• Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes

      Vitali, Francesca; Li, Qike; Schissler, A Grant; Berghout, Joanne; Kenost, Colleen; Lussier, Yves A; Univ Arizona, Ctr Biomed Informat & Biostat (OXFORD UNIV PRESS, 2019-05-21)
      The development of computational methods capable of analyzing -omics data at the individual level is critical for the success of precision medicine. Although unprecedented opportunities now exist to gather data on an individual's -omics profile (personalome'), interpreting and extracting meaningful information from single-subject -omics remain underdeveloped, particularly for quantitative non-sequence measurements, including complete transcriptome or proteome expression and metabolite abundance. Conventional bioinformatics approaches have largely been designed for making population-level inferences about average' disease processes; thus, they may not adequately capture and describe individual variability. Novel approaches intended to exploit a variety of -omics data are required for identifying individualized signals for meaningful interpretation. In this review-intended for biomedical researchers, computational biologists and bioinformaticians-we survey emerging computational and translational informatics methods capable of constructing a single subject's personalome' for predicting clinical outcomes or therapeutic responses, with an emphasis on methods that provide interpretable readouts. Key points: (i) the single-subject analytics of the transcriptome shows the greatest development to date and, (ii) the methods were all validated in simulations, cross-validations or independent retrospective data sets. This survey uncovers a growing field that offers numerous opportunities for the development of novel validation methods and opens the door for future studies focusing on the interpretation of comprehensive personalomes' through the integration of multiple -omics, providing valuable insights into individual patient outcomes and treatments.
    • Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses

      Zaim, Samir Rachid; Li, Qike; Schissler, A Grant; Lussier, Yves A; Univ Arizona, Grad Interdisciplinary Prog Statist, Dept Med, Ctr Biomed Informat & Biostat; Univ Arizona, Ctr Biomed Informat & Biostat, Dept Med, Canc Ctr; Univ Arizona (WORLD SCIENTIFIC PUBL CO PTE LTD, 2018)
      Recent precision medicine initiatives have led to the expectation of improved clinical decision-making anchored in genomic data science. However, over the last decade, only a handful of new single-gene product biomarkers have been translated to clinical practice (FDA approved) in spite of considerable discovery efforts deployed and a plethora of transcriptomes available in the Gene Expression Omnibus. With this modest outcome of current approaches in mind, we developed a pilot simulation study to demonstrate the untapped benefits of developing disease detection methods for cases where the true signal lies at the pathway level, even if the pathway's gene expression alterations may be heterogeneous across patients. In other words, we relaxed the cross-patient homogeneity assumption from the transcript level (cohort assumptions of deregulated gene expression) to the pathway level (assumptions of deregulated pathway expression). Furthermore, we have expanded previous single-subject (SS) methods into cohort analyses to illustrate the benefit of accounting for an individual's variability in cohort scenarios. We compare SS and cohort-based (CB) techniques under 54 distinct scenarios, each with 1,000 simulations, to demonstrate that the emergence of a pathway-level signal occurs through the summative effect of its altered gene expression, heterogeneous across patients. Studied variables include pathway gene set size, fraction of expressed gene responsive within gene set, fraction of expressed gene responsive up- vs down-regulated, and cohort size. We demonstrated that our SS approach was uniquely suited to detect signals in heterogeneous populations in which individuals have varying levels of baseline risks that are simultaneously confounded by patient-specific "genome -by-environment" interactions (GxE). Area under the precision-recall curve of the SS approach far surpassed that of the CB (1st quartile, median, 3 rd quartile: SS = 0.94, 0.96, 0.99; CB= 0.50, 0.52, 0.65). We conclude that single-subject pathway detection methods are uniquely suited for consistently detecting pathway dysregulation by the inclusion of a patient's individual variability.