person.01341210565.74", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01341210565.74"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/s00439-006-0171-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005782071", 
          "https://doi.org/10.1007/s00439-006-0171-8"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2007-12-18", 
    "datePublishedReg": "2007-12-18", 
    "description": "In the present paper, we used the North American Rheumatoid Arthritis Consortium data provided for Genetic Analysis Workshop 15 Problem 2 to: 1) estimate the penetrances of PTPN22 and HLA-DRB1 and, 2) test the selected model of PTPN22 conditional on the rheumatoid factor status. To achieve these aims, we used the marker association segregation chi-square method, fitting simultaneously both genotype frequency and identical by descent distributions in a sample of 3690 White individuals from 604 nuclear families. A co-dominant model fitted the rs2476601 (R620W) single-nucleotide polymorphism (SNP) of the PTPN22 gene well, whereas a lack of fit for all models was observed for the HLA-DRB1 locus. Testing genetic models of rheumatoid arthritis that include the PTPN22 SNP in addition to the HLA-DRB1 locus did not affect the results, nor did subgroup analysis of PTPN22 conditional on the rheumatoid factor status. In conclusion, PTPN22 R620W SNP is a risk factor for rheumatoid arthritis. The genetic architecture of the HLA-DRB1 locus is highly complex, and more elaborate modeling of this locus is required.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1753-6561-1-s1-s14", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1039047", 
        "issn": [
          "1753-6561"
        ], 
        "name": "BMC Proceedings", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "Suppl 1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "1"
      }
    ], 
    "keywords": [
      "single nucleotide polymorphisms", 
      "North American Rheumatoid Arthritis Consortium data", 
      "genetic architecture", 
      "Genetic Analysis Workshop 15 Problem 2", 
      "loci", 
      "genetic model", 
      "PTPN22 gene", 
      "Consortium data", 
      "PTPN22", 
      "PTPN22 single nucleotide polymorphisms", 
      "descent distributions", 
      "genotype frequencies", 
      "rs2476601 single-nucleotide polymorphism", 
      "genes", 
      "rheumatoid factor status", 
      "HLA-DRB1 locus", 
      "polymorphism", 
      "penetrance", 
      "factor status", 
      "rheumatoid arthritis", 
      "R620W single-nucleotide polymorphism", 
      "family", 
      "nuclear families", 
      "co-dominant model", 
      "subgroup analysis", 
      "risk factors", 
      "HLA-DRB1", 
      "susceptibility", 
      "Problem 2", 
      "arthritis", 
      "white individuals", 
      "status", 
      "individuals", 
      "addition", 
      "factors", 
      "marker association segregation chi-square (MASC) method", 
      "chi-square method", 
      "distribution", 
      "analysis", 
      "lack", 
      "data", 
      "model", 
      "architecture", 
      "results", 
      "conclusion", 
      "aim", 
      "samples", 
      "lack of fit", 
      "frequency", 
      "modeling", 
      "present paper", 
      "conditional", 
      "method", 
      "fit", 
      "paper", 
      "elaborate modeling", 
      "American Rheumatoid Arthritis Consortium data", 
      "Rheumatoid Arthritis Consortium data", 
      "Arthritis Consortium data", 
      "Analysis Workshop 15 Problem 2", 
      "Workshop 15 Problem 2", 
      "penetrances of PTPN22", 
      "PTPN22 conditional", 
      "association segregation chi-square method", 
      "segregation chi-square method", 
      "PTPN22 R620W SNP", 
      "Modeling of PTPN22", 
      "HLA-DRB1 susceptibility"
    ], 
    "name": "Modeling of PTPN22 and HLA-DRB1 susceptibility to rheumatoid arthritis", 
    "pagination": "s14", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1003406240"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1753-6561-1-s1-s14"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18466483"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1753-6561-1-s1-s14", 
      "https://app.dimensions.ai/details/publication/pub.1003406240"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-11-01T18:11", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_451.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1753-6561-1-s1-s14"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1753-6561-1-s1-s14'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1753-6561-1-s1-s14'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1753-6561-1-s1-s14'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1753-6561-1-s1-s14'


 

This table displays all metadata directly associated to this object as RDF triples.

