Hi @ehutchins :
For my PhD project, I’ve encountered significant challenges, starting with the DNA extraction itself, which had issues so severe that the protocol had to be fixed and couldn’t be overlooked. However, I understand that your question is more focused on sample swaps, labeling errors, and misannotations—critical risks for large cohort studies. That said, even after resolving the extraction problems and achieving the minimum DNA quantity and quality for sequencing, 23.5% of the 285 PD case samples still failed QC. Here’s the breakdown of the reasons for failure:
I think this is a really high (and quite disheartening) outcome. As a solution, I’ve been reflecting on the importance of improving training at the local centers before samples are shipped to LARGE-PD.
I’m not sure if this fully answers your question, @ehutchins, but as part of the training and mentorship Task Force, this issue needs focused attention. In Chile, we’ve struggled with small but impactful errors, which makes a big difference. Reinforcing training on sample handling and providing more context to the local teams could really help. In a way, this is more of a “mea culpa” from my side