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1. The Global Crisis of Congenital Syphilis: Vulnerable and Disenfranchised Women Most at Risk

Author

Moore A, Freyne B, and Nourse C

Subjects
syphilis, pregnancy, congenital, epidemiology., Pediatrics, RJ1-570
Abstract

Aoife Moore,1 Bridget Freyne,2 Clare Nourse3 1Department of General Paediatrics, Children’s Health Queensland, Brisbane, QLD, Australia; 2Department of Paediatric Infectious Diseases, Children’s Health Ireland, Dublin, Ireland; 3Department of Paediatric Infectious Diseases, Children’s Health Queensland, Brisbane, QLD, AustraliaCorrespondence: Aoife Moore, Queensland Children’s Hospital, South Brisbane, QLD, 4101, Tel +61 403 400 190, Email aoife.moore@bigpond.comAbstract: Congenital syphilis (CS), previously considered by many paediatricians as a “historical disease”, has re-emerged as a significant preventable neonatal infection. While low-income countries have the highest burden of disease globally, notifications have increased in many high-income countries (HIC) in recent years. This literature report provides an overview of the current strategies for testing and treating syphilis in pregnancy (SIP) and CS and describes the changing global epidemiology of SIP. National SIP guidelines are reviewed with reference to testing in pregnancy and treatment of CS. The report highlights that there is an ongoing crisis of CS in HICs worldwide and a disproportionate burden is being experienced by vulnerable populations in these countries. Action is needed to address this crisis, and interventions aimed at overcoming social and structural barriers to antenatal care access for vulnerable populations should be prioritised.Keywords: syphilis, pregnancy, congenital, epidemiology

Published
2023

2. LB1663 A multi-gene prognostic signature associated with cutaneous squamous cell carcinoma metastasis

Author

Wang, J., primary, Harwood, C., additional, Bailey, E., additional, Bewicke-Copley, F., additional, Anene, C., additional, Thomson, J., additional, Qamar, M., additional, Nourse, C., additional, Schoenherr, C., additional, Treanor-Taylor, M., additional, Healy, E., additional, Lai, C., additional, Craig, P., additional, Moyes, C., additional, Rickaby, W., additional, Martin, J., additional, Proby, C., additional, Inman, G., additional, and Leigh, I., additional

Published
2023
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7. Whole genome sequencing and molecular epidemiology of paediatric Staphylococcus aureus bacteraemia

Author

Campbell, AJ, Mowlaboccus, S, Coombs, GW, Daley, DA, Al Yazidi, LS, Phuong, LK, Leung, C, Best, EJ, Webb, RH, Voss, L, Athan, Eugene, Britton, PN, Bryant, PA, Butters, CT, Carapetis, JR, Ching, NS, Francis, J, Hung, TY, Nourse, C, Ojaimi, S, Tai, A, Vasilunas, N, McMullan, B, Bowen, AC, Blyth, CC, Campbell, AJ, Mowlaboccus, S, Coombs, GW, Daley, DA, Al Yazidi, LS, Phuong, LK, Leung, C, Best, EJ, Webb, RH, Voss, L, Athan, Eugene, Britton, PN, Bryant, PA, Butters, CT, Carapetis, JR, Ching, NS, Francis, J, Hung, TY, Nourse, C, Ojaimi, S, Tai, A, Vasilunas, N, McMullan, B, Bowen, AC, and Blyth, CC

Published
2022

8. Epidemiology and long-term neurological sequelae of childhood herpes simplex CNS infection.

Author

Berkhout, A, Kapoor, V, Heney, C, Jones, CA, Clark, JE, Britton, PN, Vaska, VL, Lai, MM, Nourse, C, Berkhout, A, Kapoor, V, Heney, C, Jones, CA, Clark, JE, Britton, PN, Vaska, VL, Lai, MM, and Nourse, C

Abstract

AIM: Herpes simplex CNS infection is a rare but important cause of neurological disability. Long term outcomes after HSV CNS infection in Australia have not yet been fully described. We sought to provide a comprehensive review of HSV CNS infection in children using a retrospective 13-year evaluation of statewide laboratory and clinical records and a parent survey conducted at least one year after the initial infection. METHODS: All positive PCR HSV 1 and 2 results from cerebrospinal fluid (CSF) or brain tissue were obtained from Queensland pathology providers for children aged 0-16 years between 1 January 2005 and 31 December 2017. Clinical data were obtained from patient records and longer-term outcomes via parent survey at least 1 year after initial infection. RESULTS: Forty-three children were identified over the 13-year period, 17 (39.5%) neonates and 26 (60.4%) non-neonates. The annual incidence for HSV CNS infection in Queensland children aged ≤16 years was 0.3/100 000 (95% confidence intervals (CIs): 0.2-0.4) with neonates at highest risk (incidence 2.5/100 000 live births, 95% CI: 1.5-3.9). HSV 1 was the predominant serotype in both neonates and non-neonates (9/17, 52.9% neonates and 19/26, 73.1% non-neonates). Seven (16.3%) children died, five (5/17, 29.4% neonates), directly attributable to HSV CNS infection (all neonates). Twenty-five (58.1%) had neurological morbidity at discharge (9/17 neonates (52.9%) vs. 16/26 (61.5%) non-neonates) and 20/27 (74.1%) reported long-term neurological morbidity at follow-up (5/9 neonates (55.6%) vs. 15/18 non-neonates (83.3%)). Seven children (two neonates and four non-neonates) with long-term neurological sequelae had no neurological morbidity identified at discharge. CONCLUSION: Significant long-term neurologic sequelae were seen in children with HSV CNS infection even in children with no neurological disability identified at discharge from hospital. Careful neurodevelopmental follow-up of all children is recommended.

Published
2022

9. The Staphylococcus aureus Network Adaptive Platform Trial Protocol: New Tools for an Old Foe

Author

Tong, S.Y.C., Mora, J., Bowen, A.C., Cheng, M.P., Daneman, N., Goodman, A.L., Heriot, G.S., Lee, T.C., Lewis, R.J., Lye, D.C., Mahar, R.K., Marsh, J., McGlothlin, A., McQuilten, Z., Morpeth, S.C., Paterson, D.L., Price, D.J., Roberts, J.A., Robinson, J.O., van Hal, S.J., Walls, G., Webb, S.A., Whiteway, L., Yahav, D., Davis, J.S., Anagnostou, N., Archuleta, S., Athan, E., Best, E., Bloomfield, M., Botheras, C., Bowen, A., Britton, P., Brown, K., Campbell, A., Carter, H., Cheng, M., Chew, K.L., Chong, R.L.M., Coombs, G., Daley, P., Davies, J., Davis, J., Dishon, Y., Dotel, R., Dunlop, A., Flack, F., Flanagan, K., Foo, H., Ghanem-Zoubi, N., Giulieri, S., Goodman, A., Grant, J., Gregson, D., Guy, S., Gwee, A., Hardy, E., Henderson, A., Heriot, G., Howden, B., Johnstone, J., Kalimuddin, S., de Kretser, D., Kwa, A., Lee, T., Legg, A., Lewis, R., Lumley, T., Lye, D., MacFadden, D., Mahar, R., Malhamé, I., Marks, M., Martinello, M., Matthews, G., McArthur, C., McKew, G., McMullan, B., Milliken, E., Morpeth, S., Murthy, S., Nourse, C., O’Sullivan, M., Paterson, D., Paul, M., Petersiel, N., Petrella, L., Price, D., Roberts, J., Rogers, B., Saville, B., Scheetz, M., Scheuerman, O., Schwartz, K., Smith, S., Snelling, T., Sommerville, C., Stewardson, A., Sud, A., Tong, S., Turner, T., van Hal, S., Vasilunas, N., Voss, L., Webb, R., Webb, S., Wilson, H., Wuerz, T., Tong, S.Y.C., Mora, J., Bowen, A.C., Cheng, M.P., Daneman, N., Goodman, A.L., Heriot, G.S., Lee, T.C., Lewis, R.J., Lye, D.C., Mahar, R.K., Marsh, J., McGlothlin, A., McQuilten, Z., Morpeth, S.C., Paterson, D.L., Price, D.J., Roberts, J.A., Robinson, J.O., van Hal, S.J., Walls, G., Webb, S.A., Whiteway, L., Yahav, D., Davis, J.S., Anagnostou, N., Archuleta, S., Athan, E., Best, E., Bloomfield, M., Botheras, C., Bowen, A., Britton, P., Brown, K., Campbell, A., Carter, H., Cheng, M., Chew, K.L., Chong, R.L.M., Coombs, G., Daley, P., Davies, J., Davis, J., Dishon, Y., Dotel, R., Dunlop, A., Flack, F., Flanagan, K., Foo, H., Ghanem-Zoubi, N., Giulieri, S., Goodman, A., Grant, J., Gregson, D., Guy, S., Gwee, A., Hardy, E., Henderson, A., Heriot, G., Howden, B., Johnstone, J., Kalimuddin, S., de Kretser, D., Kwa, A., Lee, T., Legg, A., Lewis, R., Lumley, T., Lye, D., MacFadden, D., Mahar, R., Malhamé, I., Marks, M., Martinello, M., Matthews, G., McArthur, C., McKew, G., McMullan, B., Milliken, E., Morpeth, S., Murthy, S., Nourse, C., O’Sullivan, M., Paterson, D., Paul, M., Petersiel, N., Petrella, L., Price, D., Roberts, J., Rogers, B., Saville, B., Scheetz, M., Scheuerman, O., Schwartz, K., Smith, S., Snelling, T., Sommerville, C., Stewardson, A., Sud, A., Tong, S., Turner, T., van Hal, S., Vasilunas, N., Voss, L., Webb, R., Webb, S., Wilson, H., and Wuerz, T.

