Multiple Locus Variable Number of Tandem Repeats Analysis View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2009-03-16

AUTHORS

Gilles Vergnaud , Christine Pourcel

ABSTRACT

Genotyping of bacteria through typing of loci containing a variable number of tandem repeats (VNTR) might become the gold standard for many pathogens. The development of genome sequencing has shown that such sequences were present in every species analyzed, and that polymorphism exists in at least a fraction of them. The length of these repetitions can vary from a single nucleotide to a few hundreds. This has implications for both the techniques used to measure the repeat number and the level of variability. In addition, tandem repeats can be part of coding regions or be intergenic and may play a direct role in the adaptation to the environment, thus having different observed evolution rates. For these reasons the choice of VNTR when setting a multiple-loci VNTR analysis (MLVA) assay is important. Although reasonable discrimination can be achieved with the typing of six to eight markers, in particular in species with high genomic diversity, it may be necessary to type 20 to 40 markers in monomorphic species or if an evolutionary meaningful assay is needed. Homoplasy (in the present context, two alleles containing the same repeat copy number in spite of a different history) is then compensated by the analysis of multiple markers. Finally, even if the underlying principles are relatively simple, quality standards must be implemented before this approach is widely accepted, and technology issues must be resolved to further lower the typing costs. More... »

PAGES

141-158

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_12

DOI

http://dx.doi.org/10.1007/978-1-60327-999-4_12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1045439358

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19521873


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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Electrophoresis, Agar Gel", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Electrophoresis, Capillary", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Minisatellite Repeats", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Epidemiology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "DGA/D4S -Mission pour la Recherche et l\u2019Innovation Scientifique (MRIS), Arm\u00e9es, and Department of Genetics and Microbiology, University of Paris XI, Orsay, France", 
          "id": "http://www.grid.ac/institutes/grid.5842.b", 
          "name": [
            "DGA/D4S -Mission pour la Recherche et l\u2019Innovation Scientifique (MRIS), Arm\u00e9es, and Department of Genetics and Microbiology, University of Paris XI, Orsay, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vergnaud", 
        "givenName": "Gilles", 
        "id": "sg:person.01366533021.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366533021.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Genetics and Microbiology, University of Paris XI, Orsay, France", 
          "id": "http://www.grid.ac/institutes/grid.5842.b", 
          "name": [
            "Department of Genetics and Microbiology, University of Paris XI, Orsay, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pourcel", 
        "givenName": "Christine", 
        "id": "sg:person.01021627421.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021627421.49"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2009-03-16", 
    "datePublishedReg": "2009-03-16", 
    "description": "Genotyping of bacteria through typing of loci containing a variable number of tandem repeats (VNTR) might become the gold standard for many pathogens. The development of genome sequencing has shown that such sequences were present in every species analyzed, and that polymorphism exists in at least a fraction of them. The length of these repetitions can vary from a single nucleotide to a few hundreds. This has implications for both the techniques used to measure the repeat number and the level of variability. In addition, tandem repeats can be part of coding regions or be intergenic and may play a direct role in the adaptation to the environment, thus having different observed evolution rates. For these reasons the choice of VNTR when setting a multiple-loci VNTR analysis (MLVA) assay is important. Although reasonable discrimination can be achieved with the typing of six to eight markers, in particular in species with high genomic diversity, it may be necessary to type 20 to 40 markers in monomorphic species or if an evolutionary meaningful assay is needed. Homoplasy (in the present context, two alleles containing the same repeat copy number in spite of a different history) is then compensated by the analysis of multiple markers. Finally, even if the underlying principles are relatively simple, quality standards must be implemented before this approach is widely accepted, and technology issues must be resolved to further lower the typing costs.", 
    "editor": [
      {
        "familyName": "Caugant", 
        "givenName": "Dominique A.", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-60327-999-4_12", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-60327-998-7", 
        "978-1-60327-999-4"
      ], 
      "name": "Molecular Epidemiology of Microorganisms", 
      "type": "Book"
    }, 
    "keywords": [
      "multiple-locus VNTR analysis", 
      "tandem repeats", 
      "high genomic diversity", 
      "monomorphic species", 
      "genomic diversity", 
      "genome sequencing", 
      "multiple locus variable number", 
      "single nucleotide", 
      "level of variability", 
      "typing cost", 
      "repeat number", 
      "variable number", 
      "direct role", 
      "species", 
      "repeats", 
      "tandem repeat analysis", 
      "VNTR analysis", 
      "repeat analysis", 
      "such sequences", 
      "evolution rate", 
      "multiple markers", 
      "homoplasy", 
      "markers", 
      "loci", 
      "sequencing", 
      "nucleotides", 
      "diversity", 
      "bacteria", 
      "pathogens", 
      "sequence", 
      "meaningful assays", 
      "polymorphism", 
      "assays", 
      "adaptation", 
      "VNTR", 
      "role", 
      "typing", 
      "analysis", 
      "hundreds", 
      "number", 
      "region", 
      "variability", 
      "development", 
      "levels", 
      "environment", 
      "addition", 
      "fraction", 
      "length", 
      "part", 
      "implications", 
      "discrimination", 
      "rate", 
      "approach", 
      "quality standards", 
      "reasons", 
      "technique", 
      "principles", 
      "choice", 
      "repetition", 
      "reasonable discrimination", 
      "cost", 
      "issues", 
      "gold standard", 
      "standards", 
      "technology issues", 
      "typing of loci", 
      "different observed evolution rates", 
      "observed evolution rates", 
      "choice of VNTR", 
      "evolutionary meaningful assay", 
      "Locus Variable Number"
    ], 
    "name": "Multiple Locus Variable Number of Tandem Repeats Analysis", 
    "pagination": "141-158", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1045439358"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-60327-999-4_12"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19521873"
        ]
      }
    ], 
    "publisher": {
      "name": "Springer Nature", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-60327-999-4_12", 
      "https://app.dimensions.ai/details/publication/pub.1045439358"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2022-01-01T19:12", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/chapter/chapter_217.jsonl", 
    "type": "Chapter", 
    "url": "https://doi.org/10.1007/978-1-60327-999-4_12"
  }
]
 

