Category Archives: Genetic medicine

Nathaly Sweeney, a neonatologist at Rady Children's Hospital-San Diego and researcher with Rady Children's Institute for Genomic Medicine, attends to a young patient in the hospital's neonatal intensive care unit. Jenny Siegwart/Rady Children's Institute for Genomic Medicine hide caption

Nathaly Sweeney, a neonatologist at Rady Children's Hospital-San Diego and researcher with Rady Children's Institute for Genomic Medicine, attends to a young patient in the hospital's neonatal intensive care unit.

When Nathaly Sweeney launched her career as a pediatric heart specialist a few years ago, she says, it was a struggle to anticipate which babies would need emergency surgery or when.

"We just didn't know whose heart was going to fail first," she says. "There was no rhyme or reason who was coming to the intensive care unit over and over again, versus the ones that were doing well."

Now, just a few years later, Sweeney has at her fingertips the results of the complete genome sequence of her sickest patients in a couple of days.

That's because of remarkable strides in the speed at which genomes can be sequenced and analyzed. Doctors who treat newborns in the intensive care unit are turning to this technology to help them diagnose their difficult cases.

Sweeney sees her tiny patients in the neonatal intensive care unit of Rady Children's Hospital in San Diego. Doctors there can figure out what's wrong with about two-thirds of these newborns without a pricey DNA test. The rest have been medical mysteries.

"We had patients that were lying here in the hospital for six or seven months, not doing very well," she says. "The physicians would refer them for rapid genome sequencing and would diagnose them with something we didn't even think of!"

Rady's Institute for Genomic Medicine, which has been pioneering this technology, has now sequenced the genomes of more than 1,000 newborns.

In a building across the street from the hospital, three $1 million sequencing machines form the core of the operation. Technicians tending to the NovaSeq 6000s can put DNA from babies (and often their parents) into the machine in the late afternoon and have a complete genome sequence back by 11 a.m. or noon the next day, says clinical lab scientist Luca Van der Kraan.

That fact is worth repeating: An entire genome is decoded in about 16 hours.

Kasia Ellsworth is one of the experts waiting in a nearby office to analyze the information. That task has shrunk from months to typically just four hours, thanks to increasingly sophisticated software.

Ellsworth inputs the baby's symptoms into the software, which then spits out a long list of genetic variants that might be related to the illness. She scrolls down the screen.

"I'm looking through a list of those variants and then basically deciding whether something may be truly contributing to the disease or not," she says.

About 40% of the time, a gene stands out, giving doctors a tentative diagnosis. Follow-up tests are often requested, and those can take several days. But in the meantime, doctors can sometimes act on the information they have in hand.

When she or a colleague makes a diagnosis, "You always feel very relieved, very happy and excited," she says. "But at the same time you kind of need to put it in perspective. What does it mean for the family, for the patient, for the clinician as well?"

Often it's a sense of relief. And for a minority of cases, it can affect the baby's treatment.

"We now are at the point where I think the evidence is overwhelming that a rapid genome sequence can save a child's life," says Dr. Stephen Kingsmore, the institute's director and the driving force behind this revolution.

By his reckoning, the results change the way doctors manage these cases about 40% of the time.

Treatments are available for only a small share of these rare diseases. In other cases, the information can help parents and doctors understand what's wrong with their baby even if there is no treatment or learn whether death is inevitable. "And there it's a very different conversation," Kingsmore says. "We help guide parents through picking an appropriate point at which to say enough is enough" and to end futile treatments.

Of course, Kingsmore highlights the happier outcomes. One example is a bouncy girl named Sebastiana, now approaching her third birthday.

As a newborn, Sebastiana Manuel was diagnosed with a rare disease after rapid genome sequencing. She is seen here at 11 months of age. Jenny Siegwart/Rady Children's Institute for Genomic Medicine hide caption

As a newborn, Sebastiana Manuel was diagnosed with a rare disease after rapid genome sequencing. She is seen here at 11 months of age.

He showed off her case recently in front of the Global Genes conference, a meeting of families with rare genetic conditions.

"She was critically ill in our intensive care unit," he tells the audience, "and in a couple of days we gave the doctors the answer. It's Ohtahara syndrome. It comes with this specific therapy. And she hasn't had a seizure in 2 1/2 years. She doesn't take any medication."

The audience applauds enthusiastically at an outcome that sounds miraculous. But when you meet Sebastiana and her mother, Dolores Sebastian, a more complicated story emerges.

Ohtahara syndrome isn't actually what made Sebastiana ill it's a term doctors use to describe newborn seizures. Those are actually a symptom of deeper brain issues. That was apparent the day she was born.

"She was acting weird and screaming and crying and turning purple and we weren't sure why," her mother says.

The hospital where Sebastiana was born rushed her to the neonatal intensive care unit, across town at Rady. She was having frequent seizures. The following days were a nightmare for Sebastian and her husband.

"I can't even describe it," she says. "I always keep on saying that at that moment I was kind of like dead, but I was walking."

The hospital ran a battery of tests to look for severe brain damage. They couldn't get to the bottom of it.

"They came in and offered us the genomic testing," Sebastian said. "They never told us how quick it would be."

She was surprised when the results were back in four days. The doctor told her they had identified a gene variant that can trigger seizures as well as do other harm to the brain.

"He said this is how we're going to go ahead and change her medications now and treat her," she says. And that made a "huge difference, [an] amazing difference."

Sebastiana was already on a medication that was helping control her seizures, but they sedated her to the extent that she needed a feeding tube. On the new medication, carbamazepine, she was alert and able to eat, and her seizures were still under control. Sebastian says her daughter is still taking that drug.

Controlling her seizures isn't a cure. Children who have this genetic variant, in a gene called KCNQ2, can have a range of symptoms from benign to debilitating. Sebastiana falls somewhere in between. For example, she has only a few words in her vocabulary as she approaches the age of 3.

