News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups
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Clinical Laboratories and Pathology Groups
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Proteomics-based Clinical Laboratory Testing May Get a Major Boost as Google’s DeepMind Research Lab Is Making Public Its Entire AI Database of Human Protein Predictions

Dec 20, 2021 | Clinical Laboratory Middleware, Informatics, Analytics, Digital Pathology, Laboratory Instruments & Laboratory Equipment, Laboratory Pathology, Laboratory Resources, Molecular Diagnostics, Genetic Testing, Whole Gene Sequencing, Precision Medicine

DeepMind hopes its unrivaled collection of data, enabled by artificial intelligence, may advance development of precision medicines, new medical laboratory tests, and therapeutic treatments

‘Tis the season for giving, and one United Kingdom-based artificial intelligence (AI) research laboratory is making a sizeable gift. After using AI and machine learning to create “the most comprehensive map of human proteins,” in existence, DeepMind, a subsidiary of Alphabet Inc. (NASDAQ:GOOGL), parent company of Google, plans to give away for free its database of millions of protein structure predictions to the global scientific community and to all of humanity, The Verge reported.

Pathologists and clinical laboratory scientists developing proteomic assays understand the significance of this gesture. They know how difficult and expensive it is to determine protein structures using sequencing of amino acids. That’s because the various types of amino acids in use cause the [DNA] string to “fold.” Thus, the availability of this data may accelerate the development of more diagnostic tests based on proteomics.

“For decades, scientists have been trying to find a method to reliably determine a protein’s structure just from its sequence of amino acids. Attraction and repulsion between the 20 different types of amino acids cause the string to fold in a feat of ‘spontaneous origami,’ forming the intricate curls, loops, and pleats of a protein’s 3D structure. This grand scientific challenge is known as the protein-folding problem,” a DeepMind statement noted.

Enter DeepMind’s AlphaFold AI platform to help iron things out. “Experimental techniques for determining structures are painstakingly laborious and time consuming (sometimes taking years and millions of dollars). Our latest version [of AlphaFold] can now predict the shape of a protein, at scale and in minutes, down to atomic accuracy. This is a significant breakthrough and highlights the impact AI can have on science,” DeepMind stated.

Release of Data Will Be ‘Transformative’

In July, DeepMind announced it would begin releasing data from its AlphaFold Protein Structure Database which contains “predictions for the structure of some 350,000 proteins across 20 different organisms,” The Verge reported, adding, “Most significantly, the release includes predictions for 98% of all human proteins, around 20,000 different structures, which are collectively known as the human proteome. By the end of the year, DeepMind hopes to release predictions for 100 million protein structures.”

According to Edith Heard, PhD, Director General of the European Molecular Biology Laboratory (EMBL), the open release of such a dataset will be “transformative for our understanding of how life works,” The Verge reported.  

Demis Hassabis

“I see this as the culmination of the entire 10-year-plus lifetime of DeepMind,” company CEO and co-founder Demis Hassabis (above), told The Verge. “From the beginning, this is what we set out to do: to make breakthroughs in AI, test that on games like Go and Atari, [and] apply that to real-world problems, to see if we can accelerate scientific breakthroughs and use those to benefit humanity.” The release of DeepMind’s entire protein prediction database will certainly do that. Clinical laboratory scientists worldwide will have free access to use it in developing new precision medicine treatments based on proteomics. (Photo copyright: BBC.)

Free Data about Proteins Will Accelerate Research on Diseases, Treatments

Research into how protein folds and, thereby, functions could have implications to fighting diseases and developing new medicines, according to DeepMind. 

“This will be one of the most important datasets since the mapping of the human genome,” said Ewan Birney, PhD, Deputy Director General of the EMBL, in the DeepMind statement. EMBL worked with DeepMind on the dataset.

DeepMind protein prediction data are already being used by scientists in medical research. “Anyone can use it for anything. They just need to credit the people involved in the citation,” said Demis Hassabis, DeepMind CEO and Co-founder, in The Verge.

