@article{Amambua-Ngwa2012, abstract = {Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now prioritized for functional study.}, author = {Amambua-Ngwa, Alfred and Tetteh, Kevin K. A. and Manske, Magnus and Gomez-Escobar, Natalia and Stewart, Lindsay B. and Deerhake, Me Elizabeth and Cheeseman, Ian H. and Newbold, Christopher I. and Holder, Anthony Aa and Knuepfer, Ellen and Janha, Omar and Jallow, Muminatou and Campino, Susana and MacInnis, Bronwyn and Kwiatkowski, Dominic P. and Conway, David J.}, doi = {10.1371/journal.pgen.1002992}, month = {nov}, title = {Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites}, url = {http://dx.doi.org/10.1371/journal.pgen.1002992}, year = {2012} } @article{Auburn2012, abstract = {Our understanding of the composition of multi-clonal malarial infections and the epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host diversity has been defined in terms of the multiplicity of infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be derived on genome-wide datasets facilitating the development of new statistical approaches to describe within-host diversity. In this class of measures the F(WS) metric characterizes within-host diversity and its relationship to population level diversity. Utilizing P. falciparum field isolates from patients in West Africa we here explore the relationship between the traditional MOI and F(WS) approaches. F(WS) statistics were derived from read count data at 86,158 SNPs in 64 samples sequenced on the Illumina GA platform. MOI estimates were derived by PCR at the msp-1 and -2 loci. Significant correlations were observed between the two measures, particularly with the msp-1 locus (P = 5.92×10(-5)). The F(WS) metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the F(WS) metric captures information on a range of parameters which influence out-crossing risk including the number of clones (MOI), their relative proportions and genetic divergence. This approach should provide novel insights into the factors which correlate with, and shape within-host diversity.}, author = {Auburn, Sarah and Campino, Susana and Miotto, Olivo and Djimde, Abdoulaye Aa and Zongo, Issaka and Manske, Magnus and Maslen, Gareth and Mangano, Valentina and Alcock, Daniel and MacInnis, Bronwyn and Rockett, Kirk A. and Clark, Taane G. and Doumbo, Ogobara K. and Ouédraogo, Jean Bosco and Kwiatkowski, Dominic P.}, doi = {10.1371/journal.pone.0032891}, month = {feb}, title = {Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data}, url = {http://dx.doi.org/10.1371/journal.pone.0032891}, year = {2012} } @article{Auburn2013, abstract = {Whole genome sequencing (WGS) of Plasmodium vivax is problematic due to the reliance on clinical isolates which are generally low in parasitaemia and sample volume. Furthermore, clinical isolates contain a significant contaminating background of host DNA which confounds efforts to map short read sequence of the target P. vivax DNA. Here, we discuss a methodology to significantly improve the success of P. vivax WGS on natural (non-adapted) patient isolates. Using 37 patient isolates from Indonesia, Thailand, and travellers, we assessed the application of CF11-based white blood cell filtration alone and in combination with short term ex vivo schizont maturation. Although CF11 filtration reduced human DNA contamination in 8 Indonesian isolates tested, additional short-term culture increased the P. vivax DNA yield from a median of 0.15 to 6.2 ng µl(-1) packed red blood cells (pRBCs) (p = 0.001) and reduced the human DNA percentage from a median of 33.9% to 6.22% (p = 0.008). Furthermore, post-CF11 and culture samples from Thailand gave a median P. vivax DNA yield of 2.34 ng µl(-1) pRBCs, and 2.65% human DNA. In 22 P. vivax patient isolates prepared with the 2-step method, we demonstrate high depth (median 654X coverage) and breadth (≥89%) of coverage on the Illumina GAII and HiSeq platforms. In contrast to the A+T-rich P. falciparum genome, negligible bias was observed in coverage depth between coding and non-coding regions of the P. vivax genome. This uniform coverage will greatly facilitate the detection of SNPs and copy number variants across the genome, enabling unbiased exploration of the natural diversity in P. vivax populations.