America’s sequencing boom could throw money into the wrong problem

Instead of trying to work on these issues at the national level, sequencing agreements allow individual public health agencies to request the names and contact information of positively tested individuals for variants of concern. But it only chains the same problem of data ownership.

“Some states are very good and want to know a lot about the variants that are common in their state,” says Brian Kreueger of Labcarp. “No other states.”

Public health epidemiologists often have little experience with bioinformatics, using software to analyze large datasets such as genomic sequences. A few companies have pre-existing sequencing programs; Even if they do, a small piece of the dataset gives out how much knowledge about real-world behavior can be gleaned after having each jurisdiction to analyze.

These issues revolve around – simplifying large-scale sequencing and linking clinical metadata – but require more than privacy and branch reform of privacy regulations – requiring a complete overhaul of the healthcare and public health system in the United States, with each of the four public health agencies Works and there is no concentration of information or energy.

Jonathan Quick, Managing Director of Epidemic Response, Preparedness and Prevention at the Rockefeller Foundation, said, “Metadata is the single largest uncracked nut. (Rockefeller Foundation Helps fund coverage In the MIT technology review, although it has no editorial observations)) It is so difficult to put together datasets large enough to understand the real-world alternative behavior for public health, our vaccine manufacturers and hospitals must come up with their own clinical trials, he says.

It is frustrating for him that such a huge dataset of useful information already exists in electronic treatment records, immunization registers and other sources but cannot be easily used.

“There’s a lot more that can be learned and learned quickly, we can’t rely on vaccine companies to monitor without trimming that data,” says Quick.

Boost state-level bioinformatics

If public health labs themselves are expected to focus more on tracking and understanding variants, they need all the help they can get. Above all, doing something about case-by-case forms is a public health job, while doing something about variants at the policy level is a political job.

Public health labs typically use genomics to reveal confidential information about an outbreak or as part of a track and trace effort. In the past, sequencing has been used to link E. coli outbreaks to specific farms, to identify and prevent HIV infection sequences, to isolate U.S. Ebola cases, and to follow annual flu patterns.

Even well-established programs tend to use genomics sparingly. The cost of sequencing has declined over the past decade, However, the process is still not cheap, especially for cash-strapped state and local health departments. The machines cost thousands of dollars to buy themselves and have a lot more to run: Illumina, the largest manufacturer of sequencing equipment, says labs cost an average $ 1.2 million Annually for the supply of each of its machines.

“If we pay the health department to set up programs without just a federal strategy so that everyone knows what they’re doing.”

Health organizations don’t just need money; They also need skills. Surveillance requires highly trained bioinformatics to turn the long letters of a sequence into useful information, as well as to explain to people the results and to explain any lessons learned in the conversion into policy.

Fortunately, OAMD is working to support state and local health departments as they try to understand their hierarchical data, hire regional bioinformatics experts to consult with public health officials, and facilitate agency sharing experience.

It pours in hundreds of millions to build and support those companies’ own sequencing programs. Not just for covid, but for all pathogens.

But many of those companies are under pressure to sequence as many quad genomes as possible. Without an integrated strategy for data collection and analysis, it is unclear how useful these programs will be.

“If we pay the health department to set up programs without just a federal strategy, so that they know what they’re doing,” Wormbrod said.

Early philosophy, snatching

Mark Pandori is the director of the Nevada State Public Health Laboratory, a program that OAMD supports. He has been a staunch advocate of genomic surveillance for years. Before moving to Reno, he ran a public health lab in Alameda County, California, where he helped pioneer a program using sequencing to find out how infections were going on around the hospital.

The biggest challenge for public health genomics programs is to turn order into usable data, he says.

“The CDC may say, ‘Buy a bunch of sequencing tools, do a whole bunch of sequencing’, but nothing can be done if these data customers don’t know how to use it and how to apply it.” “I’m talking to you about robotics. We need to do things consistently every day, but we need an easy way to know if the health departments are involved in the case. “

When it comes to variants, public health labs are under the same pressure facing the CDC: everyone wants to know how forms are being promoted, whether they can do anything with the information.

Pandori launched its Covid Sequencing program in the hope of reducing the labor required to investigate potential covid outbreaks by quickly identifying whether the cases caught close to each other were related or coincidental.

After his lab identified the first North American Kovid-9 patient, B1.351 was found in a hospitalized man returning from South Africa. The search for quick contact enabled the health department to prevent it from spreading.

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