| Title |
High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
|
|---|---|
| Published in |
Scientific Reports, May 2017
|
| DOI | 10.1038/s41598-017-02724-x |
| Pubmed ID | |
| Authors |
Sidsel Nag, Marlene D. Dalgaard, Poul-Erik Kofoed, Johan Ursing, Marina Crespo, Lee O’Brien Andersen, Frank Møller Aarestrup, Ole Lund, Michael Alifrangis |
| Abstract |
Genetic polymorphisms in P. falciparum can be used to indicate the parasite's susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8-100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in pfK13 are absent from the studied area of Guinea-Bissau, while the pfmdr1 86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before. |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 2 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 151 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Denmark | 1 | <1% |
| Unknown | 150 | 99% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Master | 32 | 21% |
| Student > Ph. D. Student | 27 | 18% |
| Researcher | 20 | 13% |
| Student > Bachelor | 13 | 9% |
| Other | 8 | 5% |
| Other | 20 | 13% |
| Unknown | 31 | 21% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 47 | 31% |
| Agricultural and Biological Sciences | 22 | 15% |
| Medicine and Dentistry | 11 | 7% |
| Immunology and Microbiology | 7 | 5% |
| Computer Science | 4 | 3% |
| Other | 19 | 13% |
| Unknown | 41 | 27% |
Attention Score in Context
This research output has an Altmetric Attention Score of 15. 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 November 2017.
All research outputs
#2,083,258
of 23,577,654 outputs
Outputs from Scientific Reports
#18,795
of 127,511 outputs
Outputs of similar age
#40,920
of 314,659 outputs
Outputs of similar age from Scientific Reports
#571
of 3,780 outputs
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We're also able to compare this research output to 3,780 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 84% of its contemporaries.