Parasite partner study resources

This page provides details for what is required before shipping parasite samples to MalariaGEN, as well as how data is returned to our partners.

Checklist for shipping parasite samples

We cannot accept any samples until the below checklist is complete. If you have any queries regarding any aspect in relation to your partner study, please contact samples [at] malariagen.net, particularly if you need to request collection kits, require support applying for Nagoya approval and to send your completed sample information sheet.

  1. The study has a MalariaGEN Study ID
  2. Relevant ethics approvals are in place and have been shared with MalariaGEN
  3. Agreement from National authorities in the country of sample origin in line with the Nagoya Protocol is in place and signed off by Wellcome Sanger Institute
  4. Collections of dried blood spot samples follow visual guidance, and sampling protocols have been followed
  5. Two copies of Sample Information Sheets have been fully completed following sample instructions

1. Study ID
All MalariaGEN collaborations have a Study ID. We can only accept samples from approved partner studies. This should have been completed during study set-up.

2. Ethics approvals
All relevant ethics approvals for your study should be shared with MalariaGEN prior to receipt and processing of samples in line with good ethical practice. This should have been completed during study set-up, but please provide any updated approvals as they are agreed.

3. Nagoya approval
MalariaGEN cannot accept samples at Wellcome Sanger Institute without relevant Nagoya approval. This should have been completed during study set-up but the in-country process may have changed since and must be checked prior to each sample shipment. Full details can be found on the ABSCH Clearing House, but MalariaGEN are able to help with this process. Material Transfer Agreements are often a requirement, these should use your Institutional template so MalariaGEN does not provide a template as a resource. Wellcome Sanger Institute will need to sign off that due process has been followed.

Please note that approval is required from the country the samples originated in and acquiring approval can be a lengthy process that is best started as soon as possible.

4. Collection of Plasmodium-infected whole blood as DBS
Our protocol for partners who are collecting dried blood spots samples overcomes many of the challenges of inconsistencies in materials, procedural variability, and issues with sample tracking and archiving. The visual guidance explains:

  • Preparing DBS kits for collection
  • Barcoding DBS for easy tracking and archiving
  • Consistently collecting fixed volume, evenly-sized blood spots
  • Storing and transporting DBS

The benefits of MalariaGEN's DBS system for collecting parasite samples and DNA sequencing are:

  • Small volumes of blood – this makes collection from sick patients easier, and also simplifies storage and transport.
  • No cold chain required – once spotted, the blood can be kept at room temperature.
  • Low cost – minimal training and materials needed.

We may also accept extracted DNA with a minimum volume of 200ng in 100ul.

Standard DBS protocols 

These protocols are for standard MalariaGEN parasite partner studies. All parasite partner studies are part of the SpotMalaria project.

Download collection protocol visual guide
Download full collection protocol

GenRe-Mekong protocols

These protocols are specific to partner studies that are part of the GenRe-Mekong project.

Download GenRe-Mekong SOP for sample collection
Watch the GenRe-Mekong video guide for 2 dot DBS collection
Watch the GenRe-Mekong video guide for 2 dot DBS collection with Thai subtitles
Watch the GenRe-Mekong video guide for 3 dot DBS collection

5. Sample Information Sheets (SIS)
We require two completed copies of this form: an electronic copy that must be emailed to samples [at] malariagen.net before shipping samples, and a printed copy that must be included within the sample shipment.

Each sample information sheet is an excel file that contains three tabs:

  1. An ‘Instructions’ tab, providing guidance on how to complete each sample metadata column
  2. A ‘Plasmodium Samples’ tab that must be fully completed for each sample
  3. A ‘Location’ tab that must be fully completed for all samples

Download parasite sample information sheet
Download parasite sample information sheet user guide

Data release

Our Plasmodium projects routinely release genotype data to partners via an email notification sent to the contact person(s) and designated study associates for all partner studies with data in that release. Direct access will only be given to the partner study contact person and any additional study associates specifically designated by the Principle Investigator or contact person. If you wish to query or update the contact(s) for your study, please email us at data [at] malariagen.net.

Amplicon sequence data is returned as a Genetic Report Card (GRC) as soon as it is available.

Download GRC user guide

Whole genome data is returned to partners in periodic batches e.g. Pf6.4 as detailed in data access below.

Data access (whole-genome data)

To access your data, you will need to log in to the MalariaGEN website and navigate to the relevant web tool via the dashboard or the links below.

My Studies
Use My Studies to download data packages and process reports for partner studies that you have permission to access (listed by Study ID): http://lookseq.sanger.ac.uk/mystudies/

To begin, select one or more partner studies; a tabbed box will appear at the bottom of the page.

Data downloads are available under the ‘Downloads’ tab. There are typically three downloads included in each partner data release:

  • Genotyping data – This quality-filtered data package contains our catalogue of high-quality SNPs, genotype data for your samples at each high-quality SNP, and the sequence read counts that underpin these genotype calls. Currently, genotyping data can be downloaded as vcf files. Some historical data releases are available as tab-delimited files.
  • Process report – This document provides important information to assist investigators in understanding and using these data packages, including details about the genotyping methods used and their assumptions and limitations.
  • Read counts – This exploratory data package contains the full list of unfiltered, potential SNPs, identified by sequence read alignments and the read counts at the potential SNPs for each sample.

Links to raw data are available under the ‘Sample status’ tab:

  • Sequencing reads – This column provides the sample accessions and links to the sequence read data in the European Nucleotide Archive (ENA). Please note that ENA accessions can be present before the data is available on the ENA website.

My Genotypes
Use My Genotypes to browse your sample genotypes: http://lookseq.sanger.ac.uk/mygenotypes/

If you have any questions about data access or are having trouble viewing your data, please see email us at data [at] malariagen.net.