Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.

Background: Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms.

Description: We have set up a Reference Variant Store (RVS) containing variants observed in a number of large-scale sequencing efforts, such as 1000 Genomes, ExAC, Scripps Wellderly, UK10K; various genotyping studies; and disease association databases.

ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.

Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants.

Efficient extraction of protein-protein interactions from full-text articles.

Proteins and their interactions govern virtually all cellular processes, such as regulation, signaling, metabolism, and structure. Most experimental findings pertaining to such interactions are discussed in research papers, which, in turn, get curated by protein interaction databases. Authors, editors, and publishers benefit from efforts to alleviate the tasks of searching for relevant papers, evidence for physical interactions, and proper identifiers for each protein involved.

Inter-species normalization of gene mentions with GNAT.

Motivation: Text mining in the biomedical domain aims at helping researchers to access information contained in scientific publications in a faster, easier and more complete way. One step towards this aim is the recognition of named entities and their subsequent normalization to database identifiers. Normalization helps to link objects of potential interest, such as genes, to detailed information not contained in a publication; it is also key for integrating different knowledge sources.

Manifestation, latency and management of late urological complications after curative radiotherapy for cervical carcinoma.

Background: Radiotherapy alone or in combination with radical hysterectomy remains a potentially curative treatment for cervical carcinoma. Late urological complications after curative radiotreatment are rare but often present difficult problems of management due to the progressive nature of radiogenic tissue damage. We reviewed all cases of radiogenic urologic complications after radiotherapy for cervical carcinoma treated at our institution over the past 10 years.