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Whole-Genome Sequencing Plus AI Yields Same-Day Genetic Diagnoses

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Sebastiana
Caption: Rapid whole-genome sequencing helped doctors diagnose Sebastiana Manuel with Ohtahara syndrome, a neurological condition that causes seizures. Her data are now being used as part of an effort to speed the diagnosis of other children born with unexplained illnesses. Credits: Getty Images (left); Jenny Siegwart (right).



Back in April 2003, when the international Human Genome Project successfully completed the first reference sequence of the human DNA blueprint, we were thrilled to have achieved that feat in just 13 years. Sure, the U.S. contribution to that first human reference sequence cost an estimated $400 million, but we knew (or at least we hoped) that the costs would come down quickly, and the speed would accelerate. How far we’ve come since then! A new study shows that whole genome sequencing—combined with artificial intelligence (AI)—can now be used to diagnose genetic diseases in seriously ill babies in less than 24 hours.

Take a moment to absorb this. I would submit that there is no other technology in the history of planet Earth that has experienced this degree of progress in speed and affordability. And, at the same time, DNA sequence technology has achieved spectacularly high levels of accuracy. The time-honored adage that you can only get two out of three for “faster, better, and cheaper” has been broken—all three have been dramatically enhanced by the advances of the last 16 years.

Rapid diagnosis is critical for infants born with mysterious conditions because it enables them to receive potentially life-saving interventions as soon as possible after birth. In a study in Science Translational Medicine, NIH-funded researchers describe development of a highly automated, genome-sequencing pipeline that’s capable of routinely delivering a diagnosis to anxious parents and health-care professionals dramatically earlier than typically has been possible [1].

While the cost of rapid DNA sequencing continues to fall, challenges remain in utilizing this valuable tool to make quick diagnostic decisions. In most clinical settings, the wait for whole-genome sequencing results still runs more than two weeks. Attempts to obtain faster results also have been labor intensive, requiring dedicated teams of experts to sift through the data, one sample at a time.

In the new study, a research team led by Stephen Kingsmore, Rady Children’s Institute for Genomic Medicine, San Diego, CA, describes a streamlined approach that accelerates every step in the process, making it possible to obtain whole-genome test results in a median time of about 20 hours and with much less manual labor. They propose that the system could deliver answers for 30 patients per week using a single genome sequencing instrument.

Here’s how it works: Instead of manually preparing blood samples, his team used special microbeads to isolate DNA much more rapidly with very little labor. The approach reduced the time for sample preparation from 10 hours to less than three. Then, using a state-of-the-art DNA sequencer, they sequence those samples to obtain good quality whole genome data in just 15.5 hours.

The next potentially time-consuming challenge is making sense of all that data. To speed up the analysis, Kingsmore’s team took advantage of a machine-learning system called MOON. The automated platform sifts through all the data using artificial intelligence to search for potentially disease-causing variants.

The researchers paired MOON with a clinical language processing system, which allowed them to extract relevant information from the child’s electronic health records within seconds. Teaming that patient-specific information with data on more than 13,000 known genetic diseases in the scientific literature, the machine-learning system could pick out a likely disease-causing mutation out of 4.5 million potential variants in an impressive 5 minutes or less!

To put the system to the test, the researchers first evaluated its ability to reach a correct diagnosis in a sample of 101 children with 105 previously diagnosed genetic diseases. In nearly every case, the automated diagnosis matched the opinions reached previously via the more lengthy and laborious manual interpretation of experts.

Next, the researchers tested the automated system in assisting diagnosis of seven seriously ill infants in the intensive care unit, and three previously diagnosed infants. They showed that their automated system could reach a diagnosis in less than 20 hours. That’s compared to the fastest manual approach, which typically took about 48 hours. The automated system also required about 90 percent less manpower.

The system nailed a rapid diagnosis for 3 of 7 infants without returning any false-positive results. Those diagnoses were made with an average time savings of more than 22 hours. In each case, the early diagnosis immediately influenced the treatment those children received. That’s key given that, for young children suffering from serious and unexplained symptoms such as seizures, metabolic abnormalities, or immunodeficiencies, time is of the essence.

Of course, artificial intelligence may never replace doctors and other healthcare providers. Kingsmore notes that 106 years after the invention of the autopilot, two pilots are still required to fly a commercial aircraft. Likewise, health care decisions based on genome interpretation also will continue to require the expertise of skilled physicians.

Still, such a rapid automated system will prove incredibly useful. For instance, this system can provide immediate provisional diagnosis, allowing the experts to focus their attention on more difficult unsolved cases or other needs. It may also prove useful in re-evaluating the evidence in the many cases in which manual interpretation by experts fails to provide an answer.

The automated system may also be useful for periodically reanalyzing data in the many cases that remain unsolved. Keeping up with such reanalysis is a particular challenge considering that researchers continue to discover hundreds of disease-associated genes and thousands of variants each and every year. The hope is that in the years ahead, the combination of whole genome sequencing, artificial intelligence, and expert care will make all the difference in the lives of many more seriously ill babies and their families.

