Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2017-04-18

AUTHORS

Bhavik Mehta, Samantha Venables, Paul Roffey

ABSTRACT

Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA® (KAPA Biosystems) and NEBNext® (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext® kit obtained higher genotype concordance than KAPA®. The study also established an MPS workflow that can be utilised in any operational forensic laboratory. More... »

PAGES

125-132

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s00414-017-1591-9

DOI

http://dx.doi.org/10.1007/s00414-017-1591-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1084864718

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28417259


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": "DNA Fingerprinting", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genotype", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genotyping Techniques", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Magnets", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Specialist Operations \u2013 Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia", 
          "id": "http://www.grid.ac/institutes/grid.467687.c", 
          "name": [
            "National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, ACT 2617, Bruce, Australia", 
            "Specialist Operations \u2013 Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mehta", 
        "givenName": "Bhavik", 
        "id": "sg:person.014773625615.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014773625615.04"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Specialist Operations \u2013 Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia", 
          "id": "http://www.grid.ac/institutes/grid.467687.c", 
          "name": [
            "National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, ACT 2617, Bruce, Australia", 
            "Specialist Operations \u2013 Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Venables", 
        "givenName": "Samantha", 
        "id": "sg:person.0637346072.67", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637346072.67"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Specialist Operations \u2013 Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia", 
          "id": "http://www.grid.ac/institutes/grid.467687.c", 
          "name": [
            "National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, ACT 2617, Bruce, Australia", 
            "Specialist Operations \u2013 Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Roffey", 
        "givenName": "Paul", 
        "id": "sg:person.016653704641.72", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016653704641.72"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nrg2952", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048500546", 
          "https://doi.org/10.1038/nrg2952"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00414-016-1457-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017155642", 
          "https://doi.org/10.1007/s00414-016-1457-6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-13-341", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003392841", 
          "https://doi.org/10.1186/1471-2164-13-341"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2017-04-18", 
    "datePublishedReg": "2017-04-18", 
    "description": "Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq\u2122 DNA Signature Kit on MiSeq FGx\u2122 (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA\u00ae (KAPA Biosystems) and NEBNext\u00ae (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext\u00ae kit obtained higher genotype concordance than KAPA\u00ae. The study also established an MPS workflow that can be utilised in any operational forensic laboratory.", 
    "genre": "article", 
    "id": "sg:pub.10.1007/s00414-017-1591-9", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1013672", 
        "issn": [
          "0937-9827", 
          "1437-1596"
        ], 
        "name": "International Journal of Legal Medicine", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "132"
      }
    ], 
    "keywords": [
      "single nucleotide polymorphisms", 
      "short tandem repeats", 
      "Y-chromosome short tandem repeats", 
      "identity single nucleotide polymorphisms", 
      "library preparation procedure", 
      "autosomal short tandem repeats", 
      "DNA identity", 
      "X chromosome", 
      "DNA Signature kit", 
      "parallel sequencing", 
      "tandem repeats", 
      "MPS workflow", 
      "nucleotide polymorphisms", 
      "operational forensic laboratories", 
      "MiSeq FGx", 
      "analyse hundreds", 
      "qPCR chemistry", 
      "genotype concordance", 
      "higher genotype concordance", 
      "KAPA", 
      "target amplification", 
      "chromosomes", 
      "repeats", 
      "library purification", 
      "polymerase chain reaction method", 
      "chain reaction method", 
      "sequencing", 
      "multiple samples", 
      "NEBNext", 
      "series of steps", 
      "quantitative polymerase chain reaction method", 
      "qPCR", 
      "ForenSeq", 
      "magnetic beads", 
      "polymorphism", 
      "FGx", 
      "purification", 
      "amplification", 
      "markers", 
      "normalisation methods", 
      "forensic laboratories", 
      "hundreds", 
      "forensic science", 
      "identity", 
      "kit", 
      "workflow", 
      "study", 
      "profile", 
      "step", 
      "beads", 
      "comparison", 
      "concordance", 
      "laboratory", 
      "samples", 
      "MPS", 
      "preparation procedure", 
      "chemistry", 
      "method", 
      "use", 
      "series", 
      "capability", 
      "normalisation", 
      "science", 
      "reaction method", 
      "operational use", 
      "procedure", 
      "manufacturers"
    ], 
    "name": "Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping", 
    "pagination": "125-132", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1084864718"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s00414-017-1591-9"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "28417259"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s00414-017-1591-9", 
      "https://app.dimensions.ai/details/publication/pub.1084864718"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-12-01T06:35", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_729.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/s00414-017-1591-9"
  }
]
 