"She took her first steps when she was 2 years old, so she's delayed in some things," Sebastian says, "but she's catching up very quickly. She has [physical therapy]; she's going to start speech therapy. She gets a lot of help but everything's working."

Sebastiana Manuel (second from left) with members of her family: Domingo Manuel Jr. (from left), Dolores Sebastian and Tony Manuel. Jenny Siegwart/Rady Children's Institute for Genomic Medicine hide caption

Sebastiana Manuel (second from left) with members of her family: Domingo Manuel Jr. (from left), Dolores Sebastian and Tony Manuel.

KCNQ2 variants are the most common genetic factor in epilepsy, causing about a third of all gene-linked cases and about 5% of all epilepsies. Sebastiana's case could have been diagnosed with a less expensive test. For example, Invitae geneticist Dr. Ed Esplin says his company offers a genetic screen for epilepsy that has a $1,500 list price and a two-week turnaround.

Rady's whole-genome test costs $10,000, Kingsmore says. But it casts a wider net, so it might provide useful information if a baby's seizures are caused by something other than epilepsy.

And Kingsmore says his test costs about as much as a single day in the NICU. "In some babies we avoid them being in the intensive care unit literally for months," he says.

Kingsmore and colleagues have published some evidence that their approach is cost-effective, based on an analysis of 42 cases.

Even so, most insurance companies and state Medicaid programs are still balking at the cost. Kingsmore says private donors are helping support this effort at Rady, which sequences about 10% of the babies in the NICU, and at more than a dozen others scattered from Honolulu to Miami. They send their samples to Rady for analysis.

Kingsmore is pushing to expand his network in the next few years, to reach 10,000 babies at several hundred children's hospitals.

Other providers are also starting to offer whole-genome sequencing. But Dr. Isaac Kohane, chair of the department of biomedical informatics at Harvard Medical School, worries that the technology is too unreliable.

Knowledge of genes and disease is evolving rapidly, so these analyses run the risk of either missing a diagnosis or making a mistaken one. Kohane says there's still a lot of dubious information there a typical person has 10 to 40 gene variants that the textbooks incorrectly identify as causing disease.

Kohane is part of a medical network that helps diagnose people with baffling diseases. A study from 2018 found "a third of the patients who actually come to us already had full genome sequences and interpretations," Kohane says. "They were just not correct."

Even so, Kohane sees this use in the NICU as a relatively fruitful use of gene sequencing. "This is one of the few areas where I think the Human Genome Project is really beginning to pay off in health care," he says, "but buyer beware, it's not something ready to be practiced in every hospital." (He supports the work at Rady in fact, he is a science adviser.)

Kingsmore is already looking ahead. "We want to solve the next bottleneck, which is, 'I don't have a great treatment for this baby,' " he says. That's a far greater challenge, and it's especially difficult for a mutation that has altered a baby's development in the womb. Those problems may often not be reversible.

Kingsmore is undeterred. "It's going to be an incredibly exciting time in pediatrics," he says.

You can contact NPR science correspondent Richard Harris at rharris@npr.org.

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Genome Sequencing In NICU Can Speed Diagnosis Of Rare Inherited Diseases : Shots - Health News - NPR

People should not make health decisions based on genetic tests they do at home, experts have warned.

The University of Southampton team,writing in the British Medical Journal, warn results can be unreliable.

The geneticists said the tests could be wrongly reassuring or lead to unnecessary worry.

23andMe, one of the companies offering tests, said there were many cases where results had prompted further checks and preventative treatment.

Prof Anneke Lucassen, president of the British Society for Genetic Medicine and a consultant in clinical genetics at University Hospital Southampton led the research.

She said: Genetic tests sold online and in shops should absolutely not be used to inform health decisions without further scrutiny.

Finding a health risk via these tests often does not mean a person will go on to develop the health problem in question, while reassuring results might be unreliable.

[T]he BMJ paper warns genetic tests often prioritise breadth over detail, citing a 23andMe test that checks for a few variants of Brca1 and 2, linked to breast and ovarian cancer risk, when there are actually thousands.

A 23andMe spokesman said its processes were extremely accurate and it spelt out exactly what its Brca test looked for.

Read full, original post: Genetic tests: Experts urge caution over home testing

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Consumer genetic tests shouldn't be used to make health decisions, experts warn - Genetic Literacy Project

James DeLine founded the Center for Special Children in La Farge to attend to the particular health needs of the Amish and Old Order Mennonite families in Wisconsin. The Center exists within the La Farge Medical Clinic, also started by DeLine, which is part of Vernon Memorial Health Care. Photo by David Tenenbaum

Editors note: A recent article in the Milwaukee Journal Sentinel reported on Dr. James DeLines work with the Wisconsin Amish community. This story describes how UWMadison and the Wisconsin Partnership Fund are helping the effort.

LA FARGE, Wisconsin There is no car in the driveway, neither phone nor electricity in the house. Handmade clothes dry on the line.

Its fall 2018, and La Farge physician James DeLine has brought us to talk with Barbara and Daniel Hochstetler, part of the large Amish population in Wisconsins Driftless Region.

Six of their 11 children live with siterosterolemia, an extremely rare disease that can cause joint damage, stroke or heart attack, due to accumulations of a plant-based fat akin to cholesterol.

DeLine has practiced family medicine in La Farge since 1983. In 2015 he started the Center for Special Children to care for Wisconsins large concentration of Amish or Old Order Mennonite people.

Rural doctors pride themselves on being able to treat a wide range of conditions in their patients, but DeLines practice brings him face to face with several rare genetic conditions that were present when the Amish and Mennonites immigrated from Europe to America and then Wisconsin.

And that, in turn, has brought DeLine into a close collaboration with specialists at the University of WisconsinMadison who have developed tests, and suggested treatments, for some of those conditions, including siterosterolemia.