165 TRIPLES      22 PREDICATES      95 URIs      86 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1753-6561-1-s1-s14 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N6c17c0d7f97d42579a8d3cceae5dac75
4 schema:citation sg:pub.10.1007/s00439-006-0171-8
5 schema:datePublished 2007-12-18
6 schema:datePublishedReg 2007-12-18
7 schema:description In the present paper, we used the North American Rheumatoid Arthritis Consortium data provided for Genetic Analysis Workshop 15 Problem 2 to: 1) estimate the penetrances of PTPN22 and HLA-DRB1 and, 2) test the selected model of PTPN22 conditional on the rheumatoid factor status. To achieve these aims, we used the marker association segregation chi-square method, fitting simultaneously both genotype frequency and identical by descent distributions in a sample of 3690 White individuals from 604 nuclear families. A co-dominant model fitted the rs2476601 (R620W) single-nucleotide polymorphism (SNP) of the PTPN22 gene well, whereas a lack of fit for all models was observed for the HLA-DRB1 locus. Testing genetic models of rheumatoid arthritis that include the PTPN22 SNP in addition to the HLA-DRB1 locus did not affect the results, nor did subgroup analysis of PTPN22 conditional on the rheumatoid factor status. In conclusion, PTPN22 R620W SNP is a risk factor for rheumatoid arthritis. The genetic architecture of the HLA-DRB1 locus is highly complex, and more elaborate modeling of this locus is required.
8 schema:genre article
9 schema:inLanguage en
10 schema:isAccessibleForFree true
11 schema:isPartOf N4fe9313a88a14736949e0ff410727b4d
12 N6a163c825e274845b1352eed63f1ced1
13 sg:journal.1039047
14 schema:keywords American Rheumatoid Arthritis Consortium data
15 Analysis Workshop 15 Problem 2
16 Arthritis Consortium data
17 Consortium data
18 Genetic Analysis Workshop 15 Problem 2
19 HLA-DRB1
20 HLA-DRB1 locus
21 HLA-DRB1 susceptibility
22 Modeling of PTPN22
23 North American Rheumatoid Arthritis Consortium data
24 PTPN22
25 PTPN22 R620W SNP
26 PTPN22 conditional
27 PTPN22 gene
28 PTPN22 single nucleotide polymorphisms
29 Problem 2
30 R620W single-nucleotide polymorphism
31 Rheumatoid Arthritis Consortium data
32 Workshop 15 Problem 2
33 addition
34 aim
35 analysis
36 architecture
37 arthritis
38 association segregation chi-square method
39 chi-square method
40 co-dominant model
41 conclusion
42 conditional
43 data
44 descent distributions
45 distribution
46 elaborate modeling
47 factor status
48 factors
49 family
50 fit
51 frequency
52 genes
53 genetic architecture
54 genetic model
55 genotype frequencies
56 individuals
57 lack
58 lack of fit
59 loci
60 marker association segregation chi-square (MASC) method
61 method
62 model
63 modeling
64 nuclear families
65 paper
66 penetrance
67 penetrances of PTPN22
68 polymorphism
69 present paper
70 results
71 rheumatoid arthritis
72 rheumatoid factor status
73 risk factors
74 rs2476601 single-nucleotide polymorphism
75 samples
76 segregation chi-square method
77 single nucleotide polymorphisms
78 status
79 subgroup analysis
80 susceptibility
81 white individuals
82 schema:name Modeling of PTPN22 and HLA-DRB1 susceptibility to rheumatoid arthritis
83 schema:pagination s14
84 schema:productId N70eee520809747b3b6d4361790105e6a
85 N85630803c91d47c48e7ccfd371e12acc
86 Nc82a720a20c7474eaa5fbd958b287a2f
87 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003406240
88 https://doi.org/10.1186/1753-6561-1-s1-s14
89 schema:sdDatePublished 2021-11-01T18:11
90 schema:sdLicense https://scigraph.springernature.com/explorer/license/
91 schema:sdPublisher Nbc1457441bc64695afdf0087ce62e24a
92 schema:url https://doi.org/10.1186/1753-6561-1-s1-s14
93 sgo:license sg:explorer/license/
94 sgo:sdDataset articles
95 rdf:type schema:ScholarlyArticle
96 N31b900a6d43243059ba32ebac0815301 rdf:first sg:person.0625635603.54
97 rdf:rest N8592d5dbe32545889e7a93456e8ef6a6
98 N4fe9313a88a14736949e0ff410727b4d schema:volumeNumber 1
99 rdf:type schema:PublicationVolume
100 N6a163c825e274845b1352eed63f1ced1 schema:issueNumber Suppl 1
