How We Can Help You

Grafton Clinical Genomics has the following technical expertise:
  • Nucleic acid extraction from a variety of tissues including FFPE tissue sections
  • DNA and RNA QC by Qubit, Nanodrop and Tapestation.
  • Bisulphite conversion of gDNA.
  • Assay designing for Genotyping and methylation study.
  • SNP Genotyping and Methylation analysis
  • Next Generation Sequencing Library preparation and sequencing (Ion Torrent, Illumina)
  • Whole Exome Sequencing (Ion Torrent, Illumina)
  • Whole Transcriptome sequencing (Ion Torrent, Illumina)
  • Targeted gene panel sequencing (Ion Torrent, Illumina)
  • Targeted Gene expression analysis by Nanostring technology (off the shelf or customised panel)
  • 3D Biology, miRNA analysis and many other assay types offered by Nanostring
We can help you with your Project Design

We recommend that you contact us (gcgenomics@auckland.ac.nz ) in the initial phase of your project design as it will enable us to provide you best advice in order to help you achieve best quality data suitable for your project.

Discussing your project as early as possible with one of our team will ensure that you have access to the most appropriate technology and that your project is designed robustly

If required, GCG can refer you to a bioinformatician/statistician to advise on simple but important issues such as numbers of replicates, and to help with more complex experimental designs

Some of our technologies produce large amounts of complex data.

GCG will store your data for a short period of time while analysis is being carried out. We will ask you to sign a Short Term Data Management Agreement to acknowledge the limitations of our short term storage arrangements.

As GCG cannot store data long term you must also consider a long term data management plan to suit your specific project.  We can give you some general advice as part of supporting you to design and plan your project, however, you need to contact the Centre for eResearch for more detailed support to develop an appropriate longer term plan. In the process of doing this you will be asked to complete the Data Storage and Transfer Agreement

 

How much will this cost?

Usually, initial consultations about project development and technology choice are free of charge and may be all that is required for your particular project.

In many cases subsequent assistance with analysis is also free of charge, provided it includes capability development for research groups and is not just a fee for service data analysis.

We are able to provide informal ball park costings for general budgeting purposes (see “Indicative Costings for Genomic Analysis”) but please contact us for an accurate quote depending on your specific requirements. 

Once your project has been funded and is underway

On receipt of the grant number(s),  GCG will order the required reagents and consumables and if required,  data storage and transfer will be organized based on the data management plan that was agreed to as part of your project planning phase.

You are responsible for arranging sample delivery to GCG.

Sample requirements:

Samples can be provided for extraction or as extracted nucleic acids. If you extract your own Blood/BM/Buffy coat/FFPE/Buccal/saliva samples the following paramenters should be achieved:

gDNA for Genotyping – minimum of 20ng DNA

gDNA for Methylation analysis – 1ug of high quality DNA

gDNA for Ion Torrent NGS projects – for FFPE samples 10-20ng of DNA is acceptable, though higher concentrations are desirable where possible.

gDNA for Illumina NGS projects – minimum of 500 ng of gDNA for WES, AML gene panel and WGS.

RNA for Nanostring nCounter based analysis – Sample requirement depends on the abundance of the molecules you would like to quantify in your study system. In general, 200-500 ng whole RNA would be required.

Sample/plate maps

We prefer to receive samples in 96 well plates with an accompanying excel sheet with plate map details (position & concentration).

For projects with <50 samples individual sample tubes are acceptable.

Please use the templates (Sample Management Forms) provided on this page to ensure samples are in a logical format consistent with our processing workflows.

Before commencing your extractions or for other specific applications please talk to our staff (contact us)

Sample processing

Sample processing times are generally 2-6 weeks depending on the complexity of your project

Once analysis is complete, samples can be returned to you or held for temporary storage or further analysis. Samples retained for storage are held at the required storage temperature for up to 3 months after which time you will be notified before samples are disposed of using our standard disposal process

 

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Data analysis (optional)

Once the genomics data are generated, we can help with analysis, however, we prefer to work alongside investigators as they analyse their data themselves to help research groups expand their capability.

Data transfer

Based on the agreed data management plan which was developed during your project design phase, your data will be transferred to the appropriate medium (eg portable storage device or storage on the UOA servers via the Centre for eResearch)