Overview
Extraction failure is any situation in which nucleic acid purification or recovery cannot be confirmed as adequate for reliable downstream molecular testing, requiring the laboratory to hold affected results and follow assay-specific troubleshooting.
Classification
| Pattern | Typical SOP direction |
|---|---|
| Specimen-level control failure | Invalidate specimen; re-extract or recollect |
| Batch-wide extraction failure | Hold batch; check reagents/instrument |
| Low yield / purity out of range | Do not proceed outside acceptance; follow SOP |
| Suspected inhibition | Re-extract, dilute, or recollect per assay rules |
Morphologic Features
Not applicable, troubleshooting describes workflow and quality failures, not morphologic entities. Gross specimen appearance may still contribute to the failure pattern.
Laboratory Characteristics
- Always review required controls and acceptance checks before LIS release
- Separate single-specimen problems from batch/system problems
- Document holds, repeats, and outcomes for quality tracking
Reference Intervals
Not applicable, troubleshooting uses assay control expectations and SOP acceptance limits, not patient reference intervals.
Clinical and Laboratory Significance
Releasing results from a failed extraction pathway can produce false-negative or unreliable clinical reports. Holding and correcting the pathway protects patient safety.
Differential Considerations
Laboratory differential includes extraction failure, inhibition, degradation/low yield, poor specimen, and reagent/instrument problems, resolve by SOP pathway, not clinical differential diagnosis.
Comparison Tables
Extraction failure interpretation guardrails
| Situation | Safe framing | Unsafe framing |
|---|---|---|
| Failed extraction control, no target | Invalid, hold / re-extract / recollect | Negative, release now |
| Clinician urgency on a failed run | Communicate delay; complete SOP actions | Invent a negative to clear the queue |
| One specimen fails; rest of batch OK | Invalidate that specimen only (if SOP allows) | Ignore its control because neighbors passed |
Classification Frameworks
Not applicable.
Laboratory Notes
- Invalid is not negative, say so clearly when communicating holds
- Choose recollect vs re-extract only when the SOP lists that action for the pattern
- Escalate unexplained or repeated failures rather than repeating indefinitely without documentation
References
Authoritative textbooks, guidelines, and reviews supporting this reference entry. Verify reference intervals, critical limits, and reflex criteria against institutional protocols and current guideline editions.
Textbooks
- McPherson RA, Pincus MR. Henry's Clinical Diagnosis and Management by Laboratory Methods. 24th ed. Elsevier; 2021. (Molecular diagnostics chapters, verify current edition.)
- Buckingham L. Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications. 3rd ed. F.A. Davis; 2019. (Verify current edition.)
CLSI and Professional Guidelines
- Clinical and Laboratory Standards Institute (CLSI). Consult current CLSI molecular method documents available through your laboratory, document numbers and editions change; do not treat any single CLSI title as universal.
- Institutional molecular laboratory SOPs, assay manufacturer instructions for use (IFU), and locally adopted accreditation requirements. Always verify current local practice.
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