Commercial Reference Materials Research Articles

The detection of acetone in exhaled breath using gas Pre-Concentrator by modified Metal-Organic framework nanoparticles

Volatile organic compounds (VOCs) from exhaled breath are promising indicators for the diagnostics of human health conditions. However, the composition of breath is rather complex, including water vapors and various tiny amounts of gases and biomarkers. Pre-concentrator plays a significant role in capturing and concentrating target gas in the gas mixture. In this work, the MIL-101 (Cr) nanoparticles are coated with polydimethylsiloxane (PDMS) through physical vapor deposition process to concentrate acetone under high humidity and room temperature. Experimentally, the newly developed material exhibits significant improvement in signal intensity that is 76.3 times greater than a commercial reference material under relative humility of 80 %. The detection range is also proven to be desirable (from 100 ppb to 2500 ppb), capturing the spectrum of acetone concentrations typically found in human exhaled breath. Moreover, following a thermal desorption process, the device demonstrates a high degree of linearity with a coefficient of 0.9956. The modified metal–organic framework materials are made into a flexible thin-film-shape device, that could be embedded in a facemask. The proposed device could meet the critical requirements for sampling, concentrating and detecting of exhaled breath biomarkers, thereby opening a new opportunity as part of the flexible electronic systems on face masks to facilitate quantitative breath analyses.

A highly sensitive, low input, and automated assay for molecular residual disease detection (MRD) using whole-genome sequencing (WGS).

3060 Background: Molecular residual disease (MRD) detection using cell-free DNA (cfDNA) for solid tumors requires a highly sensitive and specific assay that can overcome the limitation of low abundance circulating-tumor DNA (ctDNA) in a standard blood draw with fast sample-to-answer turn-around time (TAT). Here we describe the development and analytical performance of Illumina’s TruSight Oncology MRD WGS assay (TSO MRD, for research use only), for detecting MRD using tumor-informed whole-genome sequencing (WGS) of cfDNA extracted from plasma samples across multiple cancer types. Methods: The TSO MRD assay was built using Illumina’s best-in-class WGS library preparation, informatics and sequencing technologies. The assay is composed of two major steps, fingerprinting and ctDNA detection. At the fingerprinting step, the DNA from tumor tissue and matched normal samples is analyzed through WGS to generate a sample specific somatic variant list. At the ctDNA detection step, the cfDNA extracted from plasma is analyzed through shallow WGS and the presence of ctDNA is detected using the tumor specific fingerprint as an input in the MRD analysis pipeline. The plasma extraction and WGS library preparation workflows are fully automated for high-throughput sample processing with minimum hands-on time and touch points. Results: Testing of commercial MRD reference materials and ctDNA-positive samples serially diluted into normal cfDNA background demonstrated a limit of detection of down to 0.001% VAF or 10 parts per million (PPM) in multiple cancer types. Testing of a panel of normal plasma samples from healthy individuals assessed against 20 sets of fingerprints from multiple cancer types demonstrated an analytical specificity of 99.7%. Testing of ctDNA samples with multiple operators, instruments and library prep start days demonstrated high reproducibility in MRD detection. The ctDNA testing works at an optimal input amount of 5 ng and a minimum input amount down to 2 ng, which yields a high sample success rate from one standard 10 ml of blood draw. The TAT of the fingerprinting and the ctDNA detection steps is 5-7 days, respectively. Conclusions: The TSO MRD assay demonstrated high analytical sensitivity and specificity in detecting the presence of ctDNA from low input plasma samples with automated workflow and fast TAT. This assay enables a single streamlined solid tumor MRD platform for multiple cancer types.

Implementation of an ISO15189 accredited next-generation sequencing service with the fully automated Ion Torrent Genexus: the experience of a clinical diagnostic laboratory

AimsNext-generation sequencing (NGS) is integral to the delivery of personalised medicine for targeted cancer therapy. Average turnaround times (TAT) from reference laboratories with advanced expertise in sequencing are typically 2–3...

