Medicine (RMH) - Research Publications

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    Heterogeneity in the psychosocial and behavioral responses associated with a diagnosis of suspected Lynch syndrome in women with endometrial cancer
    Jonnagadla, S ; Joseland, SL ; Saya, S ; den Elzen, N ; Isbister, J ; Winship, IM ; Buchanan, DD (BMC, 2022-07-15)
    BACKGROUND: A suspected Lynch syndrome (SLS) diagnosis is made when a tumor exhibits DNA mismatch repair deficiency but cannot be definitively assigned to an inherited or non-inherited etiology. This diagnosis poses challenges for healthcare professionals, patients, and their families in managing future cancer risks and clinical care. METHODS: This qualitative study aimed to explore the psychosocial and behavioral responses of endometrial cancer (EC) patients receiving a SLS diagnosis (EC-SLS). Semi-structured telephone interviews were conducted with 15 EC-SLS women, transcribed, and thematically analyzed. RESULTS: Most who interpreted their result as negative for Lynch syndrome (LS) believed they were at population-level risk of cancer and felt happy and relieved. Many participants who interpreted their result as inconclusive/not definitive for LS were confused about their cancer risk and experienced negative emotions of anger and frustration. Despite variation in colorectal cancer screening recommendations reported by participants, most adhered to the advice given. Almost all participants communicated their genetic test result to immediate family members; however, communication of family cancer risk management advice was more limited due to most participants reporting not receiving family screening advice. A family history of cancer and a professional healthcare background influenced participants' engagement in regular cancer screening. CONCLUSION: These findings highlight variability in the psychosocial and behavioral responses associated with EC-SLS, providing insight into how healthcare professionals can optimally manage and support such individuals.
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    Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures
    Georgeson, P ; Harrison, TA ; Pope, BJ ; Zaidi, SH ; Qu, C ; Steinfelder, RS ; Lin, Y ; Joo, JE ; Mahmood, K ; Clendenning, M ; Walker, R ; Amitay, EL ; Berndt, S ; Brenner, H ; Campbell, PT ; Cao, Y ; Chan, AT ; Chang-Claude, J ; Doheny, KF ; Drew, DA ; Figueiredo, JC ; French, AJ ; Gallinger, S ; Giannakis, M ; Giles, GG ; Gsur, A ; Gunter, MJ ; Hoffmeister, M ; Hsu, L ; Huang, W-Y ; Limburg, P ; Manson, JE ; Moreno, V ; Nassir, R ; Nowak, JA ; Obon-Santacana, M ; Ogino, S ; Phipps, A ; Potter, JD ; Schoen, RE ; Sun, W ; Toland, AE ; Trinh, QM ; Ugai, T ; Macrae, FA ; Rosty, C ; Hudson, TJ ; Jenkins, MA ; Thibodeau, SN ; Winship, IM ; Peters, U ; Buchanan, DD (NATURE PORTFOLIO, 2022-06-06)
    Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.
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    Population DNA screening for medically actionable disease risk in adults.
    Lacaze, PA ; Tiller, J ; Winship, I ; DNA Screen Investigator Group, (Wiley, 2022-04-04)
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    Population-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing
    Southey, MC ; Dowty, JG ; Riaz, M ; Steen, JA ; Renault, A-L ; Tucker, K ; Kirk, J ; James, P ; Winship, I ; Pachter, N ; Poplawski, N ; Grist, S ; Park, DJ ; Pope, BJ ; Mahmood, K ; Hammet, F ; Mahmoodi, M ; Tsimiklis, H ; Theys, D ; Rewse, A ; Willis, A ; Morrow, A ; Speechly, C ; Harris, R ; Sebra, R ; Schadt, E ; Lacaze, P ; McNeil, JJ ; Giles, GG ; Milne, RL ; Hopper, JL ; Nguyen-Dumont, T (NATURE PORTFOLIO, 2021-12-09)
    Population-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing are urgently required. Most prior research has been based on women selected for high-risk features and more data is needed to make inference about breast cancer risk for women unselected for family history, an important consideration of population screening. We tested 1464 women diagnosed with breast cancer and 862 age-matched controls participating in the Australian Breast Cancer Family Study (ABCFS), and 6549 healthy, older Australian women enroled in the ASPirin in Reducing Events in the Elderly (ASPREE) study for rare germline variants using a 24-gene-panel. Odds ratios (ORs) were estimated using unconditional logistic regression adjusted for age and other potential confounders. We identified pathogenic variants in 11.1% of the ABCFS cases, 3.7% of the ABCFS controls and 2.2% of the ASPREE (control) participants. The estimated breast cancer OR [95% confidence interval] was 5.3 [2.1-16.2] for BRCA1, 4.0 [1.9-9.1] for BRCA2, 3.4 [1.4-8.4] for ATM and 4.3 [1.0-17.0] for PALB2. Our findings provide a population-based perspective to gene-panel testing for breast cancer predisposition and opportunities to improve predictors for identifying women who carry pathogenic variants in breast cancer predisposition genes.
