Processing sequencing data sent via CSV
Hi,
Our current process allows labs to share sequencing data via Redcap. We do have a lab that has started to send sequencing results via HL7, but have several labs that do not have HL7 capability and are sending COVID results via CSV. In MD, we have our own CSV template. I am considering how we can alter our template to allow labs submitting CSVs to do so with an updated template so we can process these results into our SS (NEDSS). Has anyone else done this?
Thanks,
Kristy
Our current process allows labs to share sequencing data via Redcap. We do have a lab that has started to send sequencing results via HL7, but have several labs that do not have HL7 capability and are sending COVID results via CSV. In MD, we have our own CSV template. I am considering how we can alter our template to allow labs submitting CSVs to do so with an updated template so we can process these results into our SS (NEDSS). Has anyone else done this?
Thanks,
Kristy
I've created a minimum csv and a larger csv template for variant reporting with the idea that we need the original PCR positive result info as well as the variant results. However, I don't think we will be getting a re-report of the original as well as the variant. We are minimally asking for the specimen ID of the original and date collected. Just getting that in place and also uploading from current lab csv files not based on the new template as well. Not automated.
We have not received sequences via HL7 yet.
"It seems like this is still referencing the specimen ID of the original PCR test, and then reporting the variant information. We are seeing right now a TON of variability where sequences initially called as one lineage get later called another lineage. I want to keep emphasizing that the primary thing we need reported is the Accession number from the database so we can be analyzing the sequence over time to make sure we have the most up-to-date variant call."
Thoughts? How do we ensure we get that accession #?
Thanks,
Chris Baumgartner
Senior Data Exchange Manager
Office of Public Health Outbreak Coordination, Informatics, and Surveillance (PHOCIS)
Division of Disease Control and Health Statistics
Washington State Department of Health
chris.baumgartner@doh.wa.gov<mailto:chris.baumgartner@doh.wa.gov>
206-418-5530 | www.doh.wa.gov<http://www.doh.wa.gov/>
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