Scientific Posters

Zymo Research's scientific posters highlight the latest breakthroughs in molecular biology, showcasing innovations spanning from epigenetics to microbiomics. We are proud to present insights from our collaborations with leading scientists and institutions worldwide, with more contributions to the field of life science on the horizon.

One Step Spin Column Solution for Optimized Purification of Nucl eic Acids from Heavily Inhibited Clinical Samples for Improved Molecular Diagnostic Accuracy
Ana Barrionuevo, Zoë Hermsen, Erica Carrasco & Aaron Clausen

Melanoma is a highly aggressive skin cancer and the fifth most common cancer worldwide, accounting for 184,416 deaths between 1999 and 2020. While localized melanoma has a 95% survival rate, this rate drops to 30% once the cancer metastasizes to distant lymph nodes, making early detection critical. Molecular detection methods such as Polymerase Chain Reaction (PCR) and Next Generation Sequencing (NGS) are routinely used to identify melanoma-specific genetic markers, such as mutations in the BRAF gene. However, PCR performance can be severely compromised by the presence of PCR inhibitors or polyphenolics such as melanin in melanoma tissue, hematin in blood, and humic acid in feces. When co-purified with nucleic acids, these molecules disrupt enzymatic reactions and can cause false negatives in diagnostic assays. In this study, we evaluated the efficacy of Zymo Research's OneStep PCR Inhibitor Removal Kit in eliminating polyphenolic inhibitors from extracted DNA samples. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) melanoma tissue or HeLa cells spiked with melanin and treated with the OneStep kit. Post-treatment analyses using PCR and Sanger sequencing resulted in successful amplification and sequencing of the GAPDH and BRAF gene from melanin containing DNA. Our findings confirm that common polyphenolics significantly inhibit PCR amplification and that the OneStep PCR Inhibitor Removal Kit effectively removes these inhibitors, restoring assay sensitivity. This work underscores the importance of optimizing nucleic acid purification and amplification protocols for inhibitor-rich clinical samples. By improving the fidelity of molecular diagnostics in polyphenolic–rich samples, this study contributes to advancing accurate, early detection of melanoma.

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Broad-Range cfDNA Capture Beyond Nucleosome-Sized Fragments Enhances Liquid
Madison Valle, Eunice Choi, Duang Ratanachan, Kaitlyn Lee, Mingda Jin, Hanjun Kim, Xiaojing Yang

Liquid biopsy is increasingly used in oncology for early detection, disease monitoring, and minimal residual disease (MRD) assessment. These applications require comprehensive recovery of circulating cell-free DNA (cfDNA), particularly in low-input and low–tumor burden samples. Conventional silica- or bead-based cfDNA purification methods and double-stranded DNA library preparation workflows are optimized for nucleosome-sized fragments and may underrepresent ultra-short and single-stranded cfDNA species. Such bias may limit analytical sensitivity and fragmentomic resolution.

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Use of Metagenomic Reference Materials to Benchmark and Optimize Lysis and Extraction Methods Against a Known Input
Michael M. Weinstein, Kristopher Locken, Brett Farthing, Elaine Wolfe, Shuiquan Tang, Venu Lagishetty, Jonathan P. Jacobs, Braden Tierney, Ryan Kemp, and Christopher Mason

This study introduces a quantitative framework using defined microbial reference standards and a novel Measurement Integrity Quotient (MIQ) to benchmark microbiome lysis and extraction methods, revealing substantial variability and bias across commonly used workflows. The findings demonstrate that optimized mechanical bead-based lysis is critical for accurate community representation, highlighting the importance of reproducible, quantitatively validated methodologies for ensuring reliable cross-study comparisons and biologically meaningful conclusions in microbiome research.

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Novel Spin Column Solution for Optimized Purification of Nucleic Acids from Heavily Inhibited Samples for Highly Accurate Sequencing and PCR Analysis
Ana Barrionuevo, Zoë Hermsen, Erica Carrasco, Xiaoxiao Cheng, Joshua Lee & Aaron Clausen

Accurate DNA sequencing analysis is essential for pathogen detection & understanding complex environmental microbiomes. However, polymerase chain reaction (PCR) and next-generation sequencing (NGS) performance can be severely compromised by the presence of PCR inhibitors, such as polyphenolic compounds. These inhibitors, including humic acids, are common in environmental samples and can co-purify with nucleic acids during extraction. Their presence disrupts enzymatic reactions, reduces amplification efficiency, and often results in costly re-runs or false-negative results. In this study, we evaluated a simple, single-step centrifugation-based spin column system for the removal of common PCR inhibitors from soil & wastewater samples. First, DNA was spiked with either humic acid or a PCR inhibitor cocktail containing bile salts, indigo, and hematin, then processed through the inhibitor removal column. Inhibitor removal and DNA recovery of the flow-through was quantified using spectrophotometry and fluorometry. Additionally, quantitative PCR was performed to evaluate DNA amplification before and after column treatment. Next, performance of this inhibitor removal technology was assessed with DNA extracted from soil and wastewater samples using commercially available DNA extraction kits. Results showed that the column removed > 96% of PCR inhibitors present without significant DNA loss. Additionally, quantitative PCR analysis demonstrated that amplification failed or was reduced in untreated soil & wastewater samples but was fully restored following treatment with the inhibitor removal column. Furthermore, 16S rRNA sequencing revealed that untreated DNA extracted from soil was too inhibited for identifying bacteria, whereas column treatment restored bacteria detection. These results demonstrate that polyphenolic compounds can significantly inhibit PCR and NGS-based analyses, and that this novel PCR inhibitor removal technology removes these inhibitors without compromising nucleic acid yield, effectively enhancing amplification sensitivity and analytical accuracy. Overall, this study underscores the importance of optimizing nucleic acid purification from inhibitor-rich environmental samples to ensure reliable downstream sequencing & microbial detection.

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A Sustainable, End-to-End Workflow for Wastewater Pathogen Surveillance
A. Damerum, J. Liu, W. Ullmer, M. Yang, E. Carrasco, X. Chen, E. Chen, A. Clausen, R. Yancey, A. Balasubramanian, J. Bhasin, K. Locken, K. Booher

Zymo's end-to-end wastewater workflow addresses the core challenges of wastewater surveillance – variability, inhibition, throughput and data interpretation – through standardized tools at each step: WSB for safer, simpler collection; automated co-purification for flexible downstream use; a deliberate choice of PCR or sequencing assays depending on the surveillance objective; and a no-install web portal for rapid data visualization and reporting.

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