MGH DNA Core

CRISPR Sequencing

To address the emerging needs of the research community, the CCIB DNA Core is continuously expanding its diverse portfolio of genomics solutions. In support of the scientific community's enthusiastic embracement of the CRISPR/Cas9 genome editing technology, we have developed a cost-effective, high-throughput strategy for identifying CRISPR/Cas-induced mutations via deep sequencing of PCR amplicons.

We are offering this service on a weekly basis.
Start of Next Service Cycle:

Individual samples must be received at the core facility no later than 4 pm on Wednesday, . If you should miss the deadline or if the total customer order volume exceeds our current production capacity, your samples will be entered into the queue and processed in the subsequent run. Results for all samples processed in our weekly run will be available within 7 to 8 business days after the start of the service cycle.

Full 96-well plates can be submitted on any business day and will be processed on a first come, first serve basis. The waiting time in queue depends on the total volume of plate orders and our processing capacity. Please contact us at least 5 business days before your sample plate arrives at our core facility so that we can schedule your project in a timely manner and process it as quickly as possible.

Service Features

Cost-effective ultra-deep sequencing of amplicons derived from CRISPR-targeted genomic regions
Highly sensitive detection of CRISPR-Cas9 induced mutations
CRISPR variant calling
No need for universal tags on target-specific amplicons
No need for time-consuming cloning steps
Sample multiplexing using validated indices
Highest possible data quality
Fast turnaround time

CRISPR Amplicon Sequencing Details

The site of interest (i.e CRISPR cut site) must be within the first 100 base pairs of the amplicon (from either the 5'-end or the 3'-end) to ensure high quality data.

Both the NGS adaptors and a unique barcode will be added as part of our NGS sample preparation process.

Our current approach has been designed to generate complete sequence coverage for 200-280 bp amplicons. If the identification of amplification primer binding sites should present a problem for designing amplicons of this size, the submission of longer amplicons (up to 500 bp) will be acceptable. In this case, however, only the 5'-end and 3'-end of the amplicon will be covered by NGS reads, i.e. the middle of the amplicon will have a gap (represented by NNNNNNN....).

To obtain complete sequence coverage of 400-600 bp CRISPR amplicons, please submit your sample(s) for our Complete Amplicon Sequencing service. Please contact us to discuss your specific project needs.

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Our guidelines for amplicon design, sample preparation and submission can be found under the section Sample Submission. A short description of our algorithm used to perform CRISPR variant detection can be found here.
If you should have any additional questions about our CRISPR Sequencing service, please contact the Core Director.