Scientists create new tool to identify genomic safe harbor sites in specific tissues

Scientists at St. Jude Children’s Research Hospital have developed a tool that can find safe locations to insert genes into human DNA. The tool is an early step in the process of improving the safety and effectiveness of gene and cell therapies. The work is published today in genomic biology.

We created the Google Maps for editing the genome. With this tool we offer a new approach to identify sites where a gene cassette can be safely integrated. We’ve created step-by-step guides so you can follow the steps and easily find safe havens in specific tissues.”

Yong Cheng, Ph.D., Co-Corresponding Author, St. Jude Department of Hematology

Gene therapy, in which a patient is given a functional copy of a dysfunctional gene, has proven successful in curing certain genetic disorders. However, the field has encountered safety issues, including unintended activation of an oncogene that led to cancer in some patients. In response, the field has been looking for ‘safe haven sites’ – spots in the genome where a gene can be inserted without causing cancer or other problems. Scientists created a pipeline that uses genomic and epigenetic information from specific tissues, such as blood cells, to find safe havens.

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A novel way to find safe port locations

The tool compares DNA sequences, which vary greatly between healthy people, using data from the 1000 Genomes Project. If a region of DNA is frequently deleted or inserted in healthy people, researchers could probably safely alter it with gene therapy, too.

“Our method is a new way to identify genomic safe harbor sites in a tissue-specific way,” Cheng said. “No one has tried it from that angle. Our first step was to find the genomic loci that have a high frequency of insertions or deletions in healthy individuals.”

If the DNA in a single cell were a string, it would be two meters long. But in addition to linear sequence, DNA can form complex 3D structures using chromatin, the proteins associated with DNA, to fit into a cell. Just like a string, DNA can have loops that affect its function. The St. Jude tool takes into account the presence of these loops and other structures when searching for accessible safe haven sites.

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“Our tool evaluates the 3D structure of DNA because human DNA is not a one-dimensional linear structure, it is actually 3D,” Chen said. “Thus, parts of the DNA can be far apart in the linear DNA sequence, but physically next to each other because of the loops of the 3D structure. In this case, 3D proximity is more important than linear distance.”

Balance between safety and therapeutic gene expression

“Safe gene therapy requires two things,” Cheng said. “First, maintaining high expression of the new gene. And second, integration must have minimal impact on the normal human genome, which is a major concern for people undergoing gene therapy.”

The scientists found that the genes placed in safe harbor locations identified by their tool maintained their expression over time. The researchers also showed that when they introduced a gene into one of the safe harbor sites identified by their tool, it affected neighboring genes less than a classic safe harbor site.

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The tool called Genomics and Epigenetic Guided Safe Harbor Mapper (GEG-SH Mapper) is freely available at

Authors and Funding

The study’s first authors are Dewan Shrestha of St. Jude and The University of Tennessee Health Science Center and Aishee Bag of Rutgers, The State University of New Jersey. The other authors of the study are

Ruiqiong Wu, Xing Tang and Qian Qi of St. Jude; Yeting Zhang and co-author Jinchuan Xing from Rutgers, The State University of New Jersey.

The study was supported by grants from the National Cancer Institute (P30 CA021765), National Institutes of Health (R35GM133614), St. Jude Collaborative Research Consortium on Novel Gene Therapies for Sickle Cell Disease (SCD), Human Genetics Institute of New Jersey and supports ALSAC, St. Jude’s fundraising and awareness organization.


St. Jude Children’s Research Hospital

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