INTERNATIONAL CANCER GENOME CONSORTIUM

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

Vanessa Lakis, Rita T Lawlor, Felicity Newell, Ann-Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T Koufariotis, Rebecca L Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michele Milella, David Chang, Peter Bailey, Nigel B Jamieson

2021-02-03

Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and ..

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Stephan B Dreyer, Rosie Upstill-Goddard, Viola Paulus-Hock, Clara Paris, Eirini-Maria Lampraki, Eloise Dray, Bryan Serrels, Giuseppina Caligiuri, Selma Rebus, Dennis Plenker, Zachary Galluzzo, Holly Brunton, Richard Cunningham, Mathias Tesson, Craig Nourse, Ulla-Maja Bailey, Marc Jones, Kim Moran-Jones, Derek W Wright, Fraser Duthie

2021-01-01

BACKGROUND & AIMS: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set ..

HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer

Holly Brunton, Giuseppina Caligiuri, Richard Cunningham, Rosie Upstill-Goddard, Ulla-Maja Bailey, Ian M Garner, Craig Nourse, Stephan Dreyer, Marc Jones, Kim Moran-Jones, Derek W Wright, Viola Paulus-Hock, Colin Nixon, Gemma Thomson, Nigel B Jamieson, Grant A McGregor, Lisa Evers, Colin J McKay, Aditi Gulati, Rachel Brough

2020-05-12

Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classic..

Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer

Dale W Garsed, Kathryn Alsop, Sian Fereday, Catherine Emmanuel, Catherine J Kennedy, Dariush Etemadmoghadam, Bo Gao, Val Gebski, Valerie Gares, Elizabeth L Christie, Maartje CA Wouters, Katy Milne, Joshy George, Ann-Marie Patch, Jason Li, Gisela Mir Arnau, Timothy Semple, Sreeja R Gadipally, Yoke-Eng Chiew, Joy Hendley

2018-02-01

Purpose: Women with epithelial ovarian cancer generally have a poor prognosis; however, a subset of patients has an unexpected dra..

EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas

Dariush Etemadmoghadam, Walid J Azar, Ying Lei, Tania Moujaber, Dale W Garsed, Catherine J Kennedy, Sian Fereday, Chris Mitchell, Yoke-Eng Chiew, Joy Hendley, Raghwa Sharma, Paul R Harnett, Jason Li, Elizabeth L Christie, Ann-Marie Patch, Joshy George, George Au-Yeung, Gisela Mir Arnau, Timothy P Holloway, Timothy Semple

2017-08-15

Low-grade serous ovarian carcinomas (LGSC) are associated with a poor response to chemotherapy and are molecularly characterized b..

Lost in translation: returning germline genetic results in genome-scale cancer research

Amber L Johns, Skye H Mckay, Jeremy L Humphris, Mark Pinese, Lorraine A Chantrill, R Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A High, Katia Nones, Ann-Marie Patch, Neil D Merrett, Nick Pavlakis, Karin S Kassahn, Jaswinder S Samra, David K Miller, David K Chang, Marina Pajic

2017-04-28

BACKGROUND: The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related..

Whole-genome landscape of pancreatic neuroendocrine tumours

Aldo Scarpa, David K Chang, Katia Nones, Vincenzo Corbo, Ann-Marie Patch, Peter Bailey, Rita T Lawlor, Amber L Johns, David K Miller, Andrea Mafficini, Borislav Rusev, Maria Scardoni, Davide Antonello, Stefano Barbi, Katarzyna O Sikora, Sara Cingarlini, Caterina Vicentini, Skye McKay, Michael CJ Quinn, Timothy JC Bruxner

2017-03-02

The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this inc..

Mitochondrial mutations and metabolic adaptation in pancreatic cancer

Rae-Anne Hardie, Ellen van Dam, Mark Cowley, Ting-Li Han, Seher Balaban, Marina Pajic, Mark Pinese, Mary Iconomou, Robert F Shearer, Jessie McKenna, David Miller, Nicola Waddell, John V Pearson, Sean M Grimmond, Leonid Sazanov, Andrew V Biankin, Silas Villas-Boas, Andrew J Hoy, Nigel Turner, Darren N Saunders

2017-01-30

BACKGROUND: Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted tre..

