Mutation Profiling Pipeline

Projects > Mutation Profiling Pipeline

CONTACT INFORMATION

Sunita Koul
Programmer Analyst II
Center for Biomedical Informatics
Washington University in St. Louis
Phone: 314-747-8097
Fax: 314-747-7999
Email: sunita@pathology.wustl.edu

Resources

Presentations

	Mutation Profiling Pipeline Overview

	Mutation Profiling Pipeline Process

Project Description

With the availability of a reference genomic sequence from various species, attention is being paid to uncovering DNA sequence variations underlying complex diseases. Identifying and cataloguing these variations is a critical component of positional and candidate gene approaches that seek to identify the genetic basis for predisposition and resistance to disease. These sequence variations serve as genetic markers in studies of diseases and traits with complex inheritance patterns and strong environmental interactions. We sensed the need for an analytical tool that can analyze large resequencing data from different sample sets. The Mutation Profiling Pipeline (MPP) is a suite of tools that facilitate large-scale comparative sequence and mutational analysis. The following are components of the MPP:

	High throughput primer design – design primers for genomic and mRNA sequences using a graphical interface.

	Specimen data mapper - This component loads specimen information from caTissue or provides a user interface to enter specimen information.

	Annotation mapper -The genomic annotation data from NCBI is acquired on regular basis, and this data is used as the reference sequence annotated with domains, SNPS, coding and non-coding exons for mutation analysis.

	Traces pipeline - This component runs the traces through our mutation identification application which aligns and assembles the traces and identifies all variations in each sample sequence with respect to the reference sequence.

	Mutation Viewer - This is a Microsoft Windows based user interface allowing end users to visualize and validate mutations/SNPs.

Availability

Sequence analysis is performed by CBMI personnel and traces may be acquired from the Genome Center or the Laboratory for Clinical Genomics. The investigator then uses Mutation Viewer to visualize and validate the mutations. Please email help@bmi.wustl.edu if you are interested in analyzing your resequencing data.

Technical Specifications

Oracle 10g is used to store all the analysis data. An integrated suite of C++ and Perl scripts are used to run the analysis on a Linux cluster. Remote procedure calls are used between the client (Windows based) and the server (Linux cluster). Mutation Viewer is developed in Builder C++ 6.0.

For more information and/or technical support please contact Phone: 314-362-8853 Email: help@bmi.wustl.edu

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