Quality Control Issues -Genotyping of samples

Analyzing and Reusing Data
, , ,
1

Given limited local sequencing capacity, we shipped a batch of DNA samples to the UK, which was then forwarded to an external sequencing facility for genotyping. In the UK facility, DNA extraction, spectrophotometric quantification, and storage at –20°C was done prior to shipment. The samples represented months of careful clinical phenotyping and community engagement.

Upon arrival at the sequencing facility, a substantial proportion of the samples failed initial quality control. Several samples showed evidence of fragmentation, reflected in poor DNA quality despite passing purity and concentration checks. Fluorometric quantification at the receiving facility revealed that concentrations were significantly lower than the NanoDrop readings in the manifest. Brief temperature excursions during shipment may have contributed to degradation.

For those of us working in settings where sample shipment to external facilities is the norm, this experience highlights several systemic considerations:

Failed samples represent not only financial cost but, more importantly, the irreplaceable loss of participant data, especially when recruiting in under-researched populations is resource-intensive.

Quality control must be viewed as a continuous thread—from collection to extraction to storage to shipment to the receiving facility’s lab bench. A breakdown at any point compromises the entire dataset.

Ultimately, reducing dependency on long-distance shipment and building or strengthening local sequencing capabilities would mitigate many of these logistical risks. This is a longer-term goal our team is actively pursuing.

I am sharing this not only to reflect on our own lessons but to invite the community to share their experiences:

  • What strategies have you implemented to maintain sample integrity across international or local shipments?

  • How do you harmonize QC standards between your laboratory and external sequencing facilities?

  • For those working in under-resourced settings, what creative or low-cost solutions have you developed to ensure sample quality?

3 Likes
2

Thanks for this post, @Vidash, this is a really important point. As you said, preserving sample integrity is crucial not only for downstream scientific analyses and ensuring maximum impact of resources, but also for building and maintaining trust within the patient community.

Wondering if community members working with genetic data have any insight regarding sample integrity maintenance, QC harmonization standards, and/or solutions particularly suited to under-resourced settings?

@cdwhelan @felipe_duartez @Roberta_Repossi @Stapapou @Francisac @mattia.volta @elahif01 @dicara @marekpiatek @mariariverapaz @Elainor @sahare

1 Like