Unlocking hidden cancer drivers using transcriptome data

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

2023-02-21

Toblerone: detecting exon deletion events in cancer using RNA-seq

Andrew Lonsdale, Andreas Halman, Lauren Brown, Hansen Kosasih, Paul Ekert, Alicia Oshlack

2023-01-01

Cancer is driven by mutations of the genome that can result in the activation of oncogenes or repression of tumour suppressor gene..

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

2022-07-16

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

2022-04-07

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

2022-01-06

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

2021-10-22

Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using exist..

Slinker: Visualising novel splicing events in RNA-Seq data.

Breon Schmidt, Marek Cmero, Paul Ekert, Nadia Davidson, Alicia Oshlack

2021-01-01

Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is due to RNA sequencing (RNA-Seq..

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

2020-12-01

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

2020-10-13

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

2020-03-10

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

2019-10-01

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..

Using equivalence class counts for fast and accurate testing of differential transcript usage

Marek Cmero, Nadia M Davidson, Alicia Oshlack

2019-04-29

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differen..

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

2018-07-04

BACKGROUND: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for i..