CRISPR results in DNA damage

New research from the University of Adelaide shows large scale DNA deletions when the CRISPR genome editing technique is used (see below).

The scientist who led the research is Paul Thomas, who is developing gene drive rats and mice for the GBIRd (Genetic Biocontrol of Invasive Rodents) programme. The aim of GBIRd is species elimination – to eradicate "problematic" rodent populations using CRISPR.

The GBIRd programme has also run into problems with CRISPR, as Thomas and his colleagues found that "The technique worked inconsistently in lab mice, and myriad technological hurdles remain before researchers could even consider releasing the tool in the wild."
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We can change human DNA. We're just not sure which bits

By Liam Mannix
The Age, 9 August 2018
https://www.theage.com.au/national/we-can-change-human-dna-we-re-just-not-sure-which-bits-20180808-p4zw83.html

It was a story covered on front pages around the world.

The first viable genetically altered human embryos.

American scientists had delicately snipped disorder-causing genes from a fertilised egg's genetic code, seemingly without harming it.

Designer babies were on the way.

But new Australian research suggests the cut wasn’t so clean. Significant damage may have been done to the DNA.

It points to a huge problem with genetic editing: it is easy to cut out one gene, but very difficult to be 100 per cent sure other genes weren’t changed in the process.

Those changes might only become clear years later.

“We’re very good at cutting,” says Professor Paul Thomas, who led the research. “We’re still learning about what happens after you cut.”

At this story's heart is a technique called CRISPR, among the most-important scientific advances in the last 20 years. It allows scientists to cut and paste segments of DNA almost as simply as you cut and paste words on a computer.

It opened up a golden age of DNA editing, one that seemed to climax last year with the spectacular announcement that a disease causing mutation in human embryos had been corrected for the first time.

A team led by Shoukhrat Mitalipov of Oregon Health and Science University announced they had sliced out genes that cause a heart condition called hypertrophic cardiomyopathy, among the most-common causes of sudden death in young athletes.

‘One Giant Step For Designer Babies,’ ran the headlines.

But in Adelaide, Paul Thomas wasn’t so sure. Professor Thomas, who works at the University of Adelaide and the South Australian Health and Medical Research Institute, had been trying to slice up mice embryos with CRISPR for years but found his ‘scissors’ often cut much bigger holes in the code than he wanted.

Why was their technique working while his failed?

So Professor Thomas delicately recreated Mitalipov’s work using mice embryos (the government bans local researchers from experimenting on human embryos).

CRISPR faithfully sliced out the target, just like in Mitalipov’s study. So far so good. But Professor Thomas kept looking, surveying a much wider region of the DNA for changes.

In almost half his samples, he found more than 100 lines of genetic code had been deleted.

“Failure to detect these large deletions could lead to disastrous outcomes in potential clinical applications,” his research team write in their paper, published Thursday in Nature.

Why didn’t Mitalipov see these changes?

The answer, Professor Thomas thinks, goes right to the heart of the deeply troubling problems posed by genetic editing.

Humans get two copies of every gene, one from mum and one from dad.

Mitalipov sliced out the diseased gene on the father’s side, then scanned the DNA to see what had happened. He saw only good, fixed DNA - so he assumed the cell simply copied the mother's good gene.

But the technique scientists usually use to scan DNA is limited in one crucial respect. It can tell if a gene is there, but not how many copies there are.

Rather than seeing two copies of the good gene, Thomas’s study suggests Mitalipov was seeing only one copy of the good gene – and a really big hole.

Mitalipov’s team has since responded to Professor Thomas’s study with more data showing, they claim, that there were no large deletions in the human embryo DNA.

Professor Thomas disagrees, while other researchers who spoke to Fairfax are divided.

“Paul is right in his system, but he did it in a mouse. The original authors did it in a human. It’s possible they could both be right,” says Professor Merlin Crossley, who leads a genetics lab at the University of NSW and was not involved in either study.

“But the bottom line is: we aren’t going to see designer babies any time soon.”