MIPgen: Optimized Modeling and Design of Molecular Inversion Probes for Targeted Resequencing.

Publication Type:

Journal Article


Bioinformatics (Oxford, England) (2014)


2014, Human Biology Division, June 2014


Molecular Inversion Probes (MIPs) enable cost-effective multiplex targeted gene resequencing in very large cohorts. However, the design of individual MIPs is a critical parameter governing the performance of this technology with respect to capture uniformity and specificity. MIPgen is a user-friendly package that simplifies the process of designing custom Molecular Inversion Probe assays to arbitrary targets. New logistic and SVM-derived models enable in silico predictions of assay success, and a redesigned assay exhibits improved coverage uniformity relative to previous methods, which in turn improves the utility of MIPs for cost-effective targeted sequencing for candidate gene validation and for diagnostic sequencing in a clinical setting. Availability and Implementation: MIPgen is implemented in C++. Source code and accompanying Python scripts are available at http://krishna.gs.washington.edu/download/mipgen with the username "download".