Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites.
We explored the potential of pooled sequencing to swiftly and economically identify selective sweeps due to emerging artemisinin (ART) resistance in a South-East Asian malaria parasite population. ART resistance is defined by slow parasite clearance from the blood of ART-treated patients and mutatio...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
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2014
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| _version_ | 1797103906707210240 |
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| author | Cheeseman, I McDew-White, M Phyo, A Sriprawat, K Nosten, F Anderson, T |
| author_facet | Cheeseman, I McDew-White, M Phyo, A Sriprawat, K Nosten, F Anderson, T |
| author_sort | Cheeseman, I |
| collection | OXFORD |
| description | We explored the potential of pooled sequencing to swiftly and economically identify selective sweeps due to emerging artemisinin (ART) resistance in a South-East Asian malaria parasite population. ART resistance is defined by slow parasite clearance from the blood of ART-treated patients and mutations in the kelch gene (chr. 13) have been strongly implicated to play a role. We constructed triplicate pools of 70 slow-clearing (resistant) and 70 fast-clearing (sensitive) infections collected from the Thai-Myanmar border and sequenced these to high (~150-fold) read depth. Allele frequency estimates from pools showed almost perfect correlation (Lin's concordance = 0.98) with allele frequencies at 93 SNPs measured directly from individual infections, giving us confidence in the accuracy of this approach. By mapping genome-wide divergence (FST) between pools of drug resistant and drug sensitive parasites we identified two large (>150kb) regions (on chrs. 13 and 14) and 17 smaller candidate genome regions. To identify individual genes within these genome regions we re-sequenced an additional 38 parasite genomes (16 slow and 22 fast-clearing) and performed rare variant association tests. These confirmed kelch as a major molecular marker for ART resistance (p=6.03×10(-6)). This two-tier approach is powerful because pooled sequencing rapidly narrows down genome regions of interest, while targeted rare variant association testing within these regions can pinpoint the genetic basis of resistance. We show that our approach is robust to recurrent mutation and the generation of soft selective sweeps, which are predicted to be common in pathogen populations with large effective population sizes, and may confound more traditional gene mapping approaches. |
| first_indexed | 2024-03-07T06:26:41Z |
| format | Journal article |
| id | oxford-uuid:f48a3fde-bbce-4ea8-a2a5-9b108c1d0513 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T06:26:41Z |
| publishDate | 2014 |
| record_format | dspace |
| spelling | oxford-uuid:f48a3fde-bbce-4ea8-a2a5-9b108c1d05132022-03-27T12:20:30ZPooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:f48a3fde-bbce-4ea8-a2a5-9b108c1d0513EnglishSymplectic Elements at Oxford2014Cheeseman, IMcDew-White, MPhyo, ASriprawat, KNosten, FAnderson, TWe explored the potential of pooled sequencing to swiftly and economically identify selective sweeps due to emerging artemisinin (ART) resistance in a South-East Asian malaria parasite population. ART resistance is defined by slow parasite clearance from the blood of ART-treated patients and mutations in the kelch gene (chr. 13) have been strongly implicated to play a role. We constructed triplicate pools of 70 slow-clearing (resistant) and 70 fast-clearing (sensitive) infections collected from the Thai-Myanmar border and sequenced these to high (~150-fold) read depth. Allele frequency estimates from pools showed almost perfect correlation (Lin's concordance = 0.98) with allele frequencies at 93 SNPs measured directly from individual infections, giving us confidence in the accuracy of this approach. By mapping genome-wide divergence (FST) between pools of drug resistant and drug sensitive parasites we identified two large (>150kb) regions (on chrs. 13 and 14) and 17 smaller candidate genome regions. To identify individual genes within these genome regions we re-sequenced an additional 38 parasite genomes (16 slow and 22 fast-clearing) and performed rare variant association tests. These confirmed kelch as a major molecular marker for ART resistance (p=6.03×10(-6)). This two-tier approach is powerful because pooled sequencing rapidly narrows down genome regions of interest, while targeted rare variant association testing within these regions can pinpoint the genetic basis of resistance. We show that our approach is robust to recurrent mutation and the generation of soft selective sweeps, which are predicted to be common in pathogen populations with large effective population sizes, and may confound more traditional gene mapping approaches. |
| spellingShingle | Cheeseman, I McDew-White, M Phyo, A Sriprawat, K Nosten, F Anderson, T Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. |
| title | Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. |
| title_full | Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. |
| title_fullStr | Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. |
| title_full_unstemmed | Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. |
| title_short | Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. |
| title_sort | pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites |
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