Abstract

Staphylococcus aureus bloodstream (SAB) infection is a common and severe infectious disease, with a 90-day mortality of 15%–30%. Despite this, <3000 people have been randomized into clinical trials of treatments for SAB infection. The limited evidence base partly results from clinical trials for SAB infections being difficult to complete at scale using traditional clinical trial methods. Here we provide the rationale and framework for an adaptive platform trial applied to SAB infections. We detail the design features of the Staphylococcus aureus Network Adaptive Platform (SNAP) trial that will enable multiple questions to be answered as efficiently as possible. The SNAP trial commenced enrolling patients across multiple countries in 2022 with an estimated target sample size of 7000 participants. This approach may serve as an exemplar to increase efficiency of clinical trials for other infectious disease syndromes.

Published
2022

10. Whole genome sequencing and molecular epidemiology of paediatric Staphylococcus aureus bacteraemia

Author

Campbell, A.J., Mowlaboccus, S., Coombs, G.W., Daley, D.A., Al Yazidi, L.S., Phuong, L.K., Leung, C., Best, E.J., Webb, R.H., Voss, L., Athan, E., Britton, P.N., Bryant, P.A., Butters, C.T., Carapetis, J.R., Ching, N.S., Francis, J., Hung, T-Y, Nourse, C., Ojaimi, S., Tai, A., Vasilunas, N., McMullan, B., Bowen, A.C., Blyth, C.C., Campbell, A.J., Mowlaboccus, S., Coombs, G.W., Daley, D.A., Al Yazidi, L.S., Phuong, L.K., Leung, C., Best, E.J., Webb, R.H., Voss, L., Athan, E., Britton, P.N., Bryant, P.A., Butters, C.T., Carapetis, J.R., Ching, N.S., Francis, J., Hung, T-Y, Nourse, C., Ojaimi, S., Tai, A., Vasilunas, N., McMullan, B., Bowen, A.C., and Blyth, C.C.

Abstract

Objectives The role Staphylococcus aureus antimicrobial resistance genes and toxins play in disease severity, management and outcome in childhood is an emerging field requiring further exploration. Methods A prospective multisite study of Australian and New Zealand children hospitalised with S. aureus bacteraemia (SAB) occurred over 24 months (2017–2018). Whole genome sequencing (WGS) data were paired with clinical information from the ISAIAH cohort. Results 353 SAB isolates were sequenced; 85% methicillin-susceptible S. aureus ([MSSA], 301/353) and 15% methicillin-resistant S. aureus ([MRSA], 52/353). There were 92 sequence types (STs), most commonly ST5 (18%) and ST30 (8%), grouped into 23 clonal complexes (CCs), most frequently CC5 (21%) and CC30 (12%). MSSA comprised the majority of healthcare-associated SAB (87%, 109/125), with principal clones CC15 (48%, 11/21) and CC8 (33%, 7/21). Panton-Valentine leukocidin (PVL)-positive SAB occurred in 22% (76/353); predominantly MSSA (59%, 45/76), community-onset (92%, 70/76) infections. For community-onset SAB, the only microbiological independent predictor of poor outcomes was PVL positivity (aOR 2.6 [CI 1.0–6.2]). Conclusion From this WGS paediatric SAB data, we demonstrate the previously under-recognized role MSSA has in harbouring genetic virulence and causing healthcare-associated infections. PVL positivity was the only molecular independent predictor of poor outcomes in children. These findings underscore the need for further research to define the potential implications PVL-producing strains may have on approaches to S. aureus clinical management.

Published
2022

14. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Author

Dreyer, SB, Upstill-Goddard, R, Paulus-Hock, V, Paris, C, Lampraki, EM, Dray, E, Serrels, B, Caligiuri, G, Rebus, S, Plenker, D, Galluzzo, Z, Brunton, H, Cunningham, R, Tesson, M, Nourse, C, Bailey, UM, Jones, MD, Moran-Jones, K, Wright, DW, Duthie, F, Oien, K, Evers, L, McKay, CJ, McGregor, GA, Gulati, A, Brough, R, Bajrami, I, Pettitt, S, Dziubinski, ML, Candido, J, Balkwill, F, Barry, ST, Grützmann, R, Rahib, L, Allison, S, Bailey, PJ, Biankin, AV, Beraldi, D, Cameron, E, Chang, DK, Cooke, SL, Grimwood, P, Kelly, S, Marshall, J, Martin, S, McDade, B, McElroy, D, Musgrove, EA, Ramsay, D, Wright, D, Hair, J, Jamieson, NB, Westwood, P, Williams, N, Johns, AL, Mawson, A, Scarlett, CJ, Brancato, MAL, Rowe, SJ, Simpson, SH, Martyn-Smith, M, Thomas, MT, Chantrill, LA, Chin, VT, Chou, A, Cowley, MJ, Humphris, JL, Mead, RS, Nagrial, AM, Pajic, M, Pettit, J, Pinese, M, Rooman, I, Wu, J, Tao, J, DiPietro, R, Watson, C, Steinmann, A, Lee, HC, Wong, R, Pinho, AV, Giry-Laterriere, M, Daly, RJ, Sutherland, RL, Grimmond, SM, Waddell, N, Kassahn, KS, Miller, DK, Wilson, PJ, Patch, AM, Song, S, Harliwong, I, Idrisoglu, S, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Anderson, M, Holmes, O, Leonard, C, Dreyer, SB, Upstill-Goddard, R, Paulus-Hock, V, Paris, C, Lampraki, EM, Dray, E, Serrels, B, Caligiuri, G, Rebus, S, Plenker, D, Galluzzo, Z, Brunton, H, Cunningham, R, Tesson, M, Nourse, C, Bailey, UM, Jones, MD, Moran-Jones, K, Wright, DW, Duthie, F, Oien, K, Evers, L, McKay, CJ, McGregor, GA, Gulati, A, Brough, R, Bajrami, I, Pettitt, S, Dziubinski, ML, Candido, J, Balkwill, F, Barry, ST, Grützmann, R, Rahib, L, Allison, S, Bailey, PJ, Biankin, AV, Beraldi, D, Cameron, E, Chang, DK, Cooke, SL, Grimwood, P, Kelly, S, Marshall, J, Martin, S, McDade, B, McElroy, D, Musgrove, EA, Ramsay, D, Wright, D, Hair, J, Jamieson, NB, Westwood, P, Williams, N, Johns, AL, Mawson, A, Scarlett, CJ, Brancato, MAL, Rowe, SJ, Simpson, SH, Martyn-Smith, M, Thomas, MT, Chantrill, LA, Chin, VT, Chou, A, Cowley, MJ, Humphris, JL, Mead, RS, Nagrial, AM, Pajic, M, Pettit, J, Pinese, M, Rooman, I, Wu, J, Tao, J, DiPietro, R, Watson, C, Steinmann, A, Lee, HC, Wong, R, Pinho, AV, Giry-Laterriere, M, Daly, RJ, Sutherland, RL, Grimmond, SM, Waddell, N, Kassahn, KS, Miller, DK, Wilson, PJ, Patch, AM, Song, S, Harliwong, I, Idrisoglu, S, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Anderson, M, Holmes, O, and Leonard, C

Abstract

Background & Aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient–derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P <.001) and PARP inhibitor therapy (P <.001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P <.018) and WEE1 inhibitor (P <.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P <.001) but was not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.

Published
2021

15. The role of Kingella kingae in pre-school aged children with bone and joint infections.

Author

Olijve L., Amarasena L., Best E., Blyth C., van den Boom M., Bowen A., Bryant P.A., Buttery J., Dobinson H.C., Davis J., Francis J., Goldsmith H., Griffiths E., Hung T.-Y., Huynh J., Kesson A., Meehan A., McMullan B., Nourse C., Palasanthiran P., Penumarthy R., Pilkington K., Searle J., Stephenson A., Webb R., Williman J., Walls T., Olijve L., Amarasena L., Best E., Blyth C., van den Boom M., Bowen A., Bryant P.A., Buttery J., Dobinson H.C., Davis J., Francis J., Goldsmith H., Griffiths E., Hung T.-Y., Huynh J., Kesson A., Meehan A., McMullan B., Nourse C., Palasanthiran P., Penumarthy R., Pilkington K., Searle J., Stephenson A., Webb R., Williman J., and Walls T.

Abstract

Objectives: The Pre-school Osteoarticular Infection (POI) study aimed to describe the burden of disease, epidemiology, microbiology and treatment of acute osteoarticular infections (OAI) and the role of Kingella kingae in these infections. Method(s): Information about children 3-60 months of age who were hospitalized with an OAI to 11 different hospitals across Australia and New Zealand between January 2012 and December 2016 was collected retrospectively. Result(s): A total of 907 cases (73%) were included. Blood cultures grew a likely pathogen in only 18% (140/781). The peak age of presentation was 12 to 24 months (466/907, 51%) and Kingella kingae was the most frequently detected microorganism in this age group (60/466, 13%). In the majority of cases, no microorganism was detected (517/907, 57%). Addition of PCR to culture increased detection rates of K. kingae. However, PCR was performed infrequently (63/907, 7%). Conclusion(s): This large multi-national study highlights the need for more widespread use of molecular diagnostic techniques for accurate microbiological diagnosis of OAI in pre-school aged children. The data from this study supports the hypothesis that a substantial proportion of pre-school aged children with OAI and no organism identified may in fact have undiagnosed K. kingae infection. Improved detection of Kingella cases is likely to reduce the average length of antimicrobial treatment.Copyright © 2021

Published
2021

16. Pediatric Staphylococcus aureus bacteremia: clinical spectrum and predictors of poor outcome.

Author

Campbell A.J., Al Yazidi L.S., Phuong L.K., Leung C., Best E.J., Webb R.H., Voss L., Athan E., Britton P.N., Bryant P.A., Butters C.T., Carapetis J.R., Ching N.S., Coombs G.W., Daley D., Francis J., Hung T.-Y., Mowlaboccus S., Nourse C., Ojaimi S., Tai A., Vasilunas N., McMullan B., Blyth C.C., Bowen A.C., Campbell A.J., Al Yazidi L.S., Phuong L.K., Leung C., Best E.J., Webb R.H., Voss L., Athan E., Britton P.N., Bryant P.A., Butters C.T., Carapetis J.R., Ching N.S., Coombs G.W., Daley D., Francis J., Hung T.-Y., Mowlaboccus S., Nourse C., Ojaimi S., Tai A., Vasilunas N., McMullan B., Blyth C.C., and Bowen A.C.

