A full list of studies and other publications from Melbourne Genomics.

Evidence for genomics

Clinicians’ views and experiences with offering and returning results from exome sequencing to parents of infants with hearing loss”, Lauren Notini, Clara L. Gaff, Julian Savulescu and Danya F. Vears, Journal of Clinical Medicine (2022) https://doi.org/10.3390/jcm11010035

"Pilot study of a combined genomic and epidemiologic surveillance program for hospital-acquired multidrug-resistant pathogens across multiple hospital networks in Australia", Norelle L. Sherry, Robyn S. Lee, Claire L. Gorrie, Jason C. Kwong, Rhonda L. Stuart, Tony M. Korman, Caroline Marshall, Charlie Higgs, Hiu Tat Chan, Maryza Graham, Paul D.R. Johnson, Marcel J. Leroi, Caroline Reed, Michael J. Richards, Monica A. Slvain, Leon J. Worth, Benjamin P. Howden, M. Lindsay Grayson, The Society for Healthcare Epidemiology of America (2021) doi:10.1017/ice.2020.1253 

"Cost effectiveness of targeted exome analysis as a diagnostic test in glomerular diseases", Kushani Jayasinghe, You Wu, Zornitza Stark, Peter G. Kerr, Andrew J. Mallett, Clara Gaff, Melissa Martyn, Ilias Goranitis and Catherine Quinlan, Kidney International Reports (2021) https://doi.org/10.1016/j.ekir.2021.08.028  

"Personal utility of genomic sequencing for infants with congenital deafness", Erin Tutty, David J. Amor, Anna Jarmolowicz, Kate Paton and Lilian Downie, American Journal of Medical Genetics (2021) https://doi.org/10.1002/ajmg.a.62411  

"Exome sequencing for isolated congenital hearing loss: a cost-effective analysis", Lilian Downie,  David J. Amor, Jane Halliday, Sharon Lewis, Melissa Martyn and Ilias Goranitis, the Laryngoscope (2020) https://doi.org/10.1002/lary.29356

"The clinical utility of exome sequencing and extended bioinformatic analyses in adolescents and adults with a broad range of neurological phenotypes: an Australian perspective", Dhamidhu Eratne, Amy Schneider, Ella Lynch, Melissa Martyn, Dennis Velakoulis, Michael Fahey, Patrick Kwan, Richard Leventer, Haloom Rafehi, Belinda Chong, Zornitza Stark, Sebastian Lunke, Dean G. Phelan, Melanie O'Keefe, Kirby Siemering, Kirsty West, Adrienne Sexton, Anna Jarmolowicz and Samuel F. Berkovic, Journal of the Neurological Sciences (2020) https://doi.org/10.1016/j.jns.2020.117260

"Introducing Edna: A trainee chatbot designed to support communication about additional (secondary) genomic findings", David Ireland, DanaKai Bradford, Emma Szepe, Ella Lynch, Melissa Martyn, David Hansen and Clara Gaff, Patient Education and Counselling (2020)  https://doi.org/10.1016/j.pec.2020.11.007

"Evaluating the resource implications of different service delivery models for offering additional genomic findings", Martin Vu, Koen Degeling, Melissa Martyn, Elly Lynch, Belinda Chong, Clara Gaff and Maarten J. IJzerman, Genetics in Medicine (2020)  https://doi.org/10.1038/s41436-020-01030-8

"Clinical impact of genomic testing in patients with suspected monogenic kidney disease", Kushani Jayasinghe, Zornitza Stark, Peter G. Kerr, Clara Gaff, Melissa Martyn, John Whitlam, Belinda Creighton, Elizabeth Donaldson, Matthew Hunter, Anna Jarmolowicz, Lilian Johnstone, Emma Krzensinski, Sebastian Lunke, Elly Lynch, Kathleen Nicholls, Chirag Patel, Yael Prawer, Jessica Ryan, Emily J. See, Andrew Talbot, Alison Trainer, Rigan Tytherleigh, Giulia Valente, Matthew Wallis, Louise Wardrop, Kirsty H. West, Susan M. White, Ella Wilkins, Andrew J. Mallet and Catherine Quinlan, Genetics in Medicine (2020)  https://doi.org/10.1038/s41436-020-00963-4

