Evaluation of the Autogen FlexSTAR automated DNA extractor, for suitability in routine diagnostic use

Transcription

1 Evaluation of the Autogen FlexSTAR automated DNA extractor, for suitability in routine diagnostic use Performed by Dr H Martin, E Gee, G Flavell and S Marshall 2015

2 Initial machine evaluation Aim: To extract 2 batches of 10 samples per batch for the purpose of orientation and specialist training. In addition to machine familiarisation the evaluation addressed the logistics of sample processing and machine loading to determine the checks required for use in a diagnostic setting. Results: A number of procedural restrictions will need to be applied to the use of the FlexSTAR extractor (Autogen, Massachusetts, USA) for sample transfer control and checking, so as to reduce the likelihood of sample cross contamination or misplacement. These controls are in line with those imposed on other extraction processes within the department and do not represent any cause for concern in the operational performance or diagnostic suitability of the equipment. Sample tracking software pre-loaded onto the FlexSTAR was also evaluated and deemed suitable to assist in the tracking of sample placement and transfers during normal operation of the equipment. Recommendations: Sample transfer checking sheets are generated and registered on QPulse to allow laboratory staff to check sample loading on to the FlexSTAR, and transfers off the extractor.

3 Full batch sample extractions Aim: To extract DNA from 3 batches of 30 whole blood samples (total 90 samples) Extraction was performed from a range of blood volumes and sample ages using the Flex Star fresh blood protocol. All samples consisted of blood that has been previously extracted using the Qiagen Autopure (compromised whole blood protocol), and were therefore a number of days older than the blood sample aliquot extracted on the Autopure. Both EDTA and lithium heparin stabilised bloods were chosen for extraction based on availability. Blood sample ages ranged from 1 day to over 10 days stored at 4 Ο C prior to extraction. DNA yields and purity were compared by analysis using a Nanodrop spectrophotometer (Thermo Scientific, Paisley, UK) DNA quality vs blood age (days) /280 reading Gentra 260/280 Flexstar260/280 Mean Gentra Mean Flexstar Blood age (days) Total DNA yield (µg) vs blood volume (ml) Total DNA yield (µg) Gentra mean Gentra yield FlexStar yield FlexStar mean Blood volume (ml)

4 Vol blood FlexStar No. samples EDTA FlexStar No. samples li hep Gentra No. samples EDTA Gentra No. samples li hep Results: DNA derived from the FlexSTAR extraction chemistry was of equivalent purity and yield in comparison to DNA extracted using the Qiagen Autopure. Whilst a stringent compromised blood protocol was used for the Autopure extractions, the FlexSTAR fresh blood protocol was used under advisement from Autogen (Massachusetts, USA), and demonstrated equal performance with regards to purity and yield. An economic evaluation will be performed to determine the cost significance of the different protocols in terms of reagent and consumable costs.

5 Partial batch sample extractions Aim: To extract DNA from alternative blood stabilisation tubes Additional extraction analysis was performed using a range of blood stabilisation products with frozen blood samples. Two ml of each blood sample were extracted on both the Qiagen Autopure and the FlexSTAR platforms using the Autopure compromised whole blood extraction protocol, and the FlexSTAR fresh blood protocol. DNA yield and purity were compared from equivalent volumes of eluted DNA*. Sample type Container Extraction worksheet sample number DNA Purity (260:280) DNA concentration (ng/µl)* Autopure Flextar Autopure Flextar Tri-sodium citrate Sarstedt 9ml Tri-sodium citrate Sarstedt 9ml Tri-sodium citrate Sarstedt 9ml EDTA Sarstedt 9ml EDTA Sarstedt 9ml EDTA Sarstedt 9ml EDTA (BTF) Sarstedt 4.5ml BTF EDTA (BTF) Sarstedt 4.5ml BTF EDTA Vacutainer 2x3ml EDTA Vacutainer 2x3ml Results FlexSTAR yields for extraction of frozen bloods, were significantly higher than those generated by the Qiagen Autopure extraction chemistry irrespective of the blood stabilisation container used. Whilst DNA purity was largely unaffected by the extraction chemistry, what was particularly evident, was the greater success of DNA extraction from sodium citrate stabilised blood using the FlexSTAR chemistry. Cross contamination assessment (30 samples) Aim: To determine whether detectable sample to sample contamination could be identified, that may have occurred during the process of sample extraction. Inter-sample contamination was assessed using the PowerPlex16 microsatellite marker system (Promega, Wisconsin, USA) and semi automated analysis of microsatellite marker allele sizes using GeneMarker analysis software (SoftGenetics, Pennsylvania, USA). Absence of contamination was evaluated based on the current clinical detection limit for contamination of a 5% level of alternative alleles, with an additional visual inspection of data to determine whether contamination at lower levels could be identified.