Abstract

BACKGROUND: Staphylococcus aureus is a common cause of bacteremia, yet the epidemiology, and predictors of poor outcome remain inadequately defined in childhood. METHOD(S): ISAIAH is a prospective, cross-sectional study of S. aureus bacteremia (SAB), in children hospitalized in Australia and New Zealand, over 24-months (2017-2018). RESULT(S): Overall, 552 SABs were identified, (incidence 4.4/100,000/yr [95% confidence interval (CI) 2.2-8.8]), with methicillin-susceptible (84%), community onset (78%) infection predominating. Indigenous children (8.1/100,000/yr [CI 4.8-14.4]), those from lower-socioeconomic areas (5.5/100,000/yr [CI 2.8-10.2]) and neonates (6.6/100,000/yr (CI 3.4-11.7) were over-represented. Although 90-day mortality was infrequent, one-third experienced the composite of: length of stay >30 days (26%), ICU admission (20%), relapse (4%), or death (3%).Predictors of mortality included prematurity (aOR 16.8 [CI 1.6-296.9]), multifocal infection (aOR 22.6 [CI 1.4-498.5]), necrotizing pneumonia (aOR 38.9 [CI 1.7 - 1754.6]), multiorgan dysfunction (aOR 26.5 [CI 4.1-268.8]) and empiric-vancomycin (aOR 15.7 [CI 1.6-434.4]); whilst Infectious Diseases (ID) consultation (aOR 0.07 [CI 0.004-0.9]) was protective. Neither MRSA nor vancomycin trough-targets impacted survival; however, empiric-vancomycin was associated with significant nephrotoxicity (OR 3.1 [CI 1.3-8.1]). CONCLUSION(S): High SAB incidence was demonstrated, with at-risk populations identified for future prioritized care. For the first time in a pediatric setting, necrotizing pneumonia and multifocal infection were predictors of mortality, whilst ID consultation was protective. The need to re-evaluate pediatric vancomycin trough-targets and limit unnecessary empiric-vancomycin exposure, to reduce poor outcomes and nephrotoxicity is highlighted. One in three children experienced considerable SAB morbidity, therefore pediatric inclusion in future SAB comparator trials is paramount to improve outcomes.C

Published
2021

17. Pediatric Staphylococcus aureus Bacteremia: Clinical Spectrum and Predictors of Poor Outcome

Author

Campbell, A.J., Al Yazidi, L.S., Phuong, L.K., Leung, C., Best, E.J., Webb, R.H., Voss, L., Athan, E., Britton, P.N., Bryant, P.A., Butters, C.T., Carapetis, J.R., Ching, N.S., Coombs, G.W., Daley, D.A., Francis, J.R., Hung, T-Y, Mowlaboccus, S., Nourse, C., Ojaimi, S., Tai, A., Vasilunas, N., McMullan, B., Blyth, C.C., Bowen, A.C., Campbell, A.J., Al Yazidi, L.S., Phuong, L.K., Leung, C., Best, E.J., Webb, R.H., Voss, L., Athan, E., Britton, P.N., Bryant, P.A., Butters, C.T., Carapetis, J.R., Ching, N.S., Coombs, G.W., Daley, D.A., Francis, J.R., Hung, T-Y, Mowlaboccus, S., Nourse, C., Ojaimi, S., Tai, A., Vasilunas, N., McMullan, B., Blyth, C.C., and Bowen, A.C.

Abstract

Background Staphylococcus aureus is a common cause of bacteremia, yet the epidemiology and predictors of poor outcome remain inadequately defined in childhood. Methods ISAIAH (Invasive Staphylococcus aureus Infections and Hospitalizations in children) is a prospective, cross-sectional study of S. aureus bacteremia (SAB) in children hospitalized in Australia and New Zealand over 24 months (2017–2018). Results Overall, 552 SABs were identified (incidence 4.4/100 000/year). Indigenous children, those from lower socioeconomic areas and neonates were overrepresented. Although 90-day mortality was infrequent, one-third experienced the composite of: length of stay >30 days (26%), intensive care unit admission (20%), relapse (4%), or death (3%). Predictors of mortality included prematurity (adjusted odds ratio [aOR],16.8; 95% confidence interval [CI], 1.6–296.9), multifocal infection (aOR, 22.6; CI, 1.4–498.5), necrotizing pneumonia (aOR, 38.9; CI, 1.7–1754.6), multiorgan dysfunction (aOR, 26.5; CI, 4.1–268.8), and empiric vancomycin (aOR, 15.7; CI, 1.6–434.4); while infectious diseases (ID) consultation (aOR, 0.07; CI .004–.9) was protective. Neither MRSA nor vancomycin trough targets impacted survival; however, empiric vancomycin was associated with nephrotoxicity (OR, 3.1; 95% CI 1.3–8.1). Conclusions High SAB incidence was demonstrated and for the first time in a pediatric setting, necrotizing pneumonia and multifocal infection were predictors of mortality, while ID consultation was protective. The need to reevaluate pediatric vancomycin trough targets and limit unnecessary empiric vancomycin exposure to reduce poor outcomes and nephrotoxicity is highlighted. One in 3 children experienced considerable SAB morbidity; therefore, pediatric inclusion in future SAB comparator trials is paramount to improve outcomes.

