Characterization of the MICA polymorphism by sequence-specific oligonucleotide probing View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1999-05

AUTHORS

Jorge Mendoza-Rincon, J. Rafael Argüello, Martha Pérez-Rodríguez, Alasdair McWhinnie, Steven G. E. Marsh, Gaby Fischer, J. A. Madrigal

ABSTRACT

A large number of diseases occur in association with specific HLA-B or -C alleles. Recently a new gene, termed major histocompatibility complex class I chain-related gene A (MICA), has been identified in close proximity to HLA-B. The function of this gene is still unknown, but, it is structurally related to HLA class I genes, is polymorphic, and is potentially associated with several diseases. Some DNA-based techniques have previously been described to type for MICA including sequencing and single-strand conformational polymorphism. In this paper we describe the application of sequence-specific oligonucleotide probe based typing for the analysis of the MICA gene. We used a set of 30 oligonucleotide probes to screen for the polymorphisms in exons 2, 3, and 4, which account for the 16 known alleles. We report here the typing results of MICA for 103 B-cell lines that have been well characterized for HLA and describe the linkage disequilibrium between MICA and HLA-B. Unequivocal MICA typing was achieved for 85 of the 103 cells tested, 6 cells gave ambiguous MICA types, and a further 12 cells showed patterns consistent with them expressing at least one new MICA allele. More... »

PAGES

471-478

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s002510050523

DOI

http://dx.doi.org/10.1007/s002510050523

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010047498

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/10380690


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Alleles", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "HLA-B Antigens", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Histocompatibility Antigens Class I", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Linkage Disequilibrium", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotide Probes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymorphism, Genetic", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mendoza-Rincon", 
        "givenName": "Jorge", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Arg\u00fcello", 
        "givenName": "J. Rafael", 
        "id": "sg:person.0736141775.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0736141775.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "P\u00e9rez-Rodr\u00edguez", 
        "givenName": "Martha", 
        "id": "sg:person.01361654070.42", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01361654070.42"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McWhinnie", 
        "givenName": "Alasdair", 
        "id": "sg:person.0666760500.31", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666760500.31"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Marsh", 
        "givenName": "Steven G. E.", 
        "id": "sg:person.011602344371.96", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011602344371.96"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fischer", 
        "givenName": "Gaby", 
        "id": "sg:person.016327265402.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016327265402.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3\u20092QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Madrigal", 
        "givenName": "J. A.", 
        "id": "sg:person.07465546124.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07465546124.13"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "1999-05", 
    "datePublishedReg": "1999-05-01", 
    "description": "A large number of diseases occur in association with specific HLA-B or -C alleles. Recently a new gene, termed major histocompatibility complex class I chain-related gene A (MICA), has been identified in close proximity to HLA-B. The function of this gene is still unknown, but, it is structurally related to HLA class I genes, is polymorphic, and is potentially associated with several diseases. Some DNA-based techniques have previously been described to type for MICA including sequencing and single-strand conformational polymorphism. In this paper we describe the application of sequence-specific oligonucleotide probe based typing for the analysis of the MICA gene. We used a set of 30 oligonucleotide probes to screen for the polymorphisms in exons 2, 3, and 4, which account for the 16 known alleles. We report here the typing results of MICA for 103 B-cell lines that have been well characterized for HLA and describe the linkage disequilibrium between MICA and HLA-B. Unequivocal MICA typing was achieved for 85 of the 103 cells tested, 6 cells gave ambiguous MICA types, and a further 12 cells showed patterns consistent with them expressing at least one new MICA allele.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/s002510050523", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1019755", 
        "issn": [
          "0093-7711", 
          "1432-1211"
        ], 
        "name": "Immunogenetics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "49"
      }
    ], 
    "name": "Characterization of the MICA polymorphism by sequence-specific oligonucleotide probing", 
    "pagination": "471-478", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "2fddbdc29ae741615f5b2121134c151c664e095ba20c06e89a82cd151407779d"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "10380690"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0420404"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s002510050523"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1010047498"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s002510050523", 
      "https://app.dimensions.ai/details/publication/pub.1010047498"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T13:04", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8659_00000480.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007/s002510050523"
  }
]
 

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.10.1007/s002510050523'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s002510050523'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s002510050523'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s002510050523'


 

