Canadian Prostate Cancer Genome Network - EGA European Genome-Phenome Archive

Study

Canadian Prostate Cancer Genome Network

Study ID	Alternative Stable ID	Type
EGAS00001000900		Other

Study Description

Over 5 years, CPC-GENE will sequence the genomes of 350 intermediate risk prostate cancers to identify genetic signatures that differ in cancers that responded well to treatment compared with those that did not. CPC-GENE will also sequence multiple regions of prostate cancer from the same gland to determine if and how the genetic make-up of prostate cancer varies within an individual man’s prostate

Study Datasets 32 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001001094	200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672 200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672	Illumina HiSeq 2500	247
EGAD00001001115	SeqControl SeqControl	Illumina HiSeq 2500	54
EGAD00001003139	200PG : WGS Aligned Sequence (fastq) : Aligned WG sequence data (bam) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672 200PG : WGS Aligned Sequence (fastq) : Aligned WG sequence data (bam) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672		262
EGAD00001003706	PRAD-CA, DCC Release 26 : This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs PRAD-CA, DCC Release 26 : This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs	Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified	616
EGAD00001003756	Prostate Cancer - RNA-Seq unmapped reads Prostate Cancer - RNA-Seq unmapped reads	Illumina HiSeq 2000	98
EGAD00001003761	This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs	Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified	617
EGAD00001003909	Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls	HiSeq X Ten,Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified	610
EGAD00001003957	Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls	Illumina HiSeq 2000,Illumina HiSeq 2500,unspecified	23
EGAD00001003975	Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls Raw lane level fastq files from Whole genome sequencing in support of ICGC PRAD-CA Variant calls	HiSeq X Ten,Illumina HiSeq 2500,unspecified	128
EGAD00001004061	200PT : WG Aligned Sequence (bam)/ Aligned WG sequence data in this dataset are from CPCGene Tumour/Normal Pairs used in the 200PT Study 200PT : WG Aligned Sequence (bam)/ Aligned WG sequence data in this dataset are from CPCGene Tumour/Normal Pairs used in the 200PT Study		404
EGAD00001004072	200PT : SNV vcf files. SNV calls generated using SomaticSniper and PhyloWGS, from the CPCGene 200PT Subclonality study 200PT : SNV vcf files. SNV calls generated using SomaticSniper and PhyloWGS, from the CPCGene 200PT Subclonality study		293
EGAD00001004073	200PT : CNA vcf files. Copy Number Abberation calls generated using TITAN and PhyloWGS, from the CPCGene 200PT Subclonality study 200PT : CNA vcf files. Copy Number Abberation calls generated using TITAN and PhyloWGS, from the CPCGene 200PT Subclonality study		292
EGAD00001004400	SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study		538
EGAD00001004401	SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study		562
EGAD00001004402	SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study		580
EGAD00001004403	CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study		538
EGAD00001004404	CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study		562
EGAD00001004405	CNA calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study CNA calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study		580
EGAD00001004424	Prostate Cancer - RNA-Seq unmapped reads Prostate Cancer - RNA-Seq unmapped reads	Illumina HiSeq 2000	148
EGAD00001004431	SNV calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions SNV calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004432	SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions SNV calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004433	SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004434	SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions SNV calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004440	CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004441	CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions CNA calls generated using the SomaticSniper-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004442	CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions CNA calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004443	CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions CNA calls generated using the MuTect-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions		40
EGAD00001004875	Aligned RNA-seq sequences in this dataset are from the Proteogenomic Landscape of Curable Prostate Cancer study Aligned RNA-seq sequences in this dataset are from the Proteogenomic Landscape of Curable Prostate Cancer study		56
EGAD00010001218	Raw Array data from the CPCGene 200PG study Raw Array data from the CPCGene 200PG study	Affymetrix OncoScan FFPE Express	502
EGAD00010001414	Raw Array data from the PRAD-CA for ICGC DCC Release26 Raw Array data from the PRAD-CA for ICGC DCC Release26	Affymetrix OncoScan FFPE Express	N/A
EGAD00010001519	Raw Array data from the PRAD-CA for ICGC DCC Release27 Raw Array data from the PRAD-CA for ICGC DCC Release27	Affymetrix OncoScan FFPE Express	110
EGAD00010001703	RNAseq reads were aligned with STAR 2.5.3a and gene expression was quantified with RSEM 1.3.0 RNAseq reads were aligned with STAR 2.5.3a and gene expression was quantified with RSEM 1.3.0		144

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