MersV1, PubMed, Checkpoint, bibRecord, 000E45

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.

Identifieur interne : 000E45 ( PubMed/Checkpoint ); précédent : 000E44; suivant : 000E46

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.

Auteurs : Samuel O. Oyola [Royaume-Uni] ; Cristina V. Ariani [Royaume-Uni] ; William L. Hamilton [Royaume-Uni] ; Mihir Kekre [Royaume-Uni] ; Lucas N. Amenga-Etego [Ghana] ; Anita Ghansah [Ghana] ; Gavin G. Rutledge [Royaume-Uni] ; Seth Redmond [États-Unis] ; Magnus Manske [Royaume-Uni] ; Dushyanth Jyothi [Royaume-Uni] ; Chris G. Jacob [Royaume-Uni] ; Thomas D. Otto [Royaume-Uni] ; Kirk Rockett [Royaume-Uni] ; Chris I. Newbold [Royaume-Uni] ; Matthew Berriman [Royaume-Uni] ; Dominic P. Kwiatkowski [Royaume-Uni]

Source :

Malaria journal [ 1475-2875 ] ; 2016.

RBID : pubmed:27998271

Descripteurs français

KwdFr :
- ADN des protozoaires (), ADN des protozoaires (génétique), ADN des protozoaires (isolement et purification), Amorces ADN (génétique), Analyse de séquence d'ADN, Dessiccation, Génome de protozoaire, Humains, Plasmodium falciparum (génétique), Plasmodium falciparum (isolement et purification), Prélèvement biologique (), Sang (parasitologie), Techniques d'amplification d'acides nucléiques ().
MESH :
- génétique : ADN des protozoaires, Amorces ADN, Plasmodium falciparum.
- isolement et purification : ADN des protozoaires, Plasmodium falciparum.
- parasitologie : Sang.
- ADN des protozoaires, Analyse de séquence d'ADN, Dessiccation, Génome de protozoaire, Humains, Prélèvement biologique, Techniques d'amplification d'acides nucléiques.

English descriptors

KwdEn :
- Blood (parasitology), DNA Primers (genetics), DNA, Protozoan (chemistry), DNA, Protozoan (genetics), DNA, Protozoan (isolation & purification), Desiccation, Genome, Protozoan, Humans, Nucleic Acid Amplification Techniques (methods), Plasmodium falciparum (genetics), Plasmodium falciparum (isolation & purification), Sequence Analysis, DNA, Specimen Handling (methods).
MESH :
- chemical , chemistry : DNA, Protozoan.
- chemical , genetics : DNA Primers, DNA, Protozoan.
- chemical , isolation & purification : DNA, Protozoan.
- genetics : Plasmodium falciparum.
- isolation & purification : Plasmodium falciparum.
- methods : Nucleic Acid Amplification Techniques, Specimen Handling.
- parasitology : Blood.
- Desiccation, Genome, Protozoan, Humans, Sequence Analysis, DNA.

Abstract

Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB.

