Translocation-Capture Sequencing

TC-Seq was developed to study chromosomal rearrangements and translocations (Klein et al., 2011). In this method, cells are infected with retrovirus expressing l-Scel sites in cells with and without activation-induced cytidine deaminase (AICDA or AID) protein. gDNA from cells is sonicated, linker-ligated, purified, and amplified via seminested ligation-mediated (LM)-PCR. The linker is cleaved, and the DNA is sequenced. Any AID-dependent chromosomal rearrangement will be amplified by LM-PCR, while AID-independent translocations will be discarded.


  • Can study chromosomal translocations within a given model or environment
  • Random sonication generates unique linker ligation points, and deep sequencing allows reading through rearrangement breakpoints


  • Does not resolve junction structures
  • Relatively higher cost and lower sensitivity compared with LAM-HTGTS (Hu et al., 2016)
  • PCR amplification errors
  • Nonlinear PCR amplification can lead to biases affecting reproducibility
  • PCR biases can underrepresent GC-rich templates


Illumina Library prep and Array Kit Selector


None available yet


Robbiani D. F., Deroubaix S., Feldhahn N., et al. Plasmodium Infection Promotes Genomic Instability and AID-Dependent B Cell Lymphoma. Cell. 2015;162:727-737

Qian J., Wang Q., Dose M., et al. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell. 2014;159:1524-1537