TABLE 2.
DNA extraction comparison (automated and manual): time and cost (currency in USD)e
| Platform | List price | Min/max samples per run | Extraction method | Total run timea/sample cost/sampled |
Pros | Cons | ||
|---|---|---|---|---|---|---|---|---|
| Samples | Time (h)f | Cost ($)f | ||||||
| QIAcube Classic | $35,360 | 2–12 | Filter/ centrifuge |
12 | 1.5 | 10.96 | DNA is eluted into tubes. Customizable protocols. |
Uses a lot of consumables. Max 12 samples per run. |
| 24 | 1.75 | 10.50 | ||||||
| 36 | 2 | 10.08 | ||||||
| 96 | 12 | 11.06 | ||||||
| QIAcube HT | $51,165 | 8–96 | Filter/ vacuum |
12 | 2 | 34.90 | DNA eluted into 96-well plate. Customizable protocols. Process up to 96 samples per run. |
Not 100% walkaway. Requires user feedback during run. |
| 24 | 2.5 | 21.61 | ||||||
| 36 | 3.25 | 17.21 | ||||||
| 96 | 5.25 | 10.39 | ||||||
| MagNA Pure 24 | $79,500 | 1–24 | Magnetic beads | 12 | 1.5 | 22.59 | DNA can be eluted into tubes. Customizable protocols. |
Kits & consumables are expensive. Lengthy hands-on setup with many consumables. |
| 24 | 2.5 | 20.33 | ||||||
| 36 | 4.5 | 22.24 | ||||||
| 96 | 8.5 | 19.04 | ||||||
| DNeasy Blood & Tissue Kit | $760.00/250 reactions ($3.04/sample) | 1–24b | Manual/ centrifuge |
12 | 2c | 36.48 | Less consumables than automated instruments. For very small sample volumes (<12), it may be more efficient than using an automated platform. |
No walkaway time, tech is at bench for the entire procedure. 100% hands-on, several transfer steps increase chance of error. |
| 24 | 4c | 72.96 | ||||||
| 36 | 6c | 109.44 | ||||||
| 96 | 2 daysc | 291.84 | ||||||
Includes instrument run time (where applicable) and hands-on time.
Maximum manual extraction sample volume is 24 samples, with the limiting factor being a 24-position benchtop centrifuge.
Bench time only. Other factors to consider when performing manual extractions of a high sample volume are technician fatigue (extraction time may be slower as workday progresses), technician break schedule, scheduling of tests in LIMS, submitting samples to sequencing core, preparing reagents, labeling tubes, and DNA quantification.
Service contract price is included in the per sample cost. The service contract cost per sample was calculated by taking the average number of samples sequenced from 2020 to 2021 (2861.50), divided by the cost of an annual service contract (2021 pricing).
Note: Both sample cost and tech time are higher for batches of 96 samples because the amount of QIAcube Classic and MagNAPure 24 instruments available to run simultaneously is a limiting factor. Tech time will vary depending on the amount of QIAcube classics available to run at the same time. All prices are based on 2021 costs in the currency of US dollars.
Bold, indicates the most cost effective option.