6 The PowerPlex 16 System assay is currently in use within the departments of molecular genetics and cytogenetics, to determine the level of maternal cell contamination present in foetal samples taken for prenatal testing. The PowerPlex 16 System consists of a collection of multiplex short tandem repeat (STR) markers that are PCR amplified and genotyped by measurement of repeat size differences between individuals. It is commonly utilised in DNA typing, including paternity testing, forensic DNA analysis, human identity testing and tissue culture strain identification. The system allows co-amplification and three-color detection of sixteen loci (fifteen STR loci and Amelogenin): Penta E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, vwa, Amelogenin, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818. One primer for each of the Penta E, D18S51, D21S11, TH01 and D3S1358 loci is labeled with fluorescein (FL); one primer for each of the FGA, TPOX, D8S1179, vwa and Amelogenin loci is labeled with carboxytetramethylrhodamine (TMR); and one primer for each of the Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818 loci is labeled with 6-carboxy-4,5 dichloro-2,7 -dimethoxy-fluorescein (JOE). All sixteen loci were amplified simultaneously in a single tube and quantified in a single injection on an ABI3130xl capillary electrophoresis sequencer (Applied Biosystems, CA, USA). List of markers analysed by the PowerPlex 16 System, including chromosomal location and expected allele range.

7 D8S1179 STR analysis in 5 adjacent samples Method PowerPlex 16 analysis was performed using 5 DNA samples (numbers 1-5), derived from adjacent blood samples loaded on to the FlexSTAR extractor. Results were visually inspected in an attempt to identify the presence of markers that would indicate cross contamination of sample material during the extraction procedure. Results Four unique STR alleles (arrows at 10, 11, 14 and 16 repeats) were identified within the 5 sample batch, that allowed cross contamination between samples to be excluded.

8 PentaE STR analysis in 5 adjacent samples Method PowerPlex 16 analysis was performed using 5 DNA samples, derived from adjacent blood samples (samples 6-10) loaded on to the FlexSTAR extractor. Results were visually inspected in an attempt to identify the presence of markers that would indicate cross contamination of sample material during the extraction procedure. Results Four unique STR alleles (arrows at 7, 8, 16 and 17 repeats) were identified within the 5 sample batch, that allowed cross contamination between samples to be excluded.

9 D13S317 STR analysis in 5 adjacent samples Method PowerPlex 16 analysis was performed using 5 DNA samples, derived from adjacent blood samples (samples 16-20) loaded on to the FlexSTAR extractor. Results were visually inspected in an attempt to identify the presence of markers that would indicate cross contamination of sample material during the extraction procedure. Results Four unique STR alleles (arrows at 9, 10, 13 and 14 repeats) were identified within the 5 sample batch, that allowed cross contamination between samples to be excluded. Summary A significant number of unique STR markers were identified within 5 adjacent sample batches, that had been simultaneously extracted as part of a 30 sample extraction batch. Inspection of these markers confirmed that cross contamination of samples could not be identified at any of the procedure stages from sample loading, through to DNA extraction and post extraction processing.

10 Penta E analysis of 15 samples from a 30 sample extraction Five unique STR markers were identified (arrows at 7, 8, 9, 16 and 17 repeats) and used to exclude cross contamination between samples processed as part of a 30 sample extraction Sample numbers correspond to the location of the sample within the batch, with samples being loaded directly opposite samples 1-5 in the FlexSTAR centrifuge

11 Cross contamination assessment at 5% and below Aim: To determine whether contamination between samples could be detected at the 5% mosaicism level Data were examined by eye to determine whether cross contamination between adjacent samples was evident at the 5% mosaicism level. The 5% level was assigned based on the intensity of STR products present in adjacent wells. Result: As detailed below, no significant cross contamination could be detected between adjacently extracted samples, either at a level of 5% or below. This result was replicated throughout the batch of 30 extracted samples that were analysed using the PowerPlex 16 system.

12 Performance evaluation based on DNA integrity Aim: Too determine DNA integrity and it s suitability for long range PCR applications. Long range amplicons were generated for BRCA1 and BRCA2 genes in a manner identical to current clinical diagnostic assay, with amplicons mplicons up to 10kb being generated. Comparison omparison of amplification efficiency of DNA derived from Flex Star and Autopure extractions was performed by visual evaluation of relative PCR product yield and amplification specificity. * * * * Patient 1 BRCA1 and BRCA22 products (17 amplicons plus water controls *) Patient 2 BRCA1 and BRCA22 products (23 amplicons plus water controls *)

13 Patient 1 detailed analysis Data show equal amplification amp performance between Autopure A and FlexSTAR extractions extraction across a range of large amplification products of up to 10kb. Product specificity is comparable between DNA derived from the Autopure extraction chemistry and the FlexSTAR chemistry

14 Patient 2 detailed analysis

15 Data show equal amplification performance in yield and specificity between Autopure and FlexSTAR extractions, across a range of large amplification products of up to 10kb. Product specificity is comparable between DNA derived from the Autopure extraction chemistry and the FlexSTAR chemistry Summary of performance validations Long range PCR amplification of BRCA amplicons confirms the integrity of DNA extracted using the FlexSTAR automated chemistry, and demonstrated equivalent long-range PCR yield and specificity compared to DNA extracted using the Autopure extraction chemistry.

16 Performance testing suitability of DNA extraction from frozen bloods, for HLA genotyping Aim: To determine suitability of FlexSTAR extracted DNA for HLA genotyping. Six blood samples were extracted in parallel using the Autopure compromised whole blood extraction protocol and the FlexSTAR fresh blood protocol. DNA concentration and purity were compared. DNA Purity (260:280) DNA yield (µg/ml blood) Extraction worksheet sample number Autopure Flextar Autopure Flextar ` DNA extracted from two of the six samples were further analysed to determine their suitability for HLA genotyping using 3 distinct genotyping techniques, sequence specific primer PCR (SSP- PCR), sequence specific oligonucleotide primed PCR (SSO-PCR), and sequence based typing (SBT-PCR). Performance of the two DNA samples derived from Autopure extraction chemistry was compared to the performance of FlexSTAR extracted DNA across the 3 genotyping assays, and analysed in accordance with current clinical assay procedures for organ transplantation matching. Results: All 6 samples reached the defined acceptable performance criteria deemed necessary for data to be used for HLA genotyping of donors and recipients for organ transplantation.

17 Overall summary and recommendations Summary A detailed analysis of the FlexSTAR automated extractor and associated chemistry, has confirmed that it s performance matches (and in many cases exceeds) the performance measured for the Qiagen Autopure extractor. DNA yield, purity and integrity are all suitable for the use of FlexSTAR chemistry in routine diagnostic testing including but not limited to, long range PCR and HLA genotyping. Despite the open tube technique used on the FlexSTAR extractor, no discernable cross contamination was detected within samples located in the same 5 sample input plastic ware assembly, or between samples co-processed as part of a larger sample batch. Recommendations The FlexSTAR automated extractor can be brought in to clinical service for routine diagnostic sample extraction on the basis of it s technical performance evaluated as part of this report. Sample transfer checking sheets specific to the platform will be required: Appropriate records of change control should be prepared, training performed and SOPs updated to reflect these changes, and local clinical governance and quality management representatives informed of the proposed changes to the DNA extraction service, prior to implementation.