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Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections

Overview of attention for article published in Malaria Journal, May 2016
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  • Above-average Attention Score compared to outputs of the same age (51st percentile)

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3 tweeters

Citations

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17 Dimensions

Readers on

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48 Mendeley
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1 CiteULike
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Title
Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections
Published in
Malaria Journal, May 2016
DOI 10.1186/s12936-016-1324-4
Pubmed ID
Authors

Lee Murray, Victor A. Mobegi, Craig W. Duffy, Samuel A. Assefa, Dominic P. Kwiatkowski, Eugene Laman, Kovana M. Loua, David J. Conway

Abstract

In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers of SNPs. As expected, the number of microsatellite loci with more than one allele in each isolate was highly significantly inversely correlated with the genome-wide F ws fixation index (r = -0.88, P < 0.001). However, the microsatellite analysis revealed that most isolates contained mixed genotypes, even those that had no detectable genome sequence heterogeneity. Random sampling of different numbers of SNPs showed that an F ws index derived from ten or more SNPs with minor allele frequencies of >10 % had high correlation (r > 0.90) with the index derived using all SNPs. Different types of data give highly correlated indices of within-infection diversity, although PCR-based analysis detects low-level minority genotypes not apparent in bulk sequence analysis. When whole-genome data are not obtainable, quantitative assay of ten or more SNPs can yield a reasonably accurate estimate of the within-infection fixation index (F ws).

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 48 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 2%
Italy 1 2%
Brazil 1 2%
Unknown 45 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 14 29%
Student > Ph. D. Student 8 17%
Student > Master 7 15%
Student > Bachelor 5 10%
Student > Postgraduate 4 8%
Other 6 13%
Unknown 4 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 27%
Biochemistry, Genetics and Molecular Biology 11 23%
Immunology and Microbiology 6 13%
Medicine and Dentistry 4 8%
Nursing and Health Professions 2 4%
Other 6 13%
Unknown 6 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 16 May 2016.
All research outputs
#3,533,456
of 7,705,951 outputs
Outputs from Malaria Journal
#1,483
of 2,596 outputs
Outputs of similar age
#122,542
of 268,336 outputs
Outputs of similar age from Malaria Journal
#103
of 154 outputs
Altmetric has tracked 7,705,951 research outputs across all sources so far. This one has received more attention than most of these and is in the 51st percentile.
So far Altmetric has tracked 2,596 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 38th percentile – i.e., 38% of its peers scored the same or lower than it.
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 268,336 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.
We're also able to compare this research output to 154 others from the same source and published within six weeks on either side of this one. This one is in the 26th percentile – i.e., 26% of its contemporaries scored the same or lower than it.