Dealing with contamination

PCR-based technology has an interesting history.  In PCR's history, contamination has often led to false results, and erroneous actions have been taken based on those results.  This has led some  investigators to discontinue and denounce the technology as being, "too sensitive."  In research, PCR-based results face routine, often vigorous scrutiny for the possibility that contamination may have influenced the results.  

But, PCR also has an unparalleled advantage of powerfully increasing the amount of DNA from small samples.  This can be a great advantage in both research and forensics.  For that reason, many investigators use PCR.  

Fortunately, there are ways of dealing with contamination, or at least limiting its influence:

1.  It is extremely important to run negative controls and background controls through the entire procedure.  Such controls are virtually the only way of detecting low-level contaminating DNA molecules.

2.  Once contamination has been detected, it is important to discard all current reagents and clean relevant equipment and work surfaces.  Bleach is useful for cleaning.  However, not all equipment can be cleaned with bleach.  Some laboratories effectively use gas flames to rid metal utensils of DNA.

3.  Thermal cyclers (where PCR is carried out) need to be cleaned.  It is not unusual for sample tubes leak DNA in the thermal cycler.   Such tubes become soft during temperature extremes and they do not always seal properly.   It is not usual for sample tubes to have minuscule pin-holes.  Sample contamination due to contaminated thermal cyclers has been documented.  Hot soapy water, a sponge and a round scrub brush are useful for cleaning thermal cyclers and their sample-tube wells. 

4.  Of course the contamination event should be discussed.  However, discussion alone is rarely, if ever, sufficient since it may lead to rationalization of the event and failure to correct it.

5.  It is critically important to store samples in proper containers and keep known samples well-segregated from other evidence, particularly evidentiary samples that have small amounts of DNA.  Paper envelopes or wax-paper folds are unsuitable containers.

6.  The laboratory should be extremely careful not to overstate the scientific value of the evidence.  For example, reports that a profile occurs in 1 in a billion, randomly selected individuals greatly overstate the proven error rate of the technology since false convictions based on DNA evidence have been established.  Perhaps such rare match probabilities could be reached if thoroughly independent samples produced the same results in multiple, independent, non-communicating laboratories.  But, for single laboratories, extremely rare match probabilities misrepresent the scientific value of technology.

            Some laboratories prefer to trace the contaminants.  But, many find it is more time-efficient to perform a general cleaning and reagent replacement.  The latter makes sense because contaminant sources often vary, and time spent tracing the contaminant can be easily wasted.  It is important for laboratories to have procedures that effectively detect, acknowledge and deal with contamination