}, author = {Auburn, Sarah and Marfurt, Jutta and Maslen, Gareth and Campino, Susana and Ruano Rubio, Valentin and Rubio, Ruano and Manske, Magnus and MacHunter, Barbara and Kenangalem, Enny and Noviyanti, Rintis and Trianty, Leily and Sebayang, Boni and Wirjanata, Grennady and Sriprawat, Kanlaya and Alcock, Daniel and MacInnis, Bronwyn and Miotto, Olivo and Clark, Taane G. and Russell, Bruce and Anstey, Nicholas M. and Nosten, François and Kwiatkowski, Dominic P. and Price, Ric N.}, doi = {10.1371/journal.pone.0053160}, month = {jan}, title = {Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing}, url = {http://dx.doi.org/10.1371/journal.pone.0053160}, year = {2013} } @article{Borrmann2013, abstract = {Early identification of causal genetic variants underlying antimalarial drug resistance could provide robust epidemiological tools for timely public health interventions. Using a novel natural genetics strategy for mapping novel candidate genes we analyzed >75,000 high quality single nucleotide polymorphisms selected from high-resolution whole-genome sequencing data in 27 isolates of Plasmodium falciparum. We identified genetic variants associated with susceptibility to dihydroartemisinin that implicate one region on chromosome 13, a candidate gene on chromosome 1 (PFA0220w, a UBP1 ortholog) and others (PFB0560w, PFB0630c, PFF0445w) with putative roles in protein homeostasis and stress response. There was a strong signal for positive selection on PFA0220w, but not the other candidate loci. Our results demonstrate the power of full-genome sequencing-based association studies for uncovering candidate genes that determine parasite sensitivity to artemisinins. Our study provides a unique reference for the interpretation of results from resistant infections.}, author = {Borrmann, Steffen and Straimer, Judith and Mwai, Leah and Abdi, Abdirahman and Rippert, Anja and Okombo, John and Muriithi, Steven and Sasi, Philip and Kortok, Moses Mosobo and Lowe, Brett and Campino, Susana and Assefa, Samuel and Auburn, Sarah and Manske, Magnus and Maslen, Gareth and Peshu, Norbert and Kwiatkowski, Dominic P. and Marsh, Kevin and Nzila, Alexis and Clark, Taane G.}, doi = {10.1038/srep03318}, month = {nov}, title = {Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya}, url = {http://dx.doi.org/10.1038/srep03318}, year = {2013} } @article{Clarkson2014, abstract = {Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation.}, author = {Clarkson, Chris S. and Weetman, David and Essandoh, John and Yawson, Alexander E. and Maslen, Gareth and Manske, Magnus and Field, Stuart G. and Webster, Mark and Antão, Tiago and MacInnis, Bronwyn and Kwiatkowski, Dominic and Donnelly, Martin J.}, doi = {10.1038/ncomms5248}, journal = {Nature Communications}, month = {jun}, title = {Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation}, url = {http://dx.doi.org/10.1038/ncomms5248}, volume = {5}, year = {2014} } @article{Li2013, abstract = {Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.}, author = {Li, Jing-Woei and Bolser, Dan and Giorgi, Federico Manuel and Manske, Magnus and Vyahhi, Nikolay and Usadel, Bj and Clavijo, Bernardo J. and Chan, Ting-Fung and Wong, Nathalie and Zerbino, Daniel and Schneider, Maria Victoria}, doi = {10.1093/bib/bbt045}, journal = {Briefings in Bioinformatics}, month = {jun}, pages = {548-555}, title = {The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771235}, volume = {14}, year = {2013} } @article{Manske2012, abstract = {Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance(1,2). Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.