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.10.1007/978-1-60327-999-4_12'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_12'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_12'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-60327-999-4_12'


 

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

180 TRIPLES      23 PREDICATES      106 URIs      99 LITERALS      17 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-60327-999-4_12 schema:about N14daf8c9ac6f45178801368a784127d4
2 N16a28ce426234eb1ac7339178c25123c
3 N31b7c2c58b2f4dbf856e0b5a58f417b2
4 N5bbbb5f05bfb4c70888a1fbfbc5ec6b2
5 N62b27d1be4b14534a5eb6894086cc85f
6 N65283dfeb14f4518af47691e90520ab9
7 Nd2bc30afa0de4d69b5690cf104ab7cd4
8 Ne5ffb4a656ef4c34a495ee4b7ce1070f
9 Neacaf73ee1824c39975c481ce5b432a9
10 anzsrc-for:06
11 anzsrc-for:0604
12 schema:author N55069c5be0944f28a6a9d0d0b1ad8e0c
13 schema:datePublished 2009-03-16
14 schema:datePublishedReg 2009-03-16
15 schema:description Genotyping of bacteria through typing of loci containing a variable number of tandem repeats (VNTR) might become the gold standard for many pathogens. The development of genome sequencing has shown that such sequences were present in every species analyzed, and that polymorphism exists in at least a fraction of them. The length of these repetitions can vary from a single nucleotide to a few hundreds. This has implications for both the techniques used to measure the repeat number and the level of variability. In addition, tandem repeats can be part of coding regions or be intergenic and may play a direct role in the adaptation to the environment, thus having different observed evolution rates. For these reasons the choice of VNTR when setting a multiple-loci VNTR analysis (MLVA) assay is important. Although reasonable discrimination can be achieved with the typing of six to eight markers, in particular in species with high genomic diversity, it may be necessary to type 20 to 40 markers in monomorphic species or if an evolutionary meaningful assay is needed. Homoplasy (in the present context, two alleles containing the same repeat copy number in spite of a different history) is then compensated by the analysis of multiple markers. Finally, even if the underlying principles are relatively simple, quality standards must be implemented before this approach is widely accepted, and technology issues must be resolved to further lower the typing costs.
16 schema:editor N3002d155f32e4a0588d3ec1bd48d7f14
17 schema:genre chapter
18 schema:inLanguage en
19 schema:isAccessibleForFree false
20 schema:isPartOf N4d9f73caafce43d2b340af540d661365
21 schema:keywords Locus Variable Number
22 VNTR
23 VNTR analysis
24 adaptation
25 addition
26 analysis
27 approach
28 assays
29 bacteria
30 choice
31 choice of VNTR
32 cost
33 development
34 different observed evolution rates
35 direct role
36 discrimination
37 diversity
38 environment
39 evolution rate
40 evolutionary meaningful assay
41 fraction
42 genome sequencing
43 genomic diversity
44 gold standard
45 high genomic diversity
46 homoplasy
47 hundreds
48 implications
49 issues
50 length
51 level of variability
52 levels
53 loci
54 markers
55 meaningful assays
56 monomorphic species
57 multiple locus variable number
58 multiple markers
59 multiple-locus VNTR analysis
60 nucleotides
61 number
62 observed evolution rates
63 part
64 pathogens
65 polymorphism
66 principles
67 quality standards
68 rate
69 reasonable discrimination
70 reasons
71 region
72 repeat analysis
73 repeat number
74 repeats
75 repetition
76 role
77 sequence
78 sequencing
79 single nucleotide
80 species
81 standards
82 such sequences
83 tandem repeat analysis
84 tandem repeats
85 technique
86 technology issues
87 typing
88 typing cost
89 typing of loci
90 variability
91 variable number
92 schema:name Multiple Locus Variable Number of Tandem Repeats Analysis
93 schema:pagination 141-158
94 schema:productId N33b1c91c86d04968b325a5f13e37a6be
95 N3ff53991456446679d2e352369535410
96 N7f1cffa2f3c1466d89454815858c3475
97 schema:publisher N33fbe2c69bdd4e2eb8b0a81f3fd2e0c4
98 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045439358
99 https://doi.org/10.1007/978-1-60327-999-4_12
