2020-01-21 at 16:33 #434936Brittany HemelgarnParticipant
I wanted to reach out and ask what method everybody is using for tests using Next-Generation Sequencing (NGS) and Sanger Sequencing (when necessary)?
Is it appropriate to use Sequencing for a method when NGS and Sanger are incorporated or is Molgen more appropriate?
Brittany2020-01-21 at 16:41 #434937Pam BanningParticipant
Happy New Year! The components will vary between these methods. If you filter RELMA for method:sequencing, you’ll locate Finding/Documents on full mutation analysis of a particular gene. The method:molgen brings about a wider set of components (chromosomes, specific point mutation, deletions, transfusion transcripts, etc). There’s also a wider set of property and scales (PrThr, Geno, Prid, Arb, Find, etc). If your assays are truly using NGS and Sanger Sequencing, I would imagine your components are full gene reports. Let me know if that’s not the case?
Thank you!2020-01-21 at 17:02 #434938Brittany HemelgarnParticipant
Yes, the tests are full gene tests. So would Sanger Sequencing alone be considered Sequencing or Molgen?
With newer technology, I’m running into tests methods changing and incorporating NGS along with Sanger. Most likely all future sequencing will incorporate NGS and Sanger. It seems like it would be better to shift any sequence-related testing under Molgen. But I’m wondering if there is and will be a distinction in the LOINC world between Sanger and NGS? If there is, I need to submit many full gene components done via Molgen.
I feel kind of stuck.2020-01-21 at 17:32 #434939Pam BanningParticipant
Are you an IVD vendor or an end user? This question of equality in sensitivity and specificity would need to go to your next line of local expertise; either your technical scientist or your pathologist/medical director. I’ve checked both the LOINC User’s Guide and the Guide to LOINC Microbiology Terms v1.1 for Regenstrief’s side of the coin. “Sequencing” is mentioned in the LOINC User’s Guide 7 times, and at no point delineates amongst types of sequencing (Sanger and NGS). WIthin the 4 times it’s brought up in the Microbiology terms guide, I only find the “evolving model” note on bacterial genotypic resistant testing, where Probe.amp.tar and Sequencing are no longer recommended for use; the Method for existing bacterial molecular resistance terms may be updated over time to Molgen.
If this doesn’t answer your scenario, let me know. I can put it on the next Lab LOINC committee call (Feb 3rd). We would need supporting information from you emailed on the type of genes you are working with.
Hope to get you feeling “unstuck” and in the right direction soon!
Pam2020-01-23 at 09:43 #434975Jamalynne DeckardModerator
Hello Pam & Brittany!
The Sequencing Method in LOINC includes methods like Sanger & NGS that are used to detect variants within the coding regions and typically intron/exon boundaries of a gene (i.e. full gene analysis).
Here’s the current description for Sequencing in LOINC:
Sequencing is a method used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes or entire genomes. Historically, most sequencing has been performed using the chain termination method developed by Frederick Sanger in 1977. [PMID: 271968] Sequencing technologies have improved dramatically, making them cheaper, faster, and more accurate. Next-generation sequencing (NGS), also known as high-throughput sequencing, deep sequencing, and second-generation sequencing, is a type of technology that uses parallel sequencing of multiple small fragments of DNA to determine sequence. This “high-throughput” technology has increased the speed and amount of DNA sequenced at a significantly reduced cost. [PMID: 18576944] Several NGS platforms (ie, sequencing instruments and associated reagents) have been developed. Third-generation sequencing is another methodology currently under development that uses parallel sequencing similar to NGS. In contrast to NGS, third-generation sequencing uses single DNA molecules rather than amplified DNA as a template. [PMID: 20858600]
As Pam mentioned above, the Method of Molgen is used when a variety of methods could be used as part of the analysis. This is common for chromosome studies, targeted variant analysis, and large deletion/duplication analysis.
LOINC Content Developer
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