Amish and Mennonite families avoid technologies that, they feel, would endanger the social cohesion that is key to their survival. Thus they do not own motor vehicles or use telephones or electricity in the home. Photo by David Tenenbaum

In quiet voices, DeLine and the Hochstetler parents recounted how they learned that the family carried a gene for the rare disease. Years previously, their son, Perry, had been seen at the La Farge clinic with painful arthritis and large lumps in his limbs. Later, when we discovered that a relative of his mother had sitosterolemia, DeLine explained, we thought back to this young man and with some searching, we found him, had gene testing done at UWMadison, and discovered that he too had the disease.

After starting medicine and changing his diet, Perrys elbow lumps began melting away, DeLine said. He has had no further arthritis, and his exercise tolerance has improved.

Eventually, with genetic testing at UWMadison, the mutation was diagnosed in six of the 11 Hochstetler children. Only then did Daniel volunteer that he had heart pain (likely just age catching up with me) during heavy exertion, was actually caused by a buildup of plaque in his heart arteries. After starting the same drug as his children, Daniel has improved, though he said he can still feel it once in a while if I exert myself.

DeLine has become an expert in the culture, family relationships, and medical needs of the Amish and Old Order Mennonites (sometimes called the Plain people).

Although their acceptance of technology is highly constricted by culture and religion, the Plain benefit from DeLines hybrid of 19th century rural doctoring with 21st century genetic medicine.

Chris Seroogy, professor of pediatrics at UWMadison, is a long-time collaborator in the effort to bring 21st century health care to Wisconsins Plain populations. Photo by Robert C. Thayer

The genetic work has relied on clinicians from the School of Medicine and Public Health, and on testing at the State Laboratory of Hygiene, both at UWMadison. The State Lab has already developed fast, low-cost diagnostic tests for more than 30 conditions afflicting Plain populations in Wisconsin.

Vanessa Horner, director of cytogenetic services and molecular genetics at the State Lab, said that once a test has been developed and validated, it becomes a clinical assay that must be performed in a certified laboratory such as hers. Its a highly regulated, rigorous testing environment.

Funding for these tests and related activities came from grants totaling $800,000 from the Wisconsin Partnership Program in the School of Medicine and Public Health. Addressing the health care needs of Wisconsin communities is a priority for the Wisconsin Partnership Program, said Richard Moss, chair of the partnership education and research committee.

This teams innovative and successful community-engaged research has resulted in increased newborn screenings and affordable genetic testing that have the potential to spare our states Plain families from fatal medical conditions and costly hospitalizations, added Moss, senior associate dean for basic research, biotechnology and graduate studies.

One newborn screening test created at UWMadison, for example, detectsmaple-syrup urine disease, whichprevents the normal breakdown of certain amino acids from food. Then, toxic byproducts attack the brain and other organsimmediately after birth.

According to Mei Baker, co-director of newborn screening at the State Laboratory of Hygiene, which developed the test, We make special arrangements for lab testing beyond regular working hours. The midwife collects a blood sample and a hired driver delivers it immediately to our lab. Six or eight hours after birth, we have the result, and the clinicians at Waisman Center advise the parents on an appropriate formula to avoid the symptoms.This service is free of charge, and you cannot do any better than that.

This team hauls logs and saw timber at the Hershberger family sawmill outside La Farge, Wisconsin. Photo by David Tenenbaum

Genetic diseases among the Plain arise from founder mutations that were present in the few Amish and Old Order Mennonites who immigrated to America in the 19th century. A second genetic bottleneck occurred among smaller groups that moved to Wisconsin, starting about a century ago.

Most of the genetic diseases he sees can be treated if not cured, DeLine said.

DeLines long and deep experience with many Amish families, and his anthropological knowledge of family relationships are part of his doctors toolkit.

So are home visits.

He talks about how helpful it is to see a child in the home environment, surrounded by siblings, grandparents, parents, said Christine Seroogy, a professor of pediatrics. Seroogy is one of several UWMadison colleagues who provide outreach clinical services with the Center for Special Children. Its been quite an experience, an honor, to take part in those home visits.

The characteristic homemade clothes of an Amish family hang just inside the back door. Photo by David Tenenbaum

Home visits were not part of my medical training, but its how doctors used to practice, and Jim DeLine still does, she added.

When Seroogy began working with DeLine in 2007, one focus was severe combined immune deficiency (SCID, or bubble boy) disease. Though fatal, SCID can be detected with newborn screening and in some cases treated with bone marrow transplant. Over the years, she has worked closely with DeLine, newborn screening experts at the State Laboratory of Hygiene, and Plain families to improve SCID diagnosis and treatment.

In many cases, a true diagnosis can keep patients out of hospitals and away from physicians who tend to order an endless series of costly tests that cause more trouble than healing.

When we must deliver news about a child with a lethal disorder, DeLine said, if the family knows whats going on, sad though it is, its a gift to the family to take the child home and care for them surrounded by their community and their family.

Its hard to treat something you dont recognize, understand, DeLine added. Each time a new condition is identified, the search for a cure can begin.

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21st century medicine helps Amish deal with rare, inherited illnesses - University of Wisconsin-Madison

Myriad Genetics is among a handful of companies that make a genetic test to help doctors choose psychiatric medicines for patients. Evidence that the tests are effective has been called "inconclusive." Myriad Genetics hide caption

Myriad Genetics is among a handful of companies that make a genetic test to help doctors choose psychiatric medicines for patients. Evidence that the tests are effective has been called "inconclusive."

As a teenager, Katie Gruman was prescribed one mental health drug after another. None seemed to help her manage symptoms of anxiety and bipolar disorder, so she self-medicated with alcohol and illicit drugs.

It would take five years, and trying more than 15 different medications, before she found meds that actually helped.

Now 28 and in recovery, Gruman has been on the same drugs for years. But when a clinician recommended a genetic test to see which drugs work best for her, she took it.

Reading the test results "was definitely vindicating," she says. Medications that hadn't worked for her as a teenager were the same ones the results marked as bad fits.