}, author = {Manske, Magnus and Miotto, Olivo and Campino, Susana and Auburn, Sarah and Almagro-Garcia, Jacob and Maslen, Gareth and O'Brien, Jack and O’Brien, Jack and Djimde, Abdoulaye and Doumbo, Ogobara and Zongo, Issaka and Ouedraogo, Jean-Bosco and Michon, Pascal and Mueller, Ivo and Siba, Peter and Nzila, Alexis and Borrmann, Steffen and Kiara, Steven M. and Marsh, Kevin and Jiang, Hongying and Su, Xin-Zhuan and Amaratunga, Chanaki and Fairhurst, Rick and Socheat, Duong and Nosten, Francois and Imwong, Mallika and White, Nicholas J. and Sanders, Mandy and Anastasi, Elisa and Alcock, Dan and Drury, Eleanor and Oyola, Samuel and Quail, Michael A. and Turner, Daniel J. and Rubio, Valentin Ruano and Jyothi, Dushyanth and Amenga-Etego, Lucas and Hubbart, Christina and Jeffreys, Anna and Rowlands, Kate and Sutherland, Colin and Roper, Cally and Mangano, Valentina and Modiano, David and Tan, John C. and Ferdig, Michael T. and Amambua-Ngwa, Alfred and Conway, David J. and Takala-Harrison, Shannon and Plowe, Christopher V. and Rayner, Julian C. and Rockett, Kirk A. and Clark, Taane G. and Newbold, Chris I. and Berriman, Matthew and MacInnis, Bronwyn and Kwiatkowski, Dominic P.}, doi = {10.1038/nature11174}, month = {jun}, title = {Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22722859}, year = {2012} } @article{Miotto2013, abstract = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural ; We describe an analysis of genome variation in 825 P. falciparum samples from Asia and Africa that identifies an unusual pattern of parasite population structure at the epicenter of artemisinin resistance in western Cambodia. Within this relatively small geographic area, we have discovered several distinct but apparently sympatric parasite subpopulations with extremely high levels of genetic differentiation. Of particular interest are three subpopulations, all associated with clinical resistance to artemisinin, which have skewed allele frequency spectra and high levels of haplotype homozygosity, indicative of founder effects and recent population expansion. We provide a catalog of SNPs that show high levels of differentiation in the artemisinin-resistant subpopulations, including codon variants in transporter proteins and DNA mismatch repair proteins. These data provide a population-level genetic framework for investigating the biological origins of artemisinin resistance and for defining molecular markers to assist in its elimination.}, author = {Miotto, Olivo and Almagro-Garcia, Jacob and Manske, Magnus and MacInnis, Bronwyn and Campino, Susana and Rockett, Kirk A. and Amaratunga, Chanaki and Lim, Pharath and Suon, Seila and Sreng, Sokunthea and Anderson, Jennifer M. and Duong, Socheat and Nguon, Chea and Chuor, Char Meng and Saunders, David and Se, Youry and Lon, Chantap and Fukuda, Mark Mm and Amenga-Etego, Lucas and Hodgson, Abraham Vo O. and Asoala, Victor and Imwong, Mallika and Takala-Harrison, Shannon and Nosten, Francois and Su, Xin-Zhuan and Ringwald, Pascal and Ariey, Frédéric and Dolecek, Christiane and Hien, Tran Tinh and Boni, Maciej F. and Thai, Cao Quang and Amambua-Ngwa, Alfred and Conway, David J. and Djimd??, Aa and Djimdé, Abdoulaye A. and Doumbo, Ogobara K. and Zongo, Issaka and Ouedraogo, Jean-Bosco and Alcock, Daniel and Drury, Eleanor and Auburn, Sarah and Koch, Oliver and Sanders, Mandy and Hubbart, Christina and Maslen, Gareth and Ruano-Rubio, Valentin and Jyothi, Dushyanth and Miles, Alistair and O'Brien, John and O’Brien, John and Gamble, Chris and Oyola, Samuel O. and Rayner, Julian C. and Newbold, Chris I. and Berriman, Matthew and Spencer, Chris Ca A. and McVean, Gilean and Day, Nicholas P. and White, Nicholas J. and Bethell, Delia and Dondorp, Arjen M. and Plowe, Christopher V. and Fairhurst, Rick M. and Kwiatkowski, Dominic P. and Medical Research Council Mrc Centre for Genomics and Global Health, University of Oxford Oxford UK}, doi = {10.1038/ng.2624}, journal = {Nature Genetics}, month = {apr}, pages = {648-655}, title = {Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23624527}, volume = {45}, year = {2013} } @article{Oyola2012, abstract = {Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences.}, author = {Oyola, So and Otto, Td and Gu, Yong and Maslen, Gareth and Manske, Magnus and Campino, Susana and Turner, Dj and Macinnis, Bronwyn and Kwiatkowski, Dp and Swerdlow, Hp and Quail, Michael A.}, doi = {10.1186/1471-2164-13-1}, month = {jan}, title = {Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.}, url = {http://dx.doi.org/10.1186/1471-2164-13-1}, year = {2012} } @article{Oyola2012_2, abstract = {The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches Plasmodium falciparum DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci.