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Category Archives: Genetic Medicine

Newborns may benefit from fast genetic test

By Elizabeth Landau

(CNN) Genome sequencing is rapidly changing modern medicine, and a new study shows its potential impact on seriously ill newborn babies.

New research published in the journal Science Translational Medicine this week makes the case for a two-day whole-genome sequencing for newborns in a neonatal intensive care unit (NICU).

After 50 hours, the test delivers to doctors a wealth of information about what could be causing newborns life-threatening illnesses. This would allow them to more efficiently and quickly tailor therapies to the babies, when possible, and identify problematic genetic variants that multiple family members may share.

We think this is going to transform the world of neonatology, by allowing neonatologists to practice medicine thats influenced by genomes, said Stephen Kingsmore, the studys senior author and director for the Center for Pediatric Genomic Medicine at Childrens Mercy Hospitals and Clinics in Kansas City, Missouri, at a press conference Tuesday.

There are more than 3,500 diseases caused by a mutation in a single gene, Kingsmore said, and only about 500 have treatments. About one in 20 babies born in the United States annually gets admitted to a neonatal intensive care unit, he said. Genetic-driven illnesses are a leading cause of these admissions at Kingsmores hospital.

One example of how a genetic test would help newborns is a condition called severe Pompe disease, Kingsmore said. Children with this disorder die if they are not treated by age 1. They will live longer, at least four years, if they receive an enzyme replacement therapy.

The study shows how two software programs, called SAGA and RUNE, work together to help physicians pinpoint the genes that could be causing problems in the children. A company called Illumina developed a rapid genome sequencing device that incorporates the programs.

Researchers reported diagnoses as a result of this genetic test in the study for six children. Two of these tests were done retrospectively, after the children had died.

The test extends beyond the ill baby; genome sequencing can also identify genetic traits in multiple family members, the researchers said. Carol Saunders, the studys lead author, explained at the news conference how one baby and his 6-year-old brother both have a congenital heart defect and heterotaxy, meaning some internal organs are located on the wrong side of the body.

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New technique provides speedy diagnosis of rare genetic disorders in infants

NEW YORK Scanning the DNA of sick infants using a new speed-reading method can diagnose rare genetic disorders in two days instead of weeks, according to research that brings gene mapping a step closer to everyday hospital use.

Researchers at Children's Mercy Hospitals and Clinics in Kansas City, Mo., created software that takes raw data from DNA-scanning machines and combs though hundreds of genetic disorders to detect disease-causing mutations. The system provided likely diagnoses for three of four sick infants in about two days, results published in Science Translational Medicine found.

The new method has the potential to make genome sequencing practical for neonatal-intensive-care units, enabling doctors to diagnose mysterious genetic diseases more quickly, said Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children's Mercy and a study senior author. Fast diagnoses of sick babies could lead to life-extending treatments sooner in some or help avoid futile, costly therapies in others.

"This is the biggest breakthrough in this technology for clinical applications we have seen in a few years," said David Dimmock, a geneticist at the Medical College of Wisconsin and Children's Hospital of Wisconsin in Milwaukee, who wasn't involved in the study. "The ability to sequence and interpret a genome in less than (a) week is huge."

Dimmock said researchers at his institution were working on a similar fast genome-interpretation system, but hadn't published the results. "They beat us to the punch," he said.

There are about 3,500 known genetic diseases of which 500 have treatments, Kingsmore said. Many of these genetic illnesses hit young children. Roughly 20 percent of infant deaths are caused by genetic conditions, according to the study released Wednesday.

The Children's Mercy Hospital system was made possible in part by a new sequencing machine developed by San Diego-based Illumina that can decode the entire DNA sequence of a person in one day.

This generates a colossal volume of raw data that must be analyzed by expert genetic researchers, a process that previously has taken weeks or months.

That's where the system devised by Children's Mercy researchers comes into play. Kingsmore and his team devised smart software that allows treating doctors to enter a sick baby's symptoms.

The software then matches these reported symptoms to known genetic diseases that have similar symptoms, and scans the baby's genome results for likely harmful mutations in relevant genes.

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Newborn Genetic Test Catches Rare Diseases Earlier

A new technology can diagnose rare genetic disorders in critically ill newborns within a few days, rather than the weeks that are needed with current methods, researchers say.

The technology involves sequencing the infant's genome, and then using new software to hone in on the genes most likely to be disease culprits.

In a new study, researchers identified the genetic cause of a newborn's illness in three out of four babies tested. The whole process takes about 50 hours, they said.

The speed of the new test is what could make it useful for sick babies in neonatal intensive care units (NICUs), the researchers said. Currently, it can take weeks for doctors to diagnose a genetic disorder in an ill infant, and many babies die before their test results are available, said study researcher Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospital in Kansas City.

A faster diagnosis for genetic conditions would allow doctors to provide earlier treatments if there are any or to give parents an earlier warning, and potentially more time together with their child, if the condition is untreatable and fatal, the researchers say.

Doctors already routinely screen newborns for a few genetic disorders that have effective treatments. But these tests look for single genes, rather than at the entire genome. There about 3,500 diseases known to be caused by mutations in a single gene, and 500 of these have some type of treatment available, Kingsmore said.

