Association of a novel mutation in the plasmodium falciparum chloroquine resistance transporter with decreased piperaquine sensitivity

Background. Amplified copy number in the plasmepsin II/III genes within Plasmodium falciparum has been associated with decreased sensitivity to piperaquine. To examine this association and test whether additional loci might also contribute, we performed a genome-wide association study of ex vivo P. falciparum susceptibility to piperaquine. Methods. Plasmodium falciparum DNA from 183 samples collected primarily from Cambodia was genotyped at 33 716 genomewide single nucleotide polymorphisms (SNPs). Linear mixed models and random forests were used to estimate associations between parasite genotypes and piperaquine susceptibility. Candidate polymorphisms were evaluated for their association with dihydroartemisinin- piperaquine treatment outcomes in an independent dataset. Results. Single nucleotide polymorphisms on multiple chromosomes were associated with piperaquine 90% inhibitory concentrations (IC90) in a genome-wide analysis. Fine-mapping of genomic regions implicated in genome-wide analyses identified multiple SNPs in linkage disequilibrium with each other that were significantly associated with piperaquine IC90, including a novel mutation within the gene encoding the P. falciparum chloroquine resistance transporter, PfCRT. This mutation (F145I) was associated with dihydroartemisinin-piperaquine treatment failure after adjusting for the presence of amplified plasmepsin II/III, which was also associated with decreased piperaquine sensitivity. Conclusions. Our data suggest that, in addition to plasmepsin II/III copy number, other loci, including pfcrt, may also be involved in piperaquine resistance

A consultation on the optimization of controlled human malaria infection by mosquito bite for evaluation of candidate malaria vaccines.

Early clinical investigations of candidate malaria vaccines and antimalarial medications increasingly employ an established model of controlled human malaria infection (CHMI). Study results are used to guide further clinical development of vaccines and antimalarial medications as CHMI results to date are generally predictive of efficacy in malaria-endemic areas. The urgency to rapidly develop an efficacious malaria vaccine has increased demand for efficacy studies that include CHMI and the need for comparability of study results among the different centres conducting CHMI. An initial meeting with the goal to optimize and standardise CHMI procedures was held in 2009 with follow-up meetings in March and June 2010 to harmonise methods used at different centres. The end result is a standardised document for the design and conduct of CHMI and a second document for the microscopy methods used to determine the patency endpoint. These documents will facilitate high accuracy and comparability of CHMI studies and will be revised commensurate with advances in the field

A consultation on the optimization of controlled human malaria infection by mosquito bite for evaluation of candidate malaria vaccines.

Item does not contain fulltextEarly clinical investigations of candidate malaria vaccines and antimalarial medications increasingly employ an established model of controlled human malaria infection (CHMI). Study results are used to guide further clinical development of vaccines and antimalarial medications as CHMI results to date are generally predictive of efficacy in malaria-endemic areas. The urgency to rapidly develop an efficacious malaria vaccine has increased demand for efficacy studies that include CHMI and the need for comparability of study results among the different centres conducting CHMI. An initial meeting with the goal to optimize and standardise CHMI procedures was held in 2009 with follow-up meetings in March and June 2010 to harmonise methods used at different centres. The end result is a standardised document for the design and conduct of CHMI and a second document for the microscopy methods used to determine the patency endpoint. These documents will facilitate high accuracy and comparability of CHMI studies and will be revised commensurate with advances in the field

Individual gene cluster statistics in noisy maps

Identification of homologous chromosomal regions is important for understanding evolutionary processes that shape genome evolution, such as genome rearrangements and large scale duplication events. If these chromosomal regions have diverged significantly, statistical tests to determine whether observed similarities in gene content are due to history or chance are imperative. Currently available methods are typically designed for genomic data and are appropriate for whole genome analyses. Statistical methods for estimating significance when a single pair of regions is under consideration are needed. We present a new statistical method, based on generating functions, for estimating the significance of orthologous gene clusters under the null hypothesis of random gene order. Our statistics is suitable for noisy comparative maps, in which a one-to-one homology mapping cannot be established. It is also designed for testing the significance of an individual gene cluster in isolation, in situations where whole genome data is not available. We implement our statistics in Mathematica and demonstrate its utility by applying it to the MHC homologous regions in human and fly