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Cell-free genomics

 

Cell-free DNA in blood or plasma is a valuable source of genetic material to diagnose and monitor human disease.  Routine analysis of plasma DNA has the potential to transform treatment strategies for cancer in particular. 

However, until now a lack of standardised methods of data analysis, quality control, and clinical reporting in New Zealand has been a major roadblock to implementing genomics into our healthcare system.

Now, methods for detecting tumour sequences using cell-free DNA in plasma samples using genomics are being developed in New Zealand, which may offer an easier route for monitoring patients, and screening for multiple types of cancer. 

Automated methods are needed so clinical practices can identify optimal tumour markers, check the quality of the data, account for tumour variability, and report on genomic results. Providing a robust and sensible protocol for the use of such diagnostic tests is therefore critical for their acceptance in clinics.

The Genomics Aotearoa Cell-free genomics project team based at the University of Otago established both ddPCR (droplet digital PCR) and NGS (next generation sequencing) methods after analysing cell free DNA tests from various technologies.  From this, they developed and implemented pipelines for quality control of sequencing and testing data, and for generating and forwarding clinical reports. They also developed a pipeline to access and utilise data from Genomics Aotearoa’s NZ Variome project.

These protocols ensure that new tests using data from cell-free DNA meet a required minimum quality standard before being applied clinically.  

The Genomics Aotearoa study was part of a larger ctDNA project being carried out by Healthier Lives National Science Challenge. It involved researchers from two universities, with the Healthier Lives National Science Challenge providing data and samples to develop and test the pipeline. The project also involved collaboration with Canterbury Health Laboratories, which is essential to the implementation of ctDNA into the public health system. 

Healthier Lives is working closely with Māori health providers over the coming three years to progress implementation into the New Zealand healthcare system. 

Outcomes

  • Pipelines to analyse, quality control and report on cell-free genomic tests
  • Increased capacity in clinical bioinformatics
  • Improved relationships with clinical diagnostic providers.

Team

  • Professor Parry Guilford (University of Otago) – co-lead researcher
  • Associate Professor Mik Black (University of Otago) – co-lead researcher
  • Fiona Hely (AbacusBio)

  • Jonah Duckles (AbacusBio)

  • Luna Zhang (AbacusBio)

  • Dr Miles Benton (ESR)