Breast Cancer PDTX Encyclopaedia - EGA European Genome-Phenome Archive

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
EGAD00001002685	Breast cancer PDTX sequencing data from Bruna et al, Cell 2016 - Exome Sequencing - Shallow Whole Genome Sequencing - RRBS Methylation Sequencing	Illumina HiSeq 2500	393
EGAD00001006307	RNA-SEQ for the Caldas Lab breast cancer PDTX collection. This includes both single and paired end runs	Illumina HiSeq 4000	117
EGAD00010001032	RNA Expression using Illumina HT12 v3	Illlumina HT12 v3	153
EGAD50000001334	This dataset contains single cell RNA sequencing (192 fastq files for 59 samples), whole exome sequencing (20 BAM files -hg38- for 20 samples) and bulk RNA sequencing (138 paired-end fastq files and 17 single-end fastq files for 8 samples)	Illumina HiSeq 2500 Illumina NovaSeq 6000	87

Publications	Citations
A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds. Bruna A, Rueda OM, Greenwood W, Batra AS, Callari M, Batra RN, Pogrebniak K, Sandoval J, Cassidy JW, Tufegdzic-Vidakovic A, Sammut SJ, Jones L, Provenzano E, Baird R, Eirew P, Hadfield J, Eldridge M, McLaren-Douglas A, Barthorpe A, Lightfoot H, O'Connor MJ, Gray J, Cortes J, Baselga J, Marangoni E, Welm AL, Aparicio S, Serra V, Garnett MJ, Caldas C. Cell 167: 2016 260-274.e22	343
Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response. Georgopoulou D, Callari M, Rueda OM, Shea A, Martin A, Giovannetti A, Qosaj F, Dariush A, Chin SF, Carnevalli LS, Provenzano E, Greenwood W, Lerda G, Esmaeilishirazifard E, O'Reilly M, Serra V, Bressan D, IMAXT Consortium, Mills GB, Ali HR, Cosulich SS, Hannon GJ, Bruna A, Caldas C. Nat Commun 12: 2021 1998	38
FOXC2 promotes vasculogenic mimicry and resistance to anti-angiogenic therapy. Cannell IG, Sawicka K, Pearsall I, Wild SA, Deighton L, Pearsall SM, Lerda G, Joud F, Khan S, Bruna A, Simpson KL, Mulvey CM, Nugent F, Qosaj F, Bressan D, CRUK IMAXT Grand Challenge Team, Dive C, Caldas C, Hannon GJ. Cell Rep 42: 2023 112791	28
Modeling Drug Responses and Evolutionary Dynamics using Patient-Derived Xenografts Reveals Precision Medicine Strategies for Triple Negative Breast Cancer. Shea A, Eyal-Lubling Y, Guerrero-Romero D, Manzano Garcia R, Greenwood W, O'Reilly M, Georgopoulou D, Callari M, Lerda G, Wix S, Giovannetti A, Masina R, Esmaeilishirazifard E, Cope W, Martin AG, Nagano A, Young L, Kupczak S, Cheng Y, Bardwell H, Provenzano E, Kane J, Lay J, Grybowicz L, McAdam K, Caldas C, Abraham J, Rueda OM, Bruna A. Cancer Res 85: 2025 567-584	1