Contamination signal in a 24-sample extraction batch
During a batch of 24 casework samples, the extraction negative control carried through the full procedure quantifies at 0.04 ng/µL. Its amplification shows D3S1358 allele 16 at 85 RFU, vWA allele 17 at 60 RFU, and D8S1179 allele 12 at 45 RFU. The amplification negative is clean. The batch contains 6 sexual assault kits and 18 trace samples, several of which quantified below 0.05 ng/µL. The laboratory's contamination action threshold for negatives is 0.02 ng/µL, and its analytical threshold is 125 RFU. The last proficiency test was satisfactory. Twenty of the 24 samples have no remaining material for re-extraction, and the batch includes a case with a court date in ten days.
1. Interpret the negative control result. What are the plausible sources, and how does the sub-threshold nature of the peaks affect the response?
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The quantitative result exceeds the laboratory's contamination action threshold, so the batch has a contamination signal that requires investigation. The peaks themselves are all below the 125 RFU analytical threshold, so they cannot be used for comparison or searched against anyone; they indicate the presence of low-level DNA, not an interpretable profile.
That distinction matters. The finding is a process signal, not a profile match. It must not be reported as if a specific person's DNA were identified in the negative.
Plausible sources include: a contaminated reagent lot or water supply; contaminated plasticware or columns; carryover from a high-yield sample extracted in the same batch or on the same instrument; environmental DNA introduced during setup; or analyst contamination. The fact that the amplification negative is clean suggests the contamination entered at or before extraction rather than at amplification, but it does not prove that.
2. What must happen before any of the 24 samples are reported, and which samples are most at risk?
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Reporting should pause for the batch until the source is identified or ruled out.
Steps: review the batch layout for a high-concentration sample extracted immediately before or adjacent to the negative; check other negatives and reagent blanks from the same lot and same period; quarantine the implicated reagent lots; re-extract a fresh negative with new reagents; swab the extraction area and equipment; review the analyst's handling records; and perform a formal root-cause assessment with corrective action before the lot is returned to service.
The samples most at risk are the low-template ones: the trace samples quantifying below 0.05 ng/µL, and any sample processed near the suspected contamination point. The sexual assault kits are generally higher-yield, but their sperm fractions may be low-yield and are equally vulnerable.
A strong, complete profile from a high-yield sample is unlikely to be explained by contamination at this level, but that determination should be made case by case and documented, not assumed.
3. For the 20 samples that cannot be re-extracted, how should results be handled and reported?
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Handle them by risk rather than uniformly.
For each sample, compare the case profile to the negative-control peaks and to staff and batch-mate profiles. If the case result is a robust, high-level profile whose alleles are not explained by the contamination signal, it can generally be reported with a statement describing the negative-control finding and the assessment that it does not account for the result.
If the case result is low-level, partial, or shares alleles with the negative-control peaks, the result should be reported as inconclusive or not suitable for comparison, with the reason stated. It should not be reported as an inclusion or an exclusion.
The report must disclose the batch-level quality issue, the corrective action taken, and the limits it places on interpretation. The ten-day court date is not a basis for shortening the investigation; if the deadline cannot be met with a defensible result, the laboratory should notify the requesting agency in writing rather than issue a compromised report.