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

Overview of attention for article published in Malaria Journal, December 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (92nd percentile)
  • High Attention Score compared to outputs of the same age and source (93rd percentile)

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1 blog
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25 X users
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2 Facebook pages

Citations

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139 Dimensions

Readers on

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225 Mendeley
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3 CiteULike
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Title
Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification
Published in
Malaria Journal, December 2016
DOI 10.1186/s12936-016-1641-7
Pubmed ID
Authors

Samuel O. Oyola, Cristina V. Ariani, William L. Hamilton, Mihir Kekre, Lucas N. Amenga-Etego, Anita Ghansah, Gavin G. Rutledge, Seth Redmond, Magnus Manske, Dushyanth Jyothi, Chris G. Jacob, Thomas D. Otto, Kirk Rockett, Chris I. Newbold, Matthew Berriman, Dominic P. Kwiatkowski

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. 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. 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. 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.

X Demographics

X Demographics

The data shown below were collected from the profiles of 25 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 225 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 2 <1%
Sweden 1 <1%
Pakistan 1 <1%
Unknown 221 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 42 19%
Researcher 38 17%
Student > Master 32 14%
Student > Bachelor 15 7%
Student > Postgraduate 14 6%
Other 39 17%
Unknown 45 20%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 72 32%
Agricultural and Biological Sciences 47 21%
Immunology and Microbiology 14 6%
Medicine and Dentistry 13 6%
Engineering 6 3%
Other 24 11%
Unknown 49 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 22. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 20 January 2023.
All research outputs
#1,674,947
of 25,202,494 outputs
Outputs from Malaria Journal
#273
of 5,881 outputs
Outputs of similar age
#33,726
of 433,430 outputs
Outputs of similar age from Malaria Journal
#8
of 103 outputs
Altmetric has tracked 25,202,494 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 5,881 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.9. This one has done particularly well, scoring higher than 95% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 433,430 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 92% of its contemporaries.
We're also able to compare this research output to 103 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.