Editorial: The Fruits of the Genomic Revolution

Invited Commentary: Standards, Inputs, and Outputs-Strategies for Improving Data-Sharing and Consortia-Based Epidemiologic Research

Data-sharing improves epidemiologic research, but the sharing of data frustrates epidemiologic researchers. The inefficiencies of current methods and options for data-sharing are increasingly documented and easily understood by any study group that has shared its data and any researcher who has received shared data. In this issue of the Journal, Temprosa et al. (Am J Epidemiol. 2021;191(1):147-158) describe how the Consortium of Metabolomics Studies (COMETS) developed and deployed a flexible analytical platform to eliminate key pain points in large-scale metabolomics research. COMETS Analytics includes an online tool, but its cloud computing and technology are the supporting rather than the leading actors in this script. The COMETS team identified the need to standardize diverse and inconsistent metabolomics and covariate data and models across its many participating cohort studies, and then developed a flexible tool that gave its member studies choices about how they wanted to meet the consortium's analytical requirements. Different specialties will have different specific research needs and will probably continue to use and develop an array of diverse analytical and technical solutions for their projects. COMETS Analytics shows how important-and enabling-the upstream attention to data standards and data consistency is to producing high-quality metabolomics, consortia-based, and large-scale epidemiology research.

Translational biomarkers in the era of precision medicine

In this chapter we discuss the past, present and future of clinical biomarker development. We explore the advent of new technologies, paving the way in which health, medicine and disease is understood. This review includes the identification of physicochemical assays, current regulations, the development and reproducibility of clinical trials, as well as, the revolution of omics technologies and state-of-the-art integration and analysis approaches.

Precancer Atlas to Drive Precision Prevention Trials

Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.