TC-Seq
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.
Advantages:
- 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
Disadvantages:
- 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
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
None available yet
References:
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
Related
History: TC-Seq
Revision by sbrumpton on 2017-06-21 07:50:21 - Show/Hide
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.
Advantages:- 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
Disadvantages:- 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
Reagents:Illumina Library prep and Array Kit SelectorReviews:None available yet
References:Robbiani D. F., Deroubaix S., Feldhahn N., et al. Plasmodium Infection Promotes Genomic Instability and AID-Dependent B Cell Lymphoma. Cell. 2015;162:727-737Qian J., Wang Q., Dose M., et al. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell. 2014;159:1524-1537