Published
2021

20. National scientific medical meeting 1997 abstracts

Author

Willison, H. J., Lastovica, A. J., Prendergast, M. M., Moran, A. P., Walsh, C., Flitcroft, I., Eustace, P., McMahon, C., Smith, J., Smith, O. P., Lakshmandass, G., Taylor, M. R. H., Holland, C. V., Cox, D., Good, B., Kearns, G. M., Gaffney, P., Shark, K., Frauenshuh, M., Ortmann, W., Messner, R., King, R., Rich, S., Behrens, T., Mahmud, N., Molloy, A., McPartlin, J., Scott, J. M., Weir, D. G., Walsh, K. M., Thorburn, D., Mills, P., Morris, A. J., Good, T., Cameron, S., McCruden, E. A. B., Bennett, M. W., O’Connell, J., Brady, C., Roche, D., Collins, J. K., Shanahan, F., O’Sullivant, G. C., Henry, M., Koston, S., McMahon, K., MacNee, W., FitzGerald, M. X., O’Connor, C. M., McGonagle, D., Gibbon, W., O’Connor, P., Emery, P., Murphy, M., Watson, R., Casey, E., Naidu, E., Murphy, M., Watson, R., Barnes, L., McCann, S., Murphy, M., Watson, R., Barnes, L., Sweeney, E., Barrett, E. J., Graham, H., Cunningham, R. T., Johnston, C. F., Curry, W. J., Buchanan, K. D., Courtney, C. H., McAllister, A. S., McCance, D. R., Hadden, D. R., Bell, P. M., Leslie, H., Sheridan, B., Atkinson, A. B., Kilbane, M. T., Smith, D. F., Murray, M. J., Shering, S. G., McDermott, E. W. M., O’Higgins, N. J., Smyth, P. P. A., McEneny, J., Trimble, E. R., Young, I. S., Sharpe, P., Mercer, C., McMaster, D., Young, I. S., Evans, A. E., Young, I. S., Cundick, J., Hasselwander, O., McMaster, D., McGeough, J., Savage, D., Maxwell, A. P., Evans, A. E., Kee, F., Larkin, C. J., Watson, R. G. P., Johnston, C., Ardill, J. E. S., Buchanan, K. D., McNamara, D. A., Walsh, T. N., Bouchier-Hayes, D. J., Madden, C., Timon, C., Gardiner, N., Lawler, M., O’Riordan, J., Duggan, C., McCann, S. R., Gowing, H., Braakman, E., Lawler, M., Byrne, C., Martens, A. C. M., Hagenbeek, A., McCann, S. R., Kinsella, N., Cusack, S., Lawler, M., Baker, H., White, B., Smith, O. P., Lawler, M., Gardiner, N., Molloy, K., Gowing, H., Wogan, A., McCann, S. R., McElwaine, S., Lawler, M., Hollywood, D., McCann, S. 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A., Harmey, J., Wang, J. H., Donovan, D., Walsh, T. N., Bouchier-Hayes, D. J., Kay, E., Pidgeon, G., Harmey, J., McNamara, D. A., Bouchier-Hayes, D. J., Dunne, P., Lambkin, H., Russell, J. M., O’Neill, A. J., Dunne, B. M., O’Donovan, M., Lawler, M., Gaffney, E. F., Gillan, J. E., Cotter, T. G., Horan, J., Jones, D., Biswas, S. K., Mulkerrin, E. C., Brady, H., O’Donnell, J., Neary, J., Healy, E., Watson, A., Keogh, B., Ryan, M., Cassidy, C., Ward, S., Stokes, E., Keoghan, F., Barrett, A., O’Connell, P., Ryall, N., O’Connell, P. A., Jenkinson, A., O’Brien, T., O’Connell, P. G., Harrison, R., Barrett, T., Bailey, D. M. D., Butler, A., Barton, D. E., Byrne, C., McElwaine, S., McCann, S. R., Lawler, M., Cusack, S., Lawler, M., White, B., Smith, O. P., Daly, G., Gill, M., Heron, S., Hawi, Z., Fitzgerald, M., Hawi, Z., Mynett-Johnson, L., Shiels, D., Kendler, K., McKeon, P., Gill, M., Straub, R., Walsh, D., Ryan, F., Barton, D. E., McCabe, D., Murphy, R., Segurado, R., Mulcahy, T., Larson, B., Comerford, C., O’Connell, R., O’Mahony, E., Gill, M., Donnelly, J., Minahan, F., O’Neill, D., Farrell, Z., O’Neill, D., Jones, D., Horan, J., Glynn, C., Biswas, S. K., Mulkerrin, E., Brady, H., Lennox, S. E., Murphy, A., Rea, I. M., McNulty, H., McMeel, C., O’Neill, D., McEvoy, H., Freaney, R., McKenna, M. J., Crowe, M., Keating, D., Colreavy, M., Hone, S., Norman, G., Widda, S., Viani, L., Galvin, Nolan, C. M., Hardiman, O., Hardiman, O., Brett, F., Droogan, O., Gallagher, P., Harmey, M., King, M., Murphy, J., Perryrnan, R., Sukumaran, S., Walsh, J., Farrell, M. A., Hughes, G., Cunningham, C., Walsh, J. B., Coakley, D., O’Neill, D., Hurson, M., Flood, P., McMonagle, P., Hardiman, O., Ryan, F., O’Sullivan, S., Merry, C., Dodd, P., Redmond, J., Mulcahy, F. M., Browne, R., Keating, S., O’Connor, J., Cassidy, B. P., Smyth, R., Sheppard, N. P., Cullivan, R., Crown, J., Walsh, N., Denihan, A., Bruce, I., Radic, A., Coakley, D., Lawlor, B. A., Bridges, P. K., O’Doherty, M., Farrington, A., O’Doherty, M., Farragher, B., Fahy, S., Kelly, R., Carey, T., Owens, J., Gallagher, O., Sloan, D., McDonough, C., Casey, P., Horgan, A., Elneihum, A., O’Neill, C., McMonagle, T., Quinn, J., Meagher, D., Murphy, P., Kinsella, A., Mullaney, J., Waddington, J. L., Rooney, S., Rooney, S., Bamford, L., Sloan, D., O’Connor, J. J., Franklin, R., O’Brien, K., Fitzpatrick, G., Laffey, J. G., Boylan, J. F., Laffey, J., Coleman, M., Boylan, J., Laffey, J. G., McShane, A. J., Boylan, J. F., Loughrey, J. P. R., Gardiner, J., McGinley, J., Leonard, I., Carey, M., Neligan, P., O’Rourke, J., Cunningham, A., Fennessy, F., Kelly, C., Bouchier-Hayes, D., Fennessy, F., Wang, J. H., Kelly, C., Bouchier-Hayes, D., Fennessy, F., Wang, J. H., Kelly, C., Bouchier-Hayes, D. J., Kellett, J., Laffey, J., Murphy, D., Regan, J., O’Keeffe, D., Mahmud, A., Hemeryck, L., Feely, J., Mahmud, A., Hemeryck, L., Hall, M., Feely, J., Menown, I. B. A., Mathew, T. P., Nesbitt, G. S., Syme, M., Young, I. S., Adgey, A. A. J., Menown, I. B. A., Turtle, F., Allen, J., Anderson, J., Adgey, A. A. J., O’Hanlon, R., Codd, M. B., Walkin, S., McCann, H. A., Sugrue, D. D., Rasheed, A. M., Chen, G., Kelly, C., Bouchier-Hayes, D. J., Leahy, A., Rasheed, A. M., Kay, E., Jina, S., Bouchier-Hayes, D. J., Leahy, A., McDowell, I., Rasheed, A. M., Wang, J. H., Wo, Q., Kelly, C., Bouchier-Hayes, D. J., Leahy, A., Shuhaibar, M. N., McGovern, E., Turtle, F., Menown, I. B. A., Manoharan, G., Kirkpatrick, R., Campbell, N. P. S., Walkin, S., Codd, M. B., O’Hanlon, R., McCarthy, C., McCann, H. A., Sugrue, D. D., Wen, Y., Killalea, S., Hall, M., Hemeryck, L., Feely, J., Fahy, C. J., Griffith, A., McGinley, J., McCabe, D., Fraser, A., Casey, E., Ryan, T., Murphy, R., Browne, M., Fenton, J., Hughes, J., Timon, C. I., Fenton, J., Curran, A., Smyth, D., Viani, L., Walsh, M., Hughes, J. P., Fenton, J., Lee, P., Kelly, A., Timon, C. I., Hughes, J. P., Fenton, J., Shine, N., Blayney, A., McShane, D. P., Timon, C. I., Hussey, J., Howlett, M., Langton, A., McEvoy, A., Slevin, J., Fitzpatrick, C., Turner, M. J., Enright, F., Goggin, N., Costigan, C., Duff, D., Osizlok, P., Wood, F., Watson, R., Fitzsimons, R. B., Flanagan, N., Enright, F., Barnes, L., Watson, R., Molloy, E., Griffin, E., Deasy, P. F., Sheridan, M., White, M. J., Moore, R., Gray, A., Hill, J., Glasgow, J. F. T., Middleton, B., Slattery, D., Donoghue, V., McMahon, A., Murphy, J., Slattery, D., McCarthy, A., Oslislok, P., Duff, D., Colreavy, M., Keogh, I., Hone, S., Walsh, M., Henry, M., Koston, S., McMahon, K., MacNee, W., FitzGerald, M. X., O’Connor, C. M., Russell, K. J., Henry, M., Fitzgerald, M. X., O’Connor, C. M., Kavanagh, P. V., McNamara, S. M., Feely, J., Barry, M., O’Brien, J. E., McCormick, P., Molony, C., Doyle, R. M., Walsh, J. B., Coakley, D., Codd, M. B., O’Connell, P. R., Dowey, L. C., McGlynn, H., Thurnham, D. I., Elborn, S. J., Flynn, L., Carton, J., Byrne, B., O’Farrelly, C., Kelehan, P., O’Herlihy, C., O’Hara, A. M., Moran, A. P., Orren, A., Fernie, B. A., Merry, C., Clarke, S., Courtney, G., de Gascun, C., Mulcahy, F. M., Merry, C., Ryan, M., Barry, M., Mulcahy, F. M., Merry, C., Ryan, M., Barry, M., Mulcahy, F. M., Byrne, M., Moylett, E., Murphy, H., Butler, K., Nourse, C., Thaker, H., Barry, C., Russell, J., Sheehan, G., Boyle, B., Hone, R., Conboy, B., Butler, C., Moris, D., Cormican, M., Flynn, J., McCormack, O., Corbally, N., Murray, A., Kirrane, S., O’Keane, C., Hone, R., Lynch, S. M., Cryan, B., Whyte, D., Morris, D., Butler, C., Cormican, M., Flynn, J., Corbett-Feeney, G., Murray, A., Corbally, N., Hone, R., Mackle, T., Colreavy, M., Perkins, J., Saidlear, C., Young, A., Eustace, P., Wrigley, M., Clifford, J., Waddington, J. L., Tighe, O., Croke, D. T., Drago, J., Sibley, D. R., Feely, J., Kelly, A., Carvalho, M., Hennessy, M., Kelly, M., Feely, J., Hughes, C., Hanlon, M., Feely, J., Sabra, K., Keane, T., Egan, D., Ryan, M., Maerry, C., Ryan, M., Barry, M., Mulcahy, F. M., Maerry, C., Ryan, M., Barry, M., Mulcahy, F. M., Sharma, S. C., Williams, D., Kelly, A., Carvalho, M., Feely, J., Williams, D., Kelly, A., Carvalho, M., Feely, J., Codd, M. B., Mahon, N. G., McCann, H. A., Sugrue, D. D., Sayers, G. M., Johnson, Z., McNamara, S. M., Kavanagh, P. V., and Feely, J.

Published
1998
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26. Copy-number signatures and mutational processes in ovarian carcinoma

Author

Macintyre, G, Goranova, T, De Silva, D, Ennis, D, Piskorz, A, Eldridge, M, Sie, D, Lewsley, L-A, Hanif, A, Wilson, C, Dowson, S, Glasspool, R, Lockley, M, Brockbank, E, Montes, A, Walther, A, Sundar, S, Edmondson, R, Hall, G, Clamp, A, Gourley, C, Hall, M, Fotopoulou, C, Gabra, H, Paul, J, Supernat, A, Millan, D, Hoyle, A, Bryson, G, Nourse, C, Mincarelli, L, Navarro Sanchez, L, Ylstra, B, Jimenez-Linan, M, Moore, L, Hofmann, O, Markowetz, F, McNeish, I, and Brenton, J

Abstract

Genomic complexity from profound copy-number aberration has prevented effective molecular stratification of ovarian and other cancers. Here we present a method for copy-number signature identification that decodes this complexity. We derived eight signatures using 117 shallow whole-genome sequenced high-grade serous ovarian cancer cases, which were validated on a further 497 cases. Mutational processes underlying the copy-number signatures were identified, including breakage-fusion-bridge cycles, homologous recombination deficiency and whole-genome duplication. We show that most tumours are heterogeneous and harbour multiple signature exposures. We also demonstrate that copy number signatures predict overall survival and changes in signature exposure observed in response to chemotherapy suggest potential treatment strategies.