"By obtaining an interpreted genome in about two days, physicians can make practical use of diagnostic results to tailor treatments to individual infants and children," Kingsmore said.

However, critics point out that the diseases identified by new technology are rare, and extra genetic information is not always helpful. In fact, some are worried the genetic testing could deliver more information than researchers know what to do with.

Diagnosing genetic diseases

To begin a diagnosis with the new technology, the researchers take a drop of the baby's blood so that his or her genome can be sequenced.

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Rapid test pinpoints newborns' genetic diseases in days

Babies with genetic disorders can have their whole genome screened for muations in just two days.

Taylor S. Kennedy/ Getty Images

A faster DNA sequencing machine and streamlined analysis of the results can diagnose genetic disorders in days rather than weeks, as reported today in Science Translational Medicine1.

Up to a third of the babies admitted to neonatal intensive care units have a genetic disease. Although symptoms may be severe, the genetic cause can be hard to pin down. Thousands of genetic diseases have been described, but relatively few tests are available, and even these may detect only the most common mutations.

Whole-genome sequencing could test for many diseases at once, but its cost, the complexity of the results and the turnaround time are prohibitive. In what they hope will be a prototype for other hospitals, a research team led by Stephen Kingsmore at Childrens Mercy Hospital in Kansas City, Missouri, has implemented a much faster, simpler systemfor finding relevant mutations in whole-genome sequences that is designed for physicians without specialized genetic training.

These kinds of innovation will help more hospitals bring sequencing into clinical care, says Richard Gibbs, director of the human genome sequencing centre at Baylor College of Medicine in Houston, Texas. A lot of people are going to realize from this that the future is now.

Sequencing has been used before to pinpoint the cause of mysterious diseases. In 2011, Gibbs led a team that sequenced 14-year-old twins with a neurological movement disorder and found a way to improve their treatment2. In another instance, whole-genome sequencing suggested that a mysterious case of severe inflammatory bowel disease had a genetic cause and could be relieved through a bone marrow transplant3. But both these examples required several weeks and a team of experts to resolve. The Childrens Mercy Hospital plans to offer routine sequencing in the neonatal intensive care unit by the end of the year.

To order a test, physicians will choose terms from pull-down boxes to describe the infant's symptoms. Software then compiles a list of potential suspect genes. After the genome is sequenced, the software hunts for and analyses mutations in only those genes, which allows it to compile a list of possible causative mutations more quickly. The team had early access to a new DNA sequencing machine from sequencing company Illumina, based in San DIego, California, that could generate a whole genome within 25 hours. The entire process, from obtaining consent to preliminary diagnosis, took 50 hours, not counting the time taken to ship DNA samples and computer hard drives between Illumina's lab in the UK, where the DNA sequencing was carried out, and the hospital, where analysis was conducted. Kingsmore estimates that the cost of sequence and analysis is $13,500 per child, including costs to verify variants in a laboratory certified to perform clinical tests.

The research team used the new system to analyse the genomes of five children, including two brothers, with undiagnosed diseases and found definite or likely causative mutations in four of them. The researchers also sequenced portions of the parents genomes to track down which flagged mutations might cause disease. This exercise revealed that some mutations had arisen for the first time in the child. In other cases, recessive disease-causing variants had been inherited by both parents.

Though none of the diagnoses reported in the study affected treatment decisions, simply having a diagnosis can be a huge comfort, says Kingsmore. Physicians can stop doing costly and invasive tests. Families can get genetic counselling for planning future pregnancies. And new disease genes and mutations generate hypotheses for basic research.

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Rapid test pinpoints newborns' genetic diseases in days

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50-Hour Whole Genome Sequencing Provides Rapid Diagnosis for Children With Genetic Disorders

KANSAS CITY, Mo., Oct. 3, 2012 /PRNewswire/ --Today investigators at Children's Mercy Hospitals and Clinics in Kansas City reported the first use of whole genome information for diagnosing critically ill infants. As reported in Science Translational Medicine, the team describes STAT-Seq, a whole genome sequencing approach - from blood sample to returning results to a physician - in about 50 hours. Currently, testing even a single gene takes six weeks or more.

Speed of diagnosis is most critical in acute care situations, as in a neonatal intensive care unit (NICU), where medical decision-making is made in hours not weeks. Using STAT-Seq, with consent from parents, the investigators diagnosed acutely ill infants from the hospital's NICU. By casting a broad net over the entire set of about 3,500 genetic diseases, STAT-Seq demonstrates for the first time the potential for genome sequencing to influence therapeutic decisions in the immediate needs of NICU patients.

"Up to one third of babies admitted to a NICU in the U.S. have genetic diseases," said Stephen Kingsmore, M.B. Ch.B., D.Sc., FRCPath, Director of the Center for Pediatric Genomic Medicine at Children's Mercy. "By obtaining an interpreted genome in about two days, physicians can make practical use of diagnostic results to tailor treatments to individual infants and children."

