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Cell-free genomics

Cell-free DNA in blood or plasma is becoming a valuable source of genetic material to diagnose and monitor human disease. Producing a complete set of plasma DNA therefore has the potential to transform treatment strategies for cancer and other non-communicable diseases.

Methods for detecting tumour sequences in plasma samples using genomics are already being developed, which may offer an easier route for monitoring patients, and screening for multiple types of cancer. However, a lack of standardised methods of data analysis, quality control, and clinical reporting in New Zealand is a major roadblock to implementing genomics into our healthcare system.

Clinical practice needs automated methods to 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 critical for their acceptance in clinics.

The project team aims to develop protocols to ensure that new tests using data from cell-free DNA, including those still being researched, meet a required minimum quality standard before being applied clinically. Making use of clinical bioinformatics expertise will improve translation, and support the uptake of genomics into clinical practice.

This project involves researchers from two universities, and will employ a PhD-level bioinformatician to support capacity. This project links closely to the Healthier Lives National Science Challenge, which will provide data and samples to develop and test the pipeline.


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


  • 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)