Format

Send to

Choose Destination
Bioinformatics. 2014 Sep 15;30(18):2670-2. doi: 10.1093/bioinformatics/btu353. Epub 2014 May 26.

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

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA 98105 and Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.

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.

AVAILABILITY AND IMPLEMENTATION:

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

PMID:
24867941
PMCID:
PMC4155255
DOI:
10.1093/bioinformatics/btu353
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center