Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness
IntroductionThe use of next-generation sequencing technologies (NGS) to study parasite populations and their response and evolution to interventions is important to support malaria control and elimination efforts. While whole-genome sequencing (WGS) is optimal in terms of assessing the entire genome...
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Frontiers Media S.A.
2025-06-01
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| author | Karamoko Niaré Karamoko Niaré Rebecca Crudale Abebe A. Fola Abebe A. Fola Neeva Wernsman Young Victor Asua Victor Asua Melissa D. Conrad Pierre Gashema Anita Ghansah Stan Hangi Deus S. Ishengoma Deus S. Ishengoma Jean-Baptiste Mazarati Ayalew Jejaw Zeleke Philip J. Rosenthal Abdoulaye A. Djimdé Abdoulaye A. Djimdé Jonathan J. Juliano Jonathan J. Juliano Jonathan J. Juliano Jeffrey A. Bailey Jeffrey A. Bailey |
| author_facet | Karamoko Niaré Karamoko Niaré Rebecca Crudale Abebe A. Fola Abebe A. Fola Neeva Wernsman Young Victor Asua Victor Asua Melissa D. Conrad Pierre Gashema Anita Ghansah Stan Hangi Deus S. Ishengoma Deus S. Ishengoma Jean-Baptiste Mazarati Ayalew Jejaw Zeleke Philip J. Rosenthal Abdoulaye A. Djimdé Abdoulaye A. Djimdé Jonathan J. Juliano Jonathan J. Juliano Jonathan J. Juliano Jeffrey A. Bailey Jeffrey A. Bailey |
| author_sort | Karamoko Niaré |
| collection | DOAJ |
| description | IntroductionThe use of next-generation sequencing technologies (NGS) to study parasite populations and their response and evolution to interventions is important to support malaria control and elimination efforts. While whole-genome sequencing (WGS) is optimal in terms of assessing the entire genome, it is costly for numerous samples. Targeted approaches selectively enriching for the sequence of interest are more affordable and have higher throughput but sometimes lack adequate information content for key analyses.MethodsWe have developed a highly multiplexed molecular inversion probe (MIP) panel (IBC2FULL) targeting 4,264 single-nucleotide polymorphisms (SNPs) with ≥5% minor allele frequency (MAF) in Sub-Saharan African regions from publicly available Plasmodium falciparum WGS (n = 3,693). We optimized the panel alone and in combination with antimalarial drug resistance MIPs in laboratory P. falciparum strains at different parasitemias and validated it by sequencing field isolates from the Democratic Republic of Congo, Ethiopia, Ghana, Mali, Rwanda, Tanzania, and Uganda and evaluating the population structure, identity-by-descent (IBD), signals of selection, and complexity of infection (COI).ResultsThe new panel IBC2FULL consisted of 2,128 MIPs (containing 4,264 common SNPs) spaced by 5.1–18.4 kb across the entire genome. While these microhaplotypes were developed based on variations from Sub-Saharan African WGS data, 59.3% (2,529) of SNPs were also common in Southeast Asia. The MIPs were balanced to produce more a uniform and higher depth of coverage at low parasitemia (100 parasites/μL) along with MIPs targeting antimalarial drug resistance genes. Comparing targeted regions extracted from public WGS, we observed that IBC2FULL provided a higher resolution of the local population structure in Sub-Saharan Africa than current PCR-based targeted sequencing panels. For sequencing field samples (n = 140), IBC2FULL approximated WGS measures of relatedness, population structure, and COI. Interestingly, genome-wide analysis of extended haplotype homozygosity detected the same major peaks of selection as WGS. We also chose a subset of 305 high-performing MIPs to create a core panel (IBC2CORE) that produced high-quality data for basic population genomic analysis and accurate estimation of COI.DiscussionIBC2FULL and IBC2CORE panels have been designed to provide an improved platform for malaria genomic epidemiology and biology that can approximate WGS for many applications and is deployable for malaria molecular surveillance in resource-limited settings. |
| format | Article |
| id | doaj-art-7b66192e4ffc4bcbbf8a67dd974c8561 |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj-art-7b66192e4ffc4bcbbf8a67dd974c85612025-08-20T03:25:33ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-06-011610.3389/fgene.2025.15260491526049Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatednessKaramoko Niaré0Karamoko Niaré1Rebecca Crudale2Abebe A. Fola3Abebe A. Fola4Neeva Wernsman Young5Victor Asua6Victor Asua7Melissa D. Conrad8Pierre Gashema9Anita Ghansah10Stan Hangi11Deus S. Ishengoma12Deus S. Ishengoma13Jean-Baptiste Mazarati14Ayalew Jejaw Zeleke15Philip J. Rosenthal16Abdoulaye A. Djimdé17Abdoulaye A. Djimdé18Jonathan J. Juliano19Jonathan J. Juliano20Jonathan J. Juliano21Jeffrey A. Bailey22Jeffrey A. Bailey23Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United StatesCenter for Computational Molecular Biology, Brown University, Providence, RI, United StatesDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, United StatesDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, United StatesCenter for Computational Molecular Biology, Brown University, Providence, RI, United StatesCenter for Computational Molecular Biology, Brown University, Providence, RI, United StatesInfectious Diseases Research Collaboration, Kampala, UgandaInstitute for Tropical Medicine, University of Tubingen, Tubingen, GermanyDepartment of Medicine, University of California, San Francisco, San