Towards Sustainable Hydrogen Peroxide Electroproduction: Activated Carbon from Sewage Sludge As an Eco-Friendly Electrode Material

Hydrogen peroxide (H2O2) has emerged as a chemical of paramount importance, finding diverse applications as a bleaching agent, medical disinfectant, and environmentally benign oxidant [1]. The industrial production of H2O2 currently relies on the anthraquinone oxidation process, primarily executed within large-scale industrial plants [1]. Herein lies a challenge— H2O2, typically concentrated to an 80% level, introduces inherent hazards concerning storage and transportation, prompting a quest for a safer alternative. One way to overcome such problems is by the in-situ electrogeneration of H2O2, which would allow an adjustable production of the chemical on demand directly for its application, avoiding storing costs and safety issues. The in-situ electrogeneration can be done by using a gaseous-diffusion electrode (GDE), which typically enables the application of elevated current densities or substantial overpotentials, consequently facilitating the generation of high concentrations of H2O2, since there is less limitation due to O2 mass transport to the electrode surface [2]. Commonly, these electrodes are constructed from amorphous carbon materials, due to their highly active surface area with oxygenated functional groups, excellent conductivity, and innate selectivity for H2O2 electroproduction. However, a notable challenge emerges – bare carbon's selectivity for H2O2 presents its highest response at high overpotentials, entailing heightened energy consumption. The studies in this field are currently focused on using these types of carbon as support for other catalytic materials that are more active and selective towards H2O2 electroproduction [3, 4]. Numerous studies in the literature have explored the use of carbon materials, with the most commonly employed carbon supports for such applications being Printex 6L (Orion) and Vulcan XC 72R (Cabot). These materials are obtained from the incomplete combustion of heavy petroleum products at high temperatures, being non-sustainable and environmentally unfriendly. A potential solution lies in the use of environmentally conscious carbon sources. While amorphous carbon can be obtained from various carbon-rich wastes through an activation process, their utility in H2O2 electrogeneration remains underexplored. This study sought to obtain activated carbon from sewage sludge, focusing on its efficacy in H2O2 electrogeneration. Acid (H3PO4) and alkaline (KOH/NaOH mixture) carbon activators were analyzed in concentrations ranging from 0 – 30 %m/v, temperatures of 400 – 900 ºC, and activation time from 0 – 2 h at the selected temperature. The obtained materials were analyzed through linear sweep voltammetry using an RRDE setup in N2-saturated and O2-saturated, in a 0.05 M K2SO4 (pH 3) electrolyte solution. Results have shown that the most successful materials for H2O2 electrogeneration were those produced under 900 ºC for 2h impregnated with 5 % m/v H3PO4 and 597 ºC, zero of plateau time impregnated with 20 % m/V mixture of KOH/NaOH in the ratio of 50.5 KOH: NaOH. These optimized materials exhibited remarkable selectivities of ≈ 90% and ≈ 81% at -0.8 V vs. Ag/AgCl, respectively. This level of electrocatalytic performance is on par with that of the commercial reference material, Printex 6L. These findings highlight the promise of our material as a viable carbon support for in-situ H2O2 electrogeneration, offering a more sustainable alternative compared to commercial black carbons. Acknowledgments The authors are sincerely grateful to the Brazilian research funding agencies, including the Brazilian National Council for Scientific and Technological Development - CNPq (grants no. 465571/2014-0, 302874/2017-8, and 427452/2018-0), São Paulo Research Foundation (FAPESP – grants no. #2023/04230-2, #2023/07750-7, 2022/04058-2, #2021/12053-8, #2019/04421-7, #2017/10118-0, and #2013/02762-5).