"A cost-effectiveness analysis of genomic sequencing in a prospective versus historical cohort of complex paediatric patients", Alison Yeung, Natalie B. Tan, Tiong Y. Tan, Zornitza Stark, Natasha Brown, Matthew F. Hunter, Martin Delatycki, Chloe Stutterd, Ravi Savarirayan, George Mcgillivray, Rachel Stapleton, Smitha Kumble, Lilian Downie, Matthew Regan, Sebastian Lunke, Belinda Chong, Dean Phelan, Gemma R. Brett, Anna Jarmolowicz, Yael prawer, Giula Valente, Yana Smagarinsky, Melissa Martyn, Callum McEwan, Ilias Goranitis, Clara Gaff and Susan M. White, Genetics in Medicine (2020) https://doi.org/10.1038/s41436-020-0929-8

“Mapping the Minnesota Living with Heart Failure Questionnaire (MLHFQ) onto the Assessment of Quality of Life 8D (AQoL-8D) utility scores", Max Catchpool, Jay Ramchand, David L. Hare, Melissa Martyn and Ilias Goranitis, Quality of Life Research (2020) https://doi.org/10.1007/s11136-020-02531-4

"Exome sequencing in newborns with congenital deafness as a model for genomic newborn screening: the Baby Beyond Hearing project", Lilian Downie, Jane Halliday, Sharon Lewis, Sebastian Lunke, Elly Lynch, Melissa Martyn, Clara Gaff, Anna Jarmolowicz and David J Amor, Genetics in Medicine (2020) doi.org/10.1038/s41436-019-0745-1

"Prospective evaluation of the utility of whole exome sequencing in dilated cardiomyopathy", Jay Ramchand, Mathew Wallis, Elly Lynch, Omar Farouque, Melissa Martyn, Dean Phelan, Belinda Chong, Siobhan Lockwood, Robert Weintraub, Tina Thompson, Alison Trainer, Dominica Zentner, Jitendra Vohra, Michael Chetrit, David L. Hare and Paul James, Journal of the American Heart Association (2020) doi.org/10.1161/JAHA.119.013346

"Utility of clinical comprehensive genomic characterisation for diagnostic categorisation in patients presenting with hypocellular bone marrow failure syndromes", Piers Blombery, Lucy Fox, Georgina L. Ryland, Ella R. Thompson, Jennifer Lickiss, Michelle MCBean, Satwica Yerneni, David Hughes, Anthea Greenway, Francoise Mechinaud, Erica M. Wood, Graham J. Lieschke, Jeff Szer, Pasquale Barbaro, John Roy, Joel Wight, Elly Lynch, Melissa Martyn, Clara Gaff and David Ritchie, Haematologica (2020) doi:10.3324/haematol.2019.237693

"Exome sequencing in infants with congenital hearing impairment: a population-based cohort study", Lilian Downie, Jane Halliday, Rachel Burt, Sebastian Lunke, Elly Lynch, Melissa Martyn, Zeffie Poulakis, Clara Gaff, Valerie Sung, Melissa Wake, Matthew F. Hunter, Kerryn Saunders, Elizabeth Rose, Sharon Lewis, Anna Jarmolowicz, Dean Phelan, Heidi L. Rehm, Melbourne Genomics Health Alliance & David J. Amor, European Journal of Human Genetics (2019) doi:10.1038/s41431-019-0553-8

"A head-to-head evaluation of the diagnostic efficacy and costs of trio versus singleton exome sequencing analysis”, Tan, T., Lunke, S., Chong, B., Phelan, D., Fanjul-Fernandez, M., Marum, J. E., Kumar, V.S., Stark, Z., Yeung, A., Brown, N.J., Stutterd, N.J., Delatyki, M.B., Sadedin, S., Martyn, M., Goranitis, I., Thorne, N., Gaff, C.L., White, S.M., European Journal of Human Genetics (2019) doi.org/10.1038/s41431-019-0471-9

