MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing

• Published in: Bioinformatics (Oxford, England) Vol. 30; no. 18; pp. 2670 - 2672
• Main Authors: Boyle, Evan A, O'Roak, Brian J, Martin, Beth K, Kumar, Akash, Shendure, Jay
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15-09-2014
• Subjects: Algorithms; Applications Notes; Computational Biology - methods; Computer Simulation; DNA Probes - genetics; Humans; Models, Statistical; Sequence Analysis - methods
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btu353

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.
MIPgen is implemented in C++. Source code and accompanying Python scripts are available at http://shendurelab.github.io/MIPGEN/.