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

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/.

SUBMITTER: Boyle EA

PROVIDER: S-EPMC4155255 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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

Boyle Evan A EA O'Roak Brian J BJ Martin Beth K BK Kumar Akash A Shendure Jay J

Bioinformatics (Oxford, England) 20140526 18

<h4>Unlabelled</h4>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 re ...[more]

PMID: 24867941

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