Tuesday, March 31, 2009
Way too Sensitive?
The techniques for detecting DNA and RNA are extremely sensitive. This sensitivity often leads to misinterpretations because it become difficult to separate signal from noise. The idea that 90% of our genome may be transcribed into functional RNA, for example, may be due to the sensitivity of an assay that can easily detect tiny amounts of accidental transcription.
Similarly, the often proclaimed ubiquity of alternative splicing may be due to the easy detection of splicing mistakes. Other examples of problems with noise might be the presumed abundance of small regulatory RNAs and the frequency of transcription factor binding sites.
The problem is acute when it comes to analyzing DNA from fossils. There, tiny amounts of contamination can really screw things up. That's why John Hawks is also interested in this problem of over-sensitive DNA assays.
Just how sensitive is the technology? Hawks has found a very interesting and informative example [The trouble with contamination]. This example is about contamination but keep in mind that it also applies to the detection of noise in transcription, DNA binding, and splicing.
Here's the original report from the BBC ['DNA bungle' haunts German police]. Over the past few years German police have been on the lookout for a mysterious woman who was linked to several murders. Her DNA was found at over 40 different crime scenes. This woman became one of the most wanted people in Europe but nothing was known about her aside from her DNA.
Finally someone became suspicious and started to look closely at the way they were collecting and analyzing DNA. To make a long story short, the alleged murderer is a factory worker in Bavaria who works in a factory that manufactures cotton swabs. The same swabs that are used to collect samples at a crime scene. Those swabs were contaminated with her DNA.
There's a lesson here. Any technology that can detect the DNA from a factory worker on a cotton swap is quite capable of detecting tiny insignificant amounts of nucleic acids inside a cell.