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Big data and computational biology strategy for personalized prognosis.

ABSTRACT: The era of big data and precision medicine has led to accumulation of massive datasets of gene expression data and clinical information of patients. For a new patient, we propose that identification of a highly similar reference patient from an existing patient database via similarity matching of both clinical and expression data could be useful for predicting the prognostic risk or therapeutic efficacy.Here, we propose a novel methodology to predict disease/treatment outcome via analysis of the similarity between any pair of patients who are each characterized by a certain set of pre-defined biological variables (biomarkers or clinical features) represented initially as a prognostic binary variable vector (PBVV) and subsequently transformed to a prognostic signature vector (PSV). Our analyses revealed that Euclidean distance rather correlation distance measure was effective in defining an unbiased similarity measure calculated between two PSVs.We implemented our methods to high-grade serous ovarian cancer (HGSC) based on a 36-mRNA predictor that was previously shown to stratify patients into 3 distinct prognostic subgroups. We studied and revealed that patient's age, when converted into binary variable, was positively correlated with the overall risk of succumbing to the disease. When applied to an independent testing dataset, the inclusion of age into the molecular predictor provided more robust personalized prognosis of overall survival correlated with the therapeutic response of HGSC and provided benefit for treatment targeting of the tumors in HGSC patients.Finally, our method can be generalized and implemented in many other diseases to accurately predict personalized patients' outcomes.

SUBMITTER: Ow GS

PROVIDER: S-EPMC5130003 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Big data and computational biology strategy for personalized prognosis.

Ow Ghim Siong GS Tang Zhiqun Z Kuznetsov Vladimir A VA

Oncotarget 20160601 26

The era of big data and precision medicine has led to accumulation of massive datasets of gene expression data and clinical information of patients. For a new patient, we propose that identification of a highly similar reference patient from an existing patient database via similarity matching of both clinical and expression data could be useful for predicting the prognostic risk or therapeutic efficacy.Here, we propose a novel methodology to predict disease/treatment outcome via analysis of the ...[more]

PMID: 27229533

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Project description:Personalized medicine (PM) operates with biological data to optimize therapy or prevention and to achieve cost reduction. Associated data may consist of large variations of informational subtypes e.g. genetic characteristics and their epigenetic modifications, biomarkers or even individual lifestyle factors. Present innovations in the field of information technology have already enabled the procession of increasingly large amounts of such data ('volume') from various sources ('variety') and varying quality in terms of data accuracy ('veracity') to facilitate the generation and analyzation of messy data sets within a short and highly efficient time period ('velocity') to provide insights into previously unknown connections and correlations between different items ('value'). As such developments are characteristics of Big Data approaches, Big Data itself has become an important catchphrase that is closely linked to the emerging foundations and approaches of PM. However, as ethical concerns have been pointed out by experts in the debate already, moral concerns by stakeholders such as patient organizations (POs) need to be reflected in this context as well. We used an empirical-ethical approach including a website-analysis and 27 telephone-interviews for gaining in-depth insight into German POs' perspectives on PM and Big Data. Our results show that not all POs are stakeholders in the same way. Comparing the perspectives and political engagement of the minority of POs that is currently actively involved in research around PM and Big Data-driven research led to four stakeholder sub-classifications: 'mediators' support research projects through facilitating researcher's access to the patient community while simultaneously selecting projects they preferably support while 'cooperators' tend to contribute more directly to research projects by providing and implemeting patient perspectives. 'Financers' provide financial resources. 'Independents' keep control over their collected samples and associated patient-related information with a strong interest in making autonomous decisions about its scientific use. A more detailed terminology for the involvement of POs as stakeholders facilitates the adressing of their aims and goals. Based on our results, the 'independents' subgroup is a promising candidate for future collaborations in scientific research. Additionally, we identified gaps in PO's knowledge about PM and Big Data. Based on these findings, approaches can be developed to increase data and statistical literacy. This way, the full potential of stakeholder involvement of POs can be made accessible in discourses around PM and Big Data.

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Big data and computational biology strategy for personalized prognosis.

Publications

Big data and computational biology strategy for personalized prognosis.

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