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What’s AlphaMissense? This new Google DeepMind tool analyses genetic mutations

What’s AlphaMissense? This new Google DeepMind tool analyses genetic mutations

Researchers at DeepMind, one of Google’s artificial intelligence (AI) companies, presented a new tool that predicts whether or not genetic mutations are potentially pathogenic, a breakthrough that could help research into rare diseases.

The tool focuses on so-called missense mutations, where there is a single nucleotide change, meaning one letter of the DNA code is affected.

If you compare DNA to the alphabet, a missense mutation is like a typo, and it’s one that can change the resulting amino acid.

An individual has around 9,000 of these mutations, most of which are benign. However, some of these mutations are responsible for diseases such as cystic fibrosis, sickle-cell anaemia, or cancer, DeepMind said.

Currently, four million of these mutations have been observed in humans, but only two per cent of them have been classified as either pathogenic or benign.

In total, there are 71 million possible mutations of this type. They were examined by the AlphaMissense tool, which was able to categorise 89 per cent of them, the company said.

How does AlphaMissense work?

Each mutation was given a score between 0 and 1, indicating the risk of it being pathogenic, i.e. causing disease. AlphaMissense predicted that 57 per cent were likely benign and 32 per cent were likely pathogenic, with the rest remaining uncertain.

The database has been made public and available to all scientists through GitHub, a platform to store and share computer code. A study on the findings was published on Tuesday in the journal Science.

“The authors demonstrate superior performance by AlphaMissense,» wrote experts Joseph Marsh and Sarah Teichmann in an article also published in Science.

The tool has been trained on a database of human and primate DNA, enabling it to recognise which genetic mutations are prevalent.

Jun Cheng, a scientist at Google DeepMind, explained that the tool can tell whether a protein sequence is worrying or not.

He added that the predictions could increase the rate of diagnosis of rare diseases and help to find new genes involved in the diseases.

Indirectly, this could lead to the development of new treatments, the researchers claim, warning, however, that AlphaMissense should not be used on its own to make a diagnosis.

AlphaMissense was based on AlphaFold, another machine learning program presented by Google DeepMind in 2018, which had published the largest database of proteins with over 200 million structures available.

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