A 2018/2019 Summer Studentship research project
We are uniquely positioned to share this potential new method with international research and diagnostic laboratories who are members of the world-leading ENIGMA consortium (expert panel for interpreting genetic variants associated with breast and ovarian cancer).
Student: Isabelle Chai
Supervisors: Dr Vanessa Lattimore, Dr Logan Walker
Sponsor: Cancer Society of New Zealand Canterbury/West Coast Division
Project brief
Introduction
Breast and ovarian cancer prevention plays a vital role in the goal of achieving zero deaths from these diseases. Genetic screening is currently undertaken for individuals thought to have a high likelihood of carrying genetic changes that increase the risk of developing breast/ovarian cancer. Identifying high-risk unaffected individuals provides a potentially lifesaving opportunity to implement surveillance and/or risk-reducing strategies to lower the likelihood of developing disease. Furthermore, this genetic information can lead to improved outcomes by facilitating the detection of early stage disease and determining the suitability of patients to different therapies. New DNA technologies offer great potential to transform the clinical care of high-risk breast cancer families. However, interpreting the test results can be a major dilemma for health care professionals. We and others have shown that laboratory assays assessing the effect of a DNA variant on BRCA1 or BRCA2 mRNA splicing may contribute to clinical classification of that variant. To date, most of our understanding of BRCA1 and BRCA2 splicing in relation to genetic changes is based on mRNA derived from patient blood cells. However, obtaining blood samples from some patients can be difficult due to factors such as the vascular effects of cancer treatment and access to the nearest blood service center. Saliva collection is less invasive than drawing blood and allows for sampling in the absence of a trained phlebotomist. Collecting saliva for RNA isolation may be a novel procedure which facilitates our ability to assess the clinical significance of potential spliceogenic gene variants.
Aim
To compare BRCA1/2 mRNA splicing patterns in saliva and blood tissue.
Method
Blood and saliva samples will be obtained from women who have been recruited to the NZ Familial Breast Cancer Study (Managed by Dr Lattimore) or kConFab, Peter MacCallum Cancer Centre (Dr Walker is a member of kConFab). We will obtain up to three saliva samples from women recruited to the NZ Familial Breast Cancer Study who are known to carry a spliceogenic variant in a cancer susceptibility gene (eg. BRCA1 and BRCA2) and up to 10 non-carrier controls. Where possible, we will also obtain matched blood samples from those women, and/or other woman from kConFab with the same variant carrier status.
Student researcher’s component of the study
The student will carry out bioinformatic analysis of the potential spliceogenic variant(s) using an array of online tools. To carry out in vitro assays, they will isolate RNA and DNA from blood and saliva tissues and examine normal and aberrant mRNA splicing patterns using PCR-based methods. To confirm the structure of mRNA isoforms, selected PCR fragments will be isolated for DNA sequencing.
