{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001002685"],"sample_count":["393"],"description":["EGA dataset EGAD00001002685"],"repository":["EGA"],"title":["Breast cancer PDTX sequencing data from Bruna et al, Cell 2016"],"pubmed_abstract":["The inter- and intra-tumor heterogeneity of breast cancer needs to be adequately captured in pre-clinical models. We have created a large collection of breast cancer patient-derived tumor xenografts (PDTXs), in which the morphological and molecular characteristics of the originating tumor are preserved through passaging in the mouse. An integrated platform combining in vivo maintenance of these PDTXs along with short-term cultures of PDTX-derived tumor cells (PDTCs) was optimized. Remarkably, the intra-tumor genomic clonal architecture present in the originating breast cancers was mostly preserved upon serial passaging in xenografts and in short-term cultured PDTCs. We assessed drug responses in PDTCs on a high-throughput platform and validated several ex vivo responses in vivo. The biobank represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies (http://caldaslab.cruk.cam.ac.uk/bcape), including identification of biomarkers of response or resistance."],"pubmed_title":["A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds."],"pubmed_authors":["Bruna Alejandra A, Rueda Oscar M OM, Greenwood Wendy W, Batra Ankita Sati AS, Callari Maurizio M, Batra Rajbir Nath RN, Pogrebniak Katherine K, Sandoval Jose J, Cassidy John W JW, Tufegdzic-Vidakovic Ana A, Sammut Stephen-John SJ, Jones Linda L, Provenzano Elena E, Baird Richard R, Eirew Peter P, Hadfield James J, Eldridge Matthew M, McLaren-Douglas Anne A, Barthorpe Andrew A, Lightfoot Howard H, O'Connor Mark J MJ, Gray Joe J, Cortes Javier J, Baselga Jose J, Marangoni Elisabetta E, Welm Alana L AL, Aparicio Samuel S, Serra Violeta V, Garnett Mathew J MJ, Caldas Carlos C"],"pubmed_title_synonyms":["Breast Carcinoma, Human Mammary Neoplasm, primary breast cancer, Carcinoma, malignant tumor of the breast, Breast Carcinomas, \"breast neoplasm\" EXACT [MTH:120], Malignant Neoplasm, heterogeneity., Neoplasms, Benign Neoplasm, mammary neoplasm, Mammary Cancers, Human Mammary Neoplasms, Tumor, \"breast tumor\" EXACT [NCI2004_11_17:C2910], Malignant, Human, Breast Malignant Neoplasm, Breast Malignant Tumor, Benign, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], Mammary Carcinomas, Breast Tumor, Neoplasm, Human Mammary Carcinoma, \"mammary tumor\" EXACT [CSP2005:2016-0671], NOS, breast tumor, cancer of the breast, Malignant Neoplasm of Breast, Carcinomas, BC, Mammary Neoplasms, malignant neoplasm of breast, Human Mammary, Breast Neoplasm, Malignancy, Mammary Neoplasm, Mammary Carcinoma, Human Mammary Carcinomas, Benign Neoplasms, Cancers, \"mammary neoplasm\" RELATED [], Cancer of the Breast, Malignant Neoplasms, Neoplasias, breast cancer, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, Breast Tumors, Breast Cancer, Breast Malignant Tumors, Cancer of Breast, Malignancies, Breast, mammary cancer, other neoplasm, cancer, mammary tumor, Breast Malignant Neoplasms, Neoplasia, breast, Tumors, Cancer"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_abstract_synonyms":["l(4)16, malignant tumor of the breast, camKII, Biological Markers, Viral Marker, Breasts, Surrogate Endpoints, PhrB photolyase