hmmIBD: software to infer pairwise identity by descent between haploid genotypes

Schaffner, Stephen F.; Taylor, Aimee R; Wong, Waichi; Wirth, Dyann F.; Neafsey, Daniel E.

doi:10.1101/188078

Cited by 35 publications

(51 citation statements)

References 12 publications

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“…Whole-genome sequencing (WGS) can be particularly useful for understanding the history of parasite populations and movement of closely related parasites over geographical distances [9,10]. Identity by descent (IBD), the sharing of discrete genomic segments inherited from a common genealogical ancestor, has been found to be a particularly good metric for studying the interconnectivity of parasite populations [11][12][13]. A major obstacle to studying IBD in microorganisms, and in particular malaria, is the presence of multiple clones in a single infection.…”

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confidence: 99%

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

Morgan

Brazeau

Ngasala

et al. 2020

Malar J

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Background: Tanzania's Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria's persistence, but this paradigm has not been studied using modern genetic tools. Methods: Whole-genome sequencing (WGS) was used to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. Ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations were assessed by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections. Results: Significant decreases in the effective population sizes were inferred in both populations that coincide with a period of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared long segments of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, two of isolates between the mainland and Zanzibar were identified that are related at the expected level of half-siblings, consistent with recent importation. Conclusions: These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.

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mentioning

confidence: 99%

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

Morgan

Brazeau

Ngasala

et al. 2020

Malar J

View full text Add to dashboard Cite

show abstract

mentioning

confidence: 99%

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

Morgan

Brazeau

Ngasala

et al. 2020

Preprint

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Background : Tanzania’s Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria’s persistence, but this paradigm has not been studied using modern genetic tools. Methods : We used whole-genome sequencing (WGS) to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. We assessed ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections. Results : We identified significant decreases in the effective population sizes in both populations in the timeframe of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared large sections of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, we identified a pair of isolates between the mainland and Zanzibar that are related at the expected level of half-siblings, consistent with recent importation Conclusions : These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.

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“…First, it was observed that polygenomic infections are more common among travellers to Richard Toll, consistent with the hypothesis that these represent infections imported from higher malaria transmission settings outside Richard Toll. Pairwise analysis [9] of genotypes from 649 Richard Toll infections and 1,555 Thiès infections revealed that 21% of Richard Toll samples genetically matched parasites from Thiès, consistent with importation of Richard Toll infections. A substantially greater proportion of malaria cases diagnosed in Richard Toll are likely to be imported;…”

Section: Discussionmentioning

confidence: 77%

“…The IBS estimate used in the software output was "fract_sites_IBD." Only sample pairs that were identical or highly related (de nitions, Table 1) were included in subsequent analyses, which corresponded to a value of 0.95 or greater [9]. This corresponded to a minimum inclusion criterion of 22/23 barcode positions matching between two parasites.…”

Section: Discussionmentioning

confidence: 99%

Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal

Volkman¹,

Sarr

Steketee³

et al. 2020

Preprint

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Background Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. Methods A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. Results Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. Conclusions These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.

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hmmIBD: software to infer pairwise identity by descent between haploid genotypes

Cited by 35 publications

References 12 publications

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal

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