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    Germline MBD4 deficiency causes a multi-tumor predisposition syndrome
    Palles, C ; West, HD ; Chew, E ; Galavotti, S ; Flensburg, C ; Grolleman, JE ; Jansen, EAM ; Curley, H ; Chegwidden, L ; Arbe-Barnes, EH ; Lander, N ; Truscott, R ; Pagan, J ; Bajel, A ; Sherwood, K ; Martin, L ; Thomas, H ; Georgiou, D ; Fostira, F ; Goldberg, Y ; Adams, DJ ; van der Biezen, SAM ; Christie, M ; Clendenning, M ; Thomas, LE ; Deltas, C ; Dimovski, AJ ; Dymerska, D ; Lubinski, J ; Mahmood, K ; van der Post, RS ; Sanders, M ; Weitz, J ; Taylor, JC ; Turnbull, C ; Vreede, L ; van Wezel, T ; Whalley, C ; Arnedo-Pac, C ; Caravagna, G ; Cross, W ; Chubb, D ; Frangou, A ; Gruber, AJ ; Kinnersley, B ; Noyvert, B ; Church, D ; Graham, T ; Houlston, R ; Lopez-Bigas, N ; Sottoriva, A ; Wedge, D ; Jenkins, MA ; Kuiper, RP ; Roberts, AW ; Cheadle, JP ; Ligtenberg, MJL ; Hoogerbrugge, N ; Koelzer, VH ; Rivas, AD ; Winship, IM ; Ponte, CR ; Buchanan, DD ; Power, DG ; Green, A ; Tomlinson, IPM ; Sampson, JR ; Majewski, IJ ; de Voer, RM (CELL PRESS, 2022-05-05)
    We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.
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    Population-based estimates of age-specific cumulative risk of breast cancer for pathogenic variants in ATM
    Renault, A-L ; Dowty, JG ; Steen, JA ; Li, S ; Winship, IM ; Giles, GG ; Hopper, JL ; Southey, MC ; Nguyen-Dumont, T (BMC, 2022-04-01)
    BACKGROUND: Multigene panel tests for breast cancer predisposition routinely include ATM as it is now a well-established breast cancer predisposition gene. METHODS: We included ATM in a multigene panel test applied to the Australian Breast Cancer Family Registry (ABCFR), a population-based case-control-family study of breast cancer, with the purpose of estimating the prevalence and penetrance of heterozygous ATM pathogenic variants from the family data, using segregation analysis. RESULTS: The estimated breast cancer hazard ratio for carriers of pathogenic ATM variants in the ABCFR was 1.32 (95% confidence interval 0.45-3.87; P = 0.6). The estimated cumulative risk of breast cancer to age 80 years for heterozygous ATM pathogenic variant carriers was estimated to be 13% (95% CI 4.6-30). CONCLUSIONS: Although ATM has been definitively identified as a breast cancer predisposition gene, further evidence, such as variant-specific penetrance estimates, are needed to inform risk management strategies for carriers of pathogenic variants to increase the clinical utility of population testing of this gene.
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    Monitoring the genetic testing and life insurance moratorium in Australia: a national research project
    Tiller, J ; Winship, I ; Otlowski, MFA ; Lacaze, PA (WILEY, 2021-02-07)
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    Mainstreaming genomics: training experience of hospital medical officers at the Royal Melbourne Hospital
    Huq, AJ ; Healy, L ; Gorelik, A ; Forrest, LE ; Winship, IM (WILEY, 2021-02-01)
    The rapid evolution and wide applicability of genomic testing means that medical practitioners outside the field are not appropriately skilled to understand the utility of genomics for their patients. Rotating junior doctors through genomic medicine provides them with the hands-on experience necessary to understand the complexities in this field. In this study, we analysed the training experience of 12 hospital medical officers who rotated through genomic medicine at the Royal Melbourne Hospital. Here, we demonstrate that immersion in clinical genomics aids in mainstreaming genomics knowledge.
