Breast Cancer PDTX Encyclopaedia

Molecular data from the collection of PDTX breast cancer models described in Bruna et al, 2016. Cell. It includes whole exome sequencing, shallow whole genome sequencing, expression arrays and reduced bisulfite representation sequencing (RRBS).

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

3 Datasets 3 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
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

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	255
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	21
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 None: 2024 None	0