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Australian Prostate Cancer Group

Principal Investigators: Chris Hovens

Canadian Prostate Cancer Genome Network (CPC-GENE)

The Canadian Prostate Cancer Genome Network (CPC-GENE) is an clinically-driven initiative to identify novel prognostic and predictive molecular biomarkers of clinical outcome for men with intermediate-risk prostate cancer. CPC-GENE is composed of two clinical cohorts: ~300 men who were treated with radical prostatectomy and, uniquely, ~150 men treatment with modern-era, dose-escalated image-guided radiotherapy. All men had at least 5 years of clinical follow-up at the time of enrolment (current median > 9.5 years). Fresh-frozen tumour tissue specimens were obtained for each patient, including a unique set of fresh-frozen tumour biopsies obtained prior to initiation of radiotherapy. Each participant also provided a whole-blood specimen at time of enrolment, for analysis of germline molecular features. ...more...

Tumour and blood-derived genomic DNA was analysed by whole-genome sequencing (60X and 40X target coverage, respectively) to identify single-nucleotide variants (SNVs) and structural variants (SVs), supplemented with array-based profiling of genome-wide DNA copy number aberrations (CNAs) and aberrant DNA methylation. In addition, the tumour transcriptome was profiled using deep RNA-seq (300 million read-pairs) and/or cDNA microarray. Finally, the core CPC-GENE dataset and tissue repository has been leveraged for additional studies of the tumour proteome and epigenome.

CPC-GENE has also profiled intra-prostatic heterogeneity, using multiple tumour foci taken from a subset of men in the main study.

The major findings of CPC-GENE, to date, are

  • Saturating discovery of recurrent coding SNVs (i.e. >1%) in localized prostate cancer
  • Identification of recurrent non-coding SNVs
  • Development and validation of a novel CNA-based prognostic signature of adverse clinical outcome
  • Identification of a multi-parametric clinico-molecular signature of rapid biochemical recurrence
  • Characterization of the comparative genomics of sporadic localized prostate cancer to familial prostate cancer in men who carry a deleterious germline BRCA2 mutation
  • Assessment and identification of prognostic variants within the tumour mitochondrial genome
  • Identification of MYCL1 as a candidate oncogene in prostate cancer
  • Characterization of a novel mechanism of tumour suppressor silencing involving inversion of the PTEN locus
  • Development of novel bioinformatics tools to assess localized hypermutation (ShatterProof) and robustness of whole-genome sequencing data (SeqControl)
The findings from CPC-GENE will be used to drive novel clinical trials for treatment escalation and/or de-escalation, to allow for the best possible treatment for men with localized, non-indolent prostate cancer.

Principal Investigators: Dr. Paul Boutros and Dr. Rob Bristow

Co-Investigators: Dr. Michael Fraser, Dr. Theo van der Kwast, and Dr. Colin Collins

Chinese Prostate Cancer Group

Principal Investigator: Yinghao Sun

CRUK-ICGC Prostate Cancer Group

This Cancer Research UK funded Prostate Cancer Group consists of a multidisciplinary team of histopathologists, urologists, molecular biologists, geneticists and experts in genome technology and bioinformatics. We have collected and analyzed 30-50 fold coverage whole genome paired-end sequence data from 250 prostate cancers representing the following groups: (i) cancers from men at different risks of progression; (ii) metastatic castration resistant disease; (iii) apparently separate and genetically distinct (multi-focal) cancers arising in a single prostate; (iii) cancer from arising in men from different ethnic groups. ...more...

In parallel it is our intention to collect transcriptomic and epigenetic data on cancers entered into this study. Analyses of the combined datasets will inform on our understanding of the molecular basis of the genetic and clinical heterogeneity of prostate cancer and will provide insights into the reasons for variation in incidence in different ethnic groups. The results may suggest etiological causes for cancer development, and help to personalized treatment for men who develop prostate cancer.

Joint Lead of Project: Colin S. Cooper and Ros A. Eeles

Principal Investigators: G. Steven Bova, Daniel S. Brewer, Christopher S. Foster, Andy G. Lynch, David Neal, David C. Wedge

Danish Prostate Cancer Group

Closely aligned with the German ICGC Prostate Cancer Group.

Principal Investigators: Joachim Weischenfeldt

Danish Aarhus University Hospital Prostate Cancer Group

Principal Investigators: Karina Sorensen

Finnish Prostate Cancer Group

Closely aligned with the CRUK-ICGC Prostate Cancer Group. Our collaborative work is focused on uncovering features of lethal prostate cancer useful for improving patient care, through deep integrated clinical-molecular study of PELICAN metastatic prostate cancer rapid autopsy study cases in collaboration Tapio Visakorpi from the University of Tampere, and William B. Isaacs from Johns Hopkins University.