Published
2017

28. Copy number signatures and mutational processes in ovarian carcinoma

Author

Macintyre, G, Goranova, TE, De Silva, D, Ennis, D, Piskorz, AM, Eldridge, M, Sie, D, Lewsley, L-A, Hanif, A, Wilson, C, Dowson, S, Glasspool, RM, Lockley, M, Brockbank, E, Montes, A, Walther, A, Sundar, S, Edmondson, R, Hall, GD, Clamp, A, Gourley, C, Hall, M, Fotopoulou, C, Gabra, H, Paul, J, Supernat, A, Millan, D, Hoyle, A, Bryson, G, Nourse, C, Mincarelli, L, Sanchez, LN, Ylstra, B, Jimenez-Linan, M, Moore, L, Hofmann, O, Markowetz, F, McNeish, IA, Brenton, JD, Macintyre, G, Goranova, TE, De Silva, D, Ennis, D, Piskorz, AM, Eldridge, M, Sie, D, Lewsley, L-A, Hanif, A, Wilson, C, Dowson, S, Glasspool, RM, Lockley, M, Brockbank, E, Montes, A, Walther, A, Sundar, S, Edmondson, R, Hall, GD, Clamp, A, Gourley, C, Hall, M, Fotopoulou, C, Gabra, H, Paul, J, Supernat, A, Millan, D, Hoyle, A, Bryson, G, Nourse, C, Mincarelli, L, Sanchez, LN, Ylstra, B, Jimenez-Linan, M, Moore, L, Hofmann, O, Markowetz, F, McNeish, IA, and Brenton, JD

Abstract

The genomic complexity of profound copy number aberrations has prevented effective molecular stratification of ovarian cancers. Here, to decode this complexity, we derived copy number signatures from shallow whole-genome sequencing of 117 high-grade serous ovarian cancer (HGSOC) cases, which were validated on 527 independent cases. We show that HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in known patterns of genomic aberration. Copy number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Measurement of signature exposures provides a rational framework to choose combination treatments that target multiple mutational processes.

Published
2018

31. Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling

Author

Nones, K, Waddell, N, Song, S, Patch, Am, Miller, D, Johns, A, Wu, J, Kassahn, Ks, Wood, D, Bailey, P, Fink, L, Manning, S, Christ, An, Nourse, C, Kazakoff, S, Taylor, D, Leonard, C, Chang, Dk, Jones, Md, Thomas, M, Watson, C, Pinese, M, Cowley, M, Rooman, I, Pajic, M, Butturini, Giovanni, Malpaga, A, Corbo, Vincenzo, Crippa, Stefano, Falconi, M, Zamboni, Giuseppe, Castelli, P, Lawlor, Rita Teresa, Gill, Aj, Scarpa, Aldo, Pearson, Jv, Biankin, Av, Grimmond, Sm, Apgi, Nones, K, Waddell, N, Song, S, Patch, Am, Miller, D, Johns, A, Wu, J, Kassahn, K, Wood, D, Bailey, P, Fink, L, Manning, S, Christ, An, Nourse, C, Kazakoff, S, Taylor, D, Leonard, C, Chang, Dk, Jones, Md, Thomas, M, Watson, C, Pinese, M, Cowley, M, Rooman, I, Pajic, M, Apgi, Butturini, G, Malpaga, A, Corbo, V, Falconi, Massimo, Zamboni, G, Castelli, P, Lawlor, Rt, Gill, Aj, Scarpa, A, Pearson, Jv, Biankin, Av, Grimmond, S. M., Crippa, Stefano, Basic (bio-) Medical Sciences, and Laboratory for Medical and Molecular Oncology

Subjects
Adult, Male, pancreatic cancer, Integrin alpha2, Nerve Tissue Proteins, Signal transduction, Epigenesis, Genetic, axon-guidance, Transforming Growth Factor beta, stellate cell activation, Humans, RNA, Messenger, Receptors, Immunologic, Promoter Regions, Genetic, Aged, DNA methylation, Base Sequence, SLIT-ROBO pathway, Gene Expression Profiling, Pancreatic Stellate Cells, Pancreatic Ducts, Membrane Proteins, cell adhesion, Sequence Analysis, DNA, Middle Aged, Proto-Oncogene Proteins c-met, SLIT-ROBO pathway, axon-guidance, methylation, pancreatic cancer, stellate cell activation, Gene Expression Regulation, Neoplastic, Pancreatic Neoplasms, Wnt Proteins, integrins, Intercellular Signaling Peptides and Proteins, Female, methylation, aged, 80 and over, Carcinoma, Pancreatic Ductal
Abstract

The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5' region of genes (including the proximal promoter, 5'UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy.

Published
2014

33. Whole-genome landscape of pancreatic neuroendocrine tumours

Author

Scarpa, A., Chang, D. K., Nones, K., Corbo, V., Patch, A. -M., Bailey, P., Lawlor, R. T., Johns, A. L., Miller, D. K., Mafficini, A., Rusev, B., Scardoni, M., Antonello, D., Barbi, S., Sikora, K. O., Cingarlini, S., Vicentini, C., Mckay, S., Quinn, M. C. J., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., Mclean, S., Nourse, C., Nourbakhsh, E., Wilson, P. J., Anderson, M. J., Fink, J. L., Newell, F., Waddell, N., Holmes, O., Kazakoff, S. H., Leonard, C., Wood, S., Xu, Q., Nagaraj, S. H., Amato, E., Dalai, I., Bersani, S., Cataldo, I., Dei Tos, A. P., Capelli, P., Davi, M. V., Landoni, L., Malpaga, A., Miotto, M., Whitehall, V. L. J., Leggett, B. A., Harris, J. L., Harris, J., Jones, M. D., Humphris, J., Chantrill, L. A., Chin, V., Nagrial, A. M., Pajic, M., Scarlett, C. J., Pinho, A., Rooman, I., Toon, C., Wu, J., Pinese, M., Cowley, M., Barbour, A., Mawson, A., Humphrey, E. S., Colvin, E. K., Chou, A., Lovell, J. A., Jamieson, N. B., Duthie, F., Gingras, M. -C., Fisher, W. E., Dagg, R. A., Lau, L. M. S., Lee, M., Pickett, H. A., Reddel, R. R., Samra, J. S., Kench, J. G., Merrett, N. D., Epari, K., Nguyen, N. Q., Zeps, N., Falconi, M., Simbolo, M., Butturini, G., Van Buren, G., Partelli, S., Fassan, M., Khanna, K. K., Gill, A. J., Wheeler, D. A., Gibbs, R. A., Musgrove, E. A., Bassi, C., Tortora, G., Pederzoli, P., Pearson, J. V., Biankin, A. V., Grimmond, S. M., Amato E., Tortora G. (ORCID:0000-0002-1378-4962), Pederzoli P., Scarpa, A., Chang, D. K., Nones, K., Corbo, V., Patch, A. -M., Bailey, P., Lawlor, R. T., Johns, A. L., Miller, D. K., Mafficini, A., Rusev, B., Scardoni, M., Antonello, D., Barbi, S., Sikora, K. O., Cingarlini, S., Vicentini, C., Mckay, S., Quinn, M. C. J., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., Mclean, S., Nourse, C., Nourbakhsh, E., Wilson, P. J., Anderson, M. J., Fink, J. L., Newell, F., Waddell, N., Holmes, O., Kazakoff, S. H., Leonard, C., Wood, S., Xu, Q., Nagaraj, S. H., Amato, E., Dalai, I., Bersani, S., Cataldo, I., Dei Tos, A. P., Capelli, P., Davi, M. V., Landoni, L., Malpaga, A., Miotto, M., Whitehall, V. L. J., Leggett, B. A., Harris, J. L., Harris, J., Jones, M. D., Humphris, J., Chantrill, L. A., Chin, V., Nagrial, A. M., Pajic, M., Scarlett, C. J., Pinho, A., Rooman, I., Toon, C., Wu, J., Pinese, M., Cowley, M., Barbour, A., Mawson, A., Humphrey, E. S., Colvin, E. K., Chou, A., Lovell, J. A., Jamieson, N. B., Duthie, F., Gingras, M. -C., Fisher, W. E., Dagg, R. A., Lau, L. M. S., Lee, M., Pickett, H. A., Reddel, R. R., Samra, J. S., Kench, J. G., Merrett, N. D., Epari, K., Nguyen, N. Q., Zeps, N., Falconi, M., Simbolo, M., Butturini, G., Van Buren, G., Partelli, S., Fassan, M., Khanna, K. K., Gill, A. J., Wheeler, D. A., Gibbs, R. A., Musgrove, E. A., Bassi, C., Tortora, G., Pederzoli, P., Pearson, J. V., Biankin, A. V., Grimmond, S. M., Amato E., Tortora G. (ORCID:0000-0002-1378-4962), and Pederzoli P.

Abstract

The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.

