Stories about: precision medicine

Forecasting the convergence of artificial intelligence and precision medicine

Image of artificial DNA, which in combination with other artificial intelligence could contribute to an artificial model of the immune system
Will an artificial model of the immune system be the key to discovering new, precision vaccines?

This is part I of a two-part blog series recapping the 2018 BIO International Convention.

At the 2018 BIO International Convention last week, it was clear what’s provoking scientific minds in industry and academia — or at least those of the Guinness-world-record-making 16,000 people in attendance. Artificial intelligence, machine learning and their implications for tailor-made medicine bubbled up across all BIO’s educational tracks and a majority of discussions about the future state of biotechnology. Panelists from Boston Children’s Hospital also contributed their insights to what’s brewing at the intersection of these burgeoning fields.

Isaac Kohane, MD, PhD, former chair of Boston Children’s Computational Health and Informatics Program, spoke on a panel about how large-scale patient data — if properly harnessed and analyzed for health and disease trends — is a virtual goldmine for precision medicine insights. Patterns gleaned from population health data or electronic health records, for example, could help identify which subgroups of patients who might respond better to specific therapies.

According to Kohane, who is currently the Marion J. Nelson Professor of Biomedical Informatics and Pediatrics at Harvard Medical School (HMS), we will soon be leveraging artificial intelligence to go through patient records and determine exactly what doctors were thinking when they saw patients.

“We’ve seen again and again that data abstraction by artificial intelligence is better than abstraction by human analysts when performed at the scale of millions of clinical notes across thousands of patients,” said Kohane.

And based on what we heard at BIO, artificial intelligence will revolutionize more than patient data mining. It will also transform the way we design precision therapeutics — and even vaccines — from the ground up.

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Precision medicine for end-stage kidney failure? 40 percent of kids needing transplants have identifiable mutations

People forming a kidney shape - indicating that not all ESRD is alike and that it can have multiple genetic causes

In adults, end-stage renal disease, or ESRD, is most commonly a complication of diabetes or hypertension. In children, teens and young adults, it’s a different picture entirely. New research finds that more than half of people needing a kidney transplant before age 25 have a congenital anomaly of the kidney or urinary tract, and that 40 percent have an identifiable genetic cause of ESRD. Knowing these genetic underpinnings can inform better care for patients with kidney disease, says study leader Friedhelm Hildebrandt, MD, chief of the Division of Nephrology at Boston Children’s Hospital.

Hildebrandt and his colleagues drew on 263 families whose child received a new kidney at Boston Children’s between 2007 and 2017, before the age of 25. In 68 families, the team was able to perform whole-exome sequencing, comparing their DNA with a normal reference sample.

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Elusive epilepsy mutations begin to yield up their secrets

mosaic epilepsy mutations concept
Fawn Gracey illustration

Anti-seizure drugs don’t work in about a third of people with epilepsy. But for people with focal epilepsy, whose seizures originate in a discrete area of the brain, surgery is sometimes an option. The diseased brain tissue that’s removed also offers a rare opportunity to discover epilepsy-related genes.

Many mutations causing epilepsy have been discovered by testing DNA taken from the blood. But it’s becoming clear that not all epilepsy mutations show up on blood tests. So-called somatic mutations can arise directly in tissues like the brain during early prenatal development. Even within the brain, these mutations may affect only a fraction of the cells — those descended from the original mutated cell. This can create a “mosaic” pattern, with affected and unaffected cells sometimes intermingling.

One of the first such mutations to be described, by Ann Poduri, MD, MPH, and colleagues at Boston Children’s Hospital in 2012, was in Dante, a young boy who was having relentless daily seizures. The entire right side of Dante’s brain was malformed and enlarged, and he underwent a drastic operation, hemispherectomy, to remove it. Only later, studying brain samples from Dante and similar children, did Poduri find the genetic cause: a mutation in the gene AKT3. It affected only about a third of Dante’s brain cells. 

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Single-shot protection? Building a better hepatitis B vaccine for newborns

newborn vaccines
(Illustrations: Elena Hartley)

The hepatitis B vaccine is one of only three vaccines that are routinely given to newborns in the first days of life. But the current hepatitis B vaccine has limitations: multiple “booster” doses are needed, and it can’t be given to premature babies weighing less than 2 kg.

Annette Scheid, MD, a neonatologist at Brigham and Women’s Hospital, is interested in leveraging infant immune differences to create a better hepatitis B vaccine for newborns. “The reality is that we have to vaccinate several times,” she says. “But we all dream of a vaccine that you give only once.”

