The genomic data platform Lifebit has teamed up with PlumCare RWE in Delaware to help a Greek genomics initiative detect rare genetic diseases in newborn babies.
The initiative, dubbed BeginNGS, is supported by the Rady Children’s Institute for Genomic Medicine in San Diego in addition to Greece’s National Organization of Public Health. The program is planned to launch in 2023, and aims to sequence the genomes of 1,000 newborns by the end of the year. The long-term ambition will be expanding the target to all newborns in Greece by 2027.
Newborn babies around the world are typically screened for rare genetic conditions via a drop of blood from their heel. For example, more than 30 genetic conditions are set as priorities to screen for in the U.S. Recommended Uniform Screening Panel for newborns. However, the tests don’t detect every condition, meaning that some genetic diseases can progress for years before they are picked up and treated.
One solution to this issue is whole genome sequencing: there are around 400 conditions that could be detected with genomic analyses of newborns. Early detection of some conditions could let healthcare systems prevent the patient from dying or suffering from severe disability, rather than focusing treatment on children that are already ill. BeginNGS and other national whole genome sequencing initiatives around the world aim to usher in this transformation.
In the initiative, PlumCare specializes in using real world evidence and multi-omics data to produce insights into healthcare for children. The partnership with Lifebit will let BeginNGS deploy a cloud-based data sharing system that allows researchers to securely analyze genomics data from different healthcare hubs.
In the early days of genomics research, relatively small genomic datasets were often relocated to and analyzed in a centralized location. Many researchers today continue to download highly sensitive datasets to their institution or a centralized platform, creating many copies of the data around the world.
“This is no longer sustainable,” said a spokesperson at Lifebit in an email to Inside Precision Medicine. “In the genomics field alone, there are now roughly 2 to 40 billion gigabytes of data generated each year: this makes data duplication or movement inefficient and expensive. Most importantly, data security and patient privacy are at risk every time data is moved.”
To overcome this challenge, Lifebit’s secured and federated system connects different data hubs, allowing trusted researchers to analyze the data without needing to copy or move it.
The BeginNGS project is one of the leading projects of its kind. In the U.K., the firm Genomics England is conducting a research study with the National Health Service to assess the feasibility of carrying out whole genome sequencing in newborns, with the aim of sequencing the genomes of 100,000 infants. In New York, meanwhile, the Guardian study is gunning to screen 100,000 newborn genomes to catch rare genetic diseases early.
One concern for many national health services at the moment is the issue of cost. Whole genome sequencing is more expensive than routine diagnostic screens for newborns, and many services face squeezes in spending amid pressures from the COVID-19 pandemic and rising inflation. However, Lifebit is confident that investing in whole genome sequencing brings big value for money, and the costs and analysis time are dropping each year.
“Whole genome sequencing can significantly shorten the diagnostic odyssey many families affected by rare diseases face,” said Lifebit’s spokesperson. “In some cases this will be the difference between a single sample taken for whole genome sequencing versus potentially 20 or more different diagnostic tests. Whole genome sequencing brings benefits at the health system level with improved diagnostic efficacy and economic value, as well as at the patient-level, providing a quicker and less invasive way to diagnose and inform treatment for rare diseases.”
Lifebit’s federated learning technology has also been used in research projects in the UK and elsewhere. In April 2022, the firm struck a deal with the Danish National Genome Center to help precision medicine research across Denmark.
There are a number of other companies working on streamlining the sharing of genomics data in collaborations. One example is DNAstack, which last year recruited the firm integrate.ai to use a federated learning and privacy-preserving platform to support research into autism. Another is DNAnexus, which raised $200 million in a financing round last year to fund the development of cloud-based data analysis software, with a focus on multi-omics and clinical data.
Nonetheless, Lifebit sees itself as the only life sciences-focused company with patented federated technology built into its platform.
“The data never moves,” said the spokesperson. “Instead we bring the analysis and computation to where the sensitive data resides, in addition to being able to run federated queries and enforce federated authentication and access controls.”