}, author = {Oyola, Samuel O. and Gu, Yong and Manske, Magnus and Otto, Thomas D. and O'Brien, John and Alcock, Daniel and MacInnis, Bronwyn and Berriman, Matthew and Newbold, Chris I. and Kwiatkowski, Dominic P. and Swerdlow, Harold P. and Quail, Michael A.}, doi = {10.1128/jcm.02507-12}, month = {dec}, title = {Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing}, url = {http://jcm.asm.org/content/51/3/745.full.pdf}, year = {2012} } @article{Oyola2014, abstract = {Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples.}, author = {Oyola, Samuel O. and Campino, Susana and Manske, Magnus and Claessens, Antoine and Hamilton, William L. and Kekre, Mihir and Drury, Eleanor and Mead, Daniel and Gu, Yong and Miles, Alistair and MacInnis, Bronwyn and Newbold, Chris and Berriman, Matthew and Kwiatkowski, Dominic P.}, doi = {10.1093/dnares/dsu028}, month = {sep}, title = {Optimized Whole-Genome Amplification Strategy for Extremely AT-Biased Template}, url = {http://dx.doi.org/10.1093/dnares/dsu028}, year = {2014} } @article{Oyola2016, abstract = {Abstract Background 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. Methods Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8â 12Â 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. Results 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 >5Ă 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. Conclusion 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.}, author = {Oyola, Samuel O. and Rutledge, Gavin R. and Ariani, Cristina Valente and Hamilton, William L. and Kekre, Mihir and Amenga-Etego, Lucas N. and Ghansah, Anita and Rutledge, Gavin G. and Redmond, Seth and Manske, Magnus and Jyothi, Dushyanth and Jacob, Chris G. and Otto, Thomas D. and Rockett, Kirk and Newbold, Chris I. and Berriman, Matthew and Kwiatkowski, Dominic P.}, doi = {10.1186/s12936-016-1641-7}, month = {dec}, title = {Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification}, url = {http://dx.doi.org/10.1186/s12936-016-1641-7}, year = {2016} } @article{Pearson2016, author = {Pearson, Richard D. and Amato, Roberto and Auburn, Sarah and Miotto, Olivo and Almagro-Garcia, Jacob and Amaratunga, Chanaki and Suon, Seila and Mao, Sivanna and Noviyanti, Rintis and Trimarsanto, Hidayat and Marfurt, Jutta and Anstey, Nicholas M. and William, Timothy and Boni, Maciej F. and Dolecek, Christiane and Tran, Hien Tinh and White, Nicholas J. and Michon, Pascal and Siba, Peter and Tavul, Livingstone and Harrison, Gabrielle and Barry, Alyssa and Mueller, Ivo and Ferreira, Marcelo U. and Karunaweera, Nadira and Randrianarivelojosia, Milijaona and Gao, Qi and Hubbart, Christina and Hart, Lee and Jeffery, Ben and Drury, Eleanor and Mead, Daniel and Kekre, Mihir and Campino, Susana and Manske, Magnus and Cornelius, Victoria J. and MacInnis, Bronwyn and Rockett, Kirk A. and Miles, Alistair and Rayner, Julian C. and Fairhurst, Rick M. and Nosten, Francois and Price, Ric N. and Kwiatkowski, Dominic P.}, doi = {10.1038/ng.3599}, journal = {Nature Genetics}, month = {jun}, pages = {959-964}, title = {Genomic analysis of local variation and recent evolution in Plasmodium vivax}, url = {http://www.nature.com/articles/ng.3599.pdf}, volume = {48}, year = {2016} } @article{Preston2012, abstract = {SUMMARY: There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats. We have developed VarB software that can be used to visualize variant call format files in real time, as well as identify regions under balancing selection and informative markers to differentiate user-defined groups (e.g. populations). We demonstrate its utility using sequence data from 50 Plasmodium falciparum isolates comprising two different continents and confirm known signals from genomic regions that contain important antigenic and anti-malarial drug-resistance genes. AVAILABILITY AND IMPLEMENTATION: The C++-based software VarB and user manual are available from www.pathogenseq.org/varb. CONTACT: taane.clark@lshtm.ac.uk}, author = {Preston, Mark D. and Oudraogo, Jean-Bosco and Manske, Magnus and Horner, Neil and Assefa, Samuel and Campino, Susana and Zongo, Issaka and Auburn, Sarah and Ouedraogo, Jean-Bosco and Nosten, Francois and Anderson, Tim and Clark, Taane G.