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Evidence for genomics

"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

 

Program design

"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

"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

 

Related publications

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

"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