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/s00414-017-1591-9'

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/s00414-017-1591-9'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00414-017-1591-9'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00414-017-1591-9'


 

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

183 TRIPLES      21 PREDICATES      102 URIs      91 LITERALS      14 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s00414-017-1591-9 schema:about N0053d350217b4052a48a672dc344c420
2 N099b7513d28842d6a69ace5eae0f1c62
3 N5e2239f6f28d4313b917a14d688dcf63
4 N6171340b2f914c7f84443c07af567b8d
5 N68dc50d88f78424bb7d6821c61c71190
6 Nc1454cf3fff34fbab7258228d831a3fd
7 Nce6d0e0912af4f2fbcb6f683427908c3
8 anzsrc-for:06
9 anzsrc-for:0604
10 schema:author Nf05556039a424ebeb5b355f0e40c91ad
11 schema:citation sg:pub.10.1007/s00414-016-1457-6
12 sg:pub.10.1038/nrg2952
13 sg:pub.10.1186/1471-2164-13-341
14 schema:datePublished 2017-04-18
15 schema:datePublishedReg 2017-04-18
16 schema:description Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA® (KAPA Biosystems) and NEBNext® (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext® kit obtained higher genotype concordance than KAPA®. The study also established an MPS workflow that can be utilised in any operational forensic laboratory.
17 schema:genre article
18 schema:isAccessibleForFree false
19 schema:isPartOf N0abf768732d84df0b4fa4d97dd7ccfd7
20 Naa907bf466e3458996fb4f46f6ce005d
21 sg:journal.1013672
22 schema:keywords DNA Signature kit
23 DNA identity
24 FGx
25 ForenSeq
26 KAPA
27 MPS
28 MPS workflow
29 MiSeq FGx
30 NEBNext
31 X chromosome
32 Y-chromosome short tandem repeats
33 amplification
34 analyse hundreds
35 autosomal short tandem repeats
36 beads
37 capability
38 chain reaction method
39 chemistry
40 chromosomes
41 comparison
42 concordance
43 forensic laboratories
44 forensic science
45 genotype concordance
46 higher genotype concordance
47 hundreds
48 identity
49 identity single nucleotide polymorphisms
50 kit
51 laboratory
52 library preparation procedure
53 library purification
54 magnetic beads
55 manufacturers
56 markers
57 method
58 multiple samples
59 normalisation
60 normalisation methods
61 nucleotide polymorphisms
62 operational forensic laboratories
63 operational use
64 parallel sequencing
65 polymerase chain reaction method
66 polymorphism
67 preparation procedure
68 procedure
69 profile
70 purification
71 qPCR
72 qPCR chemistry
73 quantitative polymerase chain reaction method
74 reaction method
75 repeats
76 samples
77 science
78 sequencing
79 series
80 series of steps
81 short tandem repeats
82 single nucleotide polymorphisms
83 step
84 study
85 tandem repeats
86 target amplification
87 use
88 workflow
89 schema:name Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping
90 schema:pagination 125-132
91 schema:productId N5feb82cfa67f4a58b53de80ec7b63d6f
92 N7e95d4c2182f4124935e7578564cffa8
93 Nf0ebfcb3a05746aba2712ca854be5824
94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084864718
95 https://doi.org/10.1007/s00414-017-1591-9
96 schema:sdDatePublished 2022-12-01T06:35
97 schema:sdLicense https://scigraph.springernature.com/explorer/license/
98 schema:sdPublisher Nfac8e0cbb0e548c49f4ff04f4462be86
99 schema:url https://doi.org/10.1007/s00414-017-1591-9
100 sgo:license sg:explorer/license/
101 sgo:sdDataset articles
102 rdf:type schema:ScholarlyArticle
103 N0053d350217b4052a48a672dc344c420 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Genotyping Techniques
105 rdf:type schema:DefinedTerm
106 N03e9c0f43a8048d88740ec1e2373e544 rdf:first sg:person.0637346072.67
107 rdf:rest Nc0fcf1f9b2f04b93b5c48669d63ffcc0
108 N099b7513d28842d6a69ace5eae0f1c62 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name High-Throughput Nucleotide Sequencing
