PMID- 34503266 OWN - NLM STAT- PubMed-not-MEDLINE VI - 13 IP - 17 TI - Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler. LA - eng PT - Guideline PL - Switzerland TA - Cancers (basel) JT - Cancers JID - 101526829 IS - 2072-6694 (Print) LID - 4456 [pii] LID - 10.3390/cancers13174456 [doi] FAU - Bergholtz, Helga AU - Bergholtz H AUID- ORCID: 0000-0003-0999-1106 AD - Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway. FAU - Carter, Jodi M AU - Carter JM AD - Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA. FAU - Cesano, Alessandra AU - Cesano A AD - ESSA Pharma Inc., South San Francisco, CA 94080, USA. FAU - Cheang, Maggie Chon U AU - Cheang MCU AUID- ORCID: 0000-0001-5718-2501 AD - ICR Clinical Trials and Statistics Unit, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK. FAU - Church, Sarah E AU - Church SE AUID- ORCID: 0000-0002-7194-4282 AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Divakar, Prajan AU - Divakar P AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Fuhrman, Christopher A AU - Fuhrman CA AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Goel, Shom AU - Goel S AD - Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia. AD - Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia. FAU - Gong, Jingjing AU - Gong J AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Guerriero, Jennifer L AU - Guerriero JL AUID- ORCID: 0000-0002-2104-5457 AD - Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA. FAU - Hoang, Margaret L AU - Hoang ML AUID- ORCID: 0000-0003-0442-855X AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Hwang, E Shelley AU - Hwang ES AD - Duke Cancer Institute, Duke University, Durham, NC 27710, USA. FAU - Kuasne, Hellen AU - Kuasne H AD - Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3A 0G4, Canada. FAU - Lee, Jinho AU - Lee J AUID- ORCID: 0000-0002-5290-3100 AD - Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. FAU - Liang, Yan AU - Liang Y AUID- ORCID: 0000-0002-8536-5951 AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Mittendorf, Elizabeth A AU - Mittendorf EA AD - Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA. AD - Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA 02215, USA. AD - Harvard Medical School, Boston, MA 02115, USA. FAU - Perez, Jessica AU - Perez J AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Prat, Aleix AU - Prat A AUID- ORCID: 0000-0003-2377-540X AD - Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute, 08036 Barcelona, Spain. FAU - Pusztai, Lajos AU - Pusztai L AUID- ORCID: 0000-0001-9632-6686 AD - Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA. FAU - Reeves, Jason W AU - Reeves JW AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Riazalhosseini, Yasser AU - Riazalhosseini Y AD - Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada. AD - McGill University Genome Centre, McGill University, Montreal, QC H3A 0G4, Canada. FAU - Richer, Jennifer K AU - Richer JK AD - Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA. FAU - Sahin, Özgür AU - Sahin Ö AUID- ORCID: 0000-0002-8033-7089 AD - Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA. FAU - Sato, Hiromi AU - Sato H AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. FAU - Schlam, Ilana AU - Schlam I AD - MedStar Washington Hospital Center, Washington, DC 20010, USA. AD - Tufts Medical Center, Boston, MA 02111, USA. FAU - Sørlie, Therese AU - Sørlie T AUID- ORCID: 0000-0002-5995-2319 AD - Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway. AD - Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway. FAU - Stover, Daniel G AU - Stover DG AD - Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA. FAU - Swain, Sandra M AU - Swain SM AD - Georgetown Lombardi Comprehensive Cancer Center, Washington, DC 20057, USA. AD - Georgetown University Medical Center, Washington, DC 20057, USA. AD - MedStar Health, Washington, DC 20057, USA. FAU - Swarbrick, Alexander AU - Swarbrick A AD - Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia. AD - St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney NSW 2052, Australia. FAU - Thompson, E Aubrey AU - Thompson EA AD - Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA. FAU - Tolaney, Sara M AU - Tolaney SM AD - Harvard Medical School, Boston, MA 02115, USA. AD - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. FAU - Warren, Sarah E AU - Warren SE AD - NanoString® Technologies Inc., Seattle, WA 98109, USA. IS - 2072-6694 (Linking) OTO - NOTNLM OT - GeoMx OT - RNA and protein profiling OT - biomarker discovery OT - breast cancer OT - cancer transcriptome atlas OT - digital spatial profiler OT - spatial biology OT - tumor heterogeneity OT - tumor microenvironment OT - whole transcriptome atlas PMC - PMC8431590 LR - 20231101 DP - 2021 Sep 04 DEP - 20210904 AB - Breast cancer is a heterogenous disease with variability in tumor cells and in the surrounding tumor microenvironment (TME). Understanding the molecular diversity in breast cancer is critical for improving prediction of therapeutic response and prognostication. High-plex spatial profiling of tumors enables characterization of heterogeneity in the breast TME, which can holistically illuminate the biology of tumor growth, dissemination and, ultimately, response to therapy. The GeoMx Digital Spatial Profiler (DSP) enables researchers to spatially resolve and quantify proteins and RNA transcripts from tissue sections. The platform is compatible with both formalin-fixed paraffin-embedded and frozen tissues. RNA profiling was developed at the whole transcriptome level for human and mouse samples and protein profiling of 100-plex for human samples. Tissue can be optically segmented for analysis of regions of interest or cell populations to study biology-directed tissue characterization. The GeoMx Breast Cancer Consortium (GBCC) is composed of breast cancer researchers who are developing innovative approaches for spatial profiling to accelerate biomarker discovery. Here, the GBCC presents best practices for GeoMx profiling to promote the collection of high-quality data, optimization of data analysis and integration of datasets to advance collaboration and meta-analyses. Although the capabilities of the platform are presented in the context of breast cancer research, they can be generalized to a variety of other tumor types that are characterized by high heterogeneity.