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

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2014 May 29

PMID 24867941

Citations 84

Authors

Evan A Boyle

Brian J ORoak

Beth K Martin

Akash Kumar

Jay Shendure

Affiliations

Soon will be listed here.

Abstract

Unlabelled: Molecular inversion probes (MIPs) enable cost-effective multiplex targeted gene resequencing in 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 MIP assays to arbitrary targets. New logistic and SVM-derived models enable in silico predictions of assay success, and assay redesign 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://shendurelab.github.io/MIPGEN/.

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