The Rakeiora Project is a programme to improve genomic knowledge that will impact on the wellbeing of New Zealanders is being co-developed and co-governed with Māori. It is a “pathfinder” to test options to acquire, protect, use and store genomic datasets for use in healthcare research in Aotearoa New Zealand. Full details about the project are available.
The sovereignty of the data in the Rakeiora portal is held by the relevant Kaitiaki and it is for them to decide who can access the data and how it can be used.
Generally, any researcher of good standing who has a working knowledge of Mātauranga Māori and is looking to do research that is relevant to Māori and Pacific peoples will be granted access. This is likely to start with korero with the relevant Kaitiaki representatives and building whirinaki with the iwi you will be working with. If you are unsure how to start this process, please have a look Te Kāhui Māngai or get in touch with the Rakieora team and we will be happy to make introductions, please email rakeiora@nesi.org.nz.
Currently the Rakeiora Portal contains whole genome sequences (aligned bam) from Māori individuals from Tairāwhiti, and Tāmaki Makaurau. The pathfinder project has a large cancer focus, in many cases there are both normal and tumour samples for each individual. Currently, we have 100 normal sequences and 50 tumour sequences. These have all been sequenced using Illumina NextSeq1000 and aligned against GRCh48.p13. We are keen to get feedback as to whether researchers would like alignment to other assemblies.
There are two levels of access over the data, in order to browse the metadata in the portal you will need to register and declare that you are a researcher of good standing who has a working knowledge of Mātauranga Māori. This will allow you to explore what data is within Rakeiora and whether it is relevant to your research.
When you have identified donor samples that you would like to access the genome sequence of, you will need to hit the apply for access button. This will take you to the REMs Interface (Resource Entitlement Management System) that will manage your application for access to Rakeiora Project data. There is a specific guideline for completing your data access application.
When access is granted, you will not be able to download the sequence files. Instead, all raw sequences are kept within a secure cloud environment where you can run standard or bespoke workflows to analyse the data. The output analysis results can then be downloaded for further analysis and visualisation. Alternatively there is software (RStudio, Jupyterlab etc) in the Rakeiora portal where this can be done.
There are 10 workflows available ‘out of the box’ these include, germline variant calling, somatic variant calling, Whakapapa genealogy analysis, etc . If you wish to run your own workflow, you can upload a containerised version to our github for checking and loading into the environment. Please email rakeiora@nesi.org.nz with details of the workflow, including any reference datasets that are needed as part of the workflow.
This will be considered on a case by case basis and should be mentioned in the data access application and can be discussed withe the Rakeiora team.
You will have access to the raw data within the Rakeiora analysis platform for a finite amount of time, this will be specified as part of your access agreement. Further discussions with the relevant Kaitiaki may allow for an extension depending on circumstances. You will be able to access and download the output analysis results for the length of your project. However, this should still only be used for the research which you outlined in your data access agreement, divergence from this should be discussed with the relevant Kaitiaki and agreed before proceeding.
If you would like to carry out further research on the data than was specified on the agreement, you will need to reapply for access via the REMs Interface explaining the new scope of the research. If you have any questions or concerns with regards to this, please reach out to the Rakeiora team, rakeiora@nesi.org.nz .
No, but you will most likely need to ethical approval before you are granted access to the data by Kaitiaki. If you already have ethical approval then please include your HDEC (Health and Disability Ethics Committee) reference number. If you don’t think you need HDEC approval for your research, please also explain this as part of your data access application.