High-Fidelity DNA Extraction for Biomarker Identification

a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 1 covaris.com truCOLLECT Solution: Features & Advantages • Decentralized Micro-Sampling: Features a user-friendly, dry-stabilized whole blood collection system designed for reliable remote sampling. • Active Desiccation Technology: Eliminates cold-chain requirements by ensuring robust sample stability. • Adaptive Focused Acoustics® (AFA)® Extraction: Utilizes AFA on the Covaris R230 Focused-ultrasonicator platform for seamless, hands-free DNA isolation. • High Molecular Weight (HMW) DNA Recovery: Extracts high quality HMW DNA from 50 μL of whole blood. • Universal Assay Compatibility: Integrates with advanced next-generation sequencing (NGS) pipelines and standard orthogonal clinical assays. Benefits and Resulting Outcomes for Laboratories • Expands Access: Enables simple, self-collection that boosts research subject enrollment and surveillance without sacrificing venipuncture-level sample quality. • Eliminates Cold-Chain Logistics: Dry-stabilized specimens remain stable during shipping with no degradation in analytical performance, completely bypassing costly cold-chain shipping. • Accelerates Lab Throughput: Replaces manual, contamination-prone extraction steps with an automated, two-hour protocol that maximizes operational efficiency. • Maximizes Genomic Fidelity: Yields clinical-grade HMW DNA optimal for NGS and long-read sequencing, overcoming the fragment length limitations inherent to saliva and traditional dried blood spots (DBS). • Drives Operational Profitability: Achieves an improved sequencing quality control (QC) success rate, compared to saliva, drastically reducing the overall cost per actionable data point across complex panels. truCOLLECT® Solution: High-Fidelity Genomic DNA Extraction from Decentralized, Dry-Stabilized Whole Blood for Biomarker Identification Authors: Eugenio Daviso1, Lia Abarzua1, Heidi Giese1, Sameer Vasantgadkar1, Greg Endress1, Ulrich Thomann1, Susanne Fox2, Lei Sabarre2, Hana Schlosser2, & Tiantian Geier2 Affiliation: 1 - Covaris LLC, a PerkinElmer Company, Woburn, MA | 2 - Ambry Genetics Corporation, Aliso Viejo, CA In collaboration with: a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 2 covaris.com Introduction The paradigm of precision medicine and population genomics is undergoing a rapid transition toward decentralized testing. As clinical trials and large-scale epidemiology studies expand, the logistical constraints of traditional phlebotomy have emerged as a critical bottleneck in the deployment of decentralized clinical trials (Kijewski et al., 2026). While venous blood draws remain the standard for obtaining high-quality HMW genomic DNA (gDNA), they require trained healthcare personnel, specialized infrastructure, and resource-intensive cold-chain logistics. These requirements not only inflate operational costs but also restrict geographic reach and participant compliance (Rogers et al., 2022). In an effort to circumvent the limitations of venipuncture, laboratories have increasingly adopted cost-effective, minimally invasive collection alternatives, such as saliva swabs and DBS. However, these methods introduce pre-analytical and analytical compromises that limit their utility in comprehensive NGS workflows. Saliva samples are frequently compromised by variable DNA yield, dilution effects, and substantial bacterial DNA contamination, averaging between 54% and 69% non-human mapped reads in clinical settings (Kumar et al., 2023; Wijaya et al., 2021). This microbial contamination can mimic human genomic regions, confounding genotyping, and variant calling. This ultimately contributes to elevated downstream sequencing failure rates and necessitates frequent resource intensive sample recollections (An et al., 2025). Additionally, alternative noninvasive collection methods, such as saliva and buccal swabs, often yield highly fragmented gDNA, which has been shown to significantly diminish copy number variant (CNV) detection sensitivity by up to 25% (Trost et al., 2019). DBS cards provide the convenience of ambient temperature shipping; however, they exhibit fundamental limitations in volumetric precision attributable to hematocrit bias (Deprez et al., 2019). Furthermore, extracting DNA from DBS cards requires laborious, manual punching procedures that impose a considerable burden on laboratory pipelines and time to result (McBride et al., 2023). While recent advancements have demonstrated that Whole Genome Sequencing (WGS) and PCRfree workflows can be successfully performed directly from DBS, the restricted overall DNA yield remains a fundamental bottleneck for extensive downstream multi-assay testing (McBride et al., 2023). Contemporary liquid capillary micro-sampling devices address volume and discomfort limitations; however, these devices maintain the blood in a liquid phase, necessitating adherence to biohazard shipping and temperature stabilization protocols (Baillargeon & Mace, 2022). To achieve decentralization without sacrificing clinical-grade genomic data, laboratories require an end-to-end workflow that pairs the logistical simplicity of a desiccated specimen with the robust DNA yield and purity of a liquid draw. This technical note provides a comprehensive overview of the truCOLLECT Solution, detailing its utility in accurate biomarker detection while offering enhanced efficiency in laboratory operations. Materials and Methods Sample Collection and Storage The collection, stabilization, and analytical performance of the truCOLLECT Whole Blood Collection Kit were evaluated using dry-stabilized blood samples containing known clinical variants. Aliquots (50 μL) from historical clinical EDTA blood samples (n=32) were loaded into the Covaris truCOLLECT devices and stored at room temperature (RT) for 48 hours to simulate decentralized ambient transit. Downstream results from these specimens were compared against historical clinical baseline data encompassing high-volume EDTA blood (n=322), saliva (n=18), and buccal swabs (n=9). a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 3 covaris.com DNA Extraction DNA from truCOLLECT samples was extracted using truCOLLECT DNA Extraction Kit (96) with the IsoPURE™ Mini (Accuris Instruments, Edison, New Jersey, USA) workflow in tandem with the R230 Focused-ultrasonicator. The AFA-based rehydration and the automated magnetic bead purification workflow processed samples in 2 hours with a final DNA elution volume of 95 μL. Control clinical samples from phlebotomy were previously extracted using the MagMAX™ Multi-Sample Ultra 2.0 Kit with the KingFisher PrestoTM (Thermo Fisher Scientific, Waltham, Massachusetts, USA), requiring 2.5 hours and eluting in 80 μL (EDTA Blood) and 60 μL (Saliva) (Table 1). Table 1. Overview of collection and extraction parameters across the three evaluated modalities. The Covaris truCOLLECT Solution, paired with the IsoPURE extraction workflow, requires a significantly lower input volume (50 μL vs. 400 μL) and reduces overall extraction time by 30 minutes compared to traditional EDTA blood and saliva processing methods. Parameter Dry-stabilized Blood EDTA Blood OGD-500 Saliva Input 50 μL 400 μL 480 μL Specimen Collection Covaris truCOLLECT Phlebotomy Self-collection Elution Volume 95 μL 80 μL 60 μL Extraction Method truCOLLECT DNA Extraction kit + IsoPURE Mini MagMAX Multi-Sample Ultra 2.0+ KingFisher Presto MagMAX Multi-Sample Ultra 2.0+ KingFisher Presto Extraction Time 2 hours 2.5 hours 2.5 hours Storage Condition Dried (48 hr RT / 2-week RT) 24 hr RT (Stored 4°C) 24 hr RT (Stored 4°C) Coagulation State No Clots No Clots N/A Resuspension Quality Easy Easy Slightly Viscous Overall Extraction Difficulty Easy Easy Moderate (requires clean up) Downstream Analysis and Quality Control Pre-sequencing QC concentration and yield analysis was conducted via fluorometric assay and purity assessment was carried out via spectrophotometry (260/280 and 260/230). NGS Library preparation QC was assessed against established clinical cutoffs. Downstream testing utilized Ambry Genetics’ clinical Cancer NGS panel. Sequencing QC metrics evaluated included Mean Coverage, PCR Duplication Rate, Specificity, and Pipeline Failure Rates. Variant concordance was calculated by comparing calls from the truCOLLECT samples directly against Ambry’s historical clinical EDTA counterparts. Orthogonal clinical testing was also performed employing Sanger Sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and Targeted Arrays. Additionally, while exact paired fragment size comparisons were not the primary focus of this study, internal evaluations indicate that the AFA-powered truCOLLECT workflow yields superior High Molecular Weight (HMW) DNA compared to traditional MagMAX extractions from EDTA blood and saliva, which are known to reduce overall fragment sizes (Ambry Genetics Corporation, internal data). This robust preservation of HMW DNA makes the truCOLLECT Solution particularly well-suited to meet the growing industry demand for long-read sequencing applications. a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 4 covaris.com Results Extraction and DNA Quality Metrics The extracted DNA from 50 μL input showed that the specimens processed (n=32) yielded an average of 1399.1 ng of total DNA with an average concentration of 15.1 ng/μL. Purity metrics of each sample consistently conformed to standard clinical parameters, supplying abundant and high-quality starting material for comprehensive downstream genomic applications. NGS Library Preparation and Sequencing Quality All specimens (n=24) successfully met NGS Library Preparation Concentration QC thresholds (>20 ng/μl). During sequencing, truCOLLECT samples consistently demonstrated performance superior to clinical saliva samples and achieved analytical parity with high-volume liquid blood. The mean coverage of truCOLLECT DNA samples reached 372x, closely approximating the value of historical clinical blood (409x) and buccal swabs (393x), while significantly exceeding saliva (255x) (Figure 1). As anticipated, due to the lower initial blood input (50 μL vs. 400 μL), truCOLLECT samples exhibited a marginally higher PCR duplication rate (0.32) compared to clinical blood (0.26); importantly, this variance had no measurable impact on variant calling accuracy, specificity (0.41 vs 0.42 for blood), or assay uniformity. Notably, none of the truCOLLECT samples failed the Sequencing Pipeline QC, in stark contrast to the 27.77% failure rate observed in clinical saliva samples. Figure 1. NGS sequencing quality metrics comparing mean coverage across Covaris truCOLLECT, clinical blood, buccal, and saliva specimens. a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 5 covaris.com Variant Concordance The truCOLLECT Solution delivered exceptional sequencing accuracy across comprehensive evaluations. An evaluation of the NGS Cancer panel utilizing the known positive samples identified 1969 common calls out of 1971, yielding a concordance rate of 99.9% when compared to traditional liquid EDTA blood draws. All expected, reported pathogenic variants were successfully detected in the truCOLLECT samples without exception (Table 2). Orthogonal Assays with DNA derived from truCOLLECT Solution proved fully compatible with the following workflows, validating a diverse array of structural alterations: • Sanger Sequencing: Amplification yielded Trace Scores (24–50) and contiguous read length (CLR) metrics equivalent to the original clinical samples, indicating no degradation in sample quality (Table 3). • MLPA: Complete concordance (100%) of calls was observed based on Coffalyser reports, with all specimens passing FRSS and PSLP metrics for genes such as CHEK2, EPCAM, NF1, MSH2, MSH6, and PALB2 (Table 4). • Targeted Array: Detection of intended variants (e.g., ALK, TMEM127, BAP1) was confirmed at 100%. While a small subset of truCOLLECT arrays exhibited marginally higher baseline noise (derivative log ratio spread (DLRS) up to 0.30 vs 0.15), all variants of interest were accurately called (Table 5). Table 2. Clinical variant concordance across the Cancer panel comparing the truCOLLECT Solution to traditional liquid EDTA blood draws. The data demonstrates analytical accuracy, achieving 99.9% concordance, and successfully detecting all expected variants. Number of Samples Common Calls Calls Unique to: Total Calls in: Concordance Concordance Clinical Run truCOLLECT Pos Run Clinical Run truCOLLECT Pos Run 23 1969 2 166 1971 2135 1969 of 1971 99.90% Table 3. Sanger sequencing performance comparing truCOLLECT-derived DNA to clinical EDTA blood. The data demonstrates identical qualitative variant confirmation and equivalent Trace Scores (TS) and CLR metrics, verifying robust target amplification without degradation. Donor Gene Alteration Result COVARIS Seq (TS / CLR) CLINICAL Seq (TS / CLR) 25-B25375 ATM c.7517_7520delGAGA Confirmed call 30 / 276 28 / 292 25-B25376 MUTYH/CEBPA p.Y179C/c.584_589delACCCGC Confirmed call 37 / 269 25 / 126 25-B25377 PMS2 p.R813L Confirmed call 50 / 507 50 / 515 25-B25378 ATM/ALU c.7374_7375insAlup.Y156C Confirmed call 49 / 265 50 / 267 25-B25379 BRCA2 c.6491_6494delAGTT Confirmed call 31 / 367 24 / 234 a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 6 covaris.com Table 4. MLPA results. truCOLLECT samples matched clinical baseline data with 100% variant concordance, successfully passing stringent fragment and probe quality metrics. Donor Gene Alteration Result truCOLLECT Coffalyser CLINICAL Coffalyser 25-B25380 CHEK 2 EX4_3'UTRdup Confirmed call FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK 25-B25381 EPCAM EX8_3'UTRdel/p.R474H Confirmed call FRSS: OK 100%, PSLP: OK- 11%, RSQ: OK, RPQ: OK FRSS: OK 100%, PSLP: WARNING -29%, RSQ: OK, RPQ: OK 25-B25382 NF1 5'UTR_3'UTRdel/p.Y1835C Confirmed call FRSS: OK 100%, PSLP: WARNING -18%, RSQ: OK, RPQ: OK FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK 25-B25383 MSH2 + MSH6 5'UTR_3'UTRdup/5'UTR_3'UTRdup Confirmed call FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK 25-B25384 PALB2 EX8_3'UTRdel Confirmed call FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK 25-B25385 GATA2 5'UTR_3'UTRdup Confirmed call FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK FRSS: OK 100%, PSLP: OK, RSQ: OK, RPQ: OK Table 5. Targeted array performance for structural variant detection. While the DLRS showed slightly higher baseline noise due to the microsample input, all critical variants (e.g., ALK, TMEM127) were unequivocally detected in the truCOLLECT specimens. Donor Gene Alteration Result truCOLLECT DLRS CLINICAL DLRS 25-B25362-B2 ALK EX12_3'UTRdup Confirmed Call 0.19 0.14 25-B25363-B2 ALK 5'UTR_EX1dup Confirmed Call 0.30 0.15 25-B25364-B2 TMEM127 5'UTR_3'UTRdel Confirmed Call 0.20 0.13 25-B25365-B2 BAP1 EX15_3'UTRdel Confirmed Call 0.18 0.15 25-B25366-B2 POT1 5'UTR_EX1del Confirmed Call 0.19 0.14 25-B25367-B2 RUNX1/POT1 5'UTR_EX1DUP Confirmed Call 0.19 0.14 25-B25368-B2 POT1 EX12_3'UTRdel Confirmed Call 0.19 0.15 25-B25369-B2 SDHA EX3_3'UTRdup Confirmed Call 0.19 0.14 Workflow and User Feedback: during laboratory processing, the Covaris workflow demonstrated facile resuspension with no observed instances of coagulation or clotting and reduced standard extraction time by 30 minutes relative to MagMAX protocol (Table 6). a PerkinElmer Company TECHNICAL NOTE truCOLLECT® Solution 7 covaris.com Table 6. Summary of laboratory workflow efficiencies and participant feedback. The Covaris AFA-powered extraction reduced processing time while maintaining optimal sample integrity without coagulation. Participant surveys indicated high comprehension and ease of use for the decentralized collection device. Category Metric truCOLLECT Result Laboratory Workflow Extraction Time 2.0 hours (25% time reduction) Resuspension Quality Facile / Easy Sample Integrity No coagulation or clotting Discussion The implementation of remote blood sampling frequently forces laboratories to accept a compromise between logistical feasibility and analytical data quality. The Ambry Genetics verification data demonstrates that the truCOLLECT Solution effectively dismantles this dichotomy. By delivering phlebotomy-grade genomic fidelity from a dry-stabilized capillary sample, the platform expands the operational scope of population screening initiatives. This capability allows clinical programs to broaden participant access and geographic reach without absorbing the prohibitive costs and complexities of cold-chain logistics. Crucially, the truCOLLECT workflow translates directly to measurable operational profitability and clinical reliability. The elimination of the ~28% sequencing QC failure rate commonly associated with saliva collection prevents the cascading financial burdens of sample re-collection and limits delays in critical clinical reporting. Furthermore, securing a 99.9% variant concordance against historical venous blood control samples ensures that diagnostic accuracy is preserved, fundamentally safeguarding the integrity of downstream NGS applications. Beyond pre-analytical stability, the physical architecture of the truCOLLECT device is engineered to optimize high-throughput laboratory accessioning and processing. The standardized format facilitates immediate integration into automated workflows, enabling a seamless transition from sample receipt to AFA-powered extraction on the Covaris R230 Focused-ultrasonicator. By eradicating the manual, contamination-prone punching procedures required for traditional DBS cards and avoiding the coagulation risks inherent to liquid micro-samplers, the system reduces extraction turnaround times by 30 minutes. Consequently, laboratories can efficiently scale their processing bandwidth to accommodate the demands of decentralized testing models while ensuring that the final genomic data maintains uncompromised depth, uniformity, and clinical utility. Conclusion Engineered specifically to address the operational gaps typically faced in decentralized testing, the Covaris truCOLLECT Whole Blood Collection Kit, combined with AFA extraction technology, presents a robust and reliable integrated solution. As demonstrated by the extensive performance evaluation conducted by Ambry Genetics, the truCOLLECT Solution enables the reliable self-collection of 50 μL of capillary blood, which is immediately stabilized in a proprietary active-desiccation format and rapidly processed upon arrival using the Covaris R230 Focused-ultrasonicator. By combining this patient-centric sampling with automated precision, the truCOLLECT Solution yields superior HMW gDNA that provides genomic fidelity comparable to traditional phlebotomy. Characterized by seamless NGS pipeline integration, including 100% library preparation success, 99.9% clinical variant concordance, and confirmed compatibility across Sanger, MLPA, and array platforms, the system effectively mitigates current operational inefficiencies. By eliminating cold-chain logistics, the truCOLLECT Solution enables laboratories to scale population genomics, and precision oncology initiatives efficiently and cost-effectively. a PerkinElmer Company TECHNICAL NOTE a PerkinElmer Company Tel: +1 781-932-3959 info@covaris.com US: +1 781.932.3959 customerservice@covaris.com EU: +44 (0)845 872 0100 emeacustomerservice@covaris.com APAC: +86 137 6427 6714 APACcustomerservice@covaris.com Applications applicationsupport@covaris.com Service and Support techsupport@covaris.com www.covaris.com | 2026© Covaris, LLC 010729_RevA_Apr2026 Covaris® and the Covaris logo are trademarks of Covaris, LLC. All other trademarks, service marks, and trade names are the property of their respective owners. Unauthorized use of Covaris trademarks is strictly prohibited. Information subject to change without notice. Learn more about truCOLLECT References • An Z, Cha JH, Lee KH, Lee I. 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