In a blog article, Hassabis listed several projects and organizations already using AlphaFold. They include:

“As researchers seek cures for diseases and pursue solutions to other big problems facing humankind—including antibiotic resistance, microplastic pollution, and climate change—they will benefit from fresh insights in the structure of proteins,” Hassabis wrote.

Because of the deep financial backing that Alphabet/Google can offer, it is reasonable to predict that DeepMind will make progress with its AI technology that regularly adds capabilities and accuracy, allowing AlphaFold to be effective for many uses.

This will be particularly true for the development of new diagnostic assays that will give clinical laboratories better tools for diagnosing disease earlier and more accurately.

—Donna Marie Pocius

Related Information:

DeepMind Creates ‘Transformative’ Map of Human Proteins Drawn by Artificial Intelligence

AlphaFold Can Accurately Predict 3D Models of Protein Structures and Has the Potential to Accelerate Research in Every Field of Biology

Putting the Power of AlphaFold into the World’s Hands

Highly Accurate Protein Structure Prediction with AlphaFold

Top-5 Diagnostics Trends Identified by Kalorama Will Impact In Vitro Diagnostics Manufacturers, Medical Laboratories in 2017

Apr 3, 2017 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations

Report states IVD companies are focusing on core lab, seeking China FDA approval, and targeting urgent care

Several of the same powerful trends reshaping healthcare and clinical laboratory services are having equally significant influence on in vitro diagnostics (IVD) manufacturers. In particular, the consolidation of hospitals and physicians, as well as the emergence of new sites of service—such as urgent care centers and retail clinics—are motivating IVD companies to tailor new diagnostic systems to the unique needs of these entities.

Kalorama, a division of MarketResearch.com, has released its list of Top-Trends that will affect IVD developers in 2017. IVDs are at the heart of the medical laboratory industry. Thus, these reports are critical to keeping clinical laboratory managers and pathology groups informed on anything that could affect the production, voracity, and availability of diagnostic testing. (more…)

Researchers at Howard Hughes Medical Institute Develop Blood Test That Reveals a Patient’s Viral History; Could Reduce Unnecessary Clinical Laboratory Testing

Dec 30, 2015 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing

The VirScan test gives doctors insight into a patient’s lifetime exposure to viruses and thus may be developed into a useful medical laboratory test

Scientists and pathologists are learning that blood is like a time capsule, holding precious information about exposure to viruses over the years—chickenpox at five, mononucleosis at 18, flu at 40. You get the idea.

Now, researchers at Howard Hughes Medical Institute (HHMI)  have found a way to tap that entire data stream, so to speak. An inexpensive blood test, they say, reveals every virus that has passed through the body over time.

New Discoveries Could Lead to a Useful Clinical Laboratory Test

The testing method, called VirScan by researchers, is an efficient alternative to current medical laboratory tests that test for specific viruses one at a time, according to an HHMI news statement about the new technology. (more…)

More Use of Whole Gene Sequencing Poised to Play Important New Roles in Microbiology and Medical Laboratory Testing

Jan 30, 2012 | Laboratory News, Laboratory Pathology

Cheaper, faster, and more accurate rapid gene sequencing technologies show great promise in identifying infectious disease agents

In clinical laboratories across the nation, microbiology has greatly benefited from the introduction of molecular diagnostics in clinical practice. Now the field of microbiology is poised to undergo a more profound transformation of clinical practice, due to advances in whole genome sequencing.

Leaders in this field are calling these developments “transformative” and say they have the potential to change “all aspects of microbiology.” The driver to this emerging trend is advanced technology that makes it possible to sequence the whole gene sequence of an organism in a day or less, for a cost that is $1,000 and falling rapidly.

In the past six months, microbiologists and pathologists at such hospitals as Methodist Hospital in Houston, Texas, have begun to do whole genome sequencing of microbes found in specimens collected from patients arriving in the emergency room. The New York Times wrote about these developments in a story titled “The New Generation of Microbe Hunters,” that it published on August 29, 2011.

(more…)

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