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Rady Children's Hospital to Launch Sequencing Initiative to Investigate Birth Defects

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NEW YORK (GenomeWeb) – On the heels of a newly created pediatric genomics center, Rady Children's Hospital-San Diego is embarking on a project to sequence children with birth defects with unknown causes. 

The effort, set to start later this year, is anticipated to last four years and aims to sequence about 200 children and their parents each year of the project, Christina Chambers, lead researcher on the project and a professor of pediatrics at the University of California, San Diego, told GenomeWeb this week. 

A spokesman for Rady's said that the sequencing will be done by an undisclosed partner using Illumina platforms. The data will be analyzed in house at Rady, which will use existing staff, as well as hire additional staff in the near term, for the analysis. 

The project follows a $160 million investment at the hospital in August to establish a pediatric genomics center, with $120 million coming from philanthropist Ernest Rady and his family and $40 million coming from the hospital. The center is still looking for a director, but in the meantime, some early research initiatives have been identified, including the one targeting birth defects.

Many of the details around the project remain a work in progress, but birth defects was chosen as a research focus because such conditions "as a whole are pretty common," and occur in about one in every 30 births, according to Chambers. There are a wide variety of types of birth defects, with some genetically inherited, some resulting from chromosomal anomalies, and others caused by environmental factors. 

The causes of the vast majority of such defects, however, are unknown, Chambers said. In some instances, even when the cause is known, such as those with environmental underpinnings, it is unclear why some individuals are susceptible while others are not, she added. 

"The genomics part of this … [has] not been well addressed," she said. The work at Rady seeks to generate genetic data about some of the defects "and it can definitely develop hypotheses about specific birth defects that we can then … test or explore in larger datasets," Chambers said. 

According to a statement from the hospital, the initial goal is to sequence the genomes of every child born with a birth defect in San DiegoCounty in which the origin of the defect or disorder is unknown. About 1,200 kids are born in San Diego each year with a major birth defect, said Chambers. The project would sequence new patients, as well as analyze existing data from earlier research. 

While the plan currently is to sequence and analyze data from 200 kids and their parents each year during the length of the project, the figure is fluid and could change based on the availability of resources to Chambers and her colleagues. As sequencing prices go down, for example, more participants could be included in the research. 

The total funding amount for the project has not yet been determined, she said. 

Chambers said that the defects to be studied in the project will be those that justify the investment required for sequencing the samples, and could include cleft palates and congenital heart defects. One consideration will be "not only the ability to look at this locally, but if something pops up … we have another place [where] we can go look at a larger sample size and be able to replicate or confirm that finding," she said. 

The project is expected to start in a few months. In the meantime, Rady plans to iron out matters around patient consent, as well as create an institutional review board. 

According to Chambers, the decision not to purchase sequencers and do the sequencing in house was based on the rapid development of the technology and concerns that technology bought today could quickly become obsolete. 

"The investment would probably be better spent having that outsourced to somebody who does that and can do it well, and the rest of the expertise, we would keep in house," she said. 

The plan initially is to conduct whole-genome sequencing of patient samples with possible targeted sequencing later. "Part of the rationale is, in the end, that may be the most cost-effective approach," Chambers said. 

She added that while other clinical sequencing projects typically may have as a goal the development of therapies and treatments, for birth defects, "it's not typically coming up with a cure. You either have the defect or you don't," and it's handled either through surgery or some other method. 

Rather, the project could identify risk factors that could be avoided in the future to prevent the defect. She also said identifying the genetic basis of defects may help in differentiating the varied manifestations of a defect. 

"All of that would be helpful for parents and for clinicians to more precisely slice and dice what this disorder is, rather than lumping them all together," Chambers said. "It's possible that in the future that there would be some sort of diagnostic contribution that could be made by running a test."

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