Radboud University in Netherlands - which as I understand it essentially handles all rare disease testing in that country - has gone to PacBio WGS as first line testing since it eliminates the need for nearly all of the other technologies required to complement short reads and with it the training complexity & upkeep costs of maintaining competency in all those techs
HiFi still struggles with a handful of mutation types - Robertsonian fusions, regions with long purine tracts on one strand - but that means retaining just a few complementary technologies.
On the cost side, false positives / ambiguous calls from short reads must also be considered & the expensive personnel time to review these
I’d agree that institutional conservatism is the biggest barrier to long read adoption
The Netherlands given the relatively small population they must be looking at a few thousand tests a year I imagine. Moving to PacBio first must make a lot of sense in that context and hopefully provides a good model for others to emulate.
I'm surprised that short read tests cost $2500, these days I think the actual sequencing costs are much cheaper (probably at most $800 for 30X coverage, including library prep, and I've seen cheaper estimates than this). So is the rest just profit margin for the provider?
I think the actual sequencing cost is much less than $800. I suspect the billing from GeneDx is much higher than $2500... margins, covering operating costs on a relatively low volume test etc. etc. I guess?
Radboud University in Netherlands - which as I understand it essentially handles all rare disease testing in that country - has gone to PacBio WGS as first line testing since it eliminates the need for nearly all of the other technologies required to complement short reads and with it the training complexity & upkeep costs of maintaining competency in all those techs
http://omicsomics.blogspot.com/2024/05/hifi-wgs-as-nearly-unified-tool-for.html
https://pubmed.ncbi.nlm.nih.gov/39809270/
https://www.medrxiv.org/content/10.1101/2024.09.17.24313798v1
HiFi still struggles with a handful of mutation types - Robertsonian fusions, regions with long purine tracts on one strand - but that means retaining just a few complementary technologies.
On the cost side, false positives / ambiguous calls from short reads must also be considered & the expensive personnel time to review these
I’d agree that institutional conservatism is the biggest barrier to long read adoption
The Netherlands given the relatively small population they must be looking at a few thousand tests a year I imagine. Moving to PacBio first must make a lot of sense in that context and hopefully provides a good model for others to emulate.
I'm surprised that short read tests cost $2500, these days I think the actual sequencing costs are much cheaper (probably at most $800 for 30X coverage, including library prep, and I've seen cheaper estimates than this). So is the rest just profit margin for the provider?
I think the actual sequencing cost is much less than $800. I suspect the billing from GeneDx is much higher than $2500... margins, covering operating costs on a relatively low volume test etc. etc. I guess?