Biology subjects
Publications and source records attributed to Tessema, S. K..
Africas diverse pathogen and human genetics present significant opportunities for genomic medicine research using artificial intelligence (AI). We surveyed 250 genomics researchers across 46 of the 55 African Union Member States to assess the state of AI use. The survey revealed that only 4% of respondents reported high familiarity with the application of AI for genomics and bioinformatics.
BackgroundTargeted next generation sequencing offers the potential for consistent, deep coverage of information rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. MethodsA bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, WGS data were generated for the same controls. ResultsUsing publicly available genomes, 4465 high diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median HE = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%) and sensitivity (90% for haplotypes with 5% within sample frequency in DBS with 100 parasites/{micro}L). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic SNP barcodes. DiscussionThe bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
BackgroundWhole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. We evaluated the effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification on the quality and fidelity of WGS data recovered from DBS. ResultsAt 100 parasites/L, Chelex-Tween-McrBC samples had higher coverage (5X depth = 93% genome) than QIAamp extracted samples (5X depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published. ConclusionsOverall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.
ABSTRACTO_ST_ABSBackgroundC_ST_ABSTo better understand transmission dynamics, we characterized Plasmodium falciparum (Pf) genetic diversity in Eswatini, where transmission is low and sustained by importation.\n\nMethods26 Pf microsatellites were genotyped in 66% of all confirmed cases from 2014-2016 (n=582). Population and within-host diversity were used to characterize differences between imported and locally-acquired infections, as determined by travel history. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone.\n\nResultsThe parasite population in Eswatini was highly diverse (HE=0.75) and complex, with 67% polyclonal infections, a mean MOI of 2.2, and mean FWS of 0.84. Imported cases had comparable diversity to local cases, but exhibited higher MOI (2.4 versus 2.0; p=0.004) and lower mean FWS (0.82 vs. 0.85; p=0.03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections.\n\nDiscussionIn contrast to the commonly held perception that Pf diversity declines with decreasing transmission intensity, isolates from Eswatini exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.