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

149 TRIPLES      20 PREDICATES      36 URIs      28 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s002510050523 schema:about N07c3269e67de412c9da94a267ebb5c62
2 N0cb6e30f2c21475592fe834a5296b16a
3 N264b002aaa9e4ed8afd09d822342ad9f
4 N34a40ebc10ba41a38d006daa1878708c
5 N4d5a42328891401d8c525ffc78454b1f
6 N8052d45349204c059be60b1a131fb386
7 Nd8ad36c29a054f5f95d69a4ab5474a00
8 anzsrc-for:06
9 anzsrc-for:0604
10 schema:author N48556376a965430491b3fcbc26e236dd
11 schema:datePublished 1999-05
12 schema:datePublishedReg 1999-05-01
13 schema:description A large number of diseases occur in association with specific HLA-B or -C alleles. Recently a new gene, termed major histocompatibility complex class I chain-related gene A (MICA), has been identified in close proximity to HLA-B. The function of this gene is still unknown, but, it is structurally related to HLA class I genes, is polymorphic, and is potentially associated with several diseases. Some DNA-based techniques have previously been described to type for MICA including sequencing and single-strand conformational polymorphism. In this paper we describe the application of sequence-specific oligonucleotide probe based typing for the analysis of the MICA gene. We used a set of 30 oligonucleotide probes to screen for the polymorphisms in exons 2, 3, and 4, which account for the 16 known alleles. We report here the typing results of MICA for 103 B-cell lines that have been well characterized for HLA and describe the linkage disequilibrium between MICA and HLA-B. Unequivocal MICA typing was achieved for 85 of the 103 cells tested, 6 cells gave ambiguous MICA types, and a further 12 cells showed patterns consistent with them expressing at least one new MICA allele.
14 schema:genre research_article
15 schema:inLanguage en
16 schema:isAccessibleForFree false
17 schema:isPartOf N543ef9422d864cdc8f83cee2e191a5c0
18 N54fa7ca7fe884bbab7e70b08d6991e28
19 sg:journal.1019755
20 schema:name Characterization of the MICA polymorphism by sequence-specific oligonucleotide probing
21 schema:pagination 471-478
22 schema:productId N74b4b17b164845e7b4ab1b02894e277c
23 Nba3f8bc226844e9f9a1f01e5376aeac5
24 Nca50db5d62804c619e3bad356f6cbb8c
25 Ncc2be1b6a0ca4688ac2c915dd5c08591
26 Nf29cab5326ca45fc95b445f8801239b0
27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010047498
28 https://doi.org/10.1007/s002510050523
29 schema:sdDatePublished 2019-04-10T13:04
30 schema:sdLicense https://scigraph.springernature.com/explorer/license/
31 schema:sdPublisher Nf702deef65c6435fa6d2c3b71da4d286
32 schema:url http://link.springer.com/10.1007/s002510050523
33 sgo:license sg:explorer/license/
34 sgo:sdDataset articles
35 rdf:type schema:ScholarlyArticle
36 N06744e93083c4b5896c3e444d3715da3 rdf:first sg:person.01361654070.42
37 rdf:rest N84c886a3ccec42728d7099fd04c61bd3
38 N06bb85ae031041db8f5c1114200abd18 schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
39 rdf:type schema:Organization
40 N07c3269e67de412c9da94a267ebb5c62 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
41 schema:name Histocompatibility Antigens Class I
42 rdf:type schema:DefinedTerm
43 N0cb6e30f2c21475592fe834a5296b16a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
44 schema:name HLA-B Antigens
45 rdf:type schema:DefinedTerm
46 N0daeaf505a8649249981a7337caf323e rdf:first sg:person.011602344371.96
47 rdf:rest N44e7e12e5d5d4c11986e155a1840433d
48 N264b002aaa9e4ed8afd09d822342ad9f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
49 schema:name Humans
50 rdf:type schema:DefinedTerm
51 N34a40ebc10ba41a38d006daa1878708c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
52 schema:name Linkage Disequilibrium
53 rdf:type schema:DefinedTerm
54 N40943247c5c04f3282d548dfc7781fc8 rdf:first sg:person.07465546124.13
55 rdf:rest rdf:nil
56 N44e7e12e5d5d4c11986e155a1840433d rdf:first sg:person.016327265402.16
57 rdf:rest N40943247c5c04f3282d548dfc7781fc8
58 N48556376a965430491b3fcbc26e236dd rdf:first Nb6b7e66559094c8faba4ef360f5a08d5
59 rdf:rest Nede8ecd406ce42998215a8c5fc057d23
60 N4d5a42328891401d8c525ffc78454b1f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
61 schema:name Oligonucleotide Probes
62 rdf:type schema:DefinedTerm
63 N543ef9422d864cdc8f83cee2e191a5c0 schema:issueNumber 6
64 rdf:type schema:PublicationIssue
