Lab Matters Summer 2021 | Page 23

INDUSTRY MATTERS

5 . To truly democratize NGS for clinical or surveillance applications , multiple options with different price points are needed to accommodate needs of laboratories with different sample throughputs .

6 . NGS methods typically have higher analytical specificity than other NAATs . But , depending on the nature of the NGS workflow ( targeted vs . non-targeted or unbiased ), the analytical sensitivity could be a function of the method itself . This can be further impacted by complexity of the sample , choice of sequencing library preparation method , depth of sequencing , and read accuracy of the sequencing technology . Assay developers must design and optimize workflows based on the specific needs of the test .

7 . While a metagenomic approach is ideal for the de novo identification of unknown pathogen ( s ) in a sample , there is a great risk of wasting the sequencing bandwidth on unwanted sequences and losing sensitivity to detect lower abundance pathogens . Targeted approaches such as 16s rRNA ( for bacteria ), ITS ( for fungi ) sequencing or multi-pathogen primer panels can be good alternatives providing higher sensitivity , especially if the pathogen composition can be narrowed down a priori .

8 . In metagenomic applications , the sample preparation steps such as lysis and nucleic acid capture must be unbiased so that all groups of microbes ( gram-positive or gramnegative bacteria , fungi , protozoa , other eukaryotes ) are included in the downstream library preparation steps .

9 . A significant hurdle to the clinical adoption of a metagenomic or a pan-pathogen sequencing approach is the difficulty in proper validation . Test developers should use microbial

standards that are well-defined and accurately characterized , preferably from certified vendors , for benchmarking their assay performance . Since complex NGS workflows can have more failure modes , the test developer should also design appropriate assay and quality controls for troubleshooting and mitigating risks such as contamination and operator error .

10 . While this is not a concern under normal circumstances , a test developer should be mindful of designing NGS assays such that critical reagents , enzymes and buffers can be sourced from alternate vendors , in times of severe global supply chain limitations . n

Clear Labs is an APHL Gold Level Sustaining Member .

The Public Health Pricing List is a membersonly listing of discounts and special offers that APHL negotiates with corporate partners .

You can get special pricing for instruments , service agreements , equipment , testing supplies , PPE and more from companies such as Bio-Rad , Luminex , Roche Diagnostics , QIAGEN , Promega , SCIEX and Waters .

Log in to APHL . org and visit MyAPHL Your Resources > Member Resources > My APHL

This list is only available to the APHL member representatives and member associates who have been given membership rights under your lab ’ s APHL membership .

For more information about the public health pricing list discount offerings , please contact Camille Walker , Manager , Corporate Relations , camille . walker @ aphl . org .