Should We Sequence the Genome of Every Newborn?

In November 2019, Matt Hancock, the United Kingdom’s health secretary announced a plan to sequence the genome of every baby born in a National Health Service hospital, beginning with a pilot of 20,000 children. Hancock, called his plan a “genomic revolution,” promising that whole genome sequencing and genomics would play a huge part in ensuring that every child receives “predictive, preventive, personalized health care.” Similar enthusiasm has been expressed in the United States, where the head of the National Institutes of Health, Francis Collins, has said that he looks forward to the day when all babies are sequenced at birth.

Such sweeping plans for collecting and sequencing the DNA of newborns may appear bold and tech-forward, but they lack nuance. Sequencing results are voluminous and variable. Some can be used to improve medical care, but others are poorly understood or uncertain, making widespread and untargeted use of the technology ill-advised. If sequencing belongs in newborn health care, as we think it does, it must be used in targeted ways that are attentive to the needs of babies, families and health systems.

The human genome contains three billion base pairs, so whole genome sequencing—mapping every base pair in a person’s genome—yields a huge amount of raw data. These data are analyzed by comparing an individual’s sequence to one or more reference databases (themselves works in progress), generating a list of differences known as “gene variants.” A minority of these variants are known to be associated with diseases, disabilities and other kinds of physical or mental traits, with many real-world cases to back up that interpretation.

Others have weak associations with specific conditions or traits, making it difficult to predict whether and how a child might be impacted. Still others are not well understood or have never been seen before. While the cost of sequencing a person’s entire genome has rapidly decreased to under $1,000, working out what all that sequence data means for a particular person’s health remains time-consuming and complex.

Researchers are working to resolve some of this complexity, but it can never be completely eliminated. Even well-understood gene variants remain uncertain in many ways. A person carrying BRCA gene variants known to be strongly associated with breast and ovarian cancer may never get sick. For those rare genes where disease is certain, the age of onset can vary significantly. Some people with Huntington disease genes get their first symptoms at age 80, others at age two, and most between ages 30 and 50. And the same gene variants can affect different people in very different ways: some people with Marfan syndrome have few troubling symptoms early in life, while others experience life-threatening heart conditions from birth. Sometimes two people in the same family express the same variant differently: one severely affected, another not. We might wish genomic sequencing to foretell, magically, all health and disease, but that hope is illusory.

All these different kinds of uncertainty and variability, across thousands of gene variants, limit the usefulness of many sequencing results. At this point, only a few can aid in a diagnosis, alter a person’s medical care, or guide important life decisions like whether to have children. Getting these useful results can be very valuable, but parents shouldn’t have to deal with dozens and dozens of unclear results of questionable value just to get those few results that they can use to help their child.

Nor can health care systems afford unfocused use of sequencing. Explaining hundreds or thousands of complex and uncertain results to patients takes time and expertise, drawing down health care resources for little direct benefit. Patients need education and counseling on the meaning and implication of their results, and may seek follow-up care, including further testing and monitoring across the life-course. For these reasons, no medical association recommends whole genome sequencing as a general screening tool in adults, let alone babies.

Indeed, caution is even more warranted in newborns, who cannot consent to testing for conditions that we know some adults prefer not to know about. In addition, very little phenotypic information is available about infants to guide interpretation of results. Further, worrying results that cannot guide care could unnecessarily distress parents and disrupt family bonding. Results can also be used in discriminatory ways across the child’s lifetime by insurers or future employers. Rather than sequencing the entire genome of all newborns, we recommend targeting this powerful technology to well-understood and usable gene variants.

Thankfully, we already have a model for how to do this: newborn screening programs such as those run by state departments of public health in the U.S., which test a drop of blood taken from each baby’s heel for several dozen conditions, including cystic fibrosis and sickle cell anemia. If a child is diagnosed, specialized programs connect the family with treatments and other resources, making these programs one of the only universally available health care programs in America.

When deciding which conditions to look for in newborns, states focus on conditions that are serious or life threatening, can be effectively treated, and that can be reliably and affordably detected. These newborn screening criteria provide the legal and ethical justification for the mandatory nature of the U.S.’s newborn screening programs: parental permission is not required. These newborn screening criteria also ensure that precious public health dollars are focused where they can do the most good. Right now, states primarily use a technology called tandem mass spectrometry to analyze newborn blood spots for conditions that meet the criteria. But they could, in theory, also use sequencing to identify conditions that meet newborn screening criteria but that right now cannot be picked up with existing technology.

This kind of focused use of sequencing technology could benefit infants, families and the health care system, as we discussed at length in our report on the use of sequencing technology in newborns. But it is very different from the indiscriminate use of whole genome sequencing in all infants, as imagined by some. As with all new technologies, health care systems must select the version of this new tool that best matches the needs of children and families in particular care contexts. The sequencing test that is right for a newborn in the NICU whose diagnosis is a puzzle might not be right for millions of seemingly healthy babies whose parents just want to make sure they give their child the best shot in life. Universal public health programs like newborn screening could be undermined by indiscriminate use of genome sequencing. Targeted and nuanced use, on the other hand, will benefit babies, families, and society for decades to come.

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