Jacob Almagro‐Garcia
A5021715874- Malaria Research and Control
- Mosquito-borne diseases and control
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Research on Leishmaniasis Studies
- Genetic and phenotypic traits in livestock
- HIV Research and Treatment
- Genetic Mapping and Diversity in Plants and Animals
- Trypanosoma species research and implications
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- Invertebrate Immune Response Mechanisms
- Genetic diversity and population structure
- Ecology and Vegetation Dynamics Studies
- Digital Imaging for Blood Diseases
- Aquaculture disease management and microbiota
- vaccines and immunoinformatics approaches
- Machine Learning in Bioinformatics
- Hepatitis Viruses Studies and Epidemiology
- Genomic variations and chromosomal abnormalities
- Evolutionary Algorithms and Applications
- Gene expression and cancer classification
- Parasites and Host Interactions
- Bioenergy crop production and management
- Microbial Natural Products and Biosynthesis
Wellcome Sanger Institute
2012-2024
University of Oxford
2013-2022
Genomics (United Kingdom)
2013-2022
Medical Research Council
2013-2019
Centre for Human Genetics
2009-2019
As the prevalence of artemisinin-resistant Plasmodium falciparum malaria increases in Greater Mekong subregion, emerging resistance to partner drugs artemisinin combination therapies seriously threatens global efforts treat and eliminate this disease. Molecular markers that predict failure therapy are urgently needed monitor spread drug resistance, recommend alternative treatments southeast Asia beyond.We did a genome-wide association study 297 P isolates from Cambodia investigate...
Antimalarial resistance is rapidly spreading across parts of southeast Asia where dihydroartemisinin-piperaquine used as first-line treatment for Plasmodium falciparum malaria. The first published reports about to antimalarial drugs came from western Cambodia in 2013. Here, we analyse genetic changes the P population 6 years before those reports.
MalariaGEN is a data-sharing network that enables groups around the world to work together on genomic epidemiology of malaria. Here we describe new release curated genome variation data 7,000 Plasmodium falciparum samples from partner studies in 28 malaria-endemic countries. High-quality genotype calls 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using standardised analysis pipeline. Copy number variants associated with drug resistance structural cause...
<ns3:p>We describe the MalariaGEN Pf7 data resource, seventh release of <ns3:italic>Plasmodium falciparum</ns3:italic> genome variation from network. It comprises over 20,000 samples 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For first time we include dried blood spot sequenced after selective whole amplification, necessitating new methods to genotype copy number variations. We identify a large newly emerging...
The increasing availability of large genomic data sets as well the advent Bayesian phylogenetics facilitates investigation phylogenetic incongruence, which can result in impossibility representing relationships using a single tree. While sometimes considered nuisance, incongruence also reflect meaningful biological processes relevant statistical uncertainty, both yield valuable insights evolutionary studies. We introduce new tool for investigating through exploration tree landscapes. Our...
Abstract Motivation The presence of multiple infecting strains the malarial parasite Plasmodium falciparum affects key phenotypic traits, including drug resistance and risk severe disease. Advances in protocols sequencing technology have made it possible to obtain high-coverage genome-wide data from blood samples spots taken field. However, analyzing interpreting such is challenging because high rate infections present. Results We developed a statistical method implementation for...
Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels relatedness. Yet, how local epidemiology affects the properties such mixed remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates number strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to Pf3k data set, find that rate infection varies 29% 63% across countries 51% involve...
<ns3:p>MalariaGEN is a data-sharing network that enables groups around the world to work together on genomic epidemiology of malaria. Here we describe new release curated genome variation data 7,000 <ns3:italic>Plasmodium falciparum</ns3:italic> samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using standardised analysis pipeline. Copy number variants associated...
Malaria results in over 600,000 deaths annually, with the highest burden of young children living sub-Saharan Africa. Molecular surveillance can provide important information for malaria control policies, including detection antimalarial drug resistance. However, genome sequencing capacity malaria-endemic countries is limited. We designed and implemented an end-to-end workflow to detect Plasmodium falciparum resistance markers diversity vaccine target circumsporozoite protein (csp) using...
