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Touch DNA on these long johns influenced DA Mary Lacy when she publicly apologized to John Ramsey for the Hell his family had been put through - because in her mind the DNA evidence - found mixed with JonBenét's blood in her panties and on these long johns - pointed to the intruder who did not innocently leave his DNA on those articles of clothing.
The collection process is vital for the 'touch dna'. By making a reasonable assumption as to where JonBenet would have had her outer garment touched while being undressed and re-dressed collection efforts are concentrated in places most likely to have incriminating dna. The results show dna that is consistent with the dna inside the panties and not inconsistent with any other dna collected. 

Of course there will always be that Borg Sneeze Theory wherein some factory worker in Vietnam happened to sneeze in the factory and it also landed on the long johns that were the outer garment. 

The problem is we do not know if that dna comes from the ONLY male intruder and we do not know who that male intruder is.
We know that from the sample mixed with JBR's blood in her underwear, the CODIS profile still most likely belongs to "unknown male 1" (DS 007-2).    See Bode's Lab reports pages 1-4  in this article from the Boulder Daily Camera:

The Bode report states that the DNA profile obtained from sample 2S07-101-05A, the t-DNA on the right side of the leggings, contains a mixture of at least two individuals including the victim and at least one male contributor.  The individual associated with the "unknown male 1" profile cannot be exluded as a possible contributor to the mixture DNA profile obtained from sample 2S07-101-05A."

One of the experts consulted by the media, William Thompson, said, "A match is an analyst's judgement that the two samples fall into the 'included' category.  A match doesn't mean that the material is necessarily identical, just that there is a sufficient consistency to think that it might have come from the same source."

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