Is the Spectrum Compact CE Instrument Right for Your Lab?
An Interview with Dr. Melanie Weissenberger
Interview Written and Condensed by Nicole Siffling, Promega
We were pleased to interview Melanie Weissenberger from the Institute of Legal Medicine in Heidelberg, Germany. Dr. Weissenbergber is the very first Spectrum Compact CE user worldwide! Melanie finished her studies of Biology at the University of Heidelberg in 2007 and got her PhD at the Institute of Legal Medicine in Heidelberg in 2010. Since December 2009, she has been the Head of the Laboratory of Forensic Genetics at that Institute.
The Spectrum Compact CE instrument was installed in her lab in early September and since then she has been doing quite a bit of testing. Read on to learn what she had to tell us about her experience with the instrument so far.
Melanie, why did you choose this instrument?
Until now, we have used a Genetic Analyzer which was purchased 18 years ago. In the past 2 years, this instrument has had numerous technical issues. Therefore, we were looking into buying a new instrument to replace it.
Our criteria for a new instrument were:
- Consumables need to be available in small quantities so that they will not expire before usage.
- Exchange of consumables must be easy and consumer friendly.
- The instrument must be compatible with STR kits of all commercial manufacturers in the forensic field. As the latest STR kits are based on a 6-dye technology, it was important that the instrument can detect 6 colors.
- For future extension of our range of services, the instrument needs to have the possibility to sequence (we currently only do fragment analysis).
- The fsa-files of the instrument must be compatible with the software that was already being used in our laboratory.
- Operation of the instrument should be simple and clear.
- The sensitivity of the new instrument must be at least as good as the sensitivity of our old instrument.
- Color separation of samples with very high DNA amounts must be successful (no pull up or loss of peak signal information due to a low cut-off).
- DNA mixtures must be well balanced.
We had the chance to test the Spectrum Compact instrument before buying to see if all of our criteria were met-and indeed, they were!
Promega Instrumentation Service Engineers install the Spectrum Compact CE instrument.
Which samples have you analyzed with it so far and which kits did you try on the Spectrum Compact System?
We looked at numerous kits including:
- PowerPlex® ESX17 System (Promega)
- PowerPlex® Y23 System (Promega)
- Investigator® Argus X-12 QS Kit (Qiagen)
- Investigator® 24plex QS Kit
- Investigator® ESSplex SE QS Kit (Qiagen)
- Investigator® IDPlex Plus Kit (Qiagen),
- NGM Detect™ Kit (Applied Biosystems®)
We tested various samples such as Chelex extracted samples (buccal swabs), complex mixture samples, GEDNAP-proficiency test samples, mixtures with high major/low minor contributors, and a dilution series.
Did you see a difference in performance of the Spectrum Compact CE System in any of the kits that you evaluated?
All went well. We probably need to improve certain things with the NGM Detect kit as the yellow channel was a bit too strong.
Editor’s note: The pre-setting of the instrument includes a 6-dye matrix with NED, whereas the yellow dye in the NGM Detect Kit is TED). Whether this difference is responsible for the deviation is yet to be determined.
Regarding the robustness of samples with small quantities of DNA (i.e., Casework samples or touch samples) or samples with large quantities of DNA (i.e., Paternity samples), have you seen any anomalies?
We tested mixtures up to 1:30. Even those samples were partially interpretable if it was a unique minor and both the minor and the major were heterozygous. There were no abnormalities with the tested samples, I do not see a need for improvement here.
As for samples with low template, all peaks were readable and clearly distinguishable, and the baseline was very low (max. 30 rfu). This is why we were able to stick to a limit of 50 rfu for the allele detection. We calculated the limit of detection (LOD, mean Baseline + 3 standard deviations) for each colour channel separately and for the kits NGM DetectTM, Powerplex® ESX 17 and Powerplex® Y23 the LODs were between 20 rfu und 50 rfu. Only for the Investigator® Argus X- 12 QS the LOD in the red colour channel was higher than 50 rfu (55 rfu).
PP ESX 17: D18S51
A minor contributor was detected with the PowerPlex® ESX 17 System down to 1:30 dilution. One microliter of amplified product was injected on the Spectrum Compact CE System at 1.6kV for 9 seconds and run at 13kV.
1 : 1,5
1 : 7
1 : 30
Were you satisfied with the resolution you saw?
The peak separation is also clear in the higher bp range (> 300 bp) and single bp peak resolution is possible, so yes!
Bsp.: GEDNAP 47 Sample 4; D1S1656
Spectrum Compact CE System achieves a 1bp resolution, as can be seen in the D1S656 locus in both the PowerPlex® ESX 17 System and the NGM Detect PCR Amplification Kit. Injection was performed at 1.6kV for 9 seconds.
Editor’s note: During development, Promega R&D ran the PowerPlex® ESI 17 Fast System Allelic Ladder on six Spectrum Compact CE System instruments. The sizing precision determined on each instrument with a maximum standard deviation observed was 0.07 bases.
What did you think about the user interface compared to other CE instruments?
Compared to our previous instrument, the interface is very easy to operate and user friendly. A new colleague was trained within 20 minutes and since then she has been working with the instrument without any issues.
Now, after having worked with this instrument for almost half a year, is there anything you would like to see improved?
Maybe you could change the communication information about empty polymer? Which would mean that the strip setup does not have to be adjusted to the number of remaining injections, but a warning at a run start that the instrument will automatically stop the run after x -injections due to empty polymer.
Also, an exportable list with the information about what was exchanged, when and with which lot/expiration date and when the matrix was installed would be really useful for the Quality Management.
Would you consider using the Spectrum Compact in the future for sequencing since this instrument gives you a sequencing window of 990bp?
You took part in the recent GEDNAP proficiency testing. How were the results? Were the results comparable to other instruments?
Since we still used our old instrument for our routine work when we were testing the new one, we were able to do all GEDNAP proficiency testing on both instruments and the results were concordant.
Just published – The Developmental Validation of the Spectrum Compact CE System for Fragment Analysis
In this article, we present a series of validation studies to showcase the performance of the Spectrum Compact CE System for Fragment Analysis. This validation summary describes a set of experiments that demonstrate the sensitivity and reliability of the Spectrum Compact CE System in meeting the FBI Quality Assurance Standards for Forensic DNA Testing Laboratories and the validation guidelines outlined by the Scientific Working Group on DNA Analysis Methods. The studies describe the following characteristics of the Spectrum Compact CE system: baseline noise and threshold evaluation, precision, accuracy, resolution, reproducibility, sensitivity, signal variability, dye balance, spectral pull-up and artifact analysis, contamination assessment, mixture samples, and direct amplification.
To learn more about how the Spectrum Compact instrument can benefit your lab, visit our webpage, contact your salesperson, or consider attending a Promega Tech Tour near you.