Genomics & Bioinformatics
Gene editing technologies, such as CRISPR-Cas, TALENs, base editors, and prime editors, offer revolutionary potential for curing severe disorders through targeted gene knockout or gene correction. Despite their high specificity, unintended off-target effects can occur, potentially impacting regulatory regions or genes, and leading to adverse outcomes like tumorigenesis. Rigorous validation of the activity and specificity of genome editors is therefore essential prior to clinical application.
Our lab has developed advanced methods to detect off-target effects, including CAST-Seq (patents US11319580B2/EP3856928B1) and Abnoba-Seq (patents EP3812472B1). Abnoba-Seq is a method for detecting off-target activity in vitro. CAST-Seq is a highly sensitive cell-based assay for identifying chromosomal rearrangements at the on-target sites, detecting off-target activity-mediated chromosomal translocations, and nominating off-target sites in both in vivo and ex vivo-edited primary cells. Coupled with robust bioinformatics pipelines, CAST-Seq provides reliable detection of on-target and off-target effects.
On- and off-target sites are then subjected to further validation using NGS-based amplicon short-read sequencing, rhAmpSeq™, or long-read sequencing, so ensuring a comprehensive characterization of genome editing outcomes.
If you are interested in our CAST-Seq technology or want to request our off-target service as a fee-for-service, please contact Sandra Ammann.
Our publications using CAST-Seq:
| Year | target(s) | Nuclease | Journal | Cells and Methode |
| 2024 | HBB, CCR5, GAPDH + DNA-PKcs inhibitor AZD7648 | spCas9 | Nature Biotech. | human HSCs, RPE
|
| 2024 | NCF1 | spCas9, Cas12a | Communications Biology | HSC CAST-Seq |
| 2024 | CD40LG + DNA-PKcs inhibitor AZD7648 | TALEN, spCas9 | Nature Biotech. | human HSCs CAST-Seq, |
| 2024 | mAlb | Cas9, AAV-Hiti | Cell Rep Med | in vivo CAST-Seq |
| 2024 | COL7A1, COL17A, LAMA3 | SpCas9, D10ASaCas9 | Mol Ther | CAST |
| 2024 | ELANE | Cas9HiFi, Cas9D10A | Mol Ther | D-CAST |
| 2023 | CCR5 (TALEN) | TALEN | Front Genome Ed. | T-CAST |
| 2023 | CD40L, CSF2 | Cas9 | Cells | double KO, CAST-Seq |
| 2023 | mUnc13d | spCas9 | JACI | in vivo, mouse HSCs, CAST-Seq |
| 2023 | CCR5 CRISPR/Cas9-CtIP-dnRNF168 | spCas9, Cas9-CtIP-dnRNF168 | NAR | CAST-Seq |
| 2023 | CD3Z | spCas9 | Blood | T and NK cells CAST-Seq |
| 2023 | CD123 | Cas9 | J Exp Med | human HSCs CAST-Seq |
| 2023 | HBB (p53i) | Cas9 | Nat Commun | human HSCs CAST-Seq |
| 2023 | globin | Cas9 | Mol Ther Nucleic Acids | human HSC, CAST-Seq |
| 2023 | mHao1 | D10ASaCas9 | EMBO Mol Med | in vivo, D-CAST |
| 2021 | rhCD33 | Cas9 | Mol Ther | NHP, CAST-Seq |
| 2021 | CCR5, HBB, FANCF, VEGFA, RAG1 | Cas9, Cas9HIFI, TALEN | Cell Stem Cell | HSCs T-CAST |
Dr. Sandra Ammann
Project Manager
Research & Development
Medical Center Freiburg
Institute for Transfusion Medicine and Gene Therapy
at Center for Translational Cell Research
Breisacher Straße 115
79106 Freiburg
+49 761 270 77748
Email:
Sandra Ammann