Dr Ann-Marie Patch is an expert in cancer genomics and a bioinformatician with a strong background in genetics and molecular biology. Her PhD from the University of Exeter, UK in 2006 combined both practical and computational components investigating genomic roles of repetitive elements in model yeast systems. She moved fields to human genetics of inherited diseases for her first post-doc investigating monogenic causes of neonatal hypo and hyper-glycaemia, Maturity Onset Diabetes of the Young (MODY) and pancreatic agenesis. This work was with Professor Andrew Hattersley at the Peninsular College of Medicine and Dentistry, Exeter, UK (now the University of Exeter, College of Medicine and Health).
The research team there were closely aligned with the diagnostic team of Professor Sian Ellard who is a Consultant Clinical Scientist and head of the Molecular Genetics Laboratory at the Royal Devon and Exeter NHS Foundation Trust hospital. Ann-Marie moved fulltime to the diagnostic Molecular Genetics laboratory as a NHS Bioinformatician in 2009, developing automated sequencing pipelines, implementing LIMS and investigating next-generation Sequencing platforms for gene panel testing assays.
In 2011 her interest in next-generation sequencing technologies led her back to research and the field of human cancer genomics. She joined Professor Sean Grimmond’s team at the Institute of Molecular Bioscience, University of Queensland, working as a senior bionformatician on the Australian International Cancer Genome Consortium projects, leading the analysis of the ovarian cancer project. In 2014 she came to QIMR Berghofer, as part of Dr Nicola Waddell’s Medical Genomics team, that continued the work on the Australian ICGC pancreatic and melanoma projects. As part of this team and in collaboration with clinicians from the National Centre for Asbestos Related Diseases, Ann-Marie led the analysis of the Australian mesothelioma genome project. She has a passion for training future bioinformatics researchers and was part of the Bioplatforms Australia training team from 2015-2018. From 2018, she began a new chapter at QIMR Berghofer as team head of the Clinical Genomics laboratory, allowing her to further develop her key research interests.
Current QIMR Berghofer appointment
- 2018 – current: Team Head, Clinical Genomics Group
- 2014 – 2018: Senior Research Scientist
- 2011 – 2014: Senior Bioinformatics Research Officer, Institute of Molecular Bioscience, University of Queensland, Australia
- 2009 – 2011: Bioinformatician, Molecular Genetics Laboratory- Royal Devon and Exeter NHS Foundation Trust Hospital, Exeter, UK.
- 2007 – 2009: Associate research Fellow, Peninsula College of Medicine & Dentistry, University of Exeter, UK
- 2006 – 2007: Research Genetic Technologist, Molecular Genetics Laboratory – Royal Devon and Exeter NHS Foundation Trust Hospital, Exeter, UK
Current Area of Research
Through the Clinical Genomics group Ann-Marie directs the bioinformatics analysis of a number of different cancer types. This work is highly collaborative relying on building interactions with clinicians and researchers to help facilitate the use of genomics analysis to answer clinically important questions. We use a range of different sequencing technologies including whole genome, exome, transcriptome and single cell sequencing as a base for the genomics investigations.
Current projects include:
- Comparison of spatially or temporally separated tumour samples e.g. primary and metastatic colorectal cancer to identify the underlying sub-clonal structure that helps the primary disease to spread to other organs particularly the liver.
- Genomics of treatment resistant pre-clinical models of cancer e.g. patient derived xenograft (PDX) and patient derived colorectal organoid cultures.
- Investigation of intra-tumour heterogeneity using single cell sequencing to profile different cell populations and investigate treatment response e.g. mesothelioma pleural effusion profiling.
Ann-Marie has over 12 years’ experience in the genetics analysis of human disease using both lab and computational approaches. Since 2010 she has used the massively parallel technologies of next-generation sequencing platforms to generate genomics level data to understand the basis complex diseases such as human cancers.
- Part of the analysis team that used whole genome sequencing to characterise the genomes of ovarian, pancreatic and melanoma as part of the Australian International Cancer Genome Consortium (ICGC) projects.
- Led the analysis that identified structural variants that extended the somatic mutational spectrum of ovarian cancer, and reported sub-clonal mutational events that contributed to the emergence of treatment resistance.
Identified disease associated structural rearrangements affecting MSH2 in hyper-mutated pancreatic cancer, underlying ERBB2 amplification also in pancreatic cancer, reported patterns of rearrangements associated with breakage-fusion-bridge, chromothripsis and homologous recombination repair deficiency in pancreatic, ovarian, oesophageal, melanoma samples.
- 2017 – current: The Australian Bioinformatics and Computational Biology Society
- 2017 – current: Australasian Genomic Technologies Association (AGTA)
- 2017 – current: Australian Society for Biochemistry and Molecular Biology (ASBMB)
- 2001 – 2011: The Genetics Society, UK
- 2017: The Columbia Hospital Research Foundation Annual Award for Research Excellence in Breast, Obstetrical and Gynecologic Disorders for work published in 2015
- 2017: QIMR Berghofer Medical Research Institute Postdoctoral Prize
- 2006: PhD, University of Exeter, UK
- 2001: BSc Hons (First Class), University of Exeter, UK