PNNL

Abstract

Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into disease pathogenic mechanisms and therapies tailored to each patient. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single cell level or in 3-Dimensional space is a significant challenge that can be a futile exercise if not well controlled. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate 3D molecular atlases of healthy and diseased kidney biopsies using multiple state-of-the art OMICS and imaging technologies. Here we describe the pipeline with pertinent examples for designing a reliable and authentic single cell/region 3D molecular atlas of human adult kidney with specific emphasis on measures for quality assurance, quality control, validation and harmonization across different OMICS and imaging methods. We present a “follow the tissue” approach from procurement to data generation, analysis and data sharing, while standardizing and harmonizing procedures at sample collection, processing, storage and shipping. Additional focus has been placed on preanalytical parameters, bioassays, post analyses, reference standards and data depositions. Analyses of the data generated from a common source tissue is incorporated to identify both unique and redundant features of the macromolecules being characterized at each tissue interrogation site, taking into account limitations and strengths of the different technologies, and how composite information can be leveraged for clinical application. A peer review system was established to critically review each technology’s quality control measures and the reproducibility of data generated using tissue from different institutions before granting approval to work on clinical biopsy specimens. This unique pipeline establishes a process that economizes the use of valuable biopsy tissue for multi-omics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and which can serve as a model for similar personalized medicine projects.