Principal Investigators: G. Steven Bova

French ICGC Prostate Cancer Group

Every year about 70,000 new cases of prostate cancer are diagnosed in France and 8,700 men died from this disease. But the incidence and the rate of mortality per 100,000 men in the French West Indies are respectively 1.5x and 2x upper than the rates observed in the metropolitan France. The aim of this project is to identify, on French Caucasian and African-Caribbean men, relevant genomic events involved in prostate carcinogenesis. The project aims to identify, through an integrative approach, genomic factors which characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer. The project hypothesizes that molecular events leading to aggressive (clinical progression to extraprostatic disease and hormone refractory disease) are present at the earliest stages of the disease and are modulated by microenvironment and genetic background. ...more...

We propose a multiple stages study design involving firstly the generation of a primary set of genome-wide genomic data (whole genome sequencing, whole exome sequencing, RNA and miRNA sequencing) on 25 tumors of aggressive (high grade) prostate cancer samples (from 15 French Caucasian and 10 African-Caribbean men who were treated by radical prostatectomy). Among the 25 prostate cancer samples, ten will be also selected for methylation analyses. The discovery data will be analysed to catalogue differences that are observed between tumour and referent DNA. We will identify target regions (e.g. somatic mutations, structural variants, and/or singular expression patterns clustering in particular genes, genomic regions or functional pathways) for next stages of the study. Secondly, we plan to validate the clinical relevance of target regions identified on different (5) and large independent sets (500) of prostate cancers specimens according the following phenotypes stratification: (i) Caucasian versus African-Caribbean; (ii) Low grade versus high grade. (iii) Early onset versus late onset; (iv) Free survival disease versus recurrent disease; (v) Metastatic versus non metastatic disease.

Principal Investigator: Olivier Cussenot

Garvan Human Comparative & Prostate Cancer Genomics (Garvan-HCPCG)

The Garvan Institute of Medical Research in Sydney, Australia, houses the Human Comparative & Prostate Cancer Genomics (HcPcG) Laboratory in partnership with the University of Sydney. Funded by the Petre Foundation of Australia, the team is focused on unraveling the genomic-basis of health disparity associated with prostate cancer risk, mortality, tumour progression and ultimately treatment. In particular significant aggressive disease presentation and outcomes associated with African ancestry. ...more...

Generating the first Southern African complete human genomes in 2010, the team heads the genomic research for the Southern African Prostate Cancer Study (SAPCS), with clinical directorship headed out of the University of Pretoria in South Africa. A resource of well over 3,000 patients, the team has generated the first ethnic-based comparative genomic study for high-risk prostate cancer, including tumour-blood deep whole genome sequencing data for six African South Africans versus nine European-Australians. Identifying a uniquely African genomic profile, the team is now funded to expand this pilot study include 200 tumour-normal pairs and as such initiating the PAN Prostate Cancer Group AFRICA project (PanPCG-AFRICA). Built on a the success of SAPCS, a flagship project for Africa, i-DZOMO, was launched with funding from the Cancer Association of South Africa (CANSA) and National Research Foundation (NRF) in April 2018. The objective of i-DZOMO is to ‘provide a voice’ for prostate cancer in Africa and includes besides South Africa, contributions from Kenya, Namibia and Rwanda. Besides whole genome sequencing, the team has also provided the first whole genome optical mapping to compliment genome sequencing data for prostate cancer via funding granted as part of a Movember Revolutionary Team Award granted together with Prostate Cancer Foundation Australia to the Garvan Institute of Medical Research (ProMis Program).

garvan

Principal Investigator: Vanessa M. Hayes

Germany ICGC Prostate Cancer Group - Early Onset

Prostate cancer is the most frequent malignant tumor in males and the second most frequent cause of cancer-related death. Currently, in Germany, more than 60,000 prostate cancers are diagnosed every year. Although most of these patients are treated in a curative attempt, more than 10,000 German men die from prostate cancer annually. Owing to the demographic changes of our society, a further doubling of prostate cancer incidences during the next 20 years is expected. Prostate cancer is generally considered a tumor of elderly men. However, a fraction of prostate cancers are diagnosed at the age of 55 years or less. For several reasons, these “early onset prostate cancers” may represent a key entity for the understanding of prostate cancer biology. ...more...

First, it is likely that early onset prostate cancers represent a distinct molecular subgroup of prostate cancer (PCa), potentially characterized by relatively small numbers of genetic changes, some of which may be particularly strong driver mutations for PCa development. Second, a fraction of prostate cancers in young individuals could represent classical prostate cancers that are detected at a very early stage and might therefore have accumulated molecular changes/mutations occurring that are most instrumental for prostate cancer early detection. Third, PCa with hereditary backgrounds are likely to accumulate in the age group below 55 years. A comparison with other sample sets (e.g. from other ICGC consortia), a systematic genomic analysis of young men with PCa could therefore lead to the detection of mechanisms for hereditary PCa. Fourth, a better understanding of these tumors is particularly relevant as finding optimal treatment regimens is most critical in young cancer patients.

