An error in one of the most widely used methods in epigenetics, DNA immunoprecipitation sequencing (DIP-seq), can cause misleading results, according to researchers at Linköping University, Sweden. Fortunately the error can be corrected in previously collected DIP-seq data, the team reports in a study published yesterday in Nature Methods.
"Our discovery highlights the importance of experimental validation when using high-throughput technologies in research. Without such experimental rigour, pervasive errors can hide in plain sight, concealed by their 'consistency' across studies" says Colm Nestor, assistant professor at the department of clinical and experimental medicine and lead investigator of the study.
By analyzing more than 125 existing datasets Nestor's group revealed that DIP-seq commonly detected DNA sequences that did not have any epigenetic marks. These false positives constitute 50-90% of the detected DNA regions, and the magnitude of the effect differs between different datasets. "Now that we know about this error, it's extremely simple to subtract it away. Correcting for these errors will allow novel discoveries to be made from the wealth of epigenetics data already in the public domain" adds Nestor.
The researchers point out that the vast majority of results from previous studies are correct. "We should continue to use these methods but correct for these errors by using appropriate experimental design" Nestor emphasizes.