Hypermutation In Pancreatic Cancer

Jeremy L Humphris, Ann-Marie Patch, Katia Nones, Peter J Bailey, Amber L Johns, Skye Mckay, David K Chang, David K Miller, Marina Pajic, Karin S Kassahn, Michael CJ Quinn, Timothy JC Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Craig Nourse, Ehsan Nourbakhsh, Andrew Stone, Peter J Wilson

2017-01-01

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are ass..

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

Lutz Krause, Katia Nones, Kelly A Loffler, Derek Nancarrow, Harald Oey, Yue Hang Tang, Nicola J Wayte, Ann Marie Patch, Kalpana Patel, Sandra Brosda, Suzanne Manning, Guy Lampe, Andrew Clouston, Janine Thomas, Jens Stoye, Damian J Hussey, David I Watson, Reginald V Lord, Wayne A Phillips, David Gotley

2016-04-01

The incidence of esophageal adenocarcinoma (EAC) has risen significantly over recent decades. Although survival has improved, cure..

Genomic analyses identify molecular subtypes of pancreatic cancer

Peter Bailey, David K Chang, Katia Nones, Amber L Johns, Ann-Marie Patch, Marie-Claude Gingras, David K Miller, Angelika N Christ, Tim JC Bruxner, Michael C Quinn, Craig Nourse, L Charles Murtaugh, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Ehsan Nourbakhsh, Shivangi Wani, Lynn Fink, Oliver Holmes, Vencssa Chin

2016-03-03

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 1..

Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation

Marie-Claude Gingras, Kyle R Covington, David K Chang, Lawrence A Donehower, Anthony J Gill, Michael M Ittmann, Chad J Creighton, Amber L Johns, Eve Shinbrot, Ninad Dewal, William E Fisher, Christian Pilarsky, Robert Gruetzmann, Michael J Overman, Nigel B Jamieson, George Van Buren, Jennifer Drummond, Kimberly Walker, Oliver A Hampton, Liu Xi

2016-02-02

The ampulla of Vater is a complex cellular environment from which adenocarcinomas arise to form a group of histopathologically het..

Pancreatic cancer genomics: where can the science take us?

JS Graham, NB Jamieson, R Rulach, SM Grimmond, DK Chang, AV Biankin

2015-09-01

The incidence of pancreatic ductal adenocarcinoma (PDAC) is steadily increasing and the annual death-to-incidence ratio approaches..

Whole-genome characterization of chemoresistant ovarian cancer

Ann-Marie Patch, Elizabeth L Christie, Dariush Etemadmoghadam, Dale W Garsed, Joshy George, Sian Fereday, Katia Nones, Prue Cowin, Kathryn Alsop, Peter J Bailey, Karin S Kassahn, Felicity Newell, Michael CJ Quinn, Stephen Kazakoff, Kelly Quek, Charlotte Wilhelm-Benartzi, Ed Curry, Huei San Leong, Anne Hamilton, Linda Mileshkin

2015-05-28

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatm..

Precision Medicine for Advanced Pancreas Cancer: The Individualized Molecular Pancreatic Cancer Therapy (IMPaCT) Trial

Lorraine A Chantrill, Adnan M Nagrial, Clare Watson, Amber L Johns, Mona Martyn-Smith, Skye Simpson, Scott Mead, Marc D Jones, Jaswinder S Samra, Anthony J Gill, Nicole Watson, Venessa T Chin, Jeremy L Humphris, Angela Chou, Belinda Brown, Adrienne Morey, Marina Pajic, Sean M Grimmond, David K Chang, David Thomas

2015-05-01

PURPOSE: Personalized medicine strategies using genomic profiling are particularly pertinent for pancreas cancer. The Individualiz..

Whole genomes redefine the mutational landscape of pancreatic cancer

Nicola Waddell, Marina Pajic, Ann-Marie Patch, David K Chang, Karin S Kassahn, Peter Bailey, Amber L Johns, David Miller, Katia Nones, Kelly Quek, Michael CJ Quinn, Alan J Robertson, Muhammad ZH Fadlullah, Tim JC Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne Manning, Craig Nourse, Ehsan Nourbakhsh

2015-02-26

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing a..