She says she wishes she had taken the test as a teenager. "I could have avoided a lot of disaster in my life," she says.

Psychiatric medications are known to be hard to match to symptoms, and many patients like Gruman live through years of trial and error with their doctors.

Companies that make genetic tests like the one Gruman used say they can save patients and doctors from prolonged searching for the right medication and save insurance companies from paying for ineffective drugs. But many researchers say the tests don't have enough evidence backing them up. The Food and Drug Administration has warned that the tests could potentially steer patients towards the wrong medications. Nonetheless, UnitedHealthcare, the nation's largest insurer, began covering them October 1 for its 27 million individual and group plans.

Test makers hailed the announcement of United's coverage, the first from an insurance company to apply to all of its commercial plans across the country.

"We expect this to be a tipping point," says Shawn Patrick O'Brien, CEO of Genomind, a company that makes one of the tests. Other insurers will cover the tests "because they don't want to be uncompetitive in the marketplace," he predicts.

If the prediction is correct, it would likely fuel a market that has seen its largest test maker, Myriad Genetics, sell about 375,000 of its psychiatric medicine tests in the 2019 fiscal year, according to Jack Meehan, an industry analyst for Barclays. Myriad reported that it sold $113 million worth of the tests.

In addition to UnitedHealthcare's coverage, Myriad Genetics' test is covered by Medicare, a regional Blue Cross Blue Shield affiliate, and the insurance network for the grocery chain Kroger, a spokesperson says.

Genomind has discussed coverage with insurers including Anthem and Blue Cross Blue Shield, O'Brien says.

Debates over efficacy

As the field of genetic testing to help diagnose and treat disease grows, medicine has embraced certain tests, such as that for the BRCA gene linked to breast cancer. But many researchers say there is not enough evidence tying genetic variants to better outcomes for most psychiatric medications.

James Potash, the head of psychiatry at Johns Hopkins Medicine and an expert on psychiatric genetics, says of all the tests claiming to improve depression treatment, GeneSight's has the most proof. That isn't saying much, though.

"I wouldn't say there's no evidence that it works," he says. "It's just the evidence at this point is still weak."

The idea behind the tests is that in some cases, people can have different reactions to the same drug, even at the same dose, because they have different gene variants. Which variant a person has can affect how quickly or slowly a medicine moves through their body.

This link between genes and drug metabolism has been known for decades, says Francis McMahon, who leads genetic research into mood and anxiety disorders at the National Institutes for Mental Health.

Usually, the longer it takes your body to process a drug, the easier it is for that medication to have an effect. But in psychiatry, McMahon says, how fast someone processes a drug, or metabolizes it, and how well they respond to the drug "are sometimes not strongly related."

This skepticism is shared by some insurance companies. "Anthem considers these tests investigational and not medically necessary," says a spokesman for the carrier, which covers 41 million people. The Blue Cross Blue Shield Federal Employee Program, which covers about two-thirds of government workers and their families, said "there is not enough evidence at this time to determine the effect of genetic testing on health outcomes," according to a spokeswoman.

Test makers are also facing FDA objections that they haven't proven some of the claims underpinning genetic tests for medications, including that antidepressants work better with some gene variants.

"Changing drug treatment based on the results from such a genetic test could lead to inappropriate treatment decisions and potentially serious health consequences for the patient," the agency warned in late 2018. It told companies to stop naming specific drugs, in marketing materials or test results, for which its tests "claim to predict a patient's response" without "scientific or clinical evidence to support this use."

Most test makers complied. One, Inova Genomics Laboratory, stopped selling a range of tests, including its test for mental health disorders, after the FDA followed up with a warning letter in April.

Several mental health advocacy groups, including the National Alliance on Mental Illness, have sided with test makers in their dispute with the FDA. Keeping the names and types of medication off of genetic test reports, as the FDA has required, will "impede the ability of psychiatrists and other front-line health care professionals to personalize medication decisions" for patients with depression, the groups wrote the FDA in September.

Some have argued that genetic tests like these shouldn't be regulated by the FDA at all. Tests conducted in a lab are a medical service, not a medical device that's shipped like a product, says Vicky Pratt, president of the Association for Molecular Pathology. As a medical service, she says, clinical laboratories are already regulated by the Centers for Medicare and Medicaid Services.

"It would be redundant to have dual regulation by both the FDA and CMS," says Pratt.

Cost-benefit analysis

Research into the tests' efficacy is ongoing and continues to be debated.

Myriad hoped to bolster evidence for its test, GeneSight, in a study it funded that was published this year in the Journal of Psychiatric Research, but the results were mixed.

In the study, doctors used genetic tests to help prescribe medications for one group of patients with depression, while another group of patients received usual care. There was overall no difference between the groups in the study's primary measure of symptom improvement, though some patients showed improved response and remission rates.

Responding to criticisms of its clinical trial results, Myriad Genetics spokesman Ron Rogers says the trial population whose average participant had tried more than three unsuccessful medications for depression was uniquely difficult to treat. He says he expects to see stronger outcomes in a forthcoming review of the trial data.

In a statement on the use of genetic testing in psychiatry, the International Society of Psychiatric Genetics, calls the existing evidence "inconclusive," and notes that if 12 patients take such a test for antidepressants, just one will benefit from it.

A low rate of success means insurers will have to pay for a lot of tests for one useful result, says Barclays analyst Meehan. Meehan pointed to a letter about the recent GeneSight study that was published in the same journal, which found that 20 patients would need to take the test for one to recover as a result. At $2,000 for a GeneSight test, the authors wrote, that means patients and insurers would have to cover $40,000 worth of tests. (While competitor Genomind does not share pricing information, a spokeswoman confirmed that it has an active contract with the Department of Veterans to supply tests for $1,886.)

Still some clinicians value the tests. Skeptics often misunderstand how the tests should be used, argues Daniel Mueller, a professor at the University of Toronto who researches how genes and drugs interact. (Mueller is involved in research comparing Myriad's GeneSight to another test developed by a University of Toronto-affiliated hospital.) Most of the time, he says, doctors who order the test already plan to prescribe medication. The test is just another tool to help them decide which one to prescribe.

