Efficient In Silico Identification of a Common Insertion in the MAK Gene which Causes Retinitis Pigmentosa.

ABSTRACT:

Background

Next generation sequencing (NGS) offers a rapid and comprehensive method of screening for mutations associated with retinitis pigmentosa and related disorders. However, certain sequence alterations such as large insertions or deletions may remain undetected using standard NGS pipelines. One such mutation is a recently-identified Alu insertion into the Male Germ Cell-Associated Kinase (MAK) gene, which is missed by standard NGS-based variant callers. Here, we developed an in silico method of searching NGS raw sequence reads to detect this mutation, without the need to recalculate sequence alignments or to screen every sample by PCR.

Methods

The Linux program grep was used to search for a 23 bp "probe" sequence containing the known junction sequence of the insert. A

SUBMITTER: Bujakowska KM 

PROVIDER: S-EPMC4641726 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature