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MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing
Evan A Boyle1, Brian J O'Roak1, Beth K Martin1
1Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
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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