We are analyzing the entire genomic DNA sequences of at least 200 PCas (and matched non-tumorous DNA) of young men (≤ 55y), to at least 30 fold coverage, and integrate single-nucleotide variants and genomic structural variations with differential methylation, mRNA and miRNA expression data.

Tissues were collected at the University Medical Center Hamburg-Eppendorf. Sequencing was performed at DKFZ and NCT (Heidelberg), EMBL (Heidelberg), and MPIMG (Berlin). Data management and bioinformatic data analyses is being conducted at DKFZ.

Head of Consortium: Christoph Plass and Guido Sauter

Principal Investigators: Thorsten Schlomm, Jan Korbel, Benedikt Brors, Marie-Laure Yaspo, Holger Sültmann, Joachim Weischenfeldt

TCGA Prostate Cancer Group

Chris Sander and Massimo Loda co-lead the prostate cancer effort for TCGA, in which molecular analysis of 333 primary prostate carcinomas revealed substantial heterogeneity and major subtypes among patients, as well as potentially actionable lesions valuable for clinical management of the disease (Schultz et al, Cell, 2015). ...more...

The National Cancer Institute and the National Human Genome Research Institute launched The Cancer Genome Atlas program to create a comprehensive atlas of the genomic changes involved in more than 20 common types of cancer. This large-scale, high-throughput effort is being carried out by a network of more than 100 researchers at many organizations across the United States. The overarching goal of TCGA is to further scientific understanding of the genomic changes in cancer, thereby improving the ability to diagnose, treat and prevent this devastating disease. All data generated by the TCGA research network are made rapidly available to the research community through the TCGA Data Portal.

Massimo Loda's group focusses on the following research areas:

  • The role of de novo lipogenesis in the initiation and maintenance of prostate cancer.
  • The role of the microenvironment in tumor progression in prostate cancer.
  • Metabolic profiling in serum and archival tissues as a predictor of clinical behavior and oncogenic drivers.

Principal Investigators: Chris Sander and Massimo Loda

world

Infrastructure providers

DKFZ ITCF Cloud

The German Cancer Research Center (DKFZ) hosts the sequencing data contributed to the PPCG project by Germany. Primary data processing of the German prostate cancer cohort is performed by the division of Applied Bioinformatics at the DKFZ. The research center's IT core facility provides the compute infrastructure to run bioinformatics workflows and to store the results. The compute cluster comprises 504 CPU cores, 9.3 TB of RAM, and up to 10 PB of storage. It builds on OpenStack, an open-source cloud management platform.

URL: https://www.dkfz.de/en/itcf/index.html

Embassy Cloud

Ever-larger scientific datasets may be a goldmine for discovery, but analysing them has become a bottleneck in life-science research. Organisations of all sizes face the challenge of providing infrastructure for managing Big Data, even when the demand for it is comparatively modest.

Embassy Cloud users (tenants) have direct access to the EMBL-EBI data, services and compute. This is a practical and cost-effective alternative to replicating services and downloading vast, public datasets locally. Tenants can access their workspace from anywhere in the world, reducing the need for capital investments in hardware and related operational costs.

Contact: Dr Steven Newhouse

URL:http://www.embassycloud.org/

European Genome-phenome Archive

The European Genome-phenome Archive (EGA) is a service for the permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data which are consented for research use. The EGA provides the necessary security required to control access and maintain participant confidentiality, while providing access to those researchers and clinicians authorised to view the data. In 2017 EGA released 1.7 PB of data, resulting in a total of over 5 PB available for authorised users, and distributed over 4.5 PB of data to users. With its background in securely managing large volumes of human genetic and phenotypic data, the EGA is working with the Pan Prostate Cancer Group to provide data co-ordination, archival, and data distribution services.

Principle Investigator: Thomas Keane

Data Co-ordinator: Giselle Kerry

URL: https://ega-archive.org/

Gilles Thomas bioinformatics facility

The French ICGC prostate group contributed to the PanProstate project by analysing the 25 French samples with the PanProstate standardised pipelines (alignment, variant calling). The sequenced samples were processed in Lyon, on the "Gilles Thomas" bioinformatics facility. This platform was founded in 2009 by Prof. Gilles Thomas in order to provide bioinformatics support to French and international cancer research projects, focusing on both basic and clinical research. This mission is carried out through several international research programmes, in particular the International Cancer Genome Consortium and the French Prostate project, under the supervision of Institut National du Cancer and INSERM.

Contact: contact-pgt@lyon.unicancer.fr

URL: http://www.synergielyoncancer.com/our-projects/bioinformatics-center

Melbourne Bioinformatics

Melbourne Bioinformatics provides computational resources and analytics expertise for the Australian component of the Pan Prostate project, working in close collaboration with Prof Chris Hovens.

Contact: Dr Bernie Pope

URL: https://www.melbournebioinformatics.org.au/project/ppgc/

Cancer Genome Collaboratory

URL: https://www.cancercollaboratory.org

Wellcome Trust Sanger Institute

Contact: Adam Butler