Key factors for successful data integration in biomarker research.

Integrating a wide range of biomedical data such as that rapidly emerging from the use of next-generation sequencing is expected to have a key role in identifying and qualifying new biomarkers to support precision medicine. Here, we highlight some of the challenges for biomedical data integration and approaches to address them.

Identifying susceptibility networks for drug-induced non-immune neutropenia.

Systems toxicology, a branch of toxicology that studies drug effects at the level of biological systems, offers exciting opportunities to discover toxicity-related sub-networks using high-throughput technologies. This paper takes a computational approach to systems toxicology and investigates the use of automated signalling path detection for discovery of potential biomarkers of drug-induced non-immune neutropenia. The algorithm utilises a gene expression change measure to mine a large protein interaction network and identify chemical-toxicity signalling paths.

A systems biology approach for detecting toxicity-related hotspots inside protein interaction networks.

Drug-induced neutropenia can be fatal when severe and therefore requires an improved understanding of its mechanism(s) of toxicity. Systems biology provides an opportunity to understand adverse events after drug administration using analysis of biomolecular networks. In this study, a human protein interaction network was analyzed to identify proteins that are most central to topological paths connecting a drug's target proteins to hematopoiesis-related proteins.

Reexamining transaminase elevation in Phase I clinical trials: the importance of baseline and change from baseline.

Purpose: The aims of the present analysis were to determine prevalence of transaminase elevation in placebo-treated healthy volunteers in our historical phase I clinical trials and to assess which factors were associated with it.

Methods: We performed a retrospective analysis of alanine transaminase (ALT) levels in 481 placebo-treated healthy volunteers from 20 phase I trials by examining ALT elevation rates using the upper limit of normal values (ULN) as the cutoff as well as changes from baseline in actual ALT values.

Results: The ULN for ALT ranged from 32 to 72 IU/L across the studies.