Plasmodium falciparum Community Project: about the version 6 data

12 Aug 2019

This page provides information about data generated by the Plasmodium falciparum Community Project using the version 6 pipeline for variant discovery and genotype calling.

Background

The Plasmodium falciparum Community Project supports groups around the world to integrate parasite genome sequencing into clinical and epidemiological studies of malaria.  It comprises multiple partner studies, each with its own research objectives and led by a local investigator.  Genome sequencing is performed centrally, and partner studies are free to analyse and publish the genetic data produced on their own samples, in line with MalariaGEN’s guiding principles on equitable data sharing.

Aggregated data from the Community Project were initially released through a companion project called Pf3k whose goal was to bring together leading analysts from multiple institutions to benchmark and standardise methods of variant discovery and genotyping calling.   The Pf3k dataset can be explored using an interactive web application.

The open dataset was enlarged in 2016 when multiple partner studies contributed to a consortial publication on 3,488 samples from 23 countries.  The variants and genotypes described in this publication used version 3 of the analysis pipeline. Data produced using an earlier version of the data analysis pipeline can be explored using an interactive web application.

About the version 6 data pipeline

In 2018 the Plasmodium falciparum Community Project upgraded to version 6 of its variant discovery and genotype calling pipeline.  Follow this link for an outline of the analytical methods.  The major change from previous versions is that the version 6 pipeline is based on GATK and utilises findings on genome accessibility generated by P. falciparum Genetic Crosses Project

Publications that use the version 6 data

Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study.  Hamilton WL, Amato R, van der Pluijm RW, Jacob CG, Quang HH, Thuy-Nhien NT, Hien TT, Hongvanthong B, Chindavongsa K, Mayxay M, Huy R, Leang R, Huch C, Dysoley L, Amaratunga C, Suon S, Fairhurst RM, Tripura R, Peto TJ, Sovann Y, Jittamala P, Hanboonkunupakarn B, Pukrittayakamee S, Chau NH, Imwong M, Dhorda M, Vongpromek R, Chan XHS, Maude RJ, Pearson RD, Nguyen T, Rockett K, Drury E, Gonçalves S, White NJ, Day NP, Kwiatkowski DP, Dondorp AM, Miotto O.  Lancet Infectious Disease, 2019 Jul 22. pii: S1473-3099(19)30392-5. doi: 10.1016/S1473-3099(19)30392-5. [Epub ahead of print]

Major subpopulations of Plasmodium falciparum in sub-Saharan Africa.  Alfred Amambua-Ngwa, Lucas Amenga-Etego, Edwin Kamau, Roberto Amato, Anita Ghansah, Lemu Golassa, Milijaona Randrianarivelojosia, Deus Ishengoma, Tobias Apinjoh, Oumou Maïga-Ascofaré, Ben Andagalu, William Yavo, Marielle Bouyou-Akotet, Oyebola Kolapo, Karim Mane, Archibald Worwui, David Jeffries, Vikki Cornelius, Umberto D’Alessandro, Dominic Kwiatkowski, Abdoulaye A. Djimde.  Science, in press.