"It's not an alternative intervention," Mueller says. "It's additional information." He orders the test for most patients who do not respond to at least one antidepressant.

"If you think about the cost of depression and weeks of suffering that you can potentially avoid for some patients," Mueller says, he thinks anyone who can afford a test should take it. (Myriad says 95% of patients pay less than $330 for their test, the cost remaining after insurance and possible financial assistance; Genomind says most privately insured customers pay no more than $325.)

A lack of watertight evidence for the tests should not stop doctors from using it to inform their choice of medication, says Reyna Taylor, who leads public policy for the National Council for Behavioral Health, one of the advocacy groups that defended the tests in a letter to the FDA. "You use the science that you currently have," she says.

"Whether our providers choose to use [a genetic test] or not, we want them to have that choice," she adds.

Disagreement among experts hasn't dissuaded UnitedHealthcare from paying for the tests.

In a statement, UnitedHealthcare spokeswoman Tracey Lempner says they "frequently review our coverage policies to ensure they reflect the most current published evidence-based medicine and specialty society recommendations."

Graison Dangor is a journalist in Brooklyn.

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Genetic Tests For Psychiatric Drugs Now Covered By Some Insurers : Shots - Health News - NPR

HOUSTON, Oct. 17, 2019 /PRNewswire/ -- Researchers fromInvitae Corporation (NYSE: NVTA), a leading medical genetics company, are presenting data showing the increasing utility of genetic information at the American Society of Human Genetics (ASHG) annual meeting this week, ranging from comprehensive screening for cancer patients, to appropriate clinical follow up for women using non-invasive prenatal screening, to the limitations of direct to consumer genetic screening health reports.

The company's research includes three platform presentations and multiple poster sessions, many performed in collaboration with leading academic researchers. Among the data presented is a study evaluating the utility of combined germline testing and tumor profiling (somatic testing) in cancer patients. Germline and somatic testing are increasingly used in precision treatment of people with cancer, although frequently are ordered separately in clinical practice. Data presented at the meeting shows a substantial number of patients with medically significant variants in hereditary cancer syndrome genes in their tumor profile carry the same variant in their germline, thereby establishing a previously unknown risk of hereditary cancer and suggesting the value of combined or concurrent testing to inform precision medicine approaches.

"The research we are presenting at this year's ASHG meeting provides meaningful insight into both the science and practice of genetics, helping identify how we as clinicians can better use deep genetic insights to help a wide array of patients, whether they are cancer patients, women having a child or healthy adults seeking to better understand their risk of disease," said Robert Nussbaum, M.D., chief medical officer of Invitae. "We are proud and grateful to be able to join our colleagues from across genetic medicine in meaningful conversations that push genetic medicine forward."

Following are research from the company and collaborators to be presented at the meeting:

Wednesday, October 16:

Poster presentation #819W | 2:00 3:00 pm Germline testing in colorectal cancer: Increased yield and precision therapy implications of comprehensive multigene panels. Presented by Shan Yang, PhD. Invitae.

Poster presentation #2427W | 2:00 3:00 pm Harmonizing tumor sequencing with germline genetic testing: identification of at-risk individuals for hereditary cancer disorders. Presented by Daniel Pineda-Alvarez, MD, FACMG, Invitae.

Poster presentation #606W | 3:00 4:00 pm A comprehensive evaluation of the importance of prenatal diagnostic testing in the era of increased utilization of non-invasive prenatal screening. Presented by Jenna Guiltinan, MS, LCGC, Invitae.

Thursday, October 17:

Platform presentation #235 | 5:00 pm, Room 370A, Level 3 Limitations of direct-to-consumer genetic screening for hereditary breast, ovarian and colorectal cancer risk. Presented by: Edward Esplin, MD, PhD, FACMG, FACP, Invitae.

Poster presentation #763T | 2:00 3:00 pm In-depth dissection of APC pathogenic variants: Spectrum of more than 400 pathogenic variants, challenges of variant interpretation, and new observations in a large clinical laboratory testing cohort. Presented by: Hio Chung Kang, PhD, Invitae.

Poster presentation #1399T | 2:00 3:00 pm Prediction of lethality and severity of osteogenesis imperfecta variants in the triple-helix regions of COL1A1 and COL1A2. Presented by: Vikas Pejaver, PhD, University of Washington.

Friday, October 18:

Platform presentation #264 | 9:00 am, Room 361D, Level 3 Million Veteran Program Return Of Actionable Results - Familial Hypercholesterolemia (MVP-ROAR-FH) Study: Considerations for variant return to mega-biobank participants. Presented by Jason Vassy, MD, MPH, VA, Boston Healthcare System.

Platform presentation #265 | 9:15 am, Room 361D, Level 3 Comprehensive secondary findings analysis of parental samples submitted for exome evaluation yields a high positive rate. Presented by Eden Haverfield, DPhil, FACMG, Invitae.

Poster presentation #698F | 2:00 3:00 pm Reporting of variants in genes with limited, disputed, or no evidence for a Mendelian condition among GenomeConnect participants. Presented by: Juliann Savatt, MS, LGC, Geisinger.

About InvitaeInvitae Corporation(NYSE: NVTA)is a leading medical genetics company, whose mission is to bring comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Invitae's goal is to aggregate the world's genetic tests into a single service with higher quality, faster turnaround time, and lower prices. For more information, visit the company's website atinvitae.com.