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Digital doctoring, big data and AI: Five takeaways

digital health

Big data and artificial intelligence are reshaping our world. Earlier this month, at Computefest 2018, organized by the Institute for Applied Computational Science at Harvard University, held the symposium, “The Digital Doctor: Health Care in an Age of AI and Big Data.” Speakers were:

  • Finale Doshi-Velez, PhD, Assistant Professor of Computer Science, Harvard University
  • Matt Might, Director, Hugh Kaul Personalized Medicine Institute, University of Alabama at Birmingham
  • John Brownstein, PhD, Chief Innovation Officer and Director, Computational Epidemiology Lab, Boston Children’s Hospital
  • Marzyeh Ghassemi, PhD, Visiting Researcher, Google’s Verily; Postdoctoral Fellow, Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology
  • Jennifer Chayes, Managing Director, Microsoft Research New England and New York City
  • Emery Brown, PhD, Professor of Medical Engineering and Computational Neuroscience, Massachusetts Institute of Technology

Here are Vector’s five takeaways from the symposium:

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Patients’ individual genomes may affect efficacy, safety of gene editing

gene editing - truck delivering code
Subtle genetic variants in or near the gene editing target site could cause reagents to miss an address or arrive at the wrong one, researchers say.

Gene editing has begun to be tested in clinical trials, using CRISPR-Cas9, zinc finger nucleases (ZFN) and other technologies to directly edit DNA inside people’s cells. Multiple trials are in the recruiting or planning stages. But a study in PNAS this week raises a note of caution, finding that person-to-person genetic differences may undercut the efficacy of the gene editing process or, in more rare cases, cause a potentially dangerous “off target” effect.

The study adds to evidence that gene editing may need to be adapted to each patient’s genome, to ensure there aren’t variants in DNA sequence in or near the target gene that would throw off the technology.

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MATCHing precision medicine to all kids with cancer

Image of human neuroblastoma tumor cells. A new nationwide clinical trial called pediatric MATCH will utilize genomic sequencing to match children with individualized, targeted drugs matched to their tumor profile.
Human neuroblastoma cells.

A multi-center clinical trial is now offering nationwide genetic profiling services to pediatric and young adult cancer patients across the U.S. The goal is to identify gene mutations that can be individually matched with targeted drugs.

“This is the first-ever nationwide precision medicine clinical trial for pediatric cancer,” says pediatric oncologist Katherine Janeway, MD, clinical director of the solid tumor center at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center.

Sponsored by the National Institute of Cancer (NCI) and the Children’s Oncology Group (COG), the so-called NCI-COG Pediatric MATCH trial will screen patients’ tumors for more than 160 gene mutations related to cancer. Nearly 1,000 patients are expected to participate in the trial and it is estimated that 10 percent of those patients will be matched with a targeted therapy.

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In search of young medical geneticists

Nina Gold, MD, is Chief Resident of Medical Genetics at Boston Children’s Hospital.

During a quiet stretch of my final year in medical school, I read Sir Arthur Conan Doyle’s Sherlock Holmes stories. A master observer, the detective found secrets in wrinkles of clothes, tints of hair, scents of perfume, never satisfied until the truth was revealed. Sherlock was, simply, an expert diagnostician.

In the spring of 2014, I became the first student in my medical school to pursue residency training in a combined pediatrics and medical genetics program. Like Sherlock, pediatric geneticists are stalwart investigators. They are often called into a case long after other consultants and tasked with bringing a family’s diagnostic odyssey to an end. But unlike the emotionally obtuse fictional detective, geneticists must describe their findings with empathy and clarity to concerned families after they solve a mystery.

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If I knew then what I know now: The need for infrastructure to enable precision medicine

precision medicine - closing the infrastructure loop
For precision medicine to happen, we need to be able to close the loop when genetic discoveries are made.

Catherine Brownstein, MPH, PhD, is scientific director of The Manton Center for Orphan Disease Research at Boston Children’s Hospital. Kelsey Graber, MSc, is a research assistant in the Developmental Neuropsychiatry Program. Joseph Gonzalez-Heydrich, MD, is director of the Developmental Neuropsychiatry Program at Boston Children’s Hospital.

Research implicating rare genetic variants in medical and psychiatric diseases is quickly accumulating. This expanding knowledge should be taken into account when making treatment decisions for patients carrying these variants — as well as other family members — even when that knowledge comes after the patient is tested. But all too often, medical institutions are unable to go back and update the information given to families. We need a better infrastructure to enable precision medicine.

This problem recently surfaced in our psychiatry practice. It came to our attention because of a young boy with mild coordination delays and learning disabilities. At age 6, he started experiencing daily hallucinations such as voices telling him to kill his classmates.

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From mice to humans: Genetic syndromes may be key to finding autism treatment

Boy and a mouse eye-to-eye
(Aliaksei Lasevich/stock.adobe.com)

A beautiful, happy little girl, Emma is the apple of her parents’ eyes and adored by her older sister. The only aspect of her day that is different from any other 6-month-old’s is the medicine she receives twice a day as part of a clinical trial for tuberous sclerosis complex (TSC).

Emma’s mother was just 20 weeks pregnant when she first heard the words “tuberous sclerosis,” a rare genetic condition that causes tumors to grow in various organs of the body. Prenatal imaging showed multiple benign tumors in Emma’s heart.

Emma displays no symptoms of her disease, except for random “spikes” on her electroencephalogram (EEG) picked up by her doctors at Boston Children’s Hospital. The medication she is receiving is part of the Preventing Epilepsy Using Vigabatrin in Infants with TSC (PREVeNT) trial. Her mother desperately hopes it is the active antiepileptic drug, vigabatrin, rather than placebo.

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