Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website

Trace metal concentration in the liver of Citharinus citharus (moon – fish) from Taylor creek

This study analysed trace metal levels in the liver of Citharinus citharus obtained from three different stations(Ogboloma, Pokaku and Agbia) along Taylor Creek The concentration of cadmium in fish liver was 0.02 + 0.01 mg/kg, 0.04 + 0.01 mg/kg, 0.03 + 0.00 mg/kg in Agbia, Ogboloma and Polaku respectively (P>0.05). The values of lead in the liver of the fish were higher than that of cadmium. Lead was 0.07 + 0.01 mg/kg at Agbia, 0.14+ 0.00 mg/kg at Ogboloma and 0.09 + 0.03 mg/kg at Polaku. Mean levels of zinc fish liver sample obtained from Agbia, Ogboloma and Polaku were 1.51 + 0.07 mg/kg, 1.66 + 0.09 mg/kg and 1.66 + 0.22 mg/kg respectively. Concentrations of zinc and lead in the liver of the fish were not significantly different at Agbia and Polaku (P>0.05), but were significantly higher at Ogboloma (P<0.05). The values of zinc were generally higher than Cd and Pb.Oil and gas exploration activities and domestic waste disposal could be linked to elevated level of metals in the fish.Keywords: Effluent, fish liver, oil and gas activities, Taylor Creek, trace Metal

Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples.

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website