Statistical Analysis of Complex Proteomics Mass Spectrometry Data

Endometrial cancer is the most common gynaecological malignancy in Australia with 2256 diagnosed cases in 2010 and 381 associated deaths in 2011. The presence or absence of lymph node metastasis (LNM) is the most important prognostic factor in endometrial cancer as patients with localised disease have a 5-year survival rate of 96%, which drops to just 17% for patients with metastatic disease. Accurate assessment of the presence of LNM is difficult and often results in radical treatment which may not be necessary. A better understanding of the underlying biological phenomena and their detection in the mass spectrometry imaging (MSI) data is vital.

In this project, we work with data from 43 patients with LNM in collaboration with Professor Peter Hoffmann’s lab at the University of South Australia. Of the 43 patients, 16 are lymph node metastasis positive, 27 are negative.

For each patient, hundreds of mass spectra on more than 4500 mass bins each have been collected in Professor Hoffmann’s lab. In this project, we plan to work explicitly with all mass spectra for each patient rather than with the simpler average spectrum. Previous classification and prediction research was based on the average for each patient and resulted in a moderate success rate only. The aim of this research is to find a cluster pattern for each patient’s spectra, investigate these patterns in a deeper analysis in order to exhibit differences between LNM positive and negative patients, and in collaboration with the data experts, to interpret these differences and relate them to proteins and biomarkers.

Sophie Giraudo

The University of Western Australia

Sophie Giraudo completed a Bachelor of Science in 2021 at The University of Western Australia with majors in data science and mathematics and statistics, and will be commencing honours in statistics in 2022. She is heavily involved in the UWA Data Science Club, holding the position of President in 2021 and Insight Impact Lead for 2022, and is the founder of the UWA Data Science Club’s Insight Impact initiative—a program where current data science students provide data engineering and analytics to not-for-profit, community and government organisations.

Professionally, Sophie currently works as a Data Science Vacation Student at Woodside. Previously she has worked as a Technology Consultant Intern at Visagio, a Research Assistant at the UWA System Health Lab, and as a Data Scientist at Omni Biotech.

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