External Quality Assessment in Molecular Diagnostics

External quality assessment (EQA) in molecular diagnostics is independent verification of the accuracy of PCR, next-generation sequencing (NGS) and genetic test results. Proficiency testing (PT) programs in this field evaluate every stage, from nucleic acid extraction to mutation interpretation. For high-tech laboratories, participation in specialized EQA programs is a prerequisite for accreditation to GOST R ISO 15189-2024.

Why EQA Matters for Molecular Testing

Molecular diagnostics is a rapidly evolving field with high demands on analytical accuracy. A false-negative PCR result can mean a dangerous infection is missed. An incorrect interpretation of an NGS mutation can mean the wrong targeted therapy in oncology.

Factors that make EQA necessary:

High method sensitivity: even minimal contamination leads to false-positive results
A wide variety of platforms and protocols: results depend on the extraction system, primer set and thermal cycler
Complex interpretation, especially for variants of uncertain significance (VUS) in NGS
Rapidly expanding panels: new targets require validation through external assessment
Regulatory requirements: ISO 15189, ISO 20186 (pre-analytical processes for molecular testing)

Areas of Molecular Diagnostics Covered by EQA

PCR and qPCR: Infectious Disease Diagnostics

Respiratory pathogens: SARS-CoV-2, Influenza A/B, RSV, MPOX
Hepatitis: HBV (viral load), HCV (genotyping and quantitation)
HIV: HIV-1 RNA, qualitative and quantitative detection
Urogenital infections: CT/NG (Chlamydia/Neisseria), HPV (genotyping)
Tuberculosis: MTB/RIF (GeneXpert), detection of rifampicin resistance
Herpesviruses: CMV, EBV, quantitative monitoring in immunosuppressed patients

NGS: Next-Generation Sequencing

Cancer genetics: EGFR, KRAS, BRAF, ALK, ROS1 mutations for targeted therapy selection
Inherited diseases: BRCA1/2, CFTR, cystic fibrosis, inherited thrombophilias
Hematologic oncology: AML-associated mutations (FLT3, NPM1, IDH1/2)
Pharmacogenomics: CYP450, DPYD, TPMT polymorphisms

Digital PCR (dPCR)

High-precision quantitation of viral loads
Detection of minimal residual disease (MRD)
Non-invasive prenatal testing (NIPT)

International EQA Programs

Provider	Program	Frequency	Scope
QCMD	Respiratory Panels	3–4×/year	SARS-CoV-2, Influenza, RSV, MPOX
QCMD	Viral Load (HBV, HCV, HIV)	2×/year	Quantitation of viral loads
QCMD	HPV, CT/NG	2×/year	Urogenital infections
CAP	Molecular ID (MOL)	2×/year	16S/18S identification from cultures
CAP	Oncology NGS Panels	2–3×/year	Somatic mutations for targeted therapy
INSTAND e.V.	Ringversuch 348, 357	2×/year	MTB, CT/NG, HPV, HBV, HCV
INSTAND e.V.	Molecular genetics	2–4×/year	Genetic tests, virology
EMQN	Germline Genetics	2–3×/year	BRCA, CFTR, AML, inherited diseases
EMQN	NGS Quality	2×/year	Assessment of the entire NGS pipeline
GenQA	Molecular Genetics	2–4×/year	Molecular genetics, oncogenomics
UK NEQAS	Molecular Diagnostics	Up to 6×/year	PCR, genotyping

Equipment Compatibility

Platform	Manufacturer	Recommended EQA programs
GeneXpert	Cepheid	QCMD (MTB, CT/NG), INSTAND 348
cobas 6800 / 8800	Roche	QCMD, CAP MOL, INSTAND
QX200 / QX600 (dPCR)	Bio-Rad	QCMD, CAP, EMQN
CFX96 / CFX Opus	Bio-Rad	QCMD, INSTAND, UK NEQAS
ABI 7500	Thermo Fisher	QCMD, CAP, INSTAND
NGS sequencers (MiSeq, NextSeq, Ion Torrent)	Illumina / Thermo Fisher	EMQN, CAP NGS, GenQA

Specific Features of EQA in Molecular Diagnostics

What Is Assessed

Unlike conventional laboratory diagnostics, molecular EQA tests the entire analytical pipeline:

1. Nucleic acid extraction: DNA/RNA quality and yield

2. Amplification: PCR sensitivity and specificity

3. Detection: correct determination of Ct values (qPCR) or copy numbers (dPCR)

4. Sequencing: depth of coverage, read quality, variant calling accuracy (NGS)

5. Bioinformatics: correct annotation and classification of variants

6. Clinical interpretation: a correct report for the clinician

Control Materials

Lyophilized panels: stable at room temperature, simplify logistics
Plasma spiked with viral particles: mimics clinical samples for quantitative tests
Reference DNA samples: for NGS and genotyping, with validated mutations

Practical Recommendations

For Infectious Disease Laboratories

Basic set: QCMD (respiratory panels, viral loads) + INSTAND (PCR proficiency testing rounds) covers the core range
If you use GeneXpert, participation in the dedicated QCMD programs for MTB/RIF is essential

For Genetics and Oncology Laboratories

EMQN: the industry standard for inherited diseases and cancer genetics
CAP NGS: for laboratories performing somatic tumor profiling
GenQA: additional assessment for molecular genetics

Quality Management of the NGS Pipeline

Participate in programs that assess the entire cycle, from the wet lab to bioinformatics analysis
Document pipeline versions, annotation databases and filtering parameters
Update variant databases regularly (ClinVar, COSMIC, gnomAD)

KombiMED's Comprehensive Approach

KombiMED supplies the full range of molecular diagnostics equipment, from PCR systems (GeneXpert, cobas 6800) and dPCR (Bio-Rad QX200) to NGS sequencers. We help laboratories enroll in specialized international EQA programs that match their testing profile.

Our specialists can help you:

Request a consultation on external quality assessment in molecular diagnostics.

Build the optimal set of EQA programs for an infectious disease or genetics laboratory
Organize the supply of control panels in line with logistics requirements
Prepare your laboratory for accreditation of molecular testing to GOST R ISO 15189-2024