Browsing by Author "Hazelhurst, Scott"

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Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
(BMC, 2018-01) Ceballos, Francisco C.; Hazelhurst, Scott; Ramsay, Michèle
Background: Runs of Homozygosity (ROH) are genomic regions where identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Results: Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. By allowing heterozygous SNPs per window, using the PLINK homozygosity function and non-parametric analysis, we were able to obtain non-significant differences in number ROH, mean ROH size and total sum of ROH between data sets using the different technologies for almost all populations. Conclusions: By allowing 3 heterozygous SNPs per ROH when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using SNP array and WGS low coverage technologies
Genomewide association study metaanalysis of blood pressure traits and hypertension in subSaharan African populations an AWIGen study
(Nature Research) Norris, Shane A.; Choudhury, Ananyo; Hazelhurst, Scott ; Crowther, Nigel ; Boua, Palwende ; Sorgho, Hermann; Agongo, Godfred; Nonterah, Engelbert A.; Micklesfield, Lisa K.; Singh, Surina; Kisiangani, Isaac; Mohamed, Shukri; Gomez-Olive, Francesc X.; Tollman, Stephen M.; Choma, Solomon; Brandenburg, J-T.; Ramsay, Michele
The Gene Catalogue and Functional Analysis of the Gut Microbiome of Lions in Etosha National Park
(University of the Witwatersrand, Johannesburg, 2024-09) Belger, Carl Warner; Hetem, Robyn; Hazelhurst, Scott
Characterising the microbiomes of free-living mammals may aid conservation efforts, yet the gut microbiome of carnivores is underrepresented. This study represents the first description of the gut microbiome of free-living African lions (Panthera leo melanochaita). Faecal samples from 20 lions were collected in Etosha National Park, Namibia and microbial DNA was extracted. Samples were then whole genome sequenced, and classified using MetaPhlAn and Genome Taxonomy Database toolkit. The two most abundant bacterial genera in the lions’ gut microbiomes were Bacteroides (16.9%) and Phocaeicola (16.6%). Microbiome diversity was similar between the sexes and across seasons as assessed through Bray-Curtis dissimilarity and Shannon diversity index. The genus Clostridium_AH was more abundant in male lions (P = 0.007; d.f. = 22), while Aphodousia (P = 0.003; d.f. = 22) was more abundant in females. Lions captured in winter had a high abundance of Plesiomonas relative to those captured in summer (P = 0.008), whereas lions captured in summer a high abundance of Dysosmobacter (P = 0.038; d.f. = 22), Pelethomonas (P = 0.021; d.f. = 22), Metalachnospira (P = 0.033; d.f. = 22) and Clostridium Q (P = 0.012; d.f. = 22) compared to those captured in winter. Following various taxonomic classification approaches, a third of the reads (33.6%) present in the lion gut microbiome remained unclassified. We constructed 272 metagenome assembled genomes, from seven bacterial phyla, representing mostly new species which will contribute to understanding of the carnivore gut microbiome.