}, doi = {10.1093/bioinformatics/bts557}, month = {sep}, title = {VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data}, url = {https://academic.oup.com/bioinformatics/article-pdf/28/22/2983/666045/bts557.pdf}, year = {2012} } @article{Robinson2011, abstract = {Naturally acquired blood-stage infections of the malaria parasite Plasmodium falciparum typically harbour multiple haploid clones. The apparent number of clones observed in any single infection depends on the diversity of the polymorphic markers used for the analysis, and the relative abundance of rare clones, which frequently fail to be detected among PCR products derived from numerically dominant clones. However, minority clones are of clinical interest as they may harbour genes conferring drug resistance, leading to enhanced survival after treatment and the possibility of subsequent therapeutic failure. We deployed new generation sequencing to derive genome data for five non-propagated parasite isolates taken directly from 4 different patients treated for clinical malaria in a UK hospital. Analysis of depth of coverage and length of sequence intervals between paired reads identified both previously described and novel gene deletions and amplifications. Full-length sequence data was extracted for 6 loci considered to be under selection by antimalarial drugs, and both known and previously unknown amino acid substitutions were identified. Full mitochondrial genomes were extracted from the sequencing data for each isolate, and these are compared against a panel of polymorphic sites derived from published or unpublished but publicly available data. Finally, genome-wide analysis of clone multiplicity was performed, and the number of infecting parasite clones estimated for each isolate. Each patient harboured at least 3 clones of P. falciparum by this analysis, consistent with results obtained with conventional PCR analysis of polymorphic merozoite antigen loci. We conclude that genome sequencing of peripheral blood P. falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity. © 2011 Robinson et al.}, author = {Robinson, Timothy and Campino, Sg and Auburn, Sarah and Assefa, Sa and Polley, Sd and Manske, Magnus and MacInnis, Bronwyn and Rockett, Ka and Maslen, Gl and Sanders, Mandy and Quail, Michael A. and Chiodini, Pl and Kwiatkowski, Dp and Clark, Tg and Sutherland, Cj}, doi = {10.1371/journal.pone.0023204}, month = {jan}, title = {Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients}, url = {http://dx.doi.org/10.1371/journal.pone.0023204}, year = {2011} } @article{Rutledge2017, author = {Rutledge, Gavin G. and Böhme, Ulrike and Sanders, Mandy and Reid, Adam J. and Cotton, James A. and Maiga-Ascofare, Oumou and Djimdé, Abdoulaye A. and Apinjoh, Tobias O. and Amenga-Etego, Lucas and Manske, Magnus and Barnwell, John W. and Renaud, François and Ollomo, Benjamin and Prugnolle, Franck and Anstey, Nicholas M. and Auburn, Sarah and Price, Ric N. and McCarthy, James S. and Kwiatkowski, Dominic P. and Newbold, Chris I. and Berriman, Matthew and Otto, Thomas D.}, doi = {10.1038/nature21038}, journal = {Nature}, month = {jan}, pages = {101-104}, title = {Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution}, url = {http://www.nature.com/nature/journal/v542/n7639/pdf/nature21038.pdf}, volume = {542}, year = {2017} } @article{Shearer2016, author = {Shearer, Freya M. and Huang, Zhi and Weiss, Daniel J. and Wiebe, Antoinette and Gibson, Harry S. and Battle, Katherine E. and Pigott, David M. and Brady, Oliver J. and Putaporntip, Chaturong and Jongwutiwes, Somchai and Lau, Yee Ling and Manske, Magnus and Amato, Roberto and Elyazar, Iqbal R. F. and Vythilingam, Indra and Bhatt, Samir and Gething, Peter W. and Singh, Balbir and Golding, Nick and Hay, Simon I. and Moyes, Catherine L.