Evaluation of an internal standard-free laser ablation-ICP-OES method for elemental analysis in solid food samples

Although the laser ablation-inductively coupled plasma-optical emission spectrometry (LA-ICP-OES) is a promising method for the elemental screening of solid food materials, the main challenge associated with this technique is the lack of commercial solid standard reference materials to serve as the external standard for quantitative calibration. In this study, a reliable internal standard-free LA-ICP-OES method for direct sampling and analysis of solid food materials was developed. The method relies on the carbon internally-standardized relative sensitivity factor (CIS-RSF) was developed, eliminating the need for calibration curves or matrix-matched external standards once the CIS-RSF has been determined. After careful evaluation of the effect of the instrumental operating parameters on the long-term stability of CIS-RSFs, this method was used to analyze a variety of microelements, including sulfur (S), phosphorus (P), zinc (Zn), iron (Fe), manganese (Mg), magnesium (Mn), copper (Cu), calcium (Ca), strontium (Sr), barium (Ba), sodium (Na), and potassium (K), with the limit of quantitation (LOQ) ranging from 0.06 (Sr) to 400 μg g−1 (S). The accuracy and reproducibility of this proposed method were evaluated through the analysis of three food NIST reference materials and six typical food samples. The results indicated that the relative error of most target elements was less than 20% and the reproducibility (SD, n = 3) more than 10%. This developed LA-ICP-OES screening method has great potential for the high-throughput multielement determination of various solid food materials.

Impact of cfDNA Reference Materials on Clinical Performance of Liquid Biopsy NGS Assays.

Liquid biopsy enables the non-invasive analysis of genetic tumor variants in circulating free DNA (cfDNA) in plasma. Accurate analytical validation of liquid biopsy NGS assays is required to detect variants with low variant allele frequencies (VAFs). Six types of commercial cfDNA reference materials and 42 patient samples were analyzed using a duplex-sequencing-based liquid biopsy NGS assay. We comprehensively evaluated the similarity of commercial cfDNA reference materials to native cfDNA. We observed significant differences between the reference materials in terms of wet-lab and sequencing quality as well as background noise. No reference material resembled native cfDNA in all performance metrics investigated. Based on our results, we established guidelines for the selection of appropriate reference materials for the different steps in performance evaluation. The use of inappropriate materials and cutoffs could eventually lead to a lower sensitivity for variant detection. Careful consideration of commercial reference materials is required for performance evaluation of liquid biopsy NGS assays. While the similarity to native cfDNA aids in the development of experimental protocols, reference materials with well-defined variants are preferable for determining sensitivity and precision, which are essential for accurate clinical interpretation.

Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors

The detection of driver oncogenic variants and the recent identification of tumor-agnostic genomic biomarkers has driven the use of comprehensive genomic profiling (CGP) for disease diagnosis, prognosis, and treatment selection. The Oncomine™ Comprehensive Assay Plus (OCA+) panel uses DNA and RNA to detect single nucleotide variants (SNVs), small insertions/deletions (Indels), and structural variants (SVs) across 501 genes. Moreover, microsatellite instability (MSI), tumor mutational burden (TMB), and homologous recombination deficiency (HRD) status are assessed in a single workflow. Herein, we present the analytical validation and clinical utilization of OCA+. By using commercial reference materials, we found good analytical sensitivity, specificity, and precision for all biomarkers analyzed. The limit of detection (LoD) was validated for SNVs and Indels at 4%, except for Indels located in homopolymeric regions, where the LoD was 10%. An additional set of 81 tumor samples, including cytology smears, were sequenced to assess the clinical utility of the OCA+ across different tumor types. Among the clinical cohort, OCA+ demonstrated 100% accuracy, sensitivity, and specificity for all biomarkers analyzed, except for MSI assessment of endometrial cancer cases, where 83% accuracy and 67% sensitivity were achieved, compared to PCR and IHC. The validation of accuracy and robustness of this assay supports the OCA+’s utility for solid tumor CGP.

Standardization of SARS-CoV-2 Cycle Threshold Values: Multisite Investigation Evaluating Viral Quantitation across Multiple Commercial COVID-19 Detection Platforms.