65 N54fa7ca7fe884bbab7e70b08d6991e28 schema:volumeNumber 49
66 rdf:type schema:PublicationVolume
67 N5f57c81ece644ffc8acda3885a42f1ef schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
68 rdf:type schema:Organization
69 N72ad0d20de0c42c081b77ab69755b0e7 schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
70 rdf:type schema:Organization
71 N731e0efcaf154fc68af31d0738e6d906 schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
72 rdf:type schema:Organization
73 N74b4b17b164845e7b4ab1b02894e277c schema:name nlm_unique_id
74 schema:value 0420404
75 rdf:type schema:PropertyValue
76 N8052d45349204c059be60b1a131fb386 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
77 schema:name Alleles
78 rdf:type schema:DefinedTerm
79 N84c886a3ccec42728d7099fd04c61bd3 rdf:first sg:person.0666760500.31
80 rdf:rest N0daeaf505a8649249981a7337caf323e
81 Naadf0f24d54c4484988cdc952a8b1de6 schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
82 rdf:type schema:Organization
83 Nb6b7e66559094c8faba4ef360f5a08d5 schema:affiliation Nead7d561ead9498ab95acea8b6794902
84 schema:familyName Mendoza-Rincon
85 schema:givenName Jorge
86 rdf:type schema:Person
87 Nba3f8bc226844e9f9a1f01e5376aeac5 schema:name readcube_id
88 schema:value 2fddbdc29ae741615f5b2121134c151c664e095ba20c06e89a82cd151407779d
89 rdf:type schema:PropertyValue
90 Nca50db5d62804c619e3bad356f6cbb8c schema:name dimensions_id
91 schema:value pub.1010047498
92 rdf:type schema:PropertyValue
93 Ncc2be1b6a0ca4688ac2c915dd5c08591 schema:name pubmed_id
94 schema:value 10380690
95 rdf:type schema:PropertyValue
96 Nd8ad36c29a054f5f95d69a4ab5474a00 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Polymorphism, Genetic
98 rdf:type schema:DefinedTerm
99 Ne20fbbcf678c498e99209082564f5827 schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
100 rdf:type schema:Organization
101 Nead7d561ead9498ab95acea8b6794902 schema:name Anthony Nolan Research Institute, The Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK E-mail: madrigal@rfhsm.ac.uk, Tel.: +44-171-2848315, Fax: +44-171-2848331, GB
102 rdf:type schema:Organization
103 Nede8ecd406ce42998215a8c5fc057d23 rdf:first sg:person.0736141775.13
104 rdf:rest N06744e93083c4b5896c3e444d3715da3
105 Nf29cab5326ca45fc95b445f8801239b0 schema:name doi
106 schema:value 10.1007/s002510050523
107 rdf:type schema:PropertyValue
108 Nf702deef65c6435fa6d2c3b71da4d286 schema:name Springer Nature - SN SciGraph project
109 rdf:type schema:Organization
110 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
111 schema:name Biological Sciences
112 rdf:type schema:DefinedTerm
113 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
114 schema:name Genetics
115 rdf:type schema:DefinedTerm
116 sg:journal.1019755 schema:issn 0093-7711
117 1432-1211
118 schema:name Immunogenetics
119 rdf:type schema:Periodical
120 sg:person.011602344371.96 schema:affiliation Ne20fbbcf678c498e99209082564f5827
121 schema:familyName Marsh
122 schema:givenName Steven G. E.
123 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011602344371.96
124 rdf:type schema:Person
125 sg:person.01361654070.42 schema:affiliation N06bb85ae031041db8f5c1114200abd18
126 schema:familyName Pérez-Rodríguez
127 schema:givenName Martha
128 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01361654070.42
129 rdf:type schema:Person
130 sg:person.016327265402.16 schema:affiliation Naadf0f24d54c4484988cdc952a8b1de6
131 schema:familyName Fischer
132 schema:givenName Gaby
133 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016327265402.16
134 rdf:type schema:Person
135 sg:person.0666760500.31 schema:affiliation N72ad0d20de0c42c081b77ab69755b0e7
136 schema:familyName McWhinnie
137 schema:givenName Alasdair
138 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666760500.31
139 rdf:type schema:Person
140 sg:person.0736141775.13 schema:affiliation N5f57c81ece644ffc8acda3885a42f1ef
141 schema:familyName Argüello
142 schema:givenName J. Rafael
143 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0736141775.13
144 rdf:type schema:Person
145 sg:person.07465546124.13 schema:affiliation N731e0efcaf154fc68af31d0738e6d906
146 schema:familyName Madrigal
147 schema:givenName J. A.
148 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07465546124.13
149 rdf:type schema:Person
 




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


...