“A cost-effectiveness model of genetic testing and periodical clinical screening for the evaluation of families with dilated cardiomyopathy”, Max Catchpool, Jay Ramchand, Melissa Martyn, David L. Hare, Paul A. James, Alison H. Trainer, Josh Knight and Ilias Goranitis, Genetics in Medicine (2019) https://doi.org/10.1038/s41436-019-0582-2

"Long-term economic impacts of exome sequencing for suspected monogenic disorders: diagnosis, management, and reproductive outcomes", Deborah Schofield, Luke Rynehart, Rupendra Shresthra,  Susan M. White,  and Zornitza Stark, Genetics in Medicine, (2019) https://doi.org/10.1038/s41436-019-0534-x

"Does genomic sequencing early in the diagnostic trajectory make a difference? A follow-up study of clinical outcomes and cost-effectiveness", Stark, Z., Schofield, D., Martyn, M., Rynehart,L., Shrestha, R., Alam, K., Lunke, S., Tan, T.Y., Gaff, C.L., White, S.M., Genetics in Medicine (2018) doi:10.1038/s41436-018-0006-8

“Delayed diagnosis and complications of predominantly antibody deficiencies in a cohort of Australian adults”, Charlotte A. Slade, Julian J. Bosco, Tran Binh Giang, Elizabeth Kruse, Robert G. Stirling, Paul U. Cameron, Fiona Hore-Lacy, Michael F. Sutherland, Sara L. Barnes, Stepehen Holdsworth, Samar Ojaimi, Gary A. Unglik, Joseph De Luca, Mittal Patel, Jeremy McComish, Kymble Spriggs, Yang Tran, Priscilla Auyeung, Katherine Nicholls, Robyn E. O’Hehir, Philip D. Hodgkin, Jo A. Douglass, Vanessa L. Bryant and Menno C. van Zelm, Frontiers in Immunology (2018), doi.org/10.3389/f”immu.2018.00694

"Meeting the challenges of implementing rapid genomic testing in acute pediatric care", Stark, Z., Lunke, S., Brett, G.R., Tan, N.B., Stapleton, R., Kumble, S., Yeung, A., Phelan, D.G., Chong, B., Fanjul-Fernandez, M., Marum, J.E., Hunter, M., Jarmolowicz, A., Prawer, Y., Riseley, J.R., Regan, M., Elliott, J., Martyn, M., Best, S., Tan, T.Y., Gaff, C.L., White, S.M., Genetics in Medicine (2018) doi:10.1038/gim.2018.37 

"Exome Sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders", Dillon, O., Lunke, S., Stark, Z., Yeung, A., Thorne, N., Gaff, C., White, S., Tan, T., European Journal of Human Genetics  (2018) doi:10.1038/s41431-018-0099-1

"Diagnostic impact and cost-effectiveness of whole-exome sequencing for ambulant children with suspected monogenic conditions", Tan, T.Y., Dillon, O.J., Stark, Z., Schofield, D., Alam, K., Shrestha, R., Chong, B., Phelan, D., Brett, G.R., Creed, E.,  Jarmolowicz, A., Yap, P., Walsh, M., Downie, L., Amor, D.A.,  Savarirayan, R., McGillivray, G., Yeung, A., Peters, H., Robertson, S.J., Robinson, A.J., Macciocca, I., Sadedin, S., Bell, K., Oshlack, A., Georgeson, P., Thorne, N., Gaff, C., White, S.M, JAMA Pediatrics (2017)  doi:10.1001/jamapediatrics.2017.1755 

“Prospective comparison of the cost-effectiveness of the clinical whole exome sequencing to usual care overwhelmingly supports early use and reimbursement”, Stark, Z., Schofield, D., Alam, K., Wilson, W., Mupfeki, N., Macciocca, I., Shrestha, R., White, S.M., Gaff, C., Genetics in Medicine (2017) doi:10.1038/gim.2016.221

“Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy”, Walsh, M., Bell, K.M., Chong, B., Creed, E., Brett, G.R., Pope, K., Thorne, N.P., Sadedin, S., Georgeson, P., Phelan, D.G., Day, T., Taylor, J.A., Sexton, A., Lockhart, P.J., Kiers, L., Fahey, M., Macciocca, I., Gaff, C.L., Annals of Clinical and Translational Neurology (2017) doi.org/10.1002/acn3.409

