HCI-PDX Trial Center for Breast Cancer Therapy

The HCI-PDX Trial Center for Breast Cancer Therapy study is a collection of patient-tumor samples that are serially established as patient-derived tumor xenografts (human tumor in mouse) and matching organoids. For this study, we describe valuable methods and resources to generate organoids and use them as cost-effective models for precision drug screens. This study leveraged whole-exome sequencing, RNAseq, and SNP-array data to illustrate how the heterogeneity of tumors is preserved in xenograft and organoid models. Sequencing files are provided for whole-exome and RNAseq data. Processed copy number variant calls from the SNP arrays are also available. A full description of the study can be found in the article entitled, "A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology," written by Guillen et al., 2022 in Nature Cancer (PMID: 35221336).

• Study Design:
  • Xenograft
• Study Type:
  • Case Set
  • Exome Sequencing
  • Genotype
  • RNA Sequencing
• Total number of consented subjects: 37
• Subject Sample Telemetry Report (SSTR)

• PubMed

Patient tumor samples were accrued and collected at the Huntsman Cancer Institute in Salt Lake City, UT. Patient samples were excluded if they did not establish (i.e., grow) as xenograft model. Additionally, five patients are excluded for the case-set study in this raw data due to IRB language permitting their use in research but not public dissemination of genomic data (HCI-025, HCI-026, HCI-027, HCI-031, and HCI-035).     

This study utilizes patient-derived tumor xenograft models to address unmet clinical needs in patients with advanced breast cancer. In addition to the PDX exome and RNAseq data deposited here, this resource also includes patient tumors, and patient-derived xenograft organoids, highlighting yet another resource to evaluate drug responses in a heterogeneous cohort of advanced breast cancer cases. 

• Primary Phenotype: Breast Neoplasms
• Xenograft Model Antitumor Assays
• Organoids

• Principal Investigators
  • Alana Welm, PhD. University of Utah, Salt Lake City, UT, USA.
  • Bryan Welm, PhD. University of Utah, Salt Lake City, UT, USA.
  • K-T Varley, PhD. University of Utah, Salt Lake City, UT, USA.
  • Gabor Marth, DSc. University of Utah, Salt Lake City, UT, USA.
• Funding Source for Alana Welm and Bryan Welm
  • U54CA224076. National Institutes of Health, Bethesda, MD, USA.
• Funding Source for K-T Varley, Bryan Welm, and Gabor Marth
  • U01CA217617. National Institutes of Health, Bethesda, MD, USA.