The demand for testing during the coronavirus disease 2019 (COVID-19) pandemic has resulted in the production of several different commercial platforms and laboratory-developed assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This has created several challenges, including, but not limited to, the standardization of diagnostic testing, utilization of cycle threshold (CT) values for quantitation and clinical interpretation, and data harmonization. Using reference standards consisting of a linear range of SARS-CoV-2 concentrations quantitated by viral culture-based methods and droplet digital PCR, we investigated the commutability and standardization of SARS-CoV-2 quantitation across different laboratories in the United States. We assessed SARS-CoV-2 CT values generated on multiple reverse transcription-PCR (RT-PCR) platforms and analyzed PCR efficiencies, linearity, gene targets, and CT value agreement. Our results demonstrate the inappropriateness of using SARS-CoV-2 CT values without established standards for viral quantitation. Further, we emphasize the importance of using reference standards and controls validated to independent assays, to compare results across different testing platforms and move toward better harmonization of COVID-19 quantitative test results. IMPORTANCE From the onset of the COVID-19 pandemic, the demand for SARS-CoV-2 testing has resulted in an explosion of analytical tests with very different approaches and designs. The variability in testing modalities, compounded by the lack of available commercial reference materials for standardization early in the pandemic, has led to several challenges regarding data harmonization for viral quantitation. In this study, we assessed multiple commercially available RT-PCR platforms across different laboratories within the United States using standardized reference materials characterized by viral culture methods and droplet digital PCR. We observed variability in the results generated by different instruments and laboratories, further emphasizing the importance of utilizing validated reference standards for quantitation, to better harmonize SARS-CoV-2 test results.

Alkali-stable polybenzimidazole anion exchange membranes tethered with N,N-dimethylpiperidinium cations for dilute aqueous KOH fed water electrolyzers

Piperidinium-functionalized polybenzimidazoles enable stable and significantly higher current densities in electrolyzers fed with dilute aq. KOH solutions than a commercial reference material with much higher electrolyte concentrations.

Intercomparison exercise on difficult to measure radionuclides in spent ion exchange resin

A need for method validation in radiochemical analyses of decommissioning waste is a challenging task due to lack of commercial reference materials. Participation in an intercomparison exercise is one way for a laboratory to assess their performance and validate their analysis results. A three-year project within the Nordic Nuclear Safety Research (NKS) community was initiated in order to carry out intercomparison exercises on difficult to measure (DTM) radionuclides in real decommissioning waste. Both Nordic and Non-Nordic laboratories participated. This paper reports the results from the final year of the project focusing on beta- and gamma emitter (i.e., easy to measure, ETM) analysis in spent ion exchange resin. The assigned values were derived from the participants’ results according to ISO 13528 standard and the performances were assessed using z scores. The results showed generally good performances for both DTMs and ETMs.

Validation of a Cell-Free DNA NGS Assay for Hematological Malignancies

Introduction: In recent years, next-generation sequencing (NGS) of cell-free DNA (cfDNA) has been applied to non-invasive assessment and molecular monitoring of patients with cancer. In this study, we present the validation data for MSK-ACCESS HEME (Memorial Sloan Kettering-Analysis of Circulating cfDNA to Examine Somatic Status), a unique molecular indexing ultra-deep sequencing assay for hematologic neoplasms. Full coding or select exons of 117 genes are targeted in this assay based on alterations identified in 10,000 patient samples sequenced with the MSK-IMPACT HEME assay. Methods: To assess the accuracy of the MSK-ACCESS Heme assay we sequenced 54 patient cfDNA samples harboring 187 somatic alterations confirmed by clinically validated orthogonal methods. Seventy-five healthy donor samples were used to control for sequencing artifacts and background error. Five commercial SeraCare ctDNA Reference Material samples were sequenced and analyzed for sensitivity studies.For reproducibility and precision analyses, three of the accuracy samples were resequencedwithin or across different sequencing runs. Results: Samples were sequenced to mean duplex and simplex/duplex coverage of 1450X and 2295X, respectively.De novo variant calling accuracy was 84.4% (160/187) and 97.5% (182/187) for tumor informed genotyping. In comparing the variant allele frequencies (VAFs) of alterations between MSK-ACCESS HEME and MSK-ACCESS solid, we calculated a coefficient of determination (R2) of 99.6. For variants detected at a VAF less than 0.05 by an orthogonal method, we calculated an R2 of 96.6%. Alterations with a VAF above 0.05 had close to perfect recall, with R2=99.4%. Precision and reproducibility analysis demonstrated very close correlation when sequencing samples within and between sequencing runs.Sensitivity analysis revealed that all variants were called down to 0.5%using stringent de-novo critria. Conclusion: These data demonstrate that the MSK-ACCESS HEME assay is a robust and reliable tool for detecting and reporting alterations in hematological malignancies with high accuracy and sensitivity. Once approved by the New York State Department of Health, this assay will be employed to prospectively monitor patients with hematological diseases in clinical setting.

