MersV1, Main, Exploration, bibRecord, 000F56

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

Identifieur interne : 000F56 ( Main/Exploration ); précédent : 000F55; suivant : 000F57

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

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

Source :

Malaria Journal [ 1475-2875 ] ; 2016.

RBID : PMC:5175302

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

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.

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.

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.

Conclusion

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1641-7) contains supplementary material, which is available to authorized users.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175302

DOI: 10.1186/s12936-016-1641-7
PubMed: 27998271
PubMed Central: 5175302

Affiliations:

Le document en format XML

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<author><name sortKey="Oyola, Samuel O" sort="Oyola, Samuel O" uniqKey="Oyola S" first="Samuel O." last="Oyola">Samuel O. Oyola</name>
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<wicri:noCountry code="subfield">CB10 1SA UK</wicri:noCountry>
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<wicri:noCountry code="subfield">CB10 1SA UK</wicri:noCountry>
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<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>
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<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" qualifier="genetics" xml:lang="en"><term>Plasmodium falciparum</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des protozoaires</term>
<term>Amorces ADN</term>
<term>Plasmodium falciparum</term>
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<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Plasmodium falciparum</term>
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<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN des protozoaires</term>
<term>Plasmodium falciparum</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Nucleic Acid Amplification Techniques</term>
<term>Specimen Handling</term>
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<keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Sang</term>
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<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>
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<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"><sec><title>Background</title>
<p>Translating genomic technologies into healthcare applications for the malaria parasite <italic>Plasmodium falciparum</italic>
 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 <italic>P. falciparum</italic>
 genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB.</p>
</sec>
<sec><title>Methods</title>
<p>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 (<italic>P. falciparum</italic>
 DNA) and contaminating (human) genomes.</p>
</sec>
<sec><title>Results</title>
<p>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 <italic>P. falciparum</italic>
 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.</p>
</sec>
<sec><title>Conclusion</title>
<p>The sWGA methods described here provide a reliable and scalable way of generating <italic>P. falciparum</italic>
 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 <italic>P. falciparum</italic>
 genome sequencing from field samples, and paves the way for large-scale epidemiological applications.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12936-016-1641-7) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<li>Kenya</li>
<li>Royaume-Uni</li>
<li>États-Unis</li>
</country>
<region><li>Angleterre</li>
<li>Massachusetts</li>
<li>Oxfordshire</li>
<li>Région du Grand Accra</li>
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<li>Oxford</li>
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<li>Université du Ghana</li>
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</region>
<name sortKey="Kwiatkowski, Dominic P" sort="Kwiatkowski, Dominic P" uniqKey="Kwiatkowski D" first="Dominic P." last="Kwiatkowski">Dominic P. Kwiatkowski</name>
<name sortKey="Kwiatkowski, Dominic P" sort="Kwiatkowski, Dominic P" uniqKey="Kwiatkowski D" first="Dominic P." last="Kwiatkowski">Dominic P. Kwiatkowski</name>
<name sortKey="Newbold, Chris I" sort="Newbold, Chris I" uniqKey="Newbold C" first="Chris I." last="Newbold">Chris I. Newbold</name>
<name sortKey="Rockett, Kirk" sort="Rockett, Kirk" uniqKey="Rockett K" first="Kirk" last="Rockett">Kirk Rockett</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000F56 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000F56 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     PMC:5175302
   |texte=   Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:27998271" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

Serveur d'exploration MERS

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

Source :

Descripteurs français

English descriptors

Abstract

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

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.