100 schema:sdDatePublished 2022-01-01T19:12
101 schema:sdLicense https://scigraph.springernature.com/explorer/license/
102 schema:sdPublisher N578649615a5a49a98fa827aed4e56eac
103 schema:url https://doi.org/10.1007/978-1-60327-999-4_12
104 sgo:license sg:explorer/license/
105 sgo:sdDataset chapters
106 rdf:type schema:Chapter
107 N14daf8c9ac6f45178801368a784127d4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Molecular Epidemiology
109 rdf:type schema:DefinedTerm
110 N16a28ce426234eb1ac7339178c25123c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Genome, Bacterial
112 rdf:type schema:DefinedTerm
113 N3002d155f32e4a0588d3ec1bd48d7f14 rdf:first N6f3c242a2c29488bb6b43a167706ed67
114 rdf:rest rdf:nil
115 N31b7c2c58b2f4dbf856e0b5a58f417b2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Bacteria
117 rdf:type schema:DefinedTerm
118 N33b1c91c86d04968b325a5f13e37a6be schema:name doi
119 schema:value 10.1007/978-1-60327-999-4_12
120 rdf:type schema:PropertyValue
121 N33fbe2c69bdd4e2eb8b0a81f3fd2e0c4 schema:name Springer Nature
122 rdf:type schema:Organisation
123 N3ff53991456446679d2e352369535410 schema:name dimensions_id
124 schema:value pub.1045439358
125 rdf:type schema:PropertyValue
126 N4d9f73caafce43d2b340af540d661365 schema:isbn 978-1-60327-998-7
127 978-1-60327-999-4
128 schema:name Molecular Epidemiology of Microorganisms
129 rdf:type schema:Book
130 N55069c5be0944f28a6a9d0d0b1ad8e0c rdf:first sg:person.01366533021.19
131 rdf:rest N5a91572f7468429db8513d59f6dea8fa
132 N578649615a5a49a98fa827aed4e56eac schema:name Springer Nature - SN SciGraph project
133 rdf:type schema:Organization
134 N5a91572f7468429db8513d59f6dea8fa rdf:first sg:person.01021627421.49
135 rdf:rest rdf:nil
136 N5bbbb5f05bfb4c70888a1fbfbc5ec6b2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
137 schema:name Humans
138 rdf:type schema:DefinedTerm
139 N62b27d1be4b14534a5eb6894086cc85f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
140 schema:name Electrophoresis, Capillary
141 rdf:type schema:DefinedTerm
142 N65283dfeb14f4518af47691e90520ab9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Minisatellite Repeats
144 rdf:type schema:DefinedTerm
145 N6f3c242a2c29488bb6b43a167706ed67 schema:familyName Caugant
146 schema:givenName Dominique A.
147 rdf:type schema:Person
148 N7f1cffa2f3c1466d89454815858c3475 schema:name pubmed_id
149 schema:value 19521873
150 rdf:type schema:PropertyValue
151 Nd2bc30afa0de4d69b5690cf104ab7cd4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
152 schema:name Electrophoresis, Agar Gel
153 rdf:type schema:DefinedTerm
154 Ne5ffb4a656ef4c34a495ee4b7ce1070f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
155 schema:name DNA, Bacterial
156 rdf:type schema:DefinedTerm
157 Neacaf73ee1824c39975c481ce5b432a9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Polymerase Chain Reaction
159 rdf:type schema:DefinedTerm
160 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
161 schema:name Biological Sciences
162 rdf:type schema:DefinedTerm
163 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
164 schema:name Genetics
165 rdf:type schema:DefinedTerm
166 sg:person.01021627421.49 schema:affiliation grid-institutes:grid.5842.b
167 schema:familyName Pourcel
168 schema:givenName Christine
169 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021627421.49
170 rdf:type schema:Person
171 sg:person.01366533021.19 schema:affiliation grid-institutes:grid.5842.b
172 schema:familyName Vergnaud
173 schema:givenName Gilles
174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366533021.19
175 rdf:type schema:Person
176 grid-institutes:grid.5842.b schema:alternateName DGA/D4S -Mission pour la Recherche et l’Innovation Scientifique (MRIS), Armées, and Department of Genetics and Microbiology, University of Paris XI, Orsay, France
177 Department of Genetics and Microbiology, University of Paris XI, Orsay, France
178 schema:name DGA/D4S -Mission pour la Recherche et l’Innovation Scientifique (MRIS), Armées, and Department of Genetics and Microbiology, University of Paris XI, Orsay, France
179 Department of Genetics and Microbiology, University of Paris XI, Orsay, France
180 rdf:type schema:Organization
 




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


...