DOI: 10.1186/s12936-016-1641-7
PubMed: 27998271

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<author><name sortKey="Jyothi, Dushyanth" sort="Jyothi, Dushyanth" uniqKey="Jyothi D" first="Dushyanth" last="Jyothi">Dushyanth Jyothi</name>
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<author><name sortKey="Rockett, Kirk" sort="Rockett, Kirk" uniqKey="Rockett K" first="Kirk" last="Rockett">Kirk Rockett</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Blood (parasitology)</term>
<term>DNA Primers (genetics)</term>
<term>DNA, Protozoan (chemistry)</term>
<term>DNA, Protozoan (genetics)</term>
<term>DNA, Protozoan (isolation & purification)</term>
<term>Desiccation</term>
<term>Genome, Protozoan</term>
<term>Humans</term>
<term>Nucleic Acid Amplification Techniques (methods)</term>
<term>Plasmodium falciparum (genetics)</term>
<term>Plasmodium falciparum (isolation & purification)</term>
<term>Sequence Analysis, DNA</term>
<term>Specimen Handling (methods)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN des protozoaires ()</term>
<term>ADN des protozoaires (génétique)</term>
<term>ADN des protozoaires (isolement et purification)</term>
<term>Amorces ADN (génétique)</term>
<term>Analyse de séquence d'ADN</term>
<term>Dessiccation</term>
<term>Génome de protozoaire</term>
<term>Humains</term>
<term>Plasmodium falciparum (génétique)</term>
<term>Plasmodium falciparum (isolement et purification)</term>
<term>Prélèvement biologique ()</term>
<term>Sang (parasitologie)</term>
<term>Techniques d'amplification d'acides nucléiques ()</term>
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<term>DNA, Protozoan</term>
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<keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Protozoan</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plasmodium falciparum</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des protozoaires</term>
<term>Amorces ADN</term>
<term>Plasmodium falciparum</term>
</keywords>
<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Plasmodium falciparum</term>
</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN des protozoaires</term>
<term>Plasmodium falciparum</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Nucleic Acid Amplification Techniques</term>
<term>Specimen Handling</term>
</keywords>
<keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Sang</term>
</keywords>
<keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Blood</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Desiccation</term>
<term>Genome, Protozoan</term>
<term>Humans</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ADN des protozoaires</term>
<term>Analyse de séquence d'ADN</term>
<term>Dessiccation</term>
<term>Génome de protozoaire</term>
<term>Humains</term>
<term>Prélèvement biologique</term>
<term>Techniques d'amplification d'acides nucléiques</term>
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<front><div type="abstract" xml:lang="en">Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27998271</PMID>
<DateCompleted><Year>2017</Year>
<Month>05</Month>
<Day>22</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1475-2875</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>15</Volume>
<Issue>1</Issue>
<PubDate><Year>2016</Year>
<Month>Dec</Month>
<Day>20</Day>
</PubDate>
</JournalIssue>
<Title>Malaria journal</Title>
<ISOAbbreviation>Malar. J.</ISOAbbreviation>
</Journal>
<ArticleTitle>Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.</ArticleTitle>
<Pagination><MedlinePgn>597</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12936-016-1641-7</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB.</AbstractText>
<AbstractText Label="METHODS" NlmCategory="METHODS">Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls.</AbstractText>
<AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Oyola</LastName>
<ForeName>Samuel O</ForeName>
<Initials>SO</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. so1@sanger.ac.uk.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>International Livestock Research Institute, Box 30709, Nairobi, Kenya. so1@sanger.ac.uk.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ariani</LastName>
<ForeName>Cristina V</ForeName>
<Initials>CV</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. cristina.ariani@sanger.ac.uk.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hamilton</LastName>
<ForeName>William L</ForeName>
<Initials>WL</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Addenbrooke's Hospital, University of Cambridge School of Clinical Medicine, Hills Rd, Cambridge, CB2 0SP, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kekre</LastName>
<ForeName>Mihir</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Amenga-Etego</LastName>
<ForeName>Lucas N</ForeName>
<Initials>LN</Initials>
<AffiliationInfo><Affiliation>Navrongo Health Research Centre, Post Office Box 114, Navrongo, Ghana.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ghansah</LastName>
<ForeName>Anita</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Noguchi Memorial Institute for Medical Research, University of Ghana, P. O. Box LG 581, Legon, Accra, Ghana.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Rutledge</LastName>
<ForeName>Gavin G</ForeName>
<Initials>GG</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Redmond</LastName>
<ForeName>Seth</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Broad Institute, 415 Main St, Cambridge, MA, 02142, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Manske</LastName>
<ForeName>Magnus</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jyothi</LastName>
<ForeName>Dushyanth</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jacob</LastName>
<ForeName>Chris G</ForeName>
<Initials>CG</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Otto</LastName>
<ForeName>Thomas D</ForeName>
<Initials>TD</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Rockett</LastName>
<ForeName>Kirk</ForeName>
<Initials>K</Initials>
<AffiliationInfo><Affiliation>MRC Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Newbold</LastName>
<ForeName>Chris I</ForeName>
<Initials>CI</Initials>
<AffiliationInfo><Affiliation>Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Berriman</LastName>
<ForeName>Matthew</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kwiatkowski</LastName>
<ForeName>Dominic P</ForeName>
<Initials>DP</Initials>
<AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>MRC Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>G0600718</GrantID>
<Agency>Medical Research Council</Agency>
<Country>United Kingdom</Country>
</Grant>
<Grant><GrantID>MR/M006212/1</GrantID>
<Agency>Medical Research Council</Agency>
<Country>United Kingdom</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2016</Year>
<Month>12</Month>
<Day>20</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Malar J</MedlineTA>
<NlmUniqueID>101139802</NlmUniqueID>
<ISSNLinking>1475-2875</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D016054">DNA, Protozoan</NameOfSubstance>
</Chemical>
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<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D001769" MajorTopicYN="N">Blood</DescriptorName>
<QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName>
</MeshHeading>
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<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
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<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D003890" MajorTopicYN="Y">Desiccation</DescriptorName>
</MeshHeading>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D021141" MajorTopicYN="N">Nucleic Acid Amplification Techniques</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010963" MajorTopicYN="N">Plasmodium falciparum</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
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</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Dried blood spot</Keyword>
<Keyword MajorTopicYN="Y">Field samples</Keyword>
<Keyword MajorTopicYN="Y">Malaria</Keyword>
<Keyword MajorTopicYN="Y">Selective whole genome amplification</Keyword>
<Keyword MajorTopicYN="Y">Whole genome sequencing</Keyword>
</KeywordList>
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Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.

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