UCSF Receives $4.5M to Study Value of Gene Sequencing in Newborns

Project with UC Berkeley and Buck Institute Will Assess Accuracy, Ethics

By Kristen Bole

A mother with a baby.

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 on Sept. 4 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 individual’s 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.”

Exploring Potential of Precision Medicine

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 exome’s 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 don’t know whether they will actually cause problems for the child," Nussbaum said. "We’d like to know whether there is something in the children’s genes that determines whether these abnormalities actually will cause disease.”

Robert Nussbaum, MD

Robert Nussbaum, MD

Jennifer Puck, MD

Jennifer Puck, MD

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 Children’s 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, Puck’s 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 child’s 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 it’s more accurate in testing for these diseases. That’s the promise of genomic technology, but putting it into practice may not be so easy.”

Pharmacogenomics Test for Adverse Drug Reactions

The third arm of the project will offer parents genetic testing for newborns at the UCSF Benioff Children’s 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 parent’s attitudes regarding testing children beyond what is currently offered in newborn screening.

Exomes & Genomes

dna strand

The genome comprises an organism’s entire hereditary information, or genetic makeup, including both genes and the DNA/RNA in between them. In humans, that represents about 3.2 billion DNA base pairs.

The exome is composed only of the genes – the protein-coding DNA that makes up an estimated 2 percent of the total genome, yet is thought to contain 85 percent of disease-causing mutations.

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. There’s 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 you’re 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.

Additional researchers on the project include Neil Risch, PhD, director of the UCSF Institute of Human Genetics; Pui-Yan Kwok, MD, PhD, a UCSF professor of dermatology whose research focuses on analysis of complex genetic traits; and Joseph Shieh, MD, PhD, an assistant professor of pediatrics and medical genetics. Sean Mooney, PhD, a bioinformatics expert at the Buck Institute for Research on Aging, and Steven Brenner, PhD, a professor of plant and microbial biology at UC Berkeley and an adjunct professor at UCSF, will contribute their expertise in bioinformatics to the project.

The four NIH pilots, which also include Brigham and Women’s Hospital in Boston, Children’s Mercy Hospital in Kansas City, and the University of North Carolina at Chapel Hill, will receive $25 million over the next five years as funds are made available through the NICHD and the National Human Genome Research Institute, both parts of the National Institutes of Health. This year’s grants were made under the Genomic Sequencing and Newborn Screening Disorders research program.

UCSF is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It includes top-ranked graduate schools of dentistry, medicine, nursing and pharmacy, a graduate division with nationally renowned programs in basic biomedical, translational and population sciences, as well as a preeminent biomedical research enterprise and two top-ranked hospitals, UCSF Medical Center and UCSF Benioff Children’s Hospital.