Genetic diseases affect about three percent of children and account for 15 percent of childhood hospitalizations. Treatments are currently available for more than 500 genetic diseases. In about 70 of these, such as infantile Pompe disease and Krabbe disease, initiation of therapy in newborns can help prevent disabilities and life-threatening illnesses.

STAT-Seq uses software that translates physician-entered clinical features in individual patients into a comprehensive set of relevant diseases. Developed at Children's Mercy, this software substantially automates identification of the DNA variations that can explain the child's condition. The team uses Illumina's HiSeq 2500 system, which sequences an entire genome at high coverage in about 25 hours.

Although further research is needed, STAT-Seq also has the potential to offer cost-saving benefits. "By shortening the time-to-diagnosis, we may markedly reduce the number of other tests performed and reduce delays to a diagnosis," said Kingsmore. "Reaching an accurate diagnosis quickly can help to shorten hospitalization and reduce costs and stress for families."

About Children's Mercy Hospitals and Clinics Children's Mercy Hospitals and Clinics, located in Kansas City, Mo., is one of the nation's top pediatric medical centers. The 333-bed hospital provides care for children from birth through the age of 21, and has been ranked by U.S. News & World Report as one of "America's Best Children's Hospitals" and recognized by the American Nurses Credentialing Center with Magnet designation for excellence in nursing services. Its faculty of 600 pediatricians and researchers across more than 40 subspecialties are actively involved in clinical care, pediatric research, and educating the next generation of pediatric subspecialists. For more information about Children's Mercy and its research, visit childrensmercy.org or download our mobile phone app CMH4YOU for all phone types. For breaking news and videos, follow us on Twitter, YouTube and Facebook.

About The Center for Pediatric Genomic Medicine at Children's Mercy Hospital The first of its kind in a pediatric setting, The Center for Pediatric Genomic Medicine combines genome, computational and analytical capabilities to bring new diagnostic and treatment options to children with genetic diseases. For more information about STAT-Seq, diagnostic tests and current research, visit http://www.pediatricgenomicmedicine.com.

Melissa Novak Phone: (816) 346-1341 E-mail: mdnovak@cmh.edu

Carin Ganz Phone: (212) 373-6002 E-mail: cganz@golinharris.com

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New DNA test can diagnose genetic disorders in newborns in just 2 days

For babies born with the rare genetic disorder phenylketonuria (PKU), their bodies are unable to break down a certain amino acid, which can lead to brain damage and seizures. If found early enough, however, PKU is easily treated, and children with the condition can go on to live a normal life. But sometimes, genetic testing for disorders such as this one come too late, and narrow windows of opportunity for treatment can close up for good.

But now, parents and physicians can have answers regarding a babys genetic abnormalities in only a few short days. Researchers from Childrens Mercy Hospitals & Clinics in Kansas City, Mo., have developed a new whole-genome sequencing technology capable of diagnosing genetic disorders in ICU newborns in just 50 hours a significantly less amount of time than the 12 to 14 days needed for current screening techniques.

The ability to diagnose infants in such a short amount of time could help to speed up available treatments as well as provide relief or knowledge to anxious parents.

There are about 500 diseases that can present in a baby for which theres a treatment, Dr. Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Childrens Mercy Hospitals and Clinics and lead author of the study, told FoxNews.com. But for diseases that dont have treatment, this info can still be useful. It gives parents and physicians an answer. You can stop doing additional testing or stop giving futile treatments. Parents can get counseling about whether this can recur in a future child and get advice about how intense treatments can be.

Currently, there are more than 3,500 known genetic disorders conditions caused by a mutation in a single gene and the definitive method diagnose them is to sequence the mutated gene. However, a big problem with gene sequencing up until now has been knowing exactly which gene to sequence, according to the researchers. Each genome contains more than 3.1 billion nucleotides, and of those, three to four million variants exist. In order to diagnose a condition, all of those variants need to be analyzed a task that can take quite a long time.

To speed up this process, Kingsmore, along with fellow Childrens Mercy Hospital researcher Neil Miller, teamed up with the company Illumina a group dedicated to technologies that analyze genetic variations. Having announced in January the Illumina high-speed 2,500 a high-speed sequencing device, the company approached Kingsmore and Miller to develop software that would go hand-in-hand with their new instrument.

That was how SAGA and RUNE were born. After the Illumina high-speed 2,500 sequences the entire genome in less than 30 hours, the software applications then come into play. First, SAGA, which stands for sign-assisted genome analysis, helps physicians to determine which parts of the genome are significant depending on the patients symptoms.

It allows them to click on buttons of symptoms that are corresponding in the baby such as difficulty breathing, etc, Kingsmore said. The computer then matches those particular symptoms and signs to the right parts of the genome and selects of those 3,500 genetic diseases, which ones are appropriate to test. So it allows us to test the variants that are likely to cause a disease.

To determine how effective SAGA was in determining a diagnosis, the researchers used the program on over 500 previously diagnosed cases, and the software was 99 percent accurate in selecting the right gene according to the patients symptoms.

RUNE solves the second part of the puzzle, which is determining how these variants impact the gene in which they occur. Standing for rapid understanding of nucleotide-variant effect, RUNE essentially ranks the order of diseases that are on possibly on target for the variants that were found.

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