101 rdf:type schema:PublicationIssue
102 N6c17c0d7f97d42579a8d3cceae5dac75 rdf:first sg:person.01021200231.89
103 rdf:rest N31b900a6d43243059ba32ebac0815301
104 N7097d0bd00c14380ad2e5b5f23f2c5a6 rdf:first sg:person.01341210565.74
105 rdf:rest rdf:nil
106 N70eee520809747b3b6d4361790105e6a schema:name pubmed_id
107 schema:value 18466483
108 rdf:type schema:PropertyValue
109 N85630803c91d47c48e7ccfd371e12acc schema:name doi
110 schema:value 10.1186/1753-6561-1-s1-s14
111 rdf:type schema:PropertyValue
112 N8592d5dbe32545889e7a93456e8ef6a6 rdf:first sg:person.0725733235.14
113 rdf:rest N7097d0bd00c14380ad2e5b5f23f2c5a6
114 Nbc1457441bc64695afdf0087ce62e24a schema:name Springer Nature - SN SciGraph project
115 rdf:type schema:Organization
116 Nc82a720a20c7474eaa5fbd958b287a2f schema:name dimensions_id
117 schema:value pub.1003406240
118 rdf:type schema:PropertyValue
119 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
120 schema:name Biological Sciences
121 rdf:type schema:DefinedTerm
122 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
123 schema:name Genetics
124 rdf:type schema:DefinedTerm
125 sg:journal.1039047 schema:issn 1753-6561
126 schema:name BMC Proceedings
127 schema:publisher Springer Nature
128 rdf:type schema:Periodical
129 sg:person.01021200231.89 schema:affiliation grid-institutes:grid.17063.33
130 schema:familyName Gagnon
131 schema:givenName France
132 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021200231.89
133 rdf:type schema:Person
134 sg:person.01341210565.74 schema:affiliation grid-institutes:grid.411439.a
135 schema:familyName Tezenas du Montcel
136 schema:givenName Sophie
137 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01341210565.74
138 rdf:type schema:Person
139 sg:person.0625635603.54 schema:affiliation grid-institutes:grid.462844.8
140 schema:familyName Hajage
141 schema:givenName David
142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0625635603.54
143 rdf:type schema:Person
144 sg:person.0725733235.14 schema:affiliation grid-institutes:grid.463939.2
145 schema:familyName Plancoulaine
146 schema:givenName Sabine
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0725733235.14
148 rdf:type schema:Person
149 sg:pub.10.1007/s00439-006-0171-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005782071
150 https://doi.org/10.1007/s00439-006-0171-8
151 rdf:type schema:CreativeWork
152 grid-institutes:grid.17063.33 schema:alternateName Department of Public Health Sciences, Faculty of Medicine, University of Toronto, 155 College Street, M5T 3M7, Toronto, Ontario, Canada
153 schema:name Department of Public Health Sciences, Faculty of Medicine, University of Toronto, 155 College Street, M5T 3M7, Toronto, Ontario, Canada
154 rdf:type schema:Organization
155 grid-institutes:grid.411439.a schema:alternateName Département de Santé Publique, Unité de Biostatistique et Information Médicale, AP-HP, Groupe Hospitalier Pitié-Salpétrière, F-75013, Paris, France
156 schema:name Département de Santé Publique, Unité de Biostatistique et Information Médicale, AP-HP, Groupe Hospitalier Pitié-Salpétrière, F-75013, Paris, France
157 Université Pierre et Marie Curie-Paris 6, EA3974 Modélisation en Recherche Clinique, F-75013, Paris, France
158 rdf:type schema:Organization
159 grid-institutes:grid.462844.8 schema:alternateName Université Pierre et Marie Curie-Paris 6, EA3974 Modélisation en Recherche Clinique, F-75013, Paris, France
160 schema:name Université Pierre et Marie Curie-Paris 6, EA3974 Modélisation en Recherche Clinique, F-75013, Paris, France
161 rdf:type schema:Organization
162 grid-institutes:grid.463939.2 schema:alternateName Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine René Descartes, Université de Paris René Descartes, site Necker, F-75015, Paris, France
163 schema:name INSERM, U550, F-75015, Paris, France
164 Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine René Descartes, Université de Paris René Descartes, site Necker, F-75015, Paris, France
165 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...