9 Benefits of Cohort Explorer and Omics Data Bank if Purchased Together

This chapter contains the following topics:

Benefits

9.1 Benefits

Using Cohort Explorer together with Omics Data Bank you can perform the following functions:

Easily and rapidly assess how many patients (or study subjects) fulfill any complex set of custom criteria coming from a combination of clinical, demographics, and omics domains.
Stratify patients (or study subjects) based on comparative analysis of certain events occurring, for example, find patients who have a specific mutation within three months after undergoing gene therapy treatment.
View details of a cohort of individuals, then drill down to the individual patient's medical history without revealing patient's identity for those users who do not have permission to see identifiable data.
For Individuals with permission to see personally identifiable data for patients, they can see PI data of individuals they have access to, and obfuscated data for those patients they do not have permission to see.
For a single patient or study subject, select categories of demographic, clinical, or genomic data to show all his/her available data in one page. A comprehensive view of all genomic results for patient's/subject's specimen is available with drill-in options to view those results in Circular Genomic Viewer. Furthermore, a hierarchical viewer shows variant profile of a given individual along with impact and location categorization of each mutation. For those patients/subjects who have lower level (for example BAM, SAM, and so on) files linked in with their interpreted results, user with appropriate permissions can see the file lineage and download file from the Cohort Explorer interface.
Quickly generate a variety of prebuilt demographic, clinical and genomic reports based on a custom cohort. You can use those reports for analysis and research into relevant features.
Sequence Variants and Copy Number Variation cohort reports let you quickly analyze the number of specimen found with mutations, no-mutations or no results for a selected set of genes. You can select to drill further and view these results in a Genome-like Browser which shown chromosomal position of each mutation or CNV, respectively. You can drill further to see what specimen/patient exactly matched for a given feature.
Structural Variation histogram cohort report performs search for the most frequently structurally mutated genes or gene pairs.
Evaluate the efficiency of your organization via the operational dashboards in the Dashboard page.
Assess what biospecimen samples are currently available for a given set of patients or study subjects.
Use Circular Genomics Viewer to get a glimpse on genomic data for a given patients/study subject. Data shown in circular viewer includes variants, single and dual channel gene expression, RNA-seq results and Copy Number Variation results.
Export genomic data into other gene browser readable formats, based on patient sample analysis. Genomic data supported includes gene expression, copy number variation, mutation data. Select to either export the data immediately or schedule a job for asynchronous file generation. Once job is completed, you can download generated file(s) from under Home > Jobs page.
Use Genomic Query interface to search for genes or gene variants across genomic result data in ODB.
Identify how many patients/subjects and specimen have been found to have genomic results for genes or gene variants, and then drill into the patient/subject list to inspect those individuals for any other features.
Keep track of your saved cohort queries, as well as cohort lists. Easily share those with other users or user groups using a simple web user interface.
View all your queries, cohort lists, gene sets under My Workspace tab where you can also see any queries or lists that have been shared with you.
Keep track of your favorite genes as a saved Gene Set.
Turn on logging to track users and any activity within the application accessing data in either the Cohort Data Mart (CDM) or in the Omics Data Bank (ODB) model.