Safe Harbor StatementsThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to the increasing utility of genetic information; the utility of combined germline and somatic testing; and the benefits of the company's research. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially, and reported results should not be considered as an indication of future performance. These risks and uncertainties include, but are not limited to: the applicability of clinical results to actual outcomes; the company's history of losses; the company's ability to compete; the company's failure to manage growth effectively; the company's need to scale its infrastructure in advance of demand for its tests and to increase demand for its tests; the company's ability to use rapidly changing genetic data to interpret test results accurately and consistently; security breaches, loss of data and other disruptions; laws and regulations applicable to the company's business; and the other risks set forth in the company's filings with the Securities and Exchange Commission, including the risks set forth in the company's Quarterly Report on Form 10-Q for the quarter ended June 30, 2019. These forward-looking statements speak only as of the date hereof, and Invitae Corporation disclaims any obligation to update these forward-looking statements.

Contact:Laura D'Angelopr@invitae.com(628) 213-3283

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Research presented by Invitae at the American Society of Human Genetics Meeting Pushes Science and Practice of Genetics Forward - P&T Community

Louisiana-based Ochsner Health System is partnering with Color to launch a population health pilot program, tyinggenetic information into preventive care.

Calling it the first "fully-digital population health program," Ochsner will work with the health technology company to incorporateclinical genomics into primarycare with a focuson impacting patients' health further downstream.

Developed by Ochsners innovation lab, innovationOchsner (iO), the health systems program willidentify patients who are at higher risk for certain hereditary cancers and heart disease so these diseases can be detected early or prevented.

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This marks another big partnership for Color this year. The company inked a similar collaboration with Chicago-based NorthShore University HealthSystem, called DNA10K, that will provide more than10,000 NorthShore patients access to Colors clinical-grade genetic testing and whole genome sequencing.Atthe time, it was touted as the largest primary care genomics program in the U.S.

RELATED:Mount Sinai to launch $100M center dedicated to AI, precision medicine

Physician practices are beginning to incorporate genomics into primary care as well.Murfreesboro Medical Clinic and SurgiCenter in Tennessee are working with technology company2bPrecise, a subsidiary of health IT company Allscripts, to integrate pharmacogenomic testresults at the point of care.

In August, Color was awarded a $4.6 million grant by the National Institutes of Health to serve as the nationwide genetic counseling service for its All of Us Research Program.

With this pilot program, Ochsner is focused on screening patients with genetic mutations that put them at increased risk for three conditionshereditary breast and ovarian cancer syndrome due to genetic mutations in the BRCA1 and BRCA2 genes; Lynch syndrome,associated with increased risk in colorectal, endometrial, ovarian and other cancers; and familial hypercholesterolemia (FH), which increases the risk for heart disease or stroke.

The Centers for Disease Control and Prevention reports thatnearly 2 million people in the U.S. are at increased risk for adverse health outcomes because they have genetic mutations with one of thosethree conditions.

Genetic screening can make a meaningful difference to patients through early detection and screening. Most consumers have access to home genetic screening tests but may not have the tools, resources, and collaboration needed to take action should they receive questionable results, said Richard Milani, M.D., chief clinical transformation officer for the Ochsner Health System and medical director for iO.

RELATED:How a Nashville-area clinic teamed up with Allscripts on precision medicine

Ochsner provides patient care across40 owned, managed and affiliated hospitals and specialty hospitals and more than 100 health centers and urgent care centers.The partnership will combine Colors capabilities inmedical-grade genetics, clinical services and patient engagement and the health system's experience withpersonalized medicineand integrating it into routine patient care, the organizations said in a press release.

As part of the program, selected patients will be enrolled into the program digitally and will receive access to genetic testing and counseling.Genetic testing results will bestored in the patients Epic electronic health record so patients and providers have access to the genetic information.

RELATED:UCLA Health deploys Microsoft Azure to accelerate medical research, precision medicine at the point of care

Ochsner also has developed clinical decision support tools and a robust provider education program for both primary care and specialty providers to integrate into clinical practice.

New technology tools like clinical genomics will enableOchsner physicians to better understand individualized risk among its patient population and create action plans that can detect or prevent disease, according to the health system.

We know there are many factors that influence health, and genetic insights provide an additional data point to allow us to develop and deliver a more personalized approach in partnership with our patients," Milani said.

"Integrating this information into the patients electronic health record so doctors can review the results and discuss proactive treatment recommendations is yet another example of how we are reengineering care, informing smarter decisions by healthcare providers and empowering patients to become more involved in their health," he said.

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Ochsner Health System teaming up with genetic testing company Color on population health pilot - FierceHealthcare

When young athletes experiences sudden cardiac death as they run down the playing field, it's usually due to arrhythmogenic cardiomyopathy (ACM), an inherited heart disease. Now, Johns Hopkins researchers have shed new light on the role of the immune system in the progression of ACM and, in the process, discovered a new drug that might help prevent ACM disease symptoms and progression to heart failure in some patients.

"We realized that heart muscle inflammation in ACM is much more complicated than we thought, but also might provide a therapeutic strategy," saysStephen Chelko, Ph.D., assistant professor of medicine at the Johns Hopkins University School of Medicine and senior author of the new paper, inSept. inCirculation.

In ACM, patients often harbor mutations in any of the five genes that make up the cardiac desmosome -- the gluelike material that holds heart cells together and helps coordinate mechanical and electrical synchronization of heart cells. Because of this, it's often called "a disease of the cardiac desmosome." In patients with ACM, heart cells pull apart over time, and these cells are replaced with damaged and inflamed scar tissue. These scars can increase risk of instances of irregular heart rhythms and lead to sudden cardiac death if the scar tissue causes the heart wall to stiffen and renders it unable to pump.

If a person is aware they carry an ACM-causing genetic mutation, doctors help them avoid cardiac death through lifestyle changes, such as exercise restriction, and medications that keep their heart rate low. However, there are currently no drugs that treat the underlying structural defects of the desmosome. People who live for many years with ACM still accumulate scar tissue and inflammation in their hearts, leading to chronic heart disease.

"We tended in the past to view ACM as something that kills due to a sudden arrhythmic event," said Chelko. "But now we're starting to also see it as a chronic inflammatory disease that can progress more slowly over time, leading to heart failure."

