title: MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing.
abstract: 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.
  
  
  METHODS
  MIPgen is implemented in C++. Source code and accompanying Python scripts are available at http://shendurelab.github.io/MIPGEN/.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Evan A
authors.initials: EA
authors.lastname: Boyle
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: O'Roak
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Beth K
authors.initials: BK
authors.lastname: Martin
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Akash
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D015342:DNA Probes / Q000235:genetics*; D006801:Humans; D015233:Models, Statistical; D017421:Sequence Analysis / Q000379:methods*
chemical_list: D015342:DNA Probes