This page provides details for what is required before sending data or shipping parasite samples to MalariaGEN, as well as how data is returned to our partners.
Checklist for shipping parasite samples
We cannot accept any data or samples until the below checklist is complete. If you have any queries regarding any aspect in relation to your partner study, please contact support@malariagen.net, particularly if you require support applying for Nagoya approval and to send your completed sample information sheet.
- The study has a MalariaGEN Study ID
- Relevant ethics approvals are in place and have been shared with MalariaGEN where applicable
- 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 where applicable
- Collections of dried blood spot samples follow visual guidance, and sampling protocols have been followed (not applicable to data only)
- A sample information sheet has been fully completed as per instructions and shared with MalariaGEN
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.
For transfer of data only to MalariaGEN, Nagoya approval is not always required but a data-sharing agreement must be in place with the Wellcome Sanger Institute.
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. Extracted DNA samples must be sent in clear 96-well skirted SuperPlate PCR plates from Abgene (Catalog number AB2800). We cannot accept any alternatives (Eppendorf tubes, cryovials, deep well plates, etc). If you have any difficulty sourcing, or any questions about the 96 well plates we require, please email support@malariagen.net
Please note that in order to carry out whole genome sequencing on P. vivax samples extracted DNA from leucocyte depleted blood is required. Only P. vivax amplicon sequencing can be carried out on samples provided as DBS. For more information on leucocyte depleted blood please see https://www.malariagen.net/get-involved/partner-study-faqs/archive-partner-study-resources/
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 2 dot DBS colllection with Vietnamese subtitles
Watch the GenRe-Mekong video guide for 3 dot DBS collection
5. Sample Information Sheets (SIS)
We require the sample information sheet to be emailed to support@malariagen.net before shipping samples or sending data, and a printed copy must be included within the sample shipment.
included within the sample shipment.
Each sample information sheet is an excel file that contains three tabs:
- An ‘Instructions’ tab, providing guidance on how to complete each sample metadata column
- A ‘Plasmodium Samples’ tab that must be fully completed for each sample
- A ‘Location’ tab that must be fully completed for all samples
Download parasite sample information sheet
Data release
Our Plasmodium projects routinely release amplicon sequence data and whole genome data as soon as it is available. Partners assigned as contacts for the relevant study will be notified by email that their data is available. 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 support@malariagen.net.
Data access – amplicon sequence data
Amplicon sequence data is returned to partners as a Genetic Report Card (GRC) via our CONFLUX online portal, the study contact person will be contacted as soon as it is available.
Download the Pf GRC User Guide and Pv GRC User Guide.
Data access – whole-genome data
Whole genome data is released in monthly data releases e.g. Pf7.16, and is available via our MyStudies portal.
Once you have selected the relevant studies on MyStudies, 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.
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.
If you have any questions about data access or are having trouble viewing your data, please email us at support@malariagen.net
Standard DBS collection protocols
GenRe-Mekong collection protocols
GenRe-Mekong collection protocol
GenRe-Mekong video guide (2 dot DBS)
[Thai] GenReMekong video guide (2 dot DBS)
Sample information sheet (SIS)
Genetic report cards