Unlocking hidden cancer drivers using transcriptome data
Grant number: 1140626 | Funding period: 2019 - 2021
New sequencing technologies allow us to get an unbiased look at the molecular signalling in a tumour. However this information is very complex and need specialised methods in statistic and computation in order to make new discoveries. Here will will develop analysis methods to find novel transcriptional variants in cancer and then test them in the lab in order to understand if our discoveries are responsible for causing cancer.
Related publications (13)
Unusual PDGFRB fusion reveals novel mechanism of kinase activation in Ph-like B-ALL
Teresa Sadras, Fatimah BB Jalud, Hansen JJ Kosasih, Christopher RR Horne, Lauren MM Brown, Sam El-Kamand, Charles EE de Bock, Lachlan McAloney, Ashley PP Ng, Nadia MM Davidson, Louise EA Ludlow, Alicia Oshlack, Mark JJ Cowley, Seong LL Khaw, James MM Murphy, Paul GG Ekert
ALLSorts: an RNA-Seq subtype classifier for B-cell acute lymphoblastic leukemia
Breon Schmidt, Lauren M Brown, Georgina L Ryland, Andrew Lonsdale, Hansen J Kosasih, Louise E Ludlow, Ian J Majewski, Piers Blombery, Paul G Ekert, Nadia M Davidson, Alicia Oshlack
B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Subtypes within B-ALL are distinguished by charac..
SFPQ-ABL1 and BCR-ABL1 use different signaling networks to drive B-cell acute lymphoblastic leukemia
Lauren M Brown, Soroor Hediyeh-Zadeh, Teresa Sadras, Hannah Huckstep, Jarrod J Sandow, Ray C Bartolo, Hansen J Kosasih, Nadia M Davidson, Breon Schmidt, Stefan Bjelosevic, Ricky Johnstone, Andrew Webb, Seong L Khaw, Alicia Oshlack, Melissa J Davis, Paul G Ekert
Philadelphia-like (Ph-like) acute lymphoblastic leukemia (ALL) is a high-risk subtype of B-cell ALL characterized by a gene expres..
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
Nadia M Davidson, Ying Chen, Teresa Sadras, Georgina L Ryland, Piers Blombery, Paul G Ekert, Jonathan Goke, Alicia Oshlack
In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discove..
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data
Marek Cmero, Breon Schmidt, Ian J Majewski, Paul G Ekert, Alicia Oshlack, Nadia M Davidson
Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using exist..
Recurrent SPECC1L-NTRK fusions in pediatric sarcoma and brain tumors
Dong-Anh Khuong-Quang, Lauren M Brown, Marie Wong, Chelsea Mayoh, Alexandra Sexton-Oates, Amit Kumar, Mark Pinese, Sumanth Nagabushan, Loretta Lau, Louise E Ludlow, Andrew J Gifford, Michael Rodriguez, Jayesh Desai, Stephen B Fox, Michelle Haber, David S Ziegler, Jordan R Hansford, Glenn M Marshall, Mark J Cowley, Paul G Ekert
The identification of rearrangements driving expression of neurotrophic receptor tyrosine kinase (NTRK) family kinases in tumors h..
MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia
Hansen J Kosasih, Nadia M Davidson, Stefan Bjelosevic, Emma Morrish, Margs S Brennan, Alicia Oshlack, Ricky W Johnstone, Gabriela Brumatti, Seong L Khaw, Paul G Ekert
A novel KMT2A-rearrangement, MLL-TFE3, was identified in an infant leukemia patient. MLL-TFE3 expression produces aggressive leuke..
The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia
Lauren M Brown, Andrew Lonsdale, Andrea Zhu, Nadia M Davidson, Breon Schmidt, Anthony Hawkins, Elise Wallach, Michelle Martin, Francoise M Mechinaud, Seong Lin Khaw, Ray C Bartolo, Louise EA Ludlow, Jackie Challis, Ian Brooks, Vida Petrovic, Nicola C Venn, Rosemary Sutton, Ian J Majewski, Alicia Oshlack, Paul G Ekert
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, and implementation of risk-adapted therapy has been in..
Targeted therapy and disease monitoring in CNTRL-FGFR1-driven leukaemia
Lauren M Brown, Ray C Bartolo, Nadia M Davidson, Breon Schmidt, Ian Brooks, Jackie Challis, Vida Petrovic, Dong-Anh Khuong-Quang, Francoise Mechinaud, Seong L Khaw, Ian J Majewski, Alicia Oshlack, Paul G Ekert
We report two patients with leukaemia driven by the rare CNTRL-FGFR1 fusion oncogene. This fusion arises from a t(8;9)(p12;q33) tr..
Clinker: visualizing fusion genes detected in RNA-seq data
Breon M Schmidt, Nadia M Davidson, Anthony DK Hawkins, Ray Bartolo, Ian J Majewski, Paul G Ekert, Alicia Oshlack
BACKGROUND: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for i..