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    Prospective Evaluation over 15 Years of Six Breast Cancer Risk Models
    Li, SX ; Milne, RL ; Nguyen-Dumont, T ; English, DR ; Giles, GG ; Southey, MC ; Antoniou, AC ; Lee, A ; Winship, I ; Hopper, JL ; Terry, MB ; MacInnis, RJ (MDPI, 2021-10-01)
    Prospective validation of risk models is needed to assess their clinical utility, particularly over the longer term. We evaluated the performance of six commonly used breast cancer risk models (IBIS, BOADICEA, BRCAPRO, BRCAPRO-BCRAT, BCRAT, and iCARE-lit). 15-year risk scores were estimated using lifestyle factors and family history measures from 7608 women in the Melbourne Collaborative Cohort Study who were aged 50-65 years and unaffected at commencement of follow-up two (conducted in 2003-2007), of whom 351 subsequently developed breast cancer. Risk discrimination was assessed using the C-statistic and calibration using the expected/observed number of incident cases across the spectrum of risk by age group (50-54, 55-59, 60-65 years) and family history of breast cancer. C-statistics were higher for BOADICEA (0.59, 95% confidence interval (CI) 0.56-0.62) and IBIS (0.57, 95% CI 0.54-0.61) than the other models (p-difference ≤ 0.04). No model except BOADICEA calibrated well across the spectrum of 15-year risk (p-value < 0.03). The performance of BOADICEA and IBIS was similar across age groups and for women with or without a family history. For middle-aged Australian women, BOADICEA and IBIS had the highest discriminatory accuracy of the six risk models, but apart from BOADICEA, no model was well-calibrated across the risk spectrum.
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    Making community voices heard in a research-health service alliance, the evolving role of the Community Advisory Group: a case study from the members' perspective.
    Wale, JL ; Di Pietro, L ; Renton, H ; Sahhar, M ; Walker, C ; Williams, P ; Meehan, K ; Lynch, E ; Martyn, M ; Bell, J ; Winship, I ; Gaff, CL (Springer Science and Business Media LLC, 2021-11-27)
    BACKGROUND: The Melbourne Genomics Health Alliance (the Alliance) is a collaboration of leading hospitals, research and academic organisations, supported by its member organisations and the Victorian Government. The Alliance was set up by its members in 2013 to steer the translation of genomics, making it an integral part of health care in Victoria, Australia. The Community Advisory Group (CAG) was formed soon after, to give input and advice across the program. This was to ensure consideration of community values, perspectives and priorities, and knowledge translation for patient care. The CAG was charged with providing a strong community voice for the duration of the program. Appointed members were experienced consumer advocates with developed connections to the community. MAIN BODY: The Alliance progressed from an initial Demonstration Project (2013-2015) to a multifaceted program (2016-2020). The CAG worked strategically to help address complex issues, for example, communication, privacy, informed consent, ethics, patient experience, measurement and evaluation standards and policies, data storage and re-use of genomic data. Many aspects of translating genomics into routine care have been tackled, such as communicating with patients invited to have genomic testing, or their caregivers, and obtaining informed consent, clinical questions across 16 areas of health care, training and education of health and laboratory professionals, genomic data management and data-sharing. Evidence generated around clinical utility and cost-effectiveness led to government funding of testing for complex genetic conditions in children. CONCLUSION: The CAG activities, recorded in a CAG-inspired Activity register, span the full spectrum of information sharing and consultation to co-design and partnership. The CAG were involved at multiple levels of participation and in all tiers of activity including governance, development of policies and procedures, program planning and evaluation. Working relationships were built up and a level of trust instilled to advance the Alliance work program in ensuring an effective patient-care model of delivery of genomics. CAG input into project deliverables has been tangible. Less tangible contributions included presentations at external meetings and conferences, direct interactions at meetings with Alliance members, interactions with visitors and external experts, taking part in consultations with experts, state and federal government.