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UCSF receives $4.5M to study value of gene sequencing in newborns

UC San Francisco will receive $4.5 million over the next five years for a pilot project to assess whether large-scale gene sequencing aimed at detecting disorders and conditions can and should become a routine part of newborn testing.

The study is one of four projects launched today by the National Institutes of Health to identify the accuracy and feasibility of providing genetic sequencing as part of, or instead of, the current newborn screening that relies on biochemical changes in the blood. It also will assess what additional information would be useful to have at birth and the ethics and public interest in having such tests performed.

Genomic sequencing has the potential to diagnose a vast array of disorders and conditions at the very start of life, said Alan E. Guttmacher, MD, director of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (ICHD), which is jointly funding the studies. But the ability to decipher an individuals genetic code rapidly also brings with it a host of clinical and ethical issues, which is why it is important that this program explores the trio of technical, clinical, and ethical aspects of genomics research in the newborn period.

The pilots are a core element of the emerging field of precision medicine, which aims to harness vast amounts of genetic and health data to create predictive, preventive and precise care for patients on an international scale. Doing so has the potential to transform medicine, but there are many logistical and ethical hurdles to resolve along the way.

The UCSF team, which also includes bioinformatics experts at UC Berkeley and the Buck Institute for Research on Aging, will study the potential of sequencing the exome the roughly 2 percent of DNA that represents genes which code for proteins as a method of newborn screening. The research will look at the exomes potential for identifying disorders that California currently includes in the newborn screen, as well as those that are not currently screened for, but for which newborns may benefit if detection can occur early in life.

The UCSF research will examine the issue from three vantage points. The first will be a partnership with the California Department of Public Health (CDPH) to test blood drops previously collected from 1,400 children statewide who received standard newborn screening, to determine whether exome sequencing would be more accurate and also whether it provides insights that could lead to improved newborn screening, care and treatment.

My hope is that this will give us solid information on the specificity of gene testing, versus standard biochemical testing, for the disorders we are already screening for, said Robert Nussbaum, MD, who leads the UCSF Division of Medical Genetics and holds the Holly Smith Distinguished Professorship in Science and Medicine at UCSF. In addition, some of the disorders we pick up during screening are chemical abnormalities, but we dont know whether they will actually cause problems for the child. Wed like to know whether there is something in the childrens genes that determines whether these abnormalities actually will cause disease.

The second project will offer genetic testing to patients in a UCSF immune system disorders clinic run by Jennifer Puck, MD, a pediatrician in the UCSF Benioff Childrens Hospital whose research laboratory pioneered the current newborn test for Severe Combined Immunodeficiency (SCID). Parents will be asked to give informed consent for this arm of the project.

While there are several known genetic mutations that lead to the immune disorder, Pucks original test simply looks at a marker of whether children lack the immune cells known as T lymphocytes, which are missing in SCID. This new project will enable the team to assess whether exome sequencing works as well or better than the current test in identifying SCID, as well as other immune system abnormalities that the current test does not cover. Exome sequencing may also give parents information on the genetic basis of their childs disease.

Although new tests can benefit affected infants, extra tests cost money and will have false positives in some patients that cause both anxiety for parents and extra testing for the child, Puck said. The question in this grant is whether we could look at the DNA and see whether its more accurate in testing for these diseases. Thats the promise of genomic technology, but putting it into practice may not be so easy.

The third arm of the project will offer parents genetic testing for newborns at the UCSF Benioff Childrens Hospital to assess whether the child is likely to have adverse reactions to medications based on their genetics an area known as pharmacogenomics. That portion will be conducted in conjunction with renowned UCSF ethicist Barbara Koenig, PhD, who will be studying parents attitudes regarding testing children beyond what is currently offered in newborn screening.

While the first two projects are mainly looking at whether genetic testing would be more accurate, specific and useful than current methods, this third element assesses how willing parents are to get genetic information about their child that may be useful later in life, but not right away.

So far, newborn screening programs have not been directed towards just letting people know about a possible disease risk. There has to be a high probability of serious illness that can be prevented with early intervention, Nussbaum said. Pharmacogenomics is perhaps the most acceptable of tests that imply potential risk. Theres very little risk, and the possibility of great benefit, to knowing whether you will react to a drug or an anesthetic, and the only way to find out besides genetic screening is if youre in the operating room or have filled a prescription and you have a bad reaction.

The research team also intends to develop a participant protection framework for conducting genomic sequencing during infancy and will explore legal issues related to using genome analysis in newborn screening programs. Together, these studies have the potential to provide public health benefit for newborns and research-based information for policy makers.


Contact: Kristen Bole
University of California - San Francisco

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