The RTS,S/AS01 malaria vaccine encompasses the central repeats and C-terminal of Plasmodium falciparum circumsporozoite protein (PfCSP). Although no Phase II clinical trial studies observed evidence strain-specific immunity, recent show a decrease in efficacy against non-vaccine strain parasites. In light goals to reduce morbidity, anticipating effectiveness is critical planning widespread introduction. We deep sequenced Pfcsp from 77 individuals living along international border Luapula...
<ns7:p><ns7:bold>Background:</ns7:bold> Antimalarial drug resistance is a major obstacle to sustainable malaria control. Here we use amplicon sequencing describe molecular markers of in <ns7:italic>Plasmodium falciparum</ns7:italic> parasites from Kilifi county the coastal region Kenya over 25-year period.</ns7:p><ns7:p> <ns7:bold>Methods:</ns7:bold> We performed <ns7:italic>P. on 1162 malaria-infected blood samples collected between 1994 and 2018 identify antimalarial...
Abstract Background Antimalarial failure is rapidly spreading across parts of Southeast Asia where dihydroartemisinin-piperaquine (DHA-PPQ) used as first line treatment. The published reports came from western Cambodia in 2013. Here we analyse genetic changes the Plasmodium falciparum population six years prior to that. Methods We analysed genome sequence data on 1492 P. samples Asia, including 464 collected between 2007 and Different epidemiological origins resistance were identified by...
ABSTRACT The population structure of the malaria parasite Plasmodium falciparum can reveal underlying demographic and adaptive evolutionary processes. Here, we analyse in 4,376 P. genomes from 21 countries across Africa. We identified a strongly differentiated cluster parasites, comprising ∼1.2% samples analysed, geographically distributed over 13 continent. Members this cluster, named AF1, carry genetic background consisting large number highly variants, rarely observed outside at multitude...
Monitoring the genomic evolution of Plasmodium falciparum - most widespread and deadliest human-infecting malaria species is critical for making decisions in response to changes drug resistance, diagnostic test failures, vaccine effectiveness. The MalariaGEN data resources are world’s largest whole genome sequencing databases parasites. size complexity such a barrier many potential end users both public health academic research. A user-friendly method accessing interpreting on genetic...
Abstract Artemisinin partial resistance (ART-R) in Plasmodium falciparum is one of the most pressing threats to global malaria control. Over last two decades, ART-R has spread widely across Southeast Asia, compromising public health strategies and hindering elimination efforts. As 2024, now emerged East Africa, with potential dramatically increase human mortality region. Mitigating requires detailed genomic surveillance point mutations kelch13 gene, primary determinant artemisinin...
Abstract Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels relatedness. Yet, how local epidemiology affects the properties such mixed remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates number strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to Pf3k data set, find that rate infection varies 29% 63% across countries 51%...
Array-based comparative genomic hybridization (CGH) technology is used to discover and validate structural variation, including copy number variants, insertions, deletions other variants (SVs). The visualization summarization of the array CGH data outputs, potentially across many samples, an important process in identification analysis SVs. We have developed a software tool for SV using from technologies, which also amenable short-read sequence data.SnoopCGH written java available...
Motivation The presence of multiple infecting strains the malarial parasite Plasmodium falciparum affects key phenotypic traits, including drug resistance and risk severe disease. Advances in protocols sequencing technology have made it possible to obtain high-coverage genome-wide data from blood samples spots taken field. However, analysing interpreting such is challenging because high rate infections present. Results We developed a statistical method implementation for deconvolving genome...
Abstract Malaria is a global public health priority causing over 600,000 deaths annually, mostly young children living in Sub-Saharan Africa. Molecular surveillance can provide key information for malaria control, such as the prevalence and distribution of antimalarial drug resistance. However, genome sequencing capacity endemic countries be limited. Here, we have implemented an end-to-end workflow P. falciparum genomic Ghana using Oxford Nanopore Technologies, targeting resistance markers...