“Real-world utility of whole exome sequencing with targeted gene analysis for focal epilepsy”, Perucca, P., Scheffer, I.E., Harvey, A.S., James, P.J., Lunke, S., Thorne, N., Gaff, C., Regan, B.M., Damiano, J.A., Hildebrand, M.S., Berkovic, S.F., O'Brien, T.J., Kwan, P., Epilepsy Research (2017) doi.org/10.1016/j.eplepsyres.2017.02.001

“A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data”, Stark Z, Dashnow H, Lunke S, Tan TY, Yeung A, Sadedin S, Thorne N, Macciocca I, Gaff C, Melbourne Genomics Health Alliance, Oshlack A, White SM, James PA., European Journal of Human Genetics (2017) doi: 10.1038/ejhg.2017.123

"A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders", Stark, Z., Tan, T.Y.,  MD, Chong, B., Brett, G.R., Yap, P., Walsh, M., Yeung, A., Peters, H., Mordaunt, D.,  Cowie, S., Amor, D.J., Savarirayan, R., McGillivray, G., Downie, L., Ekert, P.G., Theda, C., James, P.A., Yaplito-Lee, J., Ryan, M.M., Leventer, R.J., Creed, E., Macciocca, I., Bell, K.M., Oshlack, A., Sadedin, S., Georgeson, P., Anderson, C., Thorne, N., Melbourne Genomics Health Alliance, Gaff, C., White, S.M., Genetics in Medicine (2016) doi:10.1038/gim.2016.1

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Program design

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” Janet l. Wale, Louisa Di Pietro, Heather Renton, Margaret Sahhar, Christine Walker, Pamela Williams, Karen Meehan, Elly Lynch, Melissa Martyn, Jane Bell, Ingrid Winship and Clara L. Gaff, Research Involvement and Engagement (2021) https://doi.org/10.1186/s40900-021-00326-6

"Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis" , Claire L. Gorrie, Anders Goncalves Da Silva, Danielle J. Ingle, Charlie Higgs, Torsten Seemann, Timothy P Stinear, Deborah A Williamson, Jason C Kwong, Lindsay Grayson, Norelle L. Sherry and Benjamin P. Howden, The Lancet Microbe (2021) https://doi.org/10.1016/S2666-5247(21)00149-X

"'It's something I've committed to longer term': The impact of an immersion program for physicians on adoption of genomic medicine", Melissa Martyn, Belinda McClaren, Monika Janinski, Elly Lynch, Fiona Cunningham and Clara Gaff, Patient Education and Counselling (2020) https://doi.org/10.1016/j.pec.2020.10.013

Comprehensive evaluation of a prospective Australian patient cohort with suspected genetic kidney disease undergoing clinical genomic testing: A study protocol”, Kushani Jayasinghe, Zornitza Stark, Chirag Patel, Amali Mallawaarachchi, Hugh McCarthy, Randall Faull Aron Chakera, Madhivanan Sundaram, Matthew Jose, Peter Kerr, You Wu, Louise Wardrop, Ilias Goranitis, Stephanie Best, Melissa Martyn, Catherine Quinlan and Andrew J. Mallett, BMJ Open (2019) doi: 10.1136/bmjopen-2019-029541

"A transformative translational change programme to introduce genomics into healthcare: a complexity and implementation science study protocol", Taylor, N., Best, S., Martyn, M., Long, J.C., North, K.N., Braithwaite, J., Gaff, C., BMJ Open (2019)  doi:10.1136/bmjopen-2018024681

"A novel approach to offering additional genomic findings - A protocol to test a two-step approach in the healthcare system", Martyn, M., Kanga-Parabia, A., Lynch, E., James, P.A., Macciocca, I., Trainer, H.A., Halliday, J., Keogh, L., Wale, J., Winship, I., Bogwitz, M., Valente, G., Walsh, M., Downie, L., Amor, D., Wallis, M., Cunningham, F., Burgess, M., Brown, N.J., Jarmolowicz, A., Lunke, S., Goranitis, I., Melbourne Genomics Health Alliance, Gaff, C.L.,  Journal of Genetic Counselling (2019)  doi:10.1002/jgc4.1102

