Challenges of validating next generation sequencing panels
Most of us endorse that NGS can and should be used as part of clinical molecular diagnostic testing menus. On the other hand side developers of next generation sequencing-based assays agree that there are still significant challenges in developing clinical NGS-based gene panels – from the sequencing technology itself to differences in laboratories’ bioinformatics pipelines, DNA extraction and sample prep protocols, as well as differences in the sample itself.
It is important to note that the assay development process should be separated from the validation process:
- Generation of a protocol for the whole diagnostic test is the main focus of the assay development.
- The downstream process is important to validate sequencing-based clinical assays.
- Researchers should keep in mind that some of the main challenges of assay development and validation have nothing to do with the sequencing itself.
Advantages and disadvantages of FDA-cleared products
Let’s look deeper at the disadvantages and advantages of FDA-cleared products:
- FDA-cleared in vitro diagnostic tests could resolve some of the issues of developing and validating LDTs
- No development and validation costs for the lab (Instead, they must verify that the assay performs according to the FDA label)
- Expensive compared with LTD
- Dependency on the vendors for trusting their validation and that they will be able to supply reagents
- Accounting exercise for cleared products vs. LDTs
Currently, the only FDA-cleared NGS-based tests are Illumina’s 2 cystic fibrosis assays that run on its MiSeqDx system. A 139-variant assay kit for example has a list price of approx €6,800 including two runs on the MiSeqDx. Up to 45 patient samples can be multiplexed per run, which could cost €80 per patient.
It is an impressive difference if it is compared with a cystic fibrosis LDT that can be run for less than €45 per patient excluding development and validation costs.
Even more expensive is the full-gene assay by Illumina with a list price of approx. €56,000 including six runs and the ability to multiplex between six to eight patients per run meaning €1,600 per patient. Just keep in mind that costs could soar to €9,500 per patient, compared to an LDT that could sequence the entire CFTR gene for €180.