CRISPR has amazing promise – the ability to edit any gene. But it needs an RNA “guide sequence” to direct it to the gene it is supposed to edit (and ideally, only to that gene). Such guide sequences are usually made by looking at a set of reference genomes. However, these reference genomes come from only a few people, and do not capture the genetic diversity of much of humanity. CRISPR techniques will thus not work as well in populations whose genomes are not included, especially people with African ancestry, whose genomes are more diverse than those of other populations. Scientists are now working on tools that can include those who have previously been left out.
- CRISPR needs a specific RNA sequence to guide it to its target.
- Scientists unearthed ancestry issues in the Cancer Dependency Map.
- Free web tools can help generate more accurate and equitable CRISPR guide sequences.
CRISPR needs a specific RNA sequence to guide it to its target.
CRISPR has made it technically feasible to edit genes in animals, plants and people. When scientists want to design CRISPR to edit a certain gene, they start by designing an RNA sequence that matches part of that gene’s DNA sequence. This “guide RNA” is essential, as it brings CRISPR’s DNA-cutting enzyme to the proper place in the genome to cut.
“Ancestry differences mean CRISPR doesn’t always edit some genomes as intended, particularly in people of African descent, whose genomes are most likely to differ from those used to steer CRISPR to a specific gene.”
These guide RNA sequences are usually generated by looking at reference genomes to find appropriate sequences near the target gene. But these reference genomes come from only a small, relatively homogenous group of people. People from populations not represented in the reference genomes might have different DNA sequences near the gene to be edited, and, in that case, CRISPR made with the guide RNA won’t work for them because it won’t find the right gene. This is especially true for people of recent African descent, for two reasons: firstly, few if any African genomes were included in the set of reference genomes; and secondly, people of African descent tend to be genetically more diverse than Europeans or Asians, whose ancestors left Africa relatively recently in human history.
Scientists unearthed ancestry issues in the Cancer Dependency Map.
The Cancer Dependency Map is a project that used CRISPR to eliminate 18,000 genes in 1,000 cancer cell lines grown from individual human tumors. Its goal was to find genes that the cancers depend on – genes whose CRISPR-induced absence would cause the cancer cells to die. The reasoning was that if the cancer cells can’t live without these genes, the genes might be good drug targets.
“The CRISPR ancestry problem is an example of how excluding diverse populations in genomics studies ‘may inevitably contribute to cancer health inequity’.”
Overall, CRISPR didn’t knock out between 2% and 5% of the 18,000 target genes in the cancer cells. But researchers found that in the 41 cell lines that came from people with recent African ancestry, CRISPR was 20% more likely to miss these genes. Moreover, ancestry mismatches can cause CRISPR molecules to cut the genome in the wrong place, further diminishing the technique’s applicability and benefit to this population.
Free web tools can help generate more accurate and equitable CRISPR guide sequences.
The teams who found these problems developed free web tools to solve them. The Boehm and Beroukhim labs made Ancestrygarden.com, which compares a proposed CRISPR RNA guide sequence with tens of thousands of genomes from diverse populations instead of just the standard reference genomes previously used. And the Pinello lab made CRISPRme to check for off-target matches to ensure that the guide RNA leads the CRISPR only to the gene that should be cut and nowhere else.
About the Author
Jocelyn Kaiser is a staff writer for Science magazine.