Reference:

[1] Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Clark MM, Hildreth A, Batalov S, Ding Y, Chowdhury S, Watkins K, Ellsworth K, Camp B, Kint CI, Yacoubian C, Farnaes L, Bainbridge MN, Beebe C, Braun JJA, Bray M, Carroll J, Cakici JA, Caylor SA, Clarke C, Creed MP, Friedman J, Frith A, Gain R, Gaughran M, George S, Gilmer S, Gleeson J, Gore J, Grunenwald H, Hovey RL, Janes ML, Lin K, McDonagh PD, McBride K, Mulrooney P, Nahas S, Oh D, Oriol A, Puckett L, Rady Z, Reese MG, Ryu J, Salz L, Sanford E, Stewart L, Sweeney N, Tokita M, Van Der Kraan L, White S, Wigby K, Williams B, Wong T, Wright MS, Yamada C, Schols P, Reynders J, Hall K, Dimmock D, Veeraraghavan N, Defay T, Kingsmore SF. Sci Transl Med. 2019 Apr 24;11(489).

Links:

DNA Sequencing Fact Sheet (National Human Genome Research Institute/NIH)

Genomics and Medicine (NHGRI/NIH)

Genetic and Rare Disease Information Center (National Center for Advancing Translational Sciences/NIH)

Stephen Kingsmore (Rady Children’s Institute for Genomic Medicine, San Diego, CA)

NIH Support: National Institute of Child Health and Human Development; National Human Genome Research Institute; National Center for Advancing Translational Sciences


How Kids See the World Depends a Lot on Genetics

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Baby in eye gaze study

Caption: Child watches video while researchers track his eye movements.
Credit: Washington University School of Medicine, St. Louis

From the time we are born, most of us humans closely watch the world around us, paying special attention to people’s faces and expressions. Now, for the first time, an NIH-funded team has shown that the ways in which children look at faces and many other things are strongly influenced by the genes they’ve inherited from their parents.

The findings come from experiments that tracked the eye movements of toddlers watching videos of other kids or adult caregivers. The experiments showed that identical twins—who share the same genes and the same home environment—spend almost precisely the same proportion of time looking at faces, even when watching different videos. And when identical twins watched the same video, they tended to look at the same thing at almost exactly the same time! In contrast, fraternal twins—who shared the same home environment, but, on average, shared just half of their genes—had patterns of eye movement that were far less similar.

Interestingly, the researchers also found that the visual behaviors most affected in children with autism spectrum disorder (ASD)—attention to another person’s eyes and mouth—were those that also appeared to be the most heavily influenced by genetics. The discovery makes an important connection between two well-known features of ASD: a strong hereditary component and poor eye contact with other people.


Preeclampsia: Study Highlights Need for More Effective Treatment, Prevention

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Obstetrics Exam

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It’s well known that preeclampsia, a condition characterized by a progressive rise in a pregnant woman’s blood pressure and appearance of protein in the urine, can have negative, even life-threatening impacts on the health of both mother and baby. Now, NIH-funded researchers have documented that preeclampsia is also taking a very high toll on our nation’s economic well-being. In fact, their calculations show that, in 2012 alone, preeclampsia-related care cost the U.S. health care system more than $2 billion.

These findings are especially noteworthy because preeclampsia rates in the United States have been steadily rising over the past 30 years, fueled in part by increases in average maternal age and weight. This highlights the urgent need for more research to develop new and more effective strategies to protect the health of all mothers and their babies.


Autism Spectrum Disorder: Progress Toward Earlier Diagnosis

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Sleeping baby

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Research shows that the roots of autism spectrum disorder (ASD) generally start early—most likely in the womb. That’s one more reason, on top of a large number of epidemiological studies, why current claims about the role of vaccines in causing autism can’t be right. But how early is ASD detectable? It’s a critical question, since early intervention has been shown to help limit the effects of autism. The problem is there’s currently no reliable way to detect ASD until around 18–24 months, when the social deficits and repetitive behaviors associated with the condition begin to appear.

Several months ago, an NIH-funded team offered promising evidence that it may be possible to detect ASD in high-risk 1-year-olds by shifting attention from how kids act to how their brains have grown [1]. Now, new evidence from that same team suggests that neurological signs of ASD might be detectable even earlier.


Aging Research: Plasma Protein Revitalizes the Brain

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Elixir of youth?For centuries, people have yearned for an elixir capable of restoring youth to their aging bodies and minds. It sounds like pure fantasy, but, in recent years, researchers have shown that the blood of young mice can exert a regenerative effect when transfused into older animals. Now, one of the NIH-funded teams that brought us those exciting findings has taken an early step toward extending them to humans.

In their latest work published in Nature, the researchers showed that blood plasma collected from the umbilical cords of newborn infants possesses some impressive rejuvenating effects [1]. When the human plasma was infused into the bloodstream of old mice, it produced marked improvements in learning and memory. Additional experiments traced many of those cognitive benefits to a specific protein called TIMP2—an unexpected discovery that could pave the way for the development of brain-boosting drugs to slow the effects of aging.


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