Upskilling on statistical genetics to aid research on bowel cancer and beaked whales

The Summer Institute in Statistical Genetics is held in June at the Georgia Institute of Technology. It aims to introduce geneticists to current methods of statistical analysis, and statisticians to the challenges posed by genetic data. It is named in honour of Professor Emeritus Bruce Weir FRS FRSNZ, an expert in statistical and forensic genetics. 

Bayley Knofflock's PhD research at Ōtākou Whakaihu Waka – the University of Otago investigates screening for bowel cancer in New Zealand.

Currently, the healthcare system is struggling to meet the demand for screening colonoscopies, yet fewer than 10% of screened patients actually have cancer. Bayley is looking to see if DNA from tissues that circulates in the blood could identify patients more likely to have bowel cancer to prioritise for screening.  “Beyond data generation, my PhD work is to find a ‘needle in a haystack’ cancer signature from the rest of the healthy tissue in cell-free DNA and build a model that accurately predicts cancer.”

She hopes the Institute will help her build a robust foundation for applying statistics and modeling to the biological data she is gathering. Of particular interest is the Institute’s module on Bayesian statistics: “I think the ability to incorporate new data into a model will be extremely important to the future use of our cell-free DNA-methylation models into clinically applied tests.”

She plans to pass on what she learns to others working in her lab who are using the same approach to develop biomarkers for lung, prostate, and pancreatic cancers, as well as chronic fatigue syndrome. “I appreciate that it is not easy to travel from New Zealand to access specialist training, and I will do my best to teach those around me and transfer the skills that I gain.”

Fang Fei Tham, of Waipapa Taumata Rau – the University of Auckland, is working towards a PhD titled 'Using Genomic Tools to Investigate Population Structure and Phylogeography in Beaked Whales (Ziphiidae)’. With statistical genetics as a main concept in her thesis, she is using genomic tools to find levels of genetic diversity and population structure in beaked whales.

Fang explains that beaked whales may be the least understood large mammal in the world, encompassing 24 unique species.

“Several beaked whale species have yet to be observed in the wild. Yet, when they are observed, similar external morphology impedes species-identification in the field.”

She says that most studies of beaked whales are based on stranded animals rather than live observations, meaning that their DNA is often the only way to understand them.  Her research seeks to better understand the populations of beaked whales found in the Northern and Southern Hemispheres: how different species evolved and where populations live.

Fang’s project will use statistical genetics to find out if goose-beaked whales (Ziphius cavirostris) and the recently described Ramari’s beaked whale (Mesoplodon eueu) live in different geographic areas or if the two groups overlap and are evenly dispersed.

She is looking forward to the Institute’s population and evolution module, which will strengthen the statistical and genetics skills she can apply to her research.

About the Summer Institute in Statistical Genetics

The Institute is named in honour of Professor Emeritus Bruce Weir FRS FRSNZ, an expert in statistical and forensic genetics.

He was born in Aotearoa New Zealand and educated at Te Whare Wānanga o Waitaha – the University of Canterbury, before embarking on a highly successful international career. Bruce and Beth Weir now live in Palmerston North. Bruce will teach modules as part of the Summer Institute, alongside other leading researchers.