Transgene Mapping Analysis

Overview

Transgene Mapping Analysis Taconic Biosciences offers Transgene Mapping Analysis in partnership with Cergentis. This service uses targeted locus amplification technology, developed by Cergentis, to identify the exact integration site of a transgene that is randomly integrated into the genome of a mouse or rat via pronuclear injection.

The Technology

Targeted Locus Amplification (TLA)1,2 is a novel targeted enrichment technology combining the principle of proximity ligation with next generation sequencing to selectively amplify and sequence the transgene and surrounding genomic region of sizes ranging from tens to hundreds of kilobases.

Using only one primer pair, complementary to a short sequence unique to the transgene, crosslinked and ligated DNA fragments surrounding the transgene insertion site are selectively amplified and sequenced. By analyzing the coverage profile of the sequencing reads and the breakpoint sequences, TLA allows the precise identification of the transgene integration site. In addition, it enables the detection of single nucleotide variations, structural variations, and transgene-transgene fusions.

Workflow of targeted locus amplification technology for transgene mapping
Workflow of targeted locus amplification technology for transgene mapping. Credit: Illustration is kindly provided by Cergentis.

Transgene Mapping Solutions

Taconic provides end-to-end solution from sample preparation to final reporting which includes:

  • Precise identification of all transgene integration sites
  • Characterization of any structural changes in the transgene and genomic regions surrounding the transgene
  • Structural changes in the transgene sequence
  • Any Single Nucleotide Variants within the transgene
  • Founder line recommendations and breeding plan optimization as applicable
  • Recommended genotyping protocols that bridge the integration site and allow for genotyping specific integration sites and accurately differentiate homozygous vs heterozygous animals. In some cases, developing genotyping protocols may not be possible due to the nature and the site of transgene integration.
Please contact our PhD scientists to discuss your project needs.

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References:
1. Vree, P. J. P. D.; Wit, E. D.; Yilmaz, M.; Heijning, M. V. D.; Klous, P.; Verstegen, M. J. A. M.; Wan, Y.; Teunissen, H.; Krijger, P. H. L.; Geeven, G.; et al. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nature Biotechnology 2014, 32 (10), 1019-1025.
2. Cain-Hom, C.; Splinter, E.; van Min, M.; Simonis, M.; van de Heijning, M.; Martinez, M.; Asghari, V.; Cox, J.C.; Warming, S. Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification. Nucleic Acids Res. 2017, pii, gkw1329.