“Preparing for genomic medicine: a real world demonstration of the future”, Gaff, C., Winship, I.M., Forrest, S.M., Hansen, D.P., Clark, J., Waring, P.M., South, M., Sinclair, A.H., NPJ Genomic Medicine (2017) doi:10.1038/s41525-017-0017-4

"Inclusion of diverse populations in genomic research and health services: Genomix workshop report", Matthew, S.S., Barwell, J., Khan, N., Lynch, E., Parker, M., Qureshi, N., Journal of Community Genetics (2017) doi.org/10.1007/s12687-017-0317-5

"A protocol for whole-exome sequencing in newborns with congenital deafness: a prospective population-based cohort", Downie, L., Halliday, J.L., Burt, R.A., Lunke, S., Lynch, E., Martyn, M., Poulakis, Z., Gaff, C., Sung, V., Wake, M., Hunter, M., Saunders, K., Rose, E., Rehm, H.L., Amor, D.J., BMJ Paediatrics Open (2017) doi: 10.1136/bmjpo-2017-000119 

Genomic data

"aCLImatise: Automated generation of tool definitions for bioinformatics workflows", Michael Milton and Natalie Thorne, Bioinformatics (2020) https://doi.org/10.1093/bioinformatics/btaa1033

"Genovic: a secure, scalable and modular system for genomic testing" Natalie Thorne, Kate Birch, Anthony Marty, Andrew Patterson, Tim Bakker, David Hansen, Clara Gaff, Information Management Advisory Group, Diagnostic Advisory Group, Melbourne Genomics Health Alliance, Pathology: The Journal of the Royal College of Pathologists of Australasia (2019)  doi: https://doi.org/10.1016/j.pathol.2018.12.345

"Interacting with Genomic Data: Clinician Requirements Prototype Requirements", Dana Bradford, Shlomo Berkovsky, Melissa Martyn, Tim Bakkar, Martin Krahnert, Michelle Rodriguez, Denis Bauer, Derek Ireland and Clara Gaff, Integrating and Connecting Care - Studies in Health Technology and Informatics (2017) doi:10.3233/978-1-61499-783-2-1

"Evaluation of computational programs to predict HLA genotypes from genomic sequencing data", Bauer, D.C., Zadoorian, A., Wilson, L.O.W, Melbourne Genomics Health Alliance, Thorne, N.P., Briefings in Bioinformatics (2016) doi.org/10.1093/bib/bbw097

"Cpipe: a shared variant detection pipeline designed for diagnostic settings", Sadedin, S.P., Dashnow, H., James, P.A., Bahlo, M., Bauer, D.C., Lonie, A., Lunke, S., Macciocca, I., Ross, J.P., Siemering, K.R., Stark, Z., White, S.M., Melbourne Genomics Health Alliance, Taylor, G., Gaff, C., OshlacK, A., Thorne, N.P., Genome Medicine  (2015) doi.org/10.1186/s13073-015-0191-x

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Melbourne Genomics data and/or the expertise of members and the program team were involved in these publications.

"Structured approaches to implementation of clinical genomics: A scoping review", Helen L. Brown, Isabella A. Sherburn, Clara Gaff, Natalie Taylor and Stephanie Best, Genetics in Medicine (2022) https://doi.org/10.1016/j.gim.2022.03.017

"Transforming the genomics workforce to sustain high value care", Janet C. Long, Clara Gaff and Chrissy Clay, Deeble Perspectives Brief (2022) https://ahha.asn.au/sites/default/files/docs/policy-issue/perspectives_brief_no_20_genomics_workforce_0.pdf

"The value of genomic testing: a contingent valuation across six child- and adult-onset genetic conditions", Yan Meng, Philip M. Clarke and Ilias Goranitis, PharmacoEconomics (2021) https://doi.org/10.1007/s40273-021-01103-9