activity, Product, CALML2, Laboratory, acetylglucosaminyltransferase-like protein, Heterograft, DD132, Mus domesticus, Mbp1, calm1, Biochemical, mammary neoplasm, Lactiferous gland, Endpoint, Human Mammary Neoplasms, TRANSPL HETEROL, Tumor, Serum, pigmented epithelium, House Mouse, glandula mammaria, Laboratory Markers, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], Biological, responsivity, Pharmaceutical Product, 3, Cal49A, cancer of the breast, NUP96, l(4)ar, myd, epithelium, BC, DmelCG18069, Mammary Neoplasms, malignant neoplasm of breast, CDPK1, like-acetylglucosaminyltransferase, AI327027, Human Mammary Carcinomas, pigmented retina, Mbp-1, Swiss Mice, l(4)102EFb, DNA cyclobutane dipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, Calm, CAMI, Immune, Xenotransplantations, Markers, cancer of breast, medicine, Pharmaceutical, CAMC, Viral Markers, CaM kinase, C2orf34, Malignancies, house mouse, mammary cancer, Breast Malignant Neoplasms, CPVT4, Cam1, Tumors, mamma, DmCalm, PRE, Carcinoma, dCaM, Viral, \"breast neoplasm\" EXACT [MTH:120], Surrogate Endpoint, gyltl1b-b, CaM KII, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, CAMKII, mouse, Biochemical Markers, Biologic Marker, CaM II, shortened, Benign, retinal pigment, Marker, MDDGA6, mKIAA0609, Lobe of mammary gland, dipyrimidine photolyase (photosensitive), NOS, Pharmaceutic, KIAA0609, Malignant Neoplasm of Breast, retinal pigment layer, Heterologous Transplantations, acetylglucosaminyltransferase-like 1A, CLNMT, Carcinomas, fg, Xenograft, Mus musculus, CAMKIId, Xenotransplantation, resistance., gyltl1b, End Points, Transplantation, mice, mdc1d, Swiss Mouse, Benign Neoplasms, Xenografts, Immunologic, \"mammary neoplasm\" RELATED [], Laboratory Marker, LARGE_HUMAN, Malignant Neoplasms, domesticus, MDC1D, phr A photolyase activity, DNA-photoreactivating enzyme, enr, breast cancer, Patient, Biochemical Marker, Breast Tumors, Breast Malignant Tumors, Mouse, 3909, other neoplasm, short, cancer, mammary region, primary breast cancer, CaMK II, Clinical Markers, Clinical Marker, Neoplasms, Benign Neoplasm, Mammary Cancers, CAMIII, photoreactivating enzyme activity, Transplantations, Malignant, LARGE1, froggy, Gyltl1a, heterologous transplantation, Human, Surrogate End Points, Surrogate Markers, Breast Malignant Tumor, House, Breast Tumor, AL024000, Mus musculus domesticus, \"mammary tumor\" EXACT [CSP2005:2016-0671], breast tumor, KMT, stratum pigmentosa retinae, l(2)03909, CaM KMT, Mice, Drugs, CamKII, Biomarker, reactivity, Human Mammary, MOS3, l(2)3909, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Clinical, Malignancy, PRECOCIOUS, Mammary Neoplasm, Swiss, MDDGB6, Mammary Carcinoma, Biological Marker, mammary part of chest, F23A5.3, Heterografts, stubby, D-CaM, LARGE, Maintenances, Cancer of the Breast, Neoplasias, BPFD#36, Camkii, drugs, Immunologic Markers, Malignant Tumor of Breast, Mammary, Mammary Cancer, Clients, CG8472, heterogeneity, PHKD, Preparation, Breast, AI256814, mammary tumor, Immunologic Marker, F23A5_3, Heterologous, Biologic, Cancer, Pharmaceuticals, Products, Breast Carcinoma, Human Mammary Neoplasm, Breast Carcinomas, Malignant Neoplasm, CaM, drug, Serum Markers, CAMKIIalpha, End Point, \"breast tumor\" EXACT [NCI2004_11_17:C2910], Brustdruese, Client, Smp1, Cell, dCaMKII, Immune Marker, Breast Malignant