IQCP for Molecular Testing: Cartridge PCR, LDTs and Exclusions
IQCP can be used for molecular tests and LDTs in eligible specialties, per CMS. In practice it suits cartridge-based molecular infectious disease tests with built-in internal controls. CAP-accredited labs can't use IQCP for ISH, microarray, Sanger sequencing or next generation sequencing.
Molecular labs ask whether a cartridge's internal controls can replace daily external positive and negative controls. Here's the official position.
Last reviewed Oct 2026 · By Sound Lab Consultants CLIA team · General information, not legal advice.
CMS position
CMS says IQCP may be used for LDTs and molecular tests in eligible specialties and subspecialties (CMS IQCP Frequently Asked Questions (Aug 2016)). The same three parts and the same director approval apply.
CAP position
the CAP's public IQCP FAQ (updated Nov 2024) limits molecular IQCP to test systems using an internal (electronic, procedural or built-in) control system for daily QC instead of external controls. Mainly that means molecular infectious disease tests and a limited number of genetics tests using single-use cartridges. ISH, microarray, Sanger sequencing and NGS aren't eligible; their checklist QC applies.
Risks specific to molecular cartridges
Specimen: collection device, transport medium, inhibitors, stability
Reagent/cartridge: lot changes, storage temperature, shipping excursions
Test system: module failures, software, internal control coverage (sample processing control vs probe check)
Environment: contamination and amplicon control, room temperature
Personnel: cartridge loading, contamination prevention, competency
Template
ASM's IQCP protocol templates for microbiology and molecular testing includes a template for a commercial cartridge-based molecular test system. Combine it with manufacturer, accreditor and CMS materials, as ASM itself recommends.
Related: unit-use cartridge devices and IQCP for microbiology.
IQCP for Molecular Testing checklist
☐ Confirm the assay is eligible (CAP: internal-control cartridge system)
☐ Document what each internal control actually checks
☐ Collect external control history and PT
☐ Cover contamination and inhibition risks
☐ Define external control frequency and new lot/shipment QC
☐ Director approval and QA monitors
CDC resources on CLIA
CDC's overview of the CLIA program: CDC explains that CLIA applies to every U.S. site that tests human specimens to assess health or to diagnose, prevent, or treat disease. It also explains that CDC supports the program alongside CMS and FDA.
CDC on CLIA test complexity categories: CDC explains how FDA scores tests as moderate or high complexity using seven criteria. It also notes that lab-developed or modified tests default to high complexity, and that moderate and high complexity standards differ only in personnel requirements.
CDC's free CLIA educational materials: CDC offers brochures and booklets on waived testing, PPM, and IQCP.
Frequently asked questions
Can molecular tests use IQCP?
Yes. CMS says IQCP may be used for molecular tests and LDTs in eligible specialties.
Can NGS use IQCP?
Not at CAP-accredited labs. The CAP says NGS, Sanger, ISH and microarray aren't eligible.
Do cartridge internal controls replace external controls?
Only through an IQCP whose risk assessment shows the internal controls cover the risks, at a frequency no less than the manufacturer requires.
Is there a molecular IQCP template?
ASM, with CLSI and CAP, publishes a template for cartridge-based molecular test systems.
Do LDTs qualify for IQCP?
CMS says yes, in eligible specialties.
Official sources and further reading
ASM's IQCP protocol templates for microbiology and molecular testing
Developing an IQCP - A Step-By-Step Guide (CDC/CMS workbook)
Related IQCP guides
Talk to an IQCP consultant
Sound Lab Consultants helps labs nationwide build, review and maintain IQCPs from their own data and the official CMS and CDC guidance.
Sound Lab Consultants, PO Box 2135, Chandler, AZ 85244