Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer.

During cancer development, tumor cells acquire changes that enable them to invade surrounding tissues and seed metastasis at distant sites. These changes contribute to the aggressiveness of metastatic cancer and interfere with success of therapy. Our comprehensive analysis of "matched" pairs of HNSCC lines derived from primary tumors and corresponding metastatic sites identified several components of Notch3 signaling that are differentially expressed and/or altered in metastatic lines and confer a dependency on this pathway. These components were also shown to be differentially expressed between early and late stages of tumors in a TMA constructed from over 200 HNSCC patients. Finally, we show that suppression of Notch3 improves survival in mice in both subcutaneous and orthotopic models of metastatic HNSCC. Novel treatments targeting components of this pathway may prove effective in targeting metastatic HNSCC cells alone or in combination with conventional therapies.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Automatic detection and resolution of measurement-unit conflicts in aggregated data.

BACKGROUND: Measurement-unit conflicts are a perennial problem in integrative research domains such as clinical meta-analysis. As multi-national collaborations grow, as new measurement instruments appear, and as Linked Open Data infrastructures become increasingly pervasive, the number of such conflicts will similarly increase. METHODS: We propose a generic approach to the problem of (a) encoding measurement units in datasets in a machine-readable manner, (b) detecting when a dataset contained mixtures of measurement units, and (c) automatically converting any conflicting units into a desired unit, as defined for a given study. RESULTS: We utilized existing ontologies and standards for scientific data representation, measurement unit definition, and data manipulation to build a simple and flexible Semantic Web Service-based approach to measurement-unit harmonization. A cardiovascular patient cohort in which clinical measurements were recorded in a number of different units (e.g., mmHg and cmHg for blood pressure) was automatically classified into a number of clinical phenotypes, semantically defined using different measurement units. CONCLUSIONS: We demonstrate that through a combination of semantic standards and frameworks, unit integration problems can be automatically detected and resolved.

Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web.

BACKGROUND: Clinical phenotypes and disease-risk stratification are most often determined through the direct observations of clinicians in conjunction with published standards and guidelines, where the clinical expert is the final arbiter of the patient's classification. While this "human" approach is highly desirable in the context of personalized and optimal patient care, it is problematic in a healthcare research setting because the basis for the patient's classification is not transparent, and likely not reproducible from one clinical expert to another. This sits in opposition to the rigor required to execute, for example, Genome-wide association analyses and other high-throughput studies where a large number of variables are being compared to a complex disease phenotype. Most clinical classification systems and are not structured for automated classification, and similarly, clinical data is generally not represented in a form that lends itself to automated integration and interpretation. Here we apply Semantic Web technologies to the problem of automated, transparent interpretation of clinical data for use in high-throughput research environments, and explore migration-paths for existing data and legacy semantic standards. RESULTS: Using a dataset from a cardiovascular cohort collected two decades ago, we present a migration path - both for the terminologies/classification systems and the data - that enables rich automated clinical classification using well-established standards. This is achieved by establishing a simple and flexible core data model, which is combined with a layered ontological framework utilizing both logical reasoning and analytical algorithms to iteratively "lift" clinical data through increasingly complex layers of interpretation and classification. We compare our automated analysis to that of the clinical expert, and discrepancies are used to refine the ontological models, finally arriving at ontologies that mirror the expert opinion of the individual clinical researcher. Other discrepancies, however, could not be as easily modeled, and we evaluate what information we are lacking that would allow these discrepancies to be resolved in an automated manner. CONCLUSIONS: We demonstrate that the combination of semantically-explicit data, logically rigorous models of clinical guidelines, and publicly-accessible Semantic Web Services, can be used to execute automated, rigorous and reproducible clinical classifications with an accuracy approaching that of an expert. Discrepancies between the manual and automatic approaches reveal, as expected, that clinicians do not always rigorously follow established guidelines for classification; however, we demonstrate that "personalized" ontologies may represent a re-usable and transparent approach to modeling individual clinical expertise, leading to more reproducible science.

SADI, SHARE, and the in silico scientific method.

BACKGROUND: The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in "the new way", and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies. RESULTS: Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries. CONCLUSIONS: The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the "semantification" of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.