Canadian Prostate Cancer Genome Network

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

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

32 Datasets 17 Publications

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	Illumina HiSeq 2500	247
EGAD00001001115	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		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	Illumina HiSeq 2000 Illumina HiSeq 2500 unspecified	616
EGAD00001003756	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	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	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	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	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		404
EGAD00001004072	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		292
EGAD00001004400	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		562
EGAD00001004402	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		538
EGAD00001004404	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		580
EGAD00001004424	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		40
EGAD00001004432	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		40
EGAD00001004434	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		40
EGAD00001004441	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		40
EGAD00001004443	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		56
EGAD00010001218	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	Affymetrix OncoScan FFPE Express	-
EGAD00010001519	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		144

Publications	Citations
Genomic hallmarks of localized, non-indolent prostate cancer. Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, Huang V, Shiah YJ, Yousif F, Lin X, Masella AP, Fox NS, Xie M, Prokopec SD, Berlin A, Lalonde E, Ahmed M, Trudel D, Luo X, Beck TA, Meng A, Zhang J, D'Costa A, Denroche RE, Kong H, Espiritu SM, Chua ML, Wong A, Chong T, Sam M, Johns J, Timms L, Buchner NB, Orain M, Picard V, Hovington H, Murison A, Kron K, Harding NJ, P'ng C, Houlahan KE, Chu KC, Lo B, Nguyen F, Li CH, Sun RX, de Borja R, Cooper CI, Hopkins JF, Govind SK, Fung C, Waggott D, Green J, Haider S, Chan-Seng-Yue MA, Jung E, Wang Z, Bergeron A, Dal Pra A, Lacombe L, Collins CC, Sahinalp C, Lupien M, Fleshner NE, He HH, Fradet Y, Tetu B, van der Kwast T, McPherson JD, Bristow RG, Boutros PC. Nature 541: 2017 359-364	335
Molecular Hallmarks of Multiparametric Magnetic Resonance Imaging Visibility in Prostate Cancer. Houlahan KE, Salmasi A, Sadun TY, Pooli A, Felker ER, Livingstone J, Huang V, Raman SS, Ahuja P, Sisk AE, Boutros PC, Reiter RE. Eur Urol 76: 2019 18-23	36
The Proteogenomic Landscape of Curable Prostate Cancer. Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC. Cancer Cell 35: 2019 414-427.e6	117
Genome-wide germline correlates of the epigenetic landscape of prostate cancer. Houlahan KE, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shetty A, Ramanand SG, Yao CQ, Bell C, O'Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu SMG, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Têtu B, McPherson JD, Pasaniuc B, Kislinger T, Chua MLK, Pomerantz MM, van der Kwast T, Freedman ML, Mani RS, He HH, Bristow RG, Boutros PC. Nat Med 25: 2019 1615-1626	39
Quantifying the influence of mutation detection on tumour subclonal reconstruction. Liu LY, Bhandari V, Salcedo A, Espiritu SMG, Morris QD, Kislinger T, Boutros PC. Nat Commun 11: 2020 6247	12
CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer. Ahmed M, Soares F, Xia JH, Yang Y, Li J, Guo H, Su P, Tian Y, Lee HJ, Wang M, Akhtar N, Houlahan KE, Bosch A, Zhou S, Mazrooei P, Hua JT, Chen S, Petricca J, Zeng Y, Davies A, Fraser M, Quigley DA, Feng FY, Boutros PC, Lupien M, Zoubeidi A, Wang L, Walsh MJ, Wang T, Ren S, Wei GH, He HH. Nat Commun 12: 2021 1781	27
Reference-free transcriptome signatures for prostate cancer prognosis. Nguyen HTN, Xue H, Firlej V, Ponty Y, Gallopin M, Gautheret D. BMC Cancer 21: 2021 394	8
Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer. Lim Y, Arora S, Schuster SL, Corey L, Fitzgibbon M, Wladyka CL, Wu X, Coleman IM, Delrow JJ, Corey E, True LD, Nelson PS, Ha G, Hsieh AC. Nat Commun 12: 2021 4217	29
Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse. Fraser M, Livingstone J, Wrana JL, Finelli A, He HH, van der Kwast T, Zlotta AR, Bristow RG, Boutros PC. Nat Commun 12: 2021 6248	12
The telomere length landscape of prostate cancer. Livingstone J, Shiah YJ, Yamaguchi TN, Heisler LE, Huang V, Lesurf R, Gebo T, Carlin B, Eng S, Drysdale E, Green J, van der Kwast T, Bristow RG, Fraser M, Boutros PC. Nat Commun 12: 2021 6893	9
Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Zhang Y, Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Nat Commun 13: 2022 2669	83
Starfish infers signatures of complex genomic rearrangements across human cancers. Bao L, Zhong X, Yang Y, Yang L. Nat Cancer 3: 2022 1247-1259	19
The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors. Chen S, Petricca J, Ye W, Guan J, Zeng Y, Cheng N, Gong L, Shen SY, Hua JT, Crumbaker M, Fraser M, Liu S, Bratman SV, van der Kwast T, Pugh T, Joshua AM, De Carvalho DD, Chi KN, Awadalla P, Ji G, Feng F, Wyatt AW, He HH. Nat Commun 13: 2022 6467	22
A polygenic two-hit hypothesis for prostate cancer. Houlahan KE, Livingstone J, Fox NS, Kurganovs N, Zhu H, Sietsma Penington J, Jung CH, Yamaguchi TN, Heisler LE, Jovelin R, Costello AJ, Pope BJ, Kishan AU, Corcoran NM, Bristow RG, Waszak SM, Weischenfeldt J, He HH, Hung RJ, Hovens CM, Boutros PC. J Natl Cancer Inst 115: 2023 468-472	2
The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer. Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY, Small EJ, Quigley DA. Cancer Res 83: 2023 2763-2774	16
Global impact of somatic structural variation on the cancer proteome. Chen F, Zhang Y, Chandrashekar DS, Varambally S, Creighton CJ. Nat Commun 14: 2023 5637	12
Upgrading of Grade Group 1 Prostate Cancer at Prostatectomy: Germline Risk Factors in a Prospective Cohort. Liss MA, Zeltser N, Zheng Y, Lopez C, Liu M, Patel Y, Yamaguchi TN, Eng SE, Tian M, Semmes OJ, Lin DW, Brooks JD, Wei JT, Klein EA, Tewari AK, Mosquera JM, Khani F, Robinson BD, Aasad M, Troyer DA, Kagan J, Sanda MG, Thompson IM, Boutros PC, Leach RJ. Cancer Epidemiol Biomarkers Prev 33: 2024 1500-1511	0