Seventh Malaria Genome

Sequencing Meeting

21st — 23rd July 1999

Wellcome Trust Genome Campus, Hinxton,

Cambridgeshire

 

REPORT OF MEETING

 

Seventh Malaria Genome Sequencing Meeting

Hinxton July 21-23 1999

For subsequent meeting reports please refer to MFI's Malaria Genome Database page at www.malaria.org/genome.html

 

Background

As the sequencing of the P. falciparum genome progresses there is an increasingly urgent need to ensure that mechanisms (both technical, information sharing and funding) are in place to exploit the information obtained, for health care benefit. The Seventh Genome Sequencing meeting was convened with a focus on the post-genomic era and participants included experts from fields other than malaria research, who shared their experience in areas such as database development and proteomics.

Updates on Sequencing projects

Representatives from the three sequencing centres (Sanger, TIGR/NMRC and Stanford) presented reports on the P. falciparum sequencing effort. Excellent progress is being made at all three centres and the Sanger team was congratulated on the completion of chromosome 3, to be published in Nature in August.

There was an open discussion about the new 96 well format capillary sequencing machines (ABI 3700). It was generally agreed that these machines, although not as efficient as the manufacturers first suggested appeared to be showing promise and with the correct technical support could increase throughput to 5 runs per day with ~500 bp reads.

Malaria Repository

Dr Raymond Cypess from MR4 (Malaria Research and Reference Reagent Resource center) described how the repository had been set up in 1998 under the management of ATCC and with contract funding from NIAID, to provide reagents for the malaria research community. Dr. Cypess described the operation and management of the MR4. Reagents are issued in reference amounts with researchers paying only shipping costs. MR4 has an international advisory group with 14 members who meet twice each year. There is a webpage (www.malaria.MR4.org), and a newsletter detailing reagents currently available and describing opportunities for workshops. Printed and CD ROM versions of the reagent catalog are anticipated in the near future. MR4 is funded to run 2 workshops per year; these could be on any relevant topic, for example, parasite culturing, bioinformatics. Although it is expected that investigators will freely deposit reagents to the MR4, in some cases funds will be made available for the production of reagents that are deemed valuable to a large number of malaria investigators. Dr. Cypess distributed an announcement soliciting the production of high quality cDNA libraries for acquisition and distribution by MR4. Funds for the production will be provided by the MR4.

Alan Fairlamb pointed out that prohibitively restrictive legalistic conditions were placed on researchers wishing to use the repository. Dr Cypess agreed that the procedure is not ideal and steps are being taken to simplify it by developing a ‘fast track’ mechanism, subject to agreement with funders and employing institutions. David Roos commented that users in developing countries would find shipping costs prohibitive and that cheaper means such as supplying plasmid DNA on filter paper should be developed. It was also suggested that, given the problems in transporting parasite material to investigators in malaria endemic areas, a satellite repository outside the USA, would be useful.

Dr Cypess invited suggestions of desirable reagents for the repository and asked whether anyone had suitable reagents that could be donated to the repository.

Updates on Mapping projects

Dr Tom Wellems and Dr David Schwartz presented progress reports and demonstrated the utility of the mapping approach to the sequencing project.

Reports from Workshops

Following the sequencing meeting held at Hinxton in July 1998 three workshops were convened to assess the technical requirements for research in functional genomics. Delegates were given copies of the written reports of these meetings and the recommendations made at the workshops were highlighted by Dan Carucci (Expression Analysis), Alistair Craig (Molecular Tools) and Chris Newbold (Databases). These were considered further in the discussion sessions and subsequent recommendations are noted later in this document.

Post-genomic needs - current needs and future directions

In this section there were four presentations which provided insight into key techniques which will be important for the post genomic era of malaria research. Michael Ashburner talked about the FLYbase database, originally set up for the Drosophila research community but now widely used and linked to other organism databases. This was followed by a discussion of proteomics (Philip Cash), metabolomics (Alan Fairlamb) and reporter protein systems (Alan Cowman).

Ways in which sequence information might be exploited in vaccine and drug design were considered by three speakers. Steve Hoffman highlighted ways in which the genome sequence data could be used to screen novel antigens as potential vaccine candidates, but pointed out that this requires the development of high throughput screening methods. Paul Sims and David Roos demonstrated how sequence information can help identify pathways specific to parasites which are potential drug targets and provide a clearer understanding of resistance mechanisms.