110 rdf:type schema:DefinedTerm
111 N0abf768732d84df0b4fa4d97dd7ccfd7 schema:issueNumber 1
112 rdf:type schema:PublicationIssue
113 N5e2239f6f28d4313b917a14d688dcf63 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
114 schema:name DNA Fingerprinting
115 rdf:type schema:DefinedTerm
116 N5feb82cfa67f4a58b53de80ec7b63d6f schema:name pubmed_id
117 schema:value 28417259
118 rdf:type schema:PropertyValue
119 N6171340b2f914c7f84443c07af567b8d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Genotype
121 rdf:type schema:DefinedTerm
122 N68dc50d88f78424bb7d6821c61c71190 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Polymerase Chain Reaction
124 rdf:type schema:DefinedTerm
125 N7e95d4c2182f4124935e7578564cffa8 schema:name dimensions_id
126 schema:value pub.1084864718
127 rdf:type schema:PropertyValue
128 Naa907bf466e3458996fb4f46f6ce005d schema:volumeNumber 132
129 rdf:type schema:PublicationVolume
130 Nc0fcf1f9b2f04b93b5c48669d63ffcc0 rdf:first sg:person.016653704641.72
131 rdf:rest rdf:nil
132 Nc1454cf3fff34fbab7258228d831a3fd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name Magnets
134 rdf:type schema:DefinedTerm
135 Nce6d0e0912af4f2fbcb6f683427908c3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Humans
137 rdf:type schema:DefinedTerm
138 Nf05556039a424ebeb5b355f0e40c91ad rdf:first sg:person.014773625615.04
139 rdf:rest N03e9c0f43a8048d88740ec1e2373e544
140 Nf0ebfcb3a05746aba2712ca854be5824 schema:name doi
141 schema:value 10.1007/s00414-017-1591-9
142 rdf:type schema:PropertyValue
143 Nfac8e0cbb0e548c49f4ff04f4462be86 schema:name Springer Nature - SN SciGraph project
144 rdf:type schema:Organization
145 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
146 schema:name Biological Sciences
147 rdf:type schema:DefinedTerm
148 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
149 schema:name Genetics
150 rdf:type schema:DefinedTerm
151 sg:journal.1013672 schema:issn 0937-9827
152 1437-1596
153 schema:name International Journal of Legal Medicine
154 schema:publisher Springer Nature
155 rdf:type schema:Periodical
156 sg:person.014773625615.04 schema:affiliation grid-institutes:grid.467687.c
157 schema:familyName Mehta
158 schema:givenName Bhavik
159 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014773625615.04
160 rdf:type schema:Person
161 sg:person.016653704641.72 schema:affiliation grid-institutes:grid.467687.c
162 schema:familyName Roffey
163 schema:givenName Paul
164 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016653704641.72
165 rdf:type schema:Person
166 sg:person.0637346072.67 schema:affiliation grid-institutes:grid.467687.c
167 schema:familyName Venables
168 schema:givenName Samantha
169 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637346072.67
170 rdf:type schema:Person
171 sg:pub.10.1007/s00414-016-1457-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017155642
172 https://doi.org/10.1007/s00414-016-1457-6
173 rdf:type schema:CreativeWork
174 sg:pub.10.1038/nrg2952 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048500546
175 https://doi.org/10.1038/nrg2952
176 rdf:type schema:CreativeWork
177 sg:pub.10.1186/1471-2164-13-341 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003392841
178 https://doi.org/10.1186/1471-2164-13-341
179 rdf:type schema:CreativeWork
180 grid-institutes:grid.467687.c schema:alternateName Specialist Operations – Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia
181 schema:name National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, ACT 2617, Bruce, Australia
182 Specialist Operations – Forensics, Australian Federal Police, Tambreet Street, ACT 2609, Majura, Australia
183 rdf:type schema:Organization
 




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


...