Published
2017

34. Hypermutation In Pancreatic Cancer

Author

Humphris, J. L., Patch, A. -M., Nones, K., Bailey, P. J., Johns, A. L., Mckay, S., Chang, D. K., Miller, D. K., Pajic, M., Kassahn, K. S., Quinn, M. C. J., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., Manning, S., Nourse, C., Nourbakhsh, E., Stone, A., Wilson, P. J., Anderson, M., Fink, J. L., Holmes, O., Kazakoff, S., Leonard, C., Newell, F., Waddell, N., Wood, S., Mead, R. S., Xu, Q., Wu, J., Pinese, M., Cowley, M. J., Jones, M. D., Nagrial, A. M., Chin, V. T., Chantrill, L. A., Mawson, A., Chou, A., Scarlett, C. J., Pinho, A. V., Rooman, I., Giry-Laterriere, M., Samra, J. S., Kench, J. G., Merrett, N. D., Toon, C. W., Epari, K., Nguyen, N. Q., Barbour, A., Zeps, N., Jamieson, N. B., Mckay, C. J., Carter, C. R., Dickson, E. J., Graham, J. S., Duthie, F., Oien, K., Hair, J., Morton, J. P., Sansom, O. J., Grutzmann, R., Hruban, R. H., Maitra, A., Iacobuzio-Donahue, C. A., Schulick, R. D., Wolfgang, C. L., Morgan, R. A., Lawlor, R. T., Rusev, B., Corbo, V., Salvia, R., Cataldo, I., Tortora, Giampaolo, Tempero, M. A., Hofmann, O., Eshleman, J. R., Pilarsky, C., Scarpa, A., Musgrove, E. A., Gill, A. J., Pearson, J. V., Grimmond, S. M., Biankin, A. V., Tortora G. (ORCID:0000-0002-1378-4962), Humphris, J. L., Patch, A. -M., Nones, K., Bailey, P. J., Johns, A. L., Mckay, S., Chang, D. K., Miller, D. K., Pajic, M., Kassahn, K. S., Quinn, M. C. J., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., Manning, S., Nourse, C., Nourbakhsh, E., Stone, A., Wilson, P. J., Anderson, M., Fink, J. L., Holmes, O., Kazakoff, S., Leonard, C., Newell, F., Waddell, N., Wood, S., Mead, R. S., Xu, Q., Wu, J., Pinese, M., Cowley, M. J., Jones, M. D., Nagrial, A. M., Chin, V. T., Chantrill, L. A., Mawson, A., Chou, A., Scarlett, C. J., Pinho, A. V., Rooman, I., Giry-Laterriere, M., Samra, J. S., Kench, J. G., Merrett, N. D., Toon, C. W., Epari, K., Nguyen, N. Q., Barbour, A., Zeps, N., Jamieson, N. B., Mckay, C. J., Carter, C. R., Dickson, E. J., Graham, J. S., Duthie, F., Oien, K., Hair, J., Morton, J. P., Sansom, O. J., Grutzmann, R., Hruban, R. H., Maitra, A., Iacobuzio-Donahue, C. A., Schulick, R. D., Wolfgang, C. L., Morgan, R. A., Lawlor, R. T., Rusev, B., Corbo, V., Salvia, R., Cataldo, I., Tortora, Giampaolo, Tempero, M. A., Hofmann, O., Eshleman, J. R., Pilarsky, C., Scarpa, A., Musgrove, E. A., Gill, A. J., Pearson, J. V., Grimmond, S. M., Biankin, A. V., and Tortora G. (ORCID:0000-0002-1378-4962)

Abstract

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer.

Published
2017

35. Hypermutation In Pancreatic Cancer

Author

Humphris, J., Patch, A., Nones, K., Bailey, P., Johns, A., Mckay, S., Chang, D., Miller, D., Pajic, M., Kassahn, K., Quinn, M., Bruxner, T., Christ, A., Harliwong, I., Idrisoglu, S., Manning, S., Nourse, C., Nourbakhsh, E., Stone, A., Wilson, P., Anderson, M., Fink, J., Holmes, O., Kazakoff, S., Leonard, C., Newell, F., Waddell, N., Wood, S., Mead, R., Xu, Q., Wu, J., Pinese, M., Cowley, M., Jones, M., Nagrial, A., Chin, V., Chantrill, L., Mawson, A., Chou, A., Scarlett, C., Pinho, A., Rooman, I., Giry-Laterriere, M., Samra, J., Kench, J., Merrett, N., Toon, C., Epari, K., Nguyen, N., Barbour, A., Zeps, Nikolajs, Jamieson, N., McKay, C., Carter, C., Dickson, E., Graham, J., Duthie, F., Oien, K., Hair, J., Morton, J., Sansom, O., Gruetzmann, R., Hruban, R., Maitra, A., Iacobuzio-Donahue, C., Schulick, R., Wolfgang, C., Morgan, R., Lawlor, R., Rusev, B., Corbo, V., Salvia, R., Cataldo, I., Tortora, G., Tempero, M., Hofmann, O., Eshleman, J., Pilarsky, C., Scarpa, A., Musgrove, E., Gill, A., Pearson, J., Grimmond, S., Biankin, A., Humphris, J., Patch, A., Nones, K., Bailey, P., Johns, A., Mckay, S., Chang, D., Miller, D., Pajic, M., Kassahn, K., Quinn, M., Bruxner, T., Christ, A., Harliwong, I., Idrisoglu, S., Manning, S., Nourse, C., Nourbakhsh, E., Stone, A., Wilson, P., Anderson, M., Fink, J., Holmes, O., Kazakoff, S., Leonard, C., Newell, F., Waddell, N., Wood, S., Mead, R., Xu, Q., Wu, J., Pinese, M., Cowley, M., Jones, M., Nagrial, A., Chin, V., Chantrill, L., Mawson, A., Chou, A., Scarlett, C., Pinho, A., Rooman, I., Giry-Laterriere, M., Samra, J., Kench, J., Merrett, N., Toon, C., Epari, K., Nguyen, N., Barbour, A., Zeps, Nikolajs, Jamieson, N., McKay, C., Carter, C., Dickson, E., Graham, J., Duthie, F., Oien, K., Hair, J., Morton, J., Sansom, O., Gruetzmann, R., Hruban, R., Maitra, A., Iacobuzio-Donahue, C., Schulick, R., Wolfgang, C., Morgan, R., Lawlor, R., Rusev, B., Corbo, V., Salvia, R., Cataldo, I., Tortora, G., Tempero, M., Hofmann, O., Eshleman, J., Pilarsky, C., Scarpa, A., Musgrove, E., Gill, A., Pearson, J., Grimmond, S., and Biankin, A.

Abstract

© 2017 AGA Institute Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer.

Published
2017

36. Erratum

Author

Nourse, C., Murphy, H., Byrne, C., O’Meara, A., Breatnach, F., Kaufmann, M., Clarke, A., and Butler, K.

Published
1998
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37. Antibiotic duration and timing of the switch from intravenous to oral route for bacterial infections in children: systematic review and guidelines.

Author

Nourse C., Osowicki J., Palasanthiran P., Starr M., Lai T., Francis J.R., Bryant P.A., Isaacs D., McMullan B.J., Andresen D., Blyth C.C., Avent M.L., Bowen A.C., Britton P.N., Clark J.E., Cooper C.M., Curtis N., Goeman E., Hazelton B., Haeusler G.M., Khatami A., Newcombe J.P., Nourse C., Osowicki J., Palasanthiran P., Starr M., Lai T., Francis J.R., Bryant P.A., Isaacs D., McMullan B.J., Andresen D., Blyth C.C., Avent M.L., Bowen A.C., Britton P.N., Clark J.E., Cooper C.M., Curtis N., Goeman E., Hazelton B., Haeusler G.M., Khatami A., and Newcombe J.P.

Abstract

Few studies are available to inform duration of intravenous antibiotics for children and when it is safe and appropriate to switch to oral antibiotics. We have systematically reviewed antibiotic duration and timing of intravenous to oral switch for 36 paediatric infectious diseases and developed evidence-graded recommendations on the basis of the review, guidelines, and expert consensus. We searched databases and obtained information from references identified and relevant guidelines. All eligible studies were assessed for quality. 4090 articles were identified and 170 studies were included. Evidence relating antibiotic duration to outcomes in children for some infections was supported by meta-analyses or randomised controlled trials; in other infections data were from retrospective series only. Criteria for intravenous to oral switch commonly included defervescence and clinical improvement with or without improvement in laboratory markers. Evidence suggests that intravenous to oral switch can occur earlier than previously recommended for some infections. We have synthesised recommendations for antibiotic duration and intravenous to oral switch to support clinical decision making and prospective research.Copyright © 2016 Elsevier Ltd

Published
2016

38. Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells

Author

Abraham, SA, Hopcroft, LEM, Carrick, E, Drotar, ME, Dunn, K, Williamson, AJK, Korfi, K, Baquero, P, Park, LE, Scott, MT, Pellicano, F, Pierce, A, Copland, M, Nourse, C, Grimmond, SM, Vetrie, D, Whetton, AD, Holyoake, TL, Abraham, SA, Hopcroft, LEM, Carrick, E, Drotar, ME, Dunn, K, Williamson, AJK, Korfi, K, Baquero, P, Park, LE, Scott, MT, Pellicano, F, Pierce, A, Copland, M, Nourse, C, Grimmond, SM, Vetrie, D, Whetton, AD, and Holyoake, TL

Abstract

Chronic myeloid leukaemia (CML) arises after transformation of a haemopoietic stem cell (HSC) by the protein-tyrosine kinase BCR-ABL. Direct inhibition of BCR-ABL kinase has revolutionized disease management, but fails to eradicate leukaemic stem cells (LSCs), which maintain CML. LSCs are independent of BCR-ABL for survival, providing a rationale for identifying and targeting kinase-independent pathways. Here we show--using proteomics, transcriptomics and network analyses--that in human LSCs, aberrantly expressed proteins, in both imatinib-responder and non-responder patients, are modulated in concert with p53 (also known as TP53) and c-MYC regulation. Perturbation of both p53 and c-MYC, and not BCR-ABL itself, leads to synergistic cell kill, differentiation, and near elimination of transplantable human LSCs in mice, while sparing normal HSCs. This unbiased systems approach targeting connected nodes exemplifies a novel precision medicine strategy providing evidence that LSCs can be eradicated.

