Michigan Oncology Seqeuncing Portal at Michigan Center for Translational Pathology within U of M Cancer Center. This application Integrates results from Next-Gen sequence analysis conducted by a bioinformatics team. A wet lab LIMS component is used to track reagents and compute library chemistry, layout Flowcells, run quality control checks, and maintain sample metadata which associated with the analyses.

Some pipeline processing is performed directly within the Portal, but the analysis pipelines are incorporated in a plugin architecture and are managed by individual bioinformaticians. The Portal’s purpose is to integrate data sources and provide the interface for researchers and clinicians to browse, search and export this data.

The cancer analysis pipeline includes sequencing results from tumor and normal RNA and DNA libraries which are called by software, such as mutations, structural rearrangements, gene expression, copy number and zygosity variations, viral sequence detection, quality control metrics, SNP genotyping, and tumor content. These and other datasets are integrated into the Portal with sample and cohort metadata in a secure, HIPAA- CAP- and CLIA-compliant environment.

The portal runs on a LAMP stack with Yii framework. With the bioinfo teams crunching through petabytes of data on thousands of cores, extreme low latency hardware is required to solve this quintessential Big Data problem.

Chinnaiyan Lab is one of the top cancer genomics labs in the world. We know they will continue to make important discoveries.

Designed and developed by Dan Miller and other members of the Chinnaiyan lab as part of a 2 1/2 year Programmer/Analyst position with UMHS. Live app is private. © MCTP.

Example LIMS screen for entering a sequencing library record and retrieving quality control metrics