Chelko and his colleagues wanted to determine the molecular cause of inflammation in the hearts of people with ACM. So they studied mice with an ACM-causing mutation, as well as heart muscle cells generated from stem cells isolated from an ACM patient. They found that the inflammation associated with the disease arose from two separate causes. First, they noticed high levels of macrophages, a type of immune cell that's normally found at sites of inflammation, such as around cuts or scrapes that are healing.

"Macrophages are usually the good guys who help heal a wound and then leave," said Chelko. "But in ACM they're permanently setting up shop in the heart, which, over time, reduces its function."

Chelko's team also found that in ACM, the heart cells themselves are triggered by a protein known as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-B) to produce chemicals called cytokines, which act as homing beacons for other inflammatory cells and molecules. When the researchers treated mice or isolated cells with a drug blocking NF-B, heart cells stopped producing many of these cytokines, leading to decreased inflammation and infiltration of inflammatory cells. In mouse models of ACM, animals treated with the NF-B-blocking drug Bay-11-7082 had a twofold increase in heart function, measured by how much blood their hearts could pump over time compared with untreated ACM animals. They also had a twofold reduction of damaged and inflammatory scar tissue in the heart.

More than one-third of patients with ACM who die of sudden cardiac death have no previous cardiac symptoms, so wouldn't ever know to seek treatment. However, for relatives of these people who discover that they carry a genetic mutation causing ACM -- or those who discover the mutation for other reasons -- a drug could help stave off long-term heart disease, Chelko said.

While the Bay-11-7082 drug is currently only used in the lab for experimental purposes, the U.S. Food and Drug Administration has approved canakinumab, a drug that targets the same inflammatory pathway, for use in juvenile arthritis and a collection of rare auto-inflammatory syndromes. Canakinumab is also being studied for use in coronary artery disease. Chelko's group is now investigating whether this drug would have the same effect as Bay-11-7082 in ACM.

"We're very excited to have found an FDA-approved drug that can reduce heart inflammation in ACM, and we're eager to do more research to ultimately help those who carry these genetic mutations," said Chelko.

Reference:Chelko, et al. (2019) Therapeutic Modulation of the Immune Response in Arrhythmogenic Cardiomyopathy. Circulation. DOI:https://doi.org/10.1161/CIRCULATIONAHA.119.040676

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

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Drug Treats Inflammation Related to Genetic Heart Disease - Technology Networks

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Artificial intelligence and machine learning have been utilized for years in the field of healthcare and continue to grow tremendously each year with its ability to advance medicine and discoveries in the industry.

The term precision medicine, sometimes referred to as personalized medicine, is a relatively new term in the healthcare field but the idea has been around for many years in the industry. According to the U.S. National Library of Medicine, precision medicine is "an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person."

Precision medicine helps physicians determine more personalized treatments for patients considering individualized approaches instead of a blanketed approach for all patients. They do this by looking at a patients genetic history, location, environmental factors, lifestyle and habits to determine a plan of action for treatment.

With artificial intelligence, it takes precision medicine to the next level and increases the accuracy and prediction of outcome for patients. Some actually believe that precision medicine is not completely possible without the addition of machine learning algorithms to assist in the process.

In a report from Chilmark Research, it states that to achieve the full potential of precision medicine it must be accompanied by machine learning and artificial intelligence due to the deep learning technology and ability to analyze large data sets faster than clinicians and medical researchers.

Not only can AI read and analyze large sets of medical data much faster than a human, it can more accurately determine results to come to conclusions about a patients treatment options and possible outcomes of the treatment.

With AI, the ability to not only predict outcomes but also be able to predict future patients probability of having diseases is a major benefit for precision medicine. By better understanding why diseases may occur and in what environments they are more likely to occur, artificial intelligence can help in the education of medical professionals to know what to look for before a disease is showing symptoms. To be able to evaluate the risk of disease in patient populations is revolutionary for healthcare and the lives of many.

Machine learning can also help improve FDA regulations of tests, drugs and pharmaceutical partnerships to help support treatments. Fully achieving precision medicine effectively takes a collaboration of pharmaceutical companies, biotechs, academia, diagnostic companies and others to drive innovation forward.

Amplion, a leading precision medicine intelligence company, recently released Dx:Revenue, a software intelligence platform that uses machine learning to deliver insights into pharmaceutical partnerships.

The platform uses over 34 million data sources from clinical trials, scientific publications, conference abstracts, FDA approved tests, lab tests, and other information to match a test providers capabilities to pharmas specific needs.

This is particularly important in cancer, where were moving away from the one-size-fits-all approach to care toward a more targeted approach with treatments based on the biological characteristics of each patient, said CEO of Amplion Chris Capdevlia. Personalizing our approach to healthcare in this way not only results in better outcomes for patients, it also drives down drug development costs through shorter, more successful trials and reduces time to market for valuable drugs all very good news for better patient outcomes.

Precision medicine can truly improve the lives, and even save the lives, of many people and the use of artificial intelligence can increase those outcomes drastically. It can also make treatments more affordable and accessible to those who may not be able to receive those treatments due to cost and health insurance at this time. There are many challenges ahead for precision medicine to be perfect, but artificial intelligence can help drive us closer to those goals.

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How Artifical Intelligence Is Advancing Precision Medicine - Forbes

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Neurology Neuroimmunology & Neuroinflammation, Oct-2019

Newswise WINSTON-SALEM, N.C. Oct. 16, 2019 A discovery made several years ago in a lab researching asthma at Wake Forest School of Medicine may now have implications for the treatment of amyotrophic lateral sclerosis (ALS), a disease with no known cure and only two FDA-approved drugs to treat its progression and severity.

A study published in the current edition of the journal Neurology Neuroimmunology & Neuroinflammation showed that ALS patients with a commonly inherited genetic variation or polymorphism in the interleukin 6 (IL6) receptor gene may experience more severe symptoms and faster progression of the disease.

