Journal
PHYSIOLOGICAL GENOMICS
Volume 53, Issue 1, Pages 1-11Publisher
AMER PHYSIOLOGICAL SOC
DOI: 10.1152/physiolgenomics.00104.2020
Keywords
imaging; kidney disease; metabolomics; proteomics; transcriptomics
Categories
Funding
- National Institute of Diabetes and Digestive and Kidney Diseases [UH3 DK-114923, UH3 DK-114920, UH3 DK-114933, UH3 DK-114937, UH3 DK-114907, U2C DK114886]
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The Kidney Precision Medicine Project aims to generate 3-D molecular atlases of healthy and diseased kidney biopsies using state-of-the-art omics and imaging technologies. The emphasis is on quality assurance, quality control, validation, and harmonization across different technologies.
Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. We describe a follow the tissue pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.
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