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Katia Nones, Nicola Waddell, Nicci Wayte, Ann-Marie Patch, Peter Bailey, Felicity Newell, Oliver Holmes, J Lynn Fink, Michael CJ Quinn, Yue Hang Tang, Guy Lampe, Kelly Quek, Kelly A Loffler, Suzanne Manning, Senel Idrisoglu, David Miller, Qinying Xu, Nick Waddell, Peter J Wilson, Timothy JC Bruxner

2014-10-01

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins eff..

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

Katia Nones, Nic Waddell, Sarah Song, Ann-Marie Patch, David Miller, Amber Johns, Jianmin Wu, Karin S Kassahn, David Wood, Peter Bailey, Lynn Fink, Suzanne Manning, Angelika N Christ, Craig Nourse, Stephen Kazakoff, Darrin Taylor, Conrad Leonard, David K Chang, Marc D Jones, Michelle Thomas

2014-09-01

The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define t..

A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing

Kelly Quek, Katia Nones, Ann-Marie Patch, J Lynn Fink, Felicity Newell, Nicole Cloonan, David Miller, Muhammad ZH Fadlullah, Karin Kassahn, Angelika N Christ, Timothy JC Bruxner, Suzanne Manning, Ivon Harliwong, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Shivangi Wani, Anita Steptoe, Matthew Anderson, Oliver Holmes

2014-07-01

Somatic rearrangements, which are commonly found in human cancer genomes, contribute to the progression and maintenance of cancers..

Clinical and molecular characterization of HER2 amplified-pancreatic cancer

Angela Chou, Nicola Waddell, Mark J Cowley, Anthony J Gill, David K Chang, Ann-Marie Patch, Katia Nones, Jianmin Wu, Mark Pinese, Amber L Johns, David K Miller, Karin S Kassahn, Adnan M Nagrial, Harpreet Wasan, David Goldstein, Christopher W Toon, Venessa Chin, Lorraine Chantrill, Jeremy Humphris, R Scott Mead

2013-08-31

BACKGROUND: Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Repurposing of therapeutics that tar..

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Andrew V Biankin, Nicola Waddell, Karin S Kassahn, Marie-Claude Gingras, Lakshmi B Muthuswamy, Amber L Johns, David K Miller, Peter J Wilson, Ann-Marie Patch, Jianmin Wu, David K Chang, Mark J Cowley, Brooke B Gardiner, Sarah Song, Ivon Harliwong, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Shivangi Wani

2012-11-15

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analys..

qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles

Sarah Song, Katia Nones, David Miller, Ivon Harliwong, Karin S Kassahn, Mark Pinese, Marina Pajic, Anthony J Gill, Amber L Johns, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, Felicity Newell, Mark J Cowley, Jianmin Wu, Peter Wilson, Lynn Fink

2012-09-25

Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection,..

PINA v2.0: mining interactome modules

Mark J Cowley, Mark Pinese, Karin S Kassahn, Nic Waddell, John V Pearson, Sean M Grimmond, Andrew V Biankin, Sampsa Hautaniemi, Jianmin Wu

2012-01-01

The Protein Interaction Network Analysis (PINA) platform is a comprehensive web resource, which includes a database of unified pro..

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Rathi D Thiagarajan, Nicole Cloonan, Brooke B Gardiner, Tim R Mercer, Gabriel Kolle, Ehsan Nourbakhsh, Shivangi Wani, Dave Tang, Keerthana Krishnan, Kylie M Georgas, Bree A Rumballe, Han S Chiu, Jason A Steen, John S Mattick, Melissa H Little, Sean M Grimmond

2011-09-05

BACKGROUND: The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Det..

X-MATE: a flexible system for mapping short read data

David LA Wood, Qinying Xu, John V Pearson, Nicole Cloonan, Sean M Grimmond

2011-02-15

SUMMARY: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological..

The uniqueome: a mappability resource for short-tag sequencing

Ryan Koehler, Hadar Issac, Nicole Cloonan, Sean M Grimmond

2011-01-15

SUMMARY: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of ..