Francisco, CA, United StatesCenter for Genomic Biology, Institut d’Enseignement Supérieur de Ruhengeri, Ruhengeri, RwandaNoguchi Memorial Institute for Medical Research, University of Ghana, Accra, GhanaDepartment of Pediatrics, HEAL Africa, Goma, Democratic Republic of CongoNational Institute for Medical Research, Dar es Salaam, Tanzania0Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, TanzaniaCenter for Genomic Biology, Institut d’Enseignement Supérieur de Ruhengeri, Ruhengeri, Rwanda1Department of Medical Parasitology, School of Biomedical and Laboratory Science, University of Gondar, Gondar, EthiopiaDepartment of Medicine, University of California, San Francisco, San Francisco, CA, United States2Pathogens genomics Diversity Network Africa, Bamako, Mali3Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali4Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States5Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States6Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United StatesDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, United StatesCenter for Computational Molecular Biology, Brown University, Providence, RI, United StatesIntroductionThe use of next-generation sequencing technologies (NGS) to study parasite populations and their response and evolution to interventions is important to support malaria control and elimination efforts. While whole-genome sequencing (WGS) is optimal in terms of assessing the entire genome, it is costly for numerous samples. Targeted approaches selectively enriching for the sequence of interest are more affordable and have higher throughput but sometimes lack adequate information content for key analyses.MethodsWe have developed a highly multiplexed molecular inversion probe (MIP) panel (IBC2FULL) targeting 4,264 single-nucleotide polymorphisms (SNPs) with ≥5% minor allele frequency (MAF) in Sub-Saharan African regions from publicly available Plasmodium falciparum WGS (n = 3,693). We optimized the panel alone and in combination with antimalarial drug resistance MIPs in laboratory P. falciparum strains at different parasitemias and validated it by sequencing field isolates from the Democratic Republic of Congo, Ethiopia, Ghana, Mali, Rwanda, Tanzania, and Uganda and evaluating the population structure, identity-by-descent (IBD), signals of selection, and complexity of infection (COI).ResultsThe new panel IBC2FULL consisted of 2,128 MIPs (containing 4,264 common SNPs) spaced by 5.1–18.4 kb across the entire genome. While these microhaplotypes were developed based on variations from Sub-Saharan African WGS data, 59.3% (2,529) of SNPs were also common in Southeast Asia. The MIPs were balanced to produce more a uniform and higher depth of coverage at low parasitemia (100 parasites/μL) along with MIPs targeting antimalarial drug resistance genes. Comparing targeted regions extracted from public WGS, we observed that IBC2FULL provided a higher resolution of the local population structure in Sub-Saharan Africa than current PCR-based targeted sequencing panels. For sequencing field samples (n = 140), IBC2FULL approximated WGS measures of relatedness, population structure, and COI. Interestingly, genome-wide analysis of extended haplotype homozygosity detected the same major peaks of selection as WGS. We also chose a subset of 305 high-performing MIPs to create a core panel (IBC2CORE) that produced high-quality data for basic population genomic analysis and accurate estimation of COI.DiscussionIBC2FULL and IBC2CORE panels have been designed to provide an improved platform for malaria genomic epidemiology and biology that can approximate WGS for many applications and is deployable for malaria molecular surveillance in resource-limited settings.https://www.frontiersin.org/articles/10.3389/fgene.2025.1526049/fullmalariaPlasmodium falciparummolecular inversion probemolecular surveillancegenomic epidemiologytargeted sequencing |
| spellingShingle | Karamoko Niaré Karamoko Niaré Rebecca Crudale Abebe A. Fola Abebe A. Fola Neeva Wernsman Young Victor Asua Victor Asua Melissa D. Conrad Pierre Gashema Anita Ghansah Stan Hangi Deus S. Ishengoma Deus S. Ishengoma Jean-Baptiste Mazarati Ayalew Jejaw Zeleke Philip J. Rosenthal Abdoulaye A. Djimdé Abdoulaye A. Djimdé Jonathan J. Juliano Jonathan J. Juliano Jonathan J. Juliano Jeffrey A. Bailey Jeffrey A. Bailey Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness Frontiers in Genetics malaria Plasmodium falciparum molecular inversion probe molecular surveillance genomic epidemiology targeted sequencing |
| title | Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness |
| title_full | Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness |
| title_fullStr | Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness |
| title_full_unstemmed | Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness |
| title_short | Highly multiplexed molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole-genome sequencing assessments for selection and relatedness |
| title_sort | highly multiplexed molecular inversion probe panel in plasmodium falciparum targeting common snps approximates whole genome sequencing assessments for selection and relatedness |
| topic | malaria Plasmodium falciparum molecular inversion probe molecular surveillance genomic epidemiology targeted sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1526049/full |
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