This relationship was first identified in asthma patients in 2012 by Gregory A. Hawkins, Ph.D., and co-workers at Wake Forest School of Medicine, part of Wake Forest Baptist Health. He found that people who had asthma and this inherited trait got more severe asthma than those who didnt.

We knew that interlukin 6 had many functions in the lung, as shown in asthma, but also in muscle and nerves, all three of which are affected in ALS, said Carol Milligan, Ph.D., professor of neurobiology and anatomy at Wake Forest School of Medicine and senior author of the study. Therefore we wondered if what they found in asthma may also have a role in ALS patients or maybe explain why the disease progressed faster in some patients but not others.

ALS, also known as Lou Gehrigs disease, is a disease that causes the death of neurons that control voluntary muscles. As voluntary muscle action is progressively affected, people may lose the ability to speak, eat, move and breathe.

To further an understanding of the factors that influence ALS progression and severity, Milligan and her team conducted an observational, case-controlled retrospective study of two groups of people.

The researchers examined blood and spinal fluid samples, provided by the Northeastern ALS Consortium Biofluid Repository, from 47 participants with ALS and 46 healthy people. Results confirmed that samples from people with ALS who had the variation in the IL6 receptor gene accounted for increased levels of IL6 in blood and spinal fluid compared to the control groups.

To examine if presence of the variation in the IL6 receptor gene might affect disease progression, the investigators examined a second group of 35 patients from the Wake Forest Baptist ALS Center Biorepository that included clinical data collected within a year of symptom onset. The researchers compared the progression of the disease between those who had the polymorphism and those who didnt. In those with the genetic variation, the disease progressed faster.

This study is the first to show that this polymorphism may modify the course of ALS, Milligan said. We hope that our findings may provide a target for a new treatment and lay the groundwork for future clinical trials.

The study was spear-headed by Marlena Wosiski-Kuhn, a M.D./Ph.D. student at Wake Forest School of Medicine, and included members of the ALS center and Departments of Biochemistry, Neurology and Neurobiology and Anatomy at Wake Forest School of Medicine.

Support for the study was provided by Hope for Tomorrow, a gift in the memory of Murray Sherman, the Wake Forest Baptist Health Brian White Fund and the Tab A. Williams Funds at Wake Forest School of Medicine.

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Scientists at Wake Forest School of Medicine Identify Genetic Variation Linked to Severity of ALS - Newswise

News Release

Friday, October 18, 2019

HudsonAlpha awarded $7 million to expand national health dataset with uncharted genetic variants.

The All of Us Research Program has selected the HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, to evaluate the use of leading-edge DNA sequencing technologies that could someday improve diagnosis and treatment of many diseases, both common and rare. The National Center for Advancing Translational Sciences (NCATS) is funding the project with $7 million over one year. All of Us and NCATS are parts of the National Institutes of Health.

All of Us will provide one of the worlds most robust platforms for precision medicine research, with a broad range of data to drive new discoveries, said Eric Dishman, All of Us director. Through this partnership with NCATS, well be able to offer approved researchers an even greater depth of genetic information than originally planned, making the resource even more valuable for them and the diverse communities we seek to help.

With this award, HudsonAlpha will use long-read whole genome sequencing technologies to generate genetic data on about 6,000 samples from participants of different backgrounds. Long-read sequencing analyzes DNA in larger segments than standard (short-read) sequencing technologies, exposing genetic variations that may otherwise go undetected. These variations include different types of alterations to the genetic structure, such as duplication, deletion or rearrangement of the building blocks that uniquely make up ones genome and set it apart from others. Everyone has thousands of these genetic variations, most with little known effect. However, researchers are learning more about how some genetic variants underlie certain health conditions or, conversely, increase disease resistance. Understanding the genetic underpinnings of health and disease will help researchers identify more targeted interventions in the future.

This project will allow researchers to better determine the value of long-read sequencing and its strengths and limitations in exploring more elusive parts of the genome. Combined with the 1 million whole genome sequences the program already plans to deliver over the next several years, this additional infusion of genetic information will provide the research community with the largest collection of genomic structural variation data and clinical data ever produced.

Because long-read sequencing can reveal genetic changes associated with rare diseases, this project is an opportunity to assess and potentially refine the technology for advancing research across the many diseases for which there is no treatment, said Christopher P. Austin, M.D., NCATS director. This project illustrates the power of data and technology to accelerate the translation of knowledge into improved health.

The HudsonAlpha team, led by Shawn Levy, Ph.D., brings significant experience in large-scale sequencing projects and in genetic studies on inherited disorders as well as complex conditions, including autism, diabetes, cancer, schizophrenia, degenerative neurological disease and amyotrophic lateral sclerosis(ALS).

We look forward to collaborating with the other All of Us genome centers and the rest of the consortium on this exciting effort, said Dr. Levy. Contributing long-read sequencing data to reveal additional structural variants will enable the scientific community to study human diversity on a tremendous scale.Appreciating the impacts of all types of genetic variation will further unravel the genetic, environmental and behavioral influences of health.

About theAll of UsResearch Program:Themissionof theAll of UsResearch Program is to accelerate health research and medical breakthroughs, enabling individualized prevention, treatment, and care for all of us. The programwill partner with one million or more people across the United States to build the most diverse biomedical data resource of its kind, to help researchers gain better insights into the biological, environmental, and behavioral factors that influence health. For more information, visitwww.JoinAllofUs.organdwww.allofus.nih.gov.

About the National Center for Advancing Translational Sciences (NCATS):NCATS conducts and supports research on the science and operation of translation the process by which interventions to improve health are developed and implemented to allow more treatments to get to more patients more quickly. For more information about how NCATS is improving health through smarter science, visithttps://ncats.nih.gov.

About the National Institutes of Health (NIH):NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit http://www.nih.gov.

NIHTurning Discovery Into Health

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NIH funds new All of Us Research Program genome center to test advanced sequencing tools - National Institutes of Health