HTGTS
High-Throughput Genome-Wide Translocation Sequencing
HTGTS was developed to study translocation mechanisms in mammalian cells (Chiarle et al., 2011). This approach could be applied for studying antibody repertoires (HTGTS-Rep-seq) (Lin et al., 2016) and CRISPR/Cas9 genome modifications (Mei et al., 2016).
In HTGTS-Rep-seq, genomic DNA from B-cell populations is sonicated and linearly amplified with a biotinylated primer that anneals downstream of a J segment. The biotin-labeled single-stranded DNA products are enriched with streptavidin beads, and the 3ê ends are ligated to a bridge adaptor containing a 6-nucleotide UMI.
Advantages:
- Higher efficiency compared to whole-genome sequencing
Disadvantages:
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
None available yet
References:
Schwer B., Wei P. C., Chang A. N., et al. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A. 2016;113:2258-2263
Frock R. L., Hu J., Meyers R. M., Ho Y. J., Kii E. and Alt F. W. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol. 2015;33:179-186
Related
History: HTGTS
Revision by Farfaraway on 2020-05-15 18:48:26 - Show/Hide
High-Throughput Genome-Wide Translocation Sequencing
HTGTS was developed to study translocation mechanisms in mammalian cells
(Chiarle et al., 2011). This approach could be applied for studying antibody repertoires (HTGTS-Rep-seq)
(Lin et al., 2016) and CRISPR/Cas9 genome modifications
(Mei et al., 2016).
In HTGTS-Rep-seq, genomic DNA from B-cell populations is sonicated and linearly amplified with a biotinylated primer that anneals downstream of a J segment. The biotin-labeled single-stranded DNA products are enriched with streptavidin beads, and the 3ê ends are ligated to a bridge adaptor containing a 6-nucleotide UMI.
Advantages:
- Higher efficiency compared to whole-genome sequencing
Disadvantages:
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
None available yet
References:
Schwer B., Wei P. C., Chang A. N., et al. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A. 2016;113:2258-2263
Frock R. L., Hu J., Meyers R. M., Ho Y. J., Kii E. and Alt F. W. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol. 2015;33:179-186Revision by sbrumpton on 2017-06-21 09:06:26 - Show/Hide
High-Throughput Genome-Wide Translocation Sequencing
HTGTS was developed to study translocation mechanisms in mammalian cells (Chiarle et al., 2011). This approach is particularly suitable for studying for AID-dependent IgH class-switching (HTGTS-Rep-seq) (Lin et al., 2016) and CRISPR/Cas9 genome modifications (Mei et al., 2016).
In HTGTS-Rep-seq, genomic DNA from B-cell populations is sonicated and linearly amplified with a biotinylated primer that anneals downstream of a J segment. The biotin-labeled single-stranded DNA products are enriched with streptavidin beads, and the 3ê ends are ligated to a bridge adaptor containing a 6-nucleotide UMI.
Advantages:- Higher efficiency compared to whole-genome sequencing
Disadvantages:Reagents:Illumina Library prep and Array Kit SelectorReviews:None available yet
References:Schwer B., Wei P. C., Chang A. N., et al. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A. 2016;113:2258-2263Frock R. L., Hu J., Meyers R. M., Ho Y. J., Kii E. and Alt F. W. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol. 2015;33:179-186