"Ensuring best practice in genomics education and evaluation: reporting item standards for education and its evaluation in genomics (RISE2 Genomics)", Amy Niselle, Monika Janinski, Melissa Martyn, Belinda McClaren, Nadia Kaunein, the Reporting Item Standards for Education and its Evaluation in Genomics Expert Group, Kristine Barlow-Stewart, Andrea Belcher, John A. Bernat, Stephanie Best, Michelle Bishop, June C. Carroll, Martina Cornel, Vajira H. W. Dissanayake, Agnes Dods, Kate Dunlop, Gunjan Garg, Russell Gear, Debra Graves, Ken Knight, Bruce Korf, Dhavendra Kumar, Mercy Laurino, Alan Ma, Jane Maguire, Andrew Mallett, Maria McCarthy, Alison McEwen, Nicola Mulder, Chirag Patel, Catherine Quinlan, Kate Reed, Erin Rooney Riggs, Ingrid Sinnerbrink, Anne Slavotinek, Vijayaprakash Suppiah, Bronwyn Terrill, Edward S. Tobias, Emma Tonjkin, Steve Trumble, Tina-MArie Wessels, Sylvia Metcalfe, Helen Jordan and Clara Gaff, Genetics in Medicine (2021) https://doi.org/10.1038/s41436-021-01140-x

"Investigating the adoption of clinical genomics in Australia. An implementation science case study", Stephanie Best, Janet C. Long, Clara Gaff, Jeffrey Braithewaite and Natalie Taylor, Genes (2021)  https://doi.org/10.3390/genes12020317

"Failure of tofacitinib to achieve an objective response in a DDX3X-MLLT10 T-lymphoblastic leukemia with activating JAK3 mutations", Jonathan Wong, Meaghan Wall, Gregory Philip Corboy, Nadine Taubenheim, Gareth Peter Gregory, Stephen Opat,  Jake Shortt, Cold Spring Harbor Molecular Case Studies (2020)  doi:10.1101/mcs.a004994.

"Childhood Hearing Australasian Medical Professionals network: Consensus guidelines on investigation and clinical management of childhood hearing loss", Valerie Sung, Lilian Downie, Georgia A Paxton, Karen Liddle,Catherine S Birman, Wei Wei Chan, Carolyn Cottier, Alison Harris, Matthew Hunter, Elizabeth Peadon, Kenneth Peacock, Laurence Roddick, Elizabeth Rose, Kerryn Saunders, David J Amor, Journal of Paediatrics and Child Health 55 (2019) doi:10.1111/jpc.14508

"Preparing Australia for genomic medicine: data, computing and digital health" , David P Hansen, Marcel E Dinger, Oliver Hofmann, Natalie Thorne and Tiffany F Boughtwood, The Medical Journal of Australia - Expanding the evidence base in digital health (2019) doi: 10.5694/mja2.50032.

“Genetic, radiologic and clinical variability in Brown-Vialetto-van Laere syndrome”, Ian R. Woordrock, Manoj P. Menezes, Lee Coleman, Joy Yaplito-Lee, Heidi Peters, Susan M. White, Rachel Stapleton, Dean G. Phelan, Belinda Chone, Sebastian Lunke, Zornitza Stark, James Pitt, Monique M. Ryan, Colin Robertson and Eppie M. Yiu, Semin Pediatr Neurol (2018) doi: 10.1016/j.spen.2017.03.001

“Pitfalls of immunotherapy: lessons from a patient with CTLA-4 haploinsufficiency”, Leisa Rebecca Watson, Charlotte A. Slade, Sama Ojaimi, Sara Barnes, Pasquale Fedele, Prudence Smith, Justine Marum, Sebastian Lunke, Zornitza Stark, Matthew F. Hunter, Vanessa L. Bryant, Michael Sze Yuan Low, Allergy Asthma Clin Immunol. (2018), doi: 10.1186/s13223-018-0272-7

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Reports and information sheets

Information sheet: GenoVic: A clinical system for genomics (2022)


We could talk genomics all day, but we’ll send you only what’s useful and interesting.

Melbourne Genomics acknowledges the Wurundjeri people of the Kulin Nation, on whose lands we work, and all First Nations peoples across Victoria. We pay respect to Elders past and present. We also acknowledge the First Nations health professionals, researchers and leaders who are shaping the future of genomic medicine.

© 2014–2022 Melbourne Genomics Health Alliance