Phylodynamic Methods Comparison Exercise
Research groups are invited to participate in a blinded methods comparison exercise on simulated sequence data sets that capture different HIV transmission dynamics in generalized HIV-1 epidemics.
Different phylogenetic and phylodynamic methods have been adopted to characterize concentrated HIV epidemics in Europe and the US, largely from partial HIV-1 pol sequences collected through local, regional or national HIV treatment monitoring studies. There is little consensus on the ability of the various methods to accurately analyse declining, stable or increasing HIV epidemics at different scales, both in terms of geographical range and epidemic scale. Little is known on the power of the various methods in reliably assessing these HIV epidemics from data that differs in completeness and may be biased. This is particularly so for the application of these methods to HIV next generation sequencing data from generalised epidemics. We expect these methods to have - ultimately - profound implications to our understanding of HIV-1 transmission and our ability to prevent transmission. It is of critical importance to understand - now - the applicability and potential shortcomings of these methods to the kind of data that will be generated by the PANGEA consortium.
The primary objective of the PANGEA-HIV phylodynamic methods comparison exercise is to evaluate existing phylogenetic methods in their ability to accurately and reliably identify changes in HIV incidence that might occur over a few years representing a community-based intervention in sub-Saharan Africa in the simulation.
Secondary aims of the exercise are to evaluate
- improvements in accuracy and power through the use of concatenated HIV-1 gag, pol and env sequence data as compared to HIV-1 pol sequence data,
- accuracy and power with respect to different sequence sampling intensities.
- 7th November 2014: Deadline for preliminary research reports by participating groups.
- 2nd December 2014: workshop to compare and consolidate initial results in London, with publication of the findings to follow.
- February 2015: Release of simulated sequence data sets and simulated phylogenies.
- 27th February 2015: Presentation of interim results at CROI.
- 6th May 2015: Deadline for submission of analyses.
- 13th May 2015: HIV Dynamics and Evolution 2015, presentation of the results of the methods comparison exercise. Individual submissions from participants are encouraged.
- 16th May 2015: PANGEA_HIV satellite meeting to present and discuss the final results of the exercise in detail. All participating teams will have the opportunity to present their work.
The simulations can be downloaded via the following link in the "201502" folder:
If you would like further details regarding this research, please email firstname.lastname@example.org
The PANGEA methods comparison working group
Anne Cori 1, Christophe Fraser 1, Matthew Hall 2, Emma Hodcroft 2, Andrew Leigh Brown 2, Mike Pickles1 , Andrew Rambaut 2, Manon Ragonnet-Cronin 2, Oliver Ratmann 1
1Imperial College London, UK; 2University of Edinburgh, UK
Genetic sequencing is increasingly used to investigate pathogens and human genes that affect health. With this in mind, researchers at the Africa Centre strived to establish one of the world’s most advanced and respected genetic sequencing systems. The system is fully automated and uses robust laboratory and informatics methodology in order to generate high-quality genomic data at a fraction of the cost of commercial or in-house research laboratories in Africa. It is anticipated that this sustainable genomic facility will become a core scientific resource of the University of KwaZulu-Natal (UKZN) and other universities within South Africa, and the facility is essential to support the world-class genomics research which is being done as part of PANGEA_HIV.
We are therefore pleased to announce that the facility is fully functional since July 2014 and would like to invite you to witness the construction of the Genomics laboratory by watching a series of three short videos. The first video shows a pictorial tour of the facilities prior to the transformation and can be accessed via http://www.bioafrica.net/videos.php?id=21. The second video (http://www.bioafrica.net/videos.php?id=22) provides a description of the robotics system and introduces the new bioinformatics facility. The third and final video shows the completion of genomics centre. It can be accessed via http://www.bioafrica.net/videos.php?id=23.
Set-up of the Bioinformatics pipeline