Group discussions

Delegates were split into five groups with a breadth of expertise within each group. In the first breakout each group was asked to discuss what information we would hope to access from a malaria specific database, possible topics for workshops which should be set up to develop expertise in key areas and what the malaria repository should provide. In the second break out session, the focus for discussion was the prerequisites for drug and vaccine development. After one hour, the views of each breakout group were presented to the group as a whole. The major points of discussion are reported below.

 

1) Database

What do we want from a malaria database?

There is already a large amount of malaria specific information available via the internet but there is a need to develop data mining tools and a more user-friendly front end to the database so that a wider range of users are able to access the information. The database needs to be expandable, flexible and compatible with other databases and information should be provided in downloadable format (ASCI). Key issues to be addressed are effective and accurate curation/editing. One group highlighted the need for annotation to focus on vaccine candidates and drug targets. Ideally the database would be a ‘one stop shop’ for malaria researchers with links to the MR4 and other information (including other key databases) and bibliographic resources. It was generally agreed that the database should be managed by an international committee comprised of malariologists, sequencing experts and representatives from other pathogen communities, probably with a single person responsible for curation.

What is the way forward for developing a database?

There is an urgent short term need to provide sequence information in a more usable form for the general community. In the longer term the ideal would be a comprehensive database which will provide a one stop shop for the malaria community.

There are already several model organism databases which meet, at least in part, the needs identified above. It was therefore agreed that the first step in developing a malaria database must be to examine the options already available and decide which (if any) would be the best model for malaria. It would be important to identify one or two individuals with the time and motivation to drive development of the database forward quickly.

2) Workshops and technology sharing

In order to ensure the transfer of enabling technologies to the wider research community, it will be important to run training courses and workshops in areas such as microarray technologies, bioinformatics, comparative studies and molecular epidemiology. Some courses already exist and new courses should link into these if possible. There is also a clear need for transferring transfection technologies to a larger number of malaria investigators, although due to the length of time required to generate transfectants, it was felt that a short course would not provide the necessary conditions to transfer the technology. In this case, a mechanism should be available to fund visits to expert labs with costs for travel and consumables provided. By doing so more foci of expertise would develop relieving pressure on the few labs currently expert in these methods.

3) Medium term goals for consideration

Knock-outs

When the complete genome sequence is available it will be theoretically possible to knock-out all genes systematically. However, this may not be the most efficient or effective strategy to identify key genes involved in pathogenesis and most participants favoured a thematic approach to generating knockouts, based on invasion, cytoadherence etc. In any event, progress will be dependent on setting up consortia of groups with relevant expertise.

Sequencing other malaria parasites

Now that the sequencing of the P falciparum genome is almost complete it is possible to analyse polymorphic regions within the genome using other P. f alciparum isolates and to compare the sequence with that of other Plasmodium species. It was generally accepted that there are arguments for doing a 3-4X coverage of at least one rodent malaria strain. In addition there was some discussion about the need to sequence the Toxoplasma gondii genome as a good model for assessing potential drug targets.

 

Other key areas requiring immediate development were identified as:

Parasitology and cell biology, including establishment of stage specific protein expression eg. by systematic production of antibodies

Heterologous expression systems

Functional assays

High throughput screening

Outcomes and recommendations of the Seventh Genome Sequencing meeting

Repository

Suggestions of reagents for the repository are to be forward to Raymond Cypess at MR4 and researchers with reagents which could be included in the repository are invited to deposit them. Dr Cypess is to explore possible ways of simplifying the procedure for obtaining and distributing reagents. Although it is expected that investigators will freely deposit reagents to the MR4, in some cases funds will be made available for the production of reagents that are deemed valuable to a large number of malaria investigators.

Database

Ross Coppel, Chris Newbold and David Roos agreed to assess the technical options available for development of a suitable database. They will report back to the funders at the end of the summer.

Workshops

The following topics for workshops were identified:

Michael Gottlieb will investigate whether MR4 could fund some of these.

Training and technology sharing

Funders to review current training programmes with a view to expanding them.

Michael Gottlieb to talk to Yumin Wu about the possibility of setting up a bulletin board with daily updates on techniques and protocols

 

Technologies in need of development

The following areas were identified: