A survey of tools for variant analysis of next-generation genome sequencing data.

Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers.

Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages.

BACKGROUND: Cancer immunotherapy has recently entered a remarkable renaissance phase with the approval of several agents for treatment. Cancer treatment platforms have demonstrated profound tumor regressions including complete cure in patients with metastatic cancer. Moreover, technological advances in next-generation sequencing (NGS) as well as the development of devices for scanning whole-slide bioimages from tissue sections and image analysis software for quantitation of tumor-infiltrating lymphocytes (TILs) allow, for the first time, the development of personalized cancer immunotherapies that target patient specific mutations. However, there is currently no bioinformatics solution that supports the integration of these heterogeneous datasets. RESULTS: We have developed a bioinformatics platform - Personalized Oncology Suite (POS) - that integrates clinical data, NGS data and whole-slide bioimages from tissue sections. POS is a web-based platform that is scalable, flexible and expandable. The underlying database is based on a data warehouse schema, which is used to integrate information from different sources. POS stores clinical data, genomic data (SNPs and INDELs identified from NGS analysis), and scanned whole-slide images. It features a genome browser as well as access to several instances of the bioimage management application Bisque. POS provides different visualization techniques and offers sophisticated upload and download possibilities. The modular architecture of POS allows the community to easily modify and extend the application. CONCLUSIONS: The web-based integration of clinical, NGS, and imaging data represents a valuable resource for clinical researchers and future application in medical oncology. POS can be used not only in the context of cancer immunology but also in other studies in which NGS data and images of tissue sections are generated. The application is open-source and can be downloaded at http://www.icbi.at/POS.

SeqBench: integrated solution for the management and analysis of exome sequencing data.

BACKGROUND: The rapid development of next generation sequencing technologies, including the recently introduced benchtop sequencers, made sequencing affordable for smaller research institutions. A widely applied method to identify causing mutations of diseases is exome sequencing, which proved to be cost-effective and time-saving. FINDINGS: SeqBench, a web-based application, combines management and analysis of exome sequencing data into one solution. It provides a user friendly data acquisition module to facilitate comprehensive and intuitive data handling. SeqBench provides direct access to the analysis pipeline SIMPLEX, which can be configured to run locally, on a cluster, or in the cloud. Identified genomic variants are presented along with several functional annotations and can be interpreted in a family context. CONCLUSIONS: The web-based application SeqBench supports the management and analysis of exome sequencing data, is open-source and available at http://www.icbi.at/SeqBench.