Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries

BMC Genomics

Laura G Reinholdt¹  Cathleen Lutz¹  Mary Barter²  Lucy B Rowe²  Ian Greenstein¹  Vivek M Philip³  Anuj Srivastava³ 

[1] Genetic Resource Sciences, The Jackson Laboratory, Bar Harbor, ME USA;Genome Technologies, The Jackson Laboratory, Bar Harbor, ME USA;Computational Sciences, The Jackson Laboratory, Bar Harbor, ME USA

关键词: Transgene insertion sites;    Transgenic;    Mate pair library;    High-throughput sequencing;   

Others  :  1217234
DOI  :  10.1186/1471-2164-15-367

 received in 2013-10-17, accepted in 2014-05-06,  发布年份 2014

【 摘 要 】

Background

Transgenesis by random integration of a transgene into the genome of a zygote has become a reliable and powerful method for the creation of new mouse strains that express exogenous genes, including human disease genes, tissue specific reporter genes or genes that allow for tissue specific recombination. Nearly 6,500 transgenic alleles have been created by random integration in embryos over the last 30 years, but for the vast majority of these strains, the transgene insertion sites remain uncharacterized.

Results

To obtain a complete understanding of how insertion sites might contribute to phenotypic outcomes, to more cost effectively manage transgenic strains, and to fully understand mechanisms of instability in transgene expression, we’ve developed methodology and a scoring scheme for transgene insertion site discovery using high throughput sequencing data.

Conclusions

Similar to other molecular approaches to transgene insertion site discovery, high-throughput sequencing of standard paired-end libraries is hindered by low signal to noise ratios. This problem is exacerbated when the transgene consists of sequences that are also present in the host genome. We’ve found that high throughput sequencing data from mate-pair libraries are more informative when compared to data from standard paired end libraries. We also show examples of the genomic regions that harbor transgenes, which have in common a preponderance of repetitive sequences.

【 授权许可】

   
2014 Srivastava et al.; licensee BioMed Central Ltd.

【 图 表 】

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