Published
2016

39. Genomic analyses identify molecular subtypes of pancreatic cancer

Author

Bailey, P., Chang, D., Nones, K., Johns, A., Patch, A., Gingras, M., Miller, D., Christ, A., Bruxner, T., Quinn, M., Nourse, C., Murtaugh, L., Harliwong, I., Idrisoglu, S., Manning, S., Nourbakhsh, E., Wani, S., Fink, L., Holmes, O., Chin, V., Anderson, M., Kazakoff, S., Leonard, C., Newell, F., Waddell, N., Wood, S., Xu, Q., Wilson, P., Cloonan, N., Kassahn, K., Taylor, D., Quek, K., Robertson, A., Pantano, L., Mincarelli, L., Sanchez, L., Evers, L., Wu, J., Pinese, M., Cowley, M., Jones, M., Colvin, E., Nagrial, A., Humphrey, E., Chantrill, L., Mawson, A., Humphris, J., Chou, A., Pajic, M., Scarlett, C., Pinho, A., Giry-Laterriere, M., Rooman, I., Samra, J., Kench, J., Lovell, J., Merrett, N., Toon, C., Epari, K., Nguyen, N., Barbour, A., Zeps, Nikolajs, Moran-Jones, K., Jamieson, N., Graham, J., Duthie, F., Oien, K., Hair, J., Gruetzmann, R., Maitra, A., Iacobuzio-Donahue, C., Wolfgang, C., Morgan, R., Lawlor, R., Corbo, V., Bassi, C., Rusev, B., Capelli, P., Salvia, R., Tortora, G., Mukhopadhyay, D., Petersen, G., Munzy, D., Fisher, W., Karim, S., Eshleman, J., Hruban, R., Pilarsky, C., Morton, J., Sansom, O., Scarpa, A., Musgrove, E., Bailey, U., Hofmann, O., Sutherland, R., Wheeler, D., Gill, A., Gibbs, R., Pearson, J., Biankin, A., Grimmond, S., Bailey, P., Chang, D., Nones, K., Johns, A., Patch, A., Gingras, M., Miller, D., Christ, A., Bruxner, T., Quinn, M., Nourse, C., Murtaugh, L., Harliwong, I., Idrisoglu, S., Manning, S., Nourbakhsh, E., Wani, S., Fink, L., Holmes, O., Chin, V., Anderson, M., Kazakoff, S., Leonard, C., Newell, F., Waddell, N., Wood, S., Xu, Q., Wilson, P., Cloonan, N., Kassahn, K., Taylor, D., Quek, K., Robertson, A., Pantano, L., Mincarelli, L., Sanchez, L., Evers, L., Wu, J., Pinese, M., Cowley, M., Jones, M., Colvin, E., Nagrial, A., Humphrey, E., Chantrill, L., Mawson, A., Humphris, J., Chou, A., Pajic, M., Scarlett, C., Pinho, A., Giry-Laterriere, M., Rooman, I., Samra, J., Kench, J., Lovell, J., Merrett, N., Toon, C., Epari, K., Nguyen, N., Barbour, A., Zeps, Nikolajs, Moran-Jones, K., Jamieson, N., Graham, J., Duthie, F., Oien, K., Hair, J., Gruetzmann, R., Maitra, A., Iacobuzio-Donahue, C., Wolfgang, C., Morgan, R., Lawlor, R., Corbo, V., Bassi, C., Rusev, B., Capelli, P., Salvia, R., Tortora, G., Mukhopadhyay, D., Petersen, G., Munzy, D., Fisher, W., Karim, S., Eshleman, J., Hruban, R., Pilarsky, C., Morton, J., Sansom, O., Scarpa, A., Musgrove, E., Bailey, U., Hofmann, O., Sutherland, R., Wheeler, D., Gill, A., Gibbs, R., Pearson, J., Biankin, A., and Grimmond, S.

Abstract

© 2016 Macmillan Publishers Limited. All rights reserved.Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63ΔN transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

Published
2016

40. RON is not a prognostic marker for resectable pancreatic cancer

Author

Tactacan, Carole M, Chang, David K, Cowley, Mark J, Humphrey, Emily S, Jianmin, Wu, Gill, Anthony J, Chou, Angela, Nones, Katia, Grimmond, Sean M, Sutherland, Robert L, Biankin, Andrew V, Daly, Roger J, Biankin, Av, Johns, Al, Mawson, A, Chang, Dk, Scarlett, Cj, Brancato, Ma, Rowe, Sj, Simpson, Sl, Martyn-Smith, M, Chantrill, La, Chin, Vt, Chou, A, Cowley, Mj, Caplan, W, Humphris, Jl, Jones, Md, Mead, R, Nagrial, Am, Pajic, M, Pettit, J, Pinese, M, Rooman, I, Wu, Jun, Daly, Rj, Musgrove, Ea, Sutherland, Rl, Grimmond, Sm, Waddell, N, Kassahn, Ks, Miller, Dk, Wilson, Pj, Patch, Am, Song, S, Harliwong, I, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Anderson, Michela, Holmes, O, Leonard, C, Taylor, D, Wood, JOHN STEPHAN, Xu, C, Nones, K, Fink, Julika, Christ, A, Bruxner, T, Cloonan, N, Newell, F, Pearson, Jv, Samra, Js, Gill, Aj, Nickpavlakis, Guminski, A, Toon, C, Asghari, R, Merrett, Nd, Pavey, Da, Das, A, Cosman, Ph, Ismail, K, O'Connor, C, Lam, Vw, Mcleod, D, Pleass, Hc, James, V, Kench, Jg, Cooper, Cl, Joseph, D, Sandroussi, C, Crawford, M, Texler, M, Forrest, C, Laycock, A, Epari, Kp, Ballal, M, Fletcher, Dr, Mukhedkar, S, Spry, Na, Deboer, B, Chai, M, Feeney, K, Zeps, N, Beilin, M, Nguyen, Nq, Ruszkiewicz, Ar, Worthley, C, Tan, Cp, Debrencini, T, Chen, J, Brooke-Smith, Me, Papangelis, V, Tang, H, Barbour, Ap, Clouston, Ad, Martin, P, O'Rourke, Tj, Chiang, A, Fawcett, Jw, Slater, K, Yeung, S, Hatzifotis, M, Hodgkinson, P, Christophi, C, Nikfarjam, M, Eshleman, Jr, Hruban, Rh, Maitra, A, Iacobuzio-Donahue, Ca, Schulick, Rd, Wolfgang, Cl, Morgan, Ra, Scarpa, A, Lawlor, Rt, Beghelli, S, Corbo, V, Scardoni, M, Bassi, C, Tempero, Ma., and Basic (bio-) Medical Sciences

Subjects
Oncology, Male, Receptor Protein-Tyrosine Kinases/analysis, Cancer Research, Receptor tyrosine kinase, Kaplan-Meier Estimate, Surgical oncology, 80 and over, Prospective cohort study, Pancreatic Neoplasms/metabolism, Biomarker, Gemcitabine, Chemotherapy, Adenocarcinoma, Adult, Aged, Aged, 80 and over, Biomarkers, Tumor, Blotting, Western, Female, Humans, Immunohistochemistry, Middle Aged, Pancreatic Neoplasms, Prognosis, Proportional Hazards Models, Receptor Protein-Tyrosine Kinases, Tissue Array Analysis, Tumor, Blotting, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Adenocarcinoma/metabolism, CA19-9, Western, Research Article, medicine.drug, medicine.medical_specialty, lcsh:RC254-282, Biomarkers, Tumor/analysis, Breast cancer, Internal medicine, Pancreatic cancer, medicine, Genetics, business.industry, Cancer, medicine.disease, business, aged, 80 and over, Biomarkers
Abstract

Background The receptor tyrosine kinase RON exhibits increased expression during pancreatic cancer progression and promotes migration, invasion and gemcitabine resistance of pancreatic cancer cells in experimental models. However, the prognostic significance of RON expression in pancreatic cancer is unknown. Methods RON expression was characterized in several large cohorts, including a prospective study, totaling 492 pancreatic cancer patients and relationships with patient outcome and clinico-pathologic variables were assessed. Results RON expression was associated with outcome in a training set, but this was not recapitulated in the validation set, nor was there any association with therapeutic responsiveness in the validation set or the prospective study. Conclusions Although RON is implicated in pancreatic cancer progression in experimental models, and may constitute a therapeutic target, RON expression is not associated with prognosis or therapeutic responsiveness in resected pancreatic cancer.

Published
2012

41. Australia-wide point prevalence survey of antimicrobial prescribing in neonatal units: How much and how good?.

Author

Noronha J., Isaacs D., Lai T.B., Nourse C., Avent M., Moriarty P., Francis J.R., Blyth C.C., Cooper C.M., Bryant P.A., Osowicki J., Gwee A., Britton P.N., Noronha J., Isaacs D., Lai T.B., Nourse C., Avent M., Moriarty P., Francis J.R., Blyth C.C., Cooper C.M., Bryant P.A., Osowicki J., Gwee A., and Britton P.N.

Abstract

Background: There is increasing recognition of the threat to neonatal patients from antibiotic resistance. There are limited data on antimicrobial prescribing practices for hospitalized neonates. We aimed to describe antimicrobial use in hospitalized Australian neonatal patients, and to determine its appropriateness. Method(s): Multicentre single-day hospital-wide point prevalence survey in 2012, in conjunction with the Antimicrobial Resistance and Prescribing in European Children study. The appropriateness of antimicrobial prescriptions was also assessed. All patients admitted at 8 am on the survey day, in 6 neonatal units in tertiary children's hospitals across 5 states, were included in an analysis of the quantity and quality of all antimicrobial prescriptions. Result(s): The point prevalence survey included 6 neonatal units and 236 patients. Of 109 patients (46%) receiving at least 1 antimicrobial, 66 (61%) were being treated for infection, with sepsis the most common indication. There were 216 antimicrobial prescriptions, 134 (62%) for treatment of infection and 82 (38%) for prophylaxis, mostly oral nystatin. Only 15 prescriptions were for targeted as opposed to empirical treatment. Penicillin and gentamicin were the most commonly prescribed antibiotics, with vancomycin third most common. Half of all treated patients were receiving combination antimicrobial therapy. There was marked variation in vancomycin and gentamicin dosing. Overall, few prescriptions (4%) were deemed inappropriate. Conclusion(s): This is the first Australia-wide point prevalence survey of neonatal antimicrobial prescribing in tertiary children's hospitals. The findings highlight positive practices and potential targets for quality improvement.Copyright © 2015 Wolters Kluwer Health, Inc.

Published
2015

42. Australia-wide point prevalence survey of the use and appropriateness of antimicrobial prescribing for children in hospital.

Author

Isaacs D., Noronha J., Palasanthiran P., McMullan B., Britton P.N., Lai T., Bryant P.A., Cooper C.M., Blyth C.C., Francis J.R., Clark J., Moriarty P., Avent M., Nourse C., Osowicki J., Gwee A., Isaacs D., Noronha J., Palasanthiran P., McMullan B., Britton P.N., Lai T., Bryant P.A., Cooper C.M., Blyth C.C., Francis J.R., Clark J., Moriarty P., Avent M., Nourse C., Osowicki J., and Gwee A.

Abstract

Objectives: To describe antimicrobial use in hospitalised Australian children and to analyse the appropriateness of this antimicrobial use. Design: Multicentre single-day hospital-wide point prevalence survey, conducted in conjunction with the Antimicrobial Resistance and Prescribing in European Children study. Setting: Eight children's hospitals across five Australian states, surveyed during late spring and early summer 2012. Patients: Children and adolescents who were inpatients at 8 am on the day of the survey. Main outcome measures: Quantity and quality of antimicrobial prescribing. Results: Of 1373 patients, 631 (46%) were prescribed at least one antimicrobial agent, 198 (31%) of whom were < 1 year old. The highest antimicrobial prescribing rates were in haematology and oncology wards (76% [95/125]) and paediatric intensive care units (55% [44/80]). Of 1174 antimicrobial prescriptions, 550 (47%) were for community-acquired infections, 175 (15%) were for hospital-acquired infections and 437 (37%) were for prophylaxis. Empirical treatment accounted for 72% of antimicrobial prescriptions for community-acquired infections and 58% for hospital-acquired infections (395 and 102 prescriptions, respectively). A total of 915 prescriptions (78%) were for antibacterials; antifungals and antivirals were predominantly used for prophylaxis. The most commonly prescribed antibacterials were narrow-spectrum penicillins (18% [164 prescriptions]), beta-lactam-beta-lactamase inhibitor combinations (15% [136]) and aminoglycosides (14% [128]). Overall, 957 prescriptions (82%) were deemed appropriate, but this varied between hospitals (range, 66% [74/112]) to 95% [165/174]) and specialties (range, 65% [122/187] to 94% [204/217]). Among surgical patients, 65 of 187 antimicrobial prescriptions (35%) were deemed inappropriate, and a common reason for this was excessive prophylaxis duration. Conclusion: A point prevalence survey is a useful cross-sectional method for quantifying antimicro

Published
2015

43. Whole genomes redefine the mutational landscape of pancreatic cancer

Author

Waddell, N., Pajic, M., Patch, A. -M., Chang, D. K., Kassahn, K. S., Bailey, P., Johns, A. L., Miller, D., Nones, K., Quek, K., Quinn, M. C. J., Robertson, A. J., Fadlullah, M. Z. H., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., Manning, S., Nourse, C., Nourbakhsh, E., Wani, S., Wilson, P. J., Markham, E., Cloonan, N., Anderson, M. J., Fink, J. L., Holmes, O., Kazakoff, S. H., Leonard, C., Newell, F., Poudel, B., Song, S., Taylor, D., Wood, S., Xu, Q., Wu, J., Pinese, M., Cowley, M. J., Lee, H. C., Jones, M. D., Nagrial, A. M., Humphris, J., Chantrill, L. A., Chin, V., Steinmann, A. M., Mawson, A., Humphrey, E. S., Colvin, E. K., Chou, A., Scarlett, C. J., Pinho, A. V., Giry-Laterriere, M., Rooman, I., Samra, J. S., Kench, J. G., Pettitt, J. A., Merrett, N. D., Toon, C., Epari, K., Nguyen, N. Q., Barbour, A., Zeps, N., Jamieson, N. B., Graham, J. S., Niclou, S. P., Bjerkvig, R., Grutzmann, R., Aust, D., Hruban, R. H., Maitra, A., Iacobuzio-Donahue, C. A., Wolfgang, C. L., Morgan, R. A., Lawlor, R. T., Corbo, V., Bassi, C., Falconi, M., Zamboni, G., Tortora, Giampaolo, Tempero, M. A., Gill, A. J., Eshleman, J. R., Pilarsky, C., Scarpa, A., Musgrove, E. A., Pearson, J. V., Biankin, A. V., Grimmond, S. M., Tortora G. (ORCID:0000-0002-1378-4962), Waddell, N., Pajic, M., Patch, A. -M., Chang, D. K., Kassahn, K. S., Bailey, P., Johns, A. L., Miller, D., Nones, K., Quek, K., Quinn, M. C. J., Robertson, A. J., Fadlullah, M. Z. H., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., Manning, S., Nourse, C., Nourbakhsh, E., Wani, S., Wilson, P. J., Markham, E., Cloonan, N., Anderson, M. J., Fink, J. L., Holmes, O., Kazakoff, S. H., Leonard, C., Newell, F., Poudel, B., Song, S., Taylor, D., Wood, S., Xu, Q., Wu, J., Pinese, M., Cowley, M. J., Lee, H. C., Jones, M. D., Nagrial, A. M., Humphris, J., Chantrill, L. A., Chin, V., Steinmann, A. M., Mawson, A., Humphrey, E. S., Colvin, E. K., Chou, A., Scarlett, C. J., Pinho, A. V., Giry-Laterriere, M., Rooman, I., Samra, J. S., Kench, J. G., Pettitt, J. A., Merrett, N. D., Toon, C., Epari, K., Nguyen, N. Q., Barbour, A., Zeps, N., Jamieson, N. B., Graham, J. S., Niclou, S. P., Bjerkvig, R., Grutzmann, R., Aust, D., Hruban, R. H., Maitra, A., Iacobuzio-Donahue, C. A., Wolfgang, C. L., Morgan, R. A., Lawlor, R. T., Corbo, V., Bassi, C., Falconi, M., Zamboni, G., Tortora, Giampaolo, Tempero, M. A., Gill, A. J., Eshleman, J. R., Pilarsky, C., Scarpa, A., Musgrove, E. A., Pearson, J. V., Biankin, A. V., Grimmond, S. M., and Tortora G. (ORCID:0000-0002-1378-4962)

Abstract

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Published
2015

46. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Author

Nones, K, Waddell, N, Wayte, N, Patch, A-M, Bailey, P, Newell, F, Holmes, O, Fink, JL, Quinn, MCJ, Tang, YH, Lampe, G, Quek, K, Loffler, KA, Manning, S, Idrisoglu, S, Miller, D, Xu, Q, Wilson, PJ, Bruxner, TJC, Christ, AN, Harliwong, I, Nourse, C, Nourbakhsh, E, Anderson, M, Kazakoff, S, Leonard, C, Wood, S, Simpson, PT, Reid, LE, Krause, L, Hussey, DJ, Watson, DI, Lord, RV, Nancarrow, D, Phillips, WA, Gotley, D, Smithers, BM, Whiteman, DC, Hayward, NK, Campbell, PJ, Pearson, JV, Grimmond, SM, Barbour, AP, Nones, K, Waddell, N, Wayte, N, Patch, A-M, Bailey, P, Newell, F, Holmes, O, Fink, JL, Quinn, MCJ, Tang, YH, Lampe, G, Quek, K, Loffler, KA, Manning, S, Idrisoglu, S, Miller, D, Xu, Q, Wilson, PJ, Bruxner, TJC, Christ, AN, Harliwong, I, Nourse, C, Nourbakhsh, E, Anderson, M, Kazakoff, S, Leonard, C, Wood, S, Simpson, PT, Reid, LE, Krause, L, Hussey, DJ, Watson, DI, Lord, RV, Nancarrow, D, Phillips, WA, Gotley, D, Smithers, BM, Whiteman, DC, Hayward, NK, Campbell, PJ, Pearson, JV, Grimmond, SM, and Barbour, AP

Abstract

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-of-function mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n=40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC.

Published
2014

47. Somatic Point Mutation Calling in Low Cellularity Tumors

Author

Jordan, IK, Kassahn, KS, Holmes, O, Nones, K, Patch, A-M, Miller, DK, Christ, AN, Harliwong, I, Bruxner, TJ, Xu, Q, Anderson, M, Wood, S, Leonard, C, Taylor, D, Newell, F, Song, S, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Steptoe, A, Pajic, M, Cowley, MJ, Pinese, M, Chang, DK, Gill, AJ, Johns, AL, Wu, J, Wilson, PJ, Fink, L, Biankin, AV, Waddell, N, Grimmond, SM, Pearson, JV, Jordan, IK, Kassahn, KS, Holmes, O, Nones, K, Patch, A-M, Miller, DK, Christ, AN, Harliwong, I, Bruxner, TJ, Xu, Q, Anderson, M, Wood, S, Leonard, C, Taylor, D, Newell, F, Song, S, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Steptoe, A, Pajic, M, Cowley, MJ, Pinese, M, Chang, DK, Gill, AJ, Johns, AL, Wu, J, Wilson, PJ, Fink, L, Biankin, AV, Waddell, N, Grimmond, SM, and Pearson, JV

Abstract

Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.

Published
2013

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