}, doi = {10.1371/journal.pntd.0004915}, journal = {PLoS Neglected Tropical Diseases}, month = {aug}, pages = {e0004915}, title = {Estimating Geographical Variation in the Risk of Zoonotic Plasmodium knowlesi Infection in Countries Eliminating Malaria}, url = {https://doi.org/10.1371/journal.pntd.0004915}, volume = {10}, year = {2016} } @article{Sundararaman2013, abstract = { Wild-living chimpanzees and gorillas harbor a multitude of Plasmodium species, including six of the subgenus Laverania , one of which served as the progenitor of Plasmodium falciparum . Despite the magnitude of this reservoir, it is unknown whether apes represent a source of human infections. Here, we used Plasmodium species-specific PCR, single-genome amplification, and 454 sequencing to screen humans from remote areas of southern Cameroon for ape Laverania infections. Among 1,402 blood samples, we found 1,000 to be Plasmodium mitochondrial DNA (mtDNA) positive, all of which contained human parasites as determined by sequencing and/or restriction enzyme digestion. To exclude low-abundance infections, we subjected 514 of these samples to 454 sequencing, targeting a region of the mtDNA genome that distinguishes ape from human Laverania species. Using algorithms specifically developed to differentiate rare Plasmodium variants from 454-sequencing error, we identified single and mixed-species infections with P. falciparum , Plasmodium malariae , and/or Plasmodium ovale . However, none of the human samples contained ape Laverania parasites, including the gorilla precursor of P. falciparum . To characterize further the diversity of P. falciparum in Cameroon, we used single-genome amplification to amplify 3.4-kb mtDNA fragments from 229 infected humans. Phylogenetic analysis identified 62 new variants, all of which clustered with extant P. falciparum , providing further evidence that P. falciparum emerged following a single gorilla-to-human transmission. Thus, unlike Plasmodium knowlesi -infected macaques in southeast Asia, African apes harboring Laverania parasites do not seem to serve as a recurrent source of human malaria, a finding of import to ongoing control and eradication measures. }, author = {Sundararaman, Sesh A. and Liu, Weimin and Keele, Brandon F. and Learn, Gerald H. and Bittinger, Kyle and Mouacha, Fatima and Ahuka-Mundeke, Steve and Manske, Magnus and Sherrill-Mix, Scott and Li, Yingying and Malenke, Jordan A. and Delaporte, Eric and Laurent, Christian and Mpoudi Ngole, Eitel and Kwiatkowski, Dominic P. and Shaw, George M. and Rayner, Julian C. and Peeters, Martine and Sharp, Paul M. and Bushman, Frederic D. and Hahn, Beatrice H.}, doi = {10.1073/pnas.1305201110}, journal = {Proceedings of the National Academy of Sciences}, month = {apr}, pages = {7020-7025}, title = {Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria}, url = {https://doi.org/10.1073/pnas.1305201110}, volume = {110}, year = {2013} } @article{Waagmeester2020, abstract = {Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.}, author = {Waagmeester, Andra and Stupp, Gregory and Burgstaller-Muehlbacher, Sebastian and Good, Benjamin M. and Griffith, Malachi and Griffith, Obi L. and Hanspers, Kristina and Hermjakob, Henning and Hudson, Toby S. and Hybiske, Kevin and Keating, Sarah M. and Manske, Magnus and Mayers, Michael and Mietchen, Daniel and Mitraka, Elvira and Pico, Alexander R. and Putman, Timothy and Riutta, Anders and Queralt-Rosinach, Nuria and Schriml, Lynn M. and Shafee, Thomas and Slenter, Denise and Stephan, Ralf and Thornton, Katherine and Tsueng, Ginger and Tu, Roger and Ul-Hasan, Sabah and Willighagen, Egon and Wu, Chunlei and Su, Andrew I.}, doi = {10.7554/elife.52614}, journal = {eLife}, month = {mar}, title = {Wikidata as a knowledge graph for the life sciences}, url = {https://doi.org/10.7554/elife.52614}, volume = {9}, year = {2020} } @article{Wendler2014, author = {Wendler, Jason P. and Okombo, John and Amato, Roberto and Miotto, Olivo and Kiara, Steven M. and Mwai, Leah and Pole, Lewa and O'Brien, John and Manske, Magnus and Alcock, Dan and Drury, Eleanor and Sanders, Mandy and Oyola, Samuel O. and Malangone, Cinzia and Jyothi, Dushyanth and Miles, Alistair and Rockett, Kirk A. and MacInnis, Bronwyn L. and Marsh, Kevin and Bejon, Philip and Nzila, Alexis and Kwiatkowski, Dominic P.}, doi = {10.1371/journal.pone.0096486}, journal = {PLoS ONE}, month = {may}, pages = {e96486}, title = {A Genome Wide Association Study of Plasmodium falciparum Susceptibility to 22 Antimalarial Drugs in Kenya}, url = {https://doi.org/10.1371/journal.pone.0096486}, volume = {9}, year = {2014} }