Complex sentence: Possible contamination with extraneous DNA or primer multimer formation is routinely assessed with a (negative) control PCR reaction, set up in the same way as the experimental PCRs but without template DNA added, which is performed alongside the experimental PCRs.
Split into simpler sentences: Possible contamination with extraneous DNA or primer-multimer formation is routinely assessed with a (negative) control PCR reaction. This control reaction is set up in the same way as the experimental PCRs, but without template DNA added, and is performed alongside the experimental PCRs.