Neoplasm, calcium/calmodulin-dependent protein kinase II, MODIFIER OF SNC1, XENOTRANSPL, Mammary Carcinomas, Mus, AI461935, Surrogate End Point, DCK, Cam, caM, CAM, deoxyribonucleic photolyase activity, Calcium/calmodulin-dependent protein kinase, Cal, Neoplasm, Human Mammary Carcinoma, 3200001F09Rik, CG18069, DmelCG8472, Biologic Markers, Breast Neoplasm, Serum Marker, RPE, Pharmaceutic Preparations, photolyase activity, Surrogate, CamKIIalpha, cam, Endpoints, Lobe of breast, HETEROL TRANSPL, House Mice, patient, CaMK-II, Cancers, Surrogate Marker, p. pigmentosa retinae, Laboratory Mice, Drug, Preparations, like-glycosyltransferase, Breast Cancer, Cancer of Breast, deoxyribonucleate pyrimidine dimer lyase (photosensitive), response, Pharmaceutical Products, Laboratory Mouse, CCM1, Neoplasia, anon-EST:Posey59, breast, glycosyltransferase-like protein LARGE1, Pharmaceutical Preparation, Ca2+/calmodulin-dependent protein kinase II, Immune Markers"],"description_synonyms":["primary breast cancer, malignant tumor of the breast, d230, Complete Exome, Neoplasms, mammary neoplasm, Mammary Cancers, Human Mammary Neoplasms, dTAFII250, Tumor, EfW1, Human, dmTAF[[II]]230, Breast Malignant Tumor, low depth, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], dmTAF1, Breast Tumor, Taf230, \"mammary tumor\" EXACT [CSP2005:2016-0671], breast tumor, cancer of the breast, Whole Transcriptome, Transcriptome Sequencing, TAF250, BC, Mammary Neoplasms, malignant neoplasm of breast, Taf200, WES, Human Mammary, Complete, reduced representation bisulfite-seq, dTAF[[II]]250, Exome Sequencings, Whole Genome, TFIID TAF250, cel, Mammary Neoplasm, cell, Complete Exome Sequencing, Mammary Carcinoma, Whole Transcriptome Sequencing, Complete Genome Sequencing, Human Mammary Carcinomas, Taf1p, Sequencing, Cancer of the Breast, dTAF250, Whole Exome, RRBS assay, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, Whole, Breast, mammary cancer, TAF, mammary tumor, shallow, Breast Malignant Neoplasms, Tumors, Cancer, Breast Carcinoma, Human Mammary Neoplasm, Carcinoma, dTAF[[II]]230, TAF[[II]]250, Breast Carcinomas, \"breast neoplasm\" EXACT [MTH:120], Complete Exome Sequencings, Exome, TAF200, Genome Sequencing, l(3)84Ab, BG:DS00004.13, TAFII-250, \"breast tumor\" EXACT [NCI2004_11_17:C2910], TAF250/230, Cell, dTAF230, Breast Malignant Neoplasm, Exome Sequencing, TAFII250, Complete Genome, Mammary Carcinomas, p230, Neoplasm, TAF[[II]]250/230, Human Mammary Carcinoma, TFIID, NOS, methylation, RRBS, Malignant Neoplasm of Breast, Carcinomas, Taf[[II]]250, Complete Transcriptome, Breast Neoplasm, Methylations., TAF[[II]]230, Complete Transcriptome Sequencing, TAF[II]250, Cancers, \"mammary neoplasm\" RELATED [], CG17603, TAF[[II]], DmelCG17603, breast cancer, Taf250, SR3-5, Breast Tumors, Breast Cancer, Whole Exome Sequencing, Breast Malignant Tumors, Cancer of Breast, cancer, Transcriptome Sequencings, breast, TAF230, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-CRUK-CI-15-09-2016-11:30:35:546-51 - samples","description":"Breast cancer PDTX sequencing data from Bruna et al, Cell 2016\n- Exome Sequencing\n- Shallow Whole Genome Sequencing\n- RRBS Methylation Sequencing","dates":{"updated":"2020-07-30 15:02:22"},"accession":"EGAD00001002685","cross_references":{"TAXONOMY":["9606"],"pubmed":["27641504"],"EGA":["EGAC00001000540","EGAS00001001913"]}}