HTAN Pilot Project: Single-Cell Transcriptomics Toolbox for Fresh and Frozen Human Tumors (Lung, Breast, Ovarian, Melanoma, Neuroblastoma, Sarcoma, Glioblastoma, Glioma, and Leukemia)

Single cell transcriptomics is a powerful tool to map the complex tumor microenvironment, providing unprecedented resolution into cell types, cell states, cell interactions, and tumor heterogeneity. Depending on their tissue site and whether processing begins from a fresh or frozen sample, different tumors require different optimizations in order to obtain high quality single cell transcriptomic data. In this study, we profiled a range of tumor types, varying in cell-of-origin, solid and non-solid forms, patient ages, and transitions. The tumors also further varied in their tissue site and in their sample collection method. To enable profiling of such diverse samples, we developed a systematic toolbox for single cell RNA-Seq and single nucleus RNA-Seq of fresh and frozen clinical tumor samples. We validated this toolbox for 216,490 cells and nuclei extracted from 39 samples across 23 tumors (some tumors were split into multiple samples). The 23 tumors represented eight unique tumor types. This toolbox comprises both experimental and computational protocols as well as guidelines for comparing and selecting protocols for the biological problem of interest.]]>
Population characteristics: This research was not designed as a population study. Only a small number of samples (2-7) are profiled and analyzed per cancer type. Most samples are from adults, with the remaining samples being pediatric (pediatric high-grade glioma, sarcoma, and neuroblastoma). Recruitment: Patients were not actively recruited for this secondary-use study. Instead, patients were recruited under the initial IRB protocols approved by our collaborating institutions (see "Ethics oversight" section). External sample cohorts were then added to the Broad's Molecular Classification of Cancer protocol (15-370B) and reviewed and approved by the Dana Farber Cancer Institute (DFCI) IRB. Patient population compositions are not expected to impact our results as our analyses were done on a per sample basis, rather than on patient populations. Ethics oversight: Ethics oversight for the Molecular Classification of Cancer protocol (15-370B) is performed by the DFCI IRB. Samples added to this protocol also underwent IRB review and approval at the institutions where the samples were originally collected. Specifically, Dana-Farber Cancer Institute IRB approved the following protocols: lung cancer (IRB protocol 98-063), metastatic breast cancer (IRB protocol 05-246), neuroblastoma (IRB protocols 11-104 and 17-104), ovarian cancer (IRB protocol 02-051), melanoma (IRB protocol 11-104), sarcoma (IRB protocol 17-104), GBM(IRB protocol 10-417), and chronic lymphocytic leukemia (IRB protocol 99-224), and the St. Jude Children's Research Hospital IRB approved the following protocol: pediatric high-grade glioma (IRB protocol 97BANK). Below is a breakdown of the cancer types included in this study: Lung cancer: number of patient(s) who provided specimen: 2 number of specimen(s) collected: 2 number of sample(s) derived from specimen(s): 5 Metastatic breast cancer: number of patient(s) who provided specimen: 6 number of specimen(s) collected: 6 number of sample(s) derived from specimen(s): 10 Ovarian cancer: number of patient(s) who provided specimen: 3 number of specimen(s) collected: 3 number of sample(s) derived from specimen(s): 5 Melanoma: number of patient(s) who provided specimen: 2 number of specimen(s) collected: 2 number of sample(s) derived from specimen(s): 2 Neuroblastoma: number of patient(s) who provided specimen: 4 number of specimen(s) collected: 5 number of sample(s) derived from specimen(s): 10 Pediatric sarcoma: number of patient(s) who provided specimen: 2 number of specimen(s) collected: 2 number of sample(s) derived from specimen(s): 4 Glioma (glioblastoma and pediatric high-grade glioma): number of patient(s) who provided specimen: 2 number of specimen(s) collected: 2 number of sample(s) derived from specimen(s): 2 Chronic lymphocytic leukemia: number of patient(s) who provided specimen: 1 number of specimen(s) collected: 1 number of sample(s) derived from specimen(s): 2 ]]>
December 2017 - start of sample collection March 2019 - end of sample collection]]>