Melt Synthesis of Lithium Manganese Iron Phosphate: Part II. Particle Size, Electrochemical Performance, and Solid-State Lithium Diffusion

Melt synthesis is a fast and simple process to make dense LiMnyFe1−yPO4 (LMFP with 0 ≤ y ≤ 1) from all-dry, low-cost precursors with zero waste. Part one of this study confirmed that highly crystalline and phase pure LMFP materials can be made by melt synthesis. This part shows that planetary milling can reduce the primary particle size of melt LMFP (0%–75% Mn) to ∼200 nm, which is smaller than the primary particles in commercial LFP reference material (0% Mn). However, further particle size reduction is needed to reach particle sizes below 70 nm observed in reference LMFP (79% Mn). Melt LFP shows almost identical specific capacity and charge/discharge voltage as reference LFP. Melt LMFP materials show a high voltage Mn plateau at ∼4 V associated with the Mn2+/3+ redox, the length of which scales with Mn content. The Mn plateau raises the average discharge voltage of LMFP; hence a minimum specific discharge capacity between 160 mAh g−1 (0% Mn) and 145 mAh g−1 (80% Mn) is sufficient to match the volumetric energy density of LFP. The Atlung Method for Intercalant Diffusion shows that the lithium diffusion coefficient in LMFP is ∼1 order of magnitude higher in the voltage region of the Fe2+/3+ redox couple (3.75–3.1 V vs Li+/Li) than in the voltage region of the Mn2+/3+ redox couple (4.3–3.75 V vs Li+/Li). This emphasizes the need for very small primary particles when making LMFP with relatively high Mn content.

Abstract 551: Clinical utility of cell-free DNA based PTEN copy number loss in prostate cancer

Abstract Loss of expression of the PTEN gene is associated with poorer prognosis in many solid tumors. While cfDNA-based liquid biopsy testing are gradually adopted as the routine testing method in the clinical setting, most of them are unable to reliably detect copy number loss and/or are limited reporting copy number amplification events only. Method: We have developed a capture-based CLIA-certified NGS assay, PredicineCARE, to robustly identify tumor-derived aberrations including SNVs, Indels, fusions, copy number amplifications and deletions from blood samples. Analytical validation of the assay was performed with commercial standard reference materials and contrived cell lines. Copy number loss of PTEN was also confirmed by Immunohistochemistry (IHC) assay in 15 clinical samples. Clinical utility of PTEN copy number loss was further established by its significant association with poor outcome in clinical patients with metastatic castration-resistant prostate cancer (mCRPC). Results: Analytical validation of the PredicineCARE assay demonstrated its super sensitivity and robustness of detecting homozygous copy number loss at approximately 10% tumor fraction. Both the sensitivity and Positive Prediction Value reached 100% when overall gene copy number is below 1.75 copies. When comparing to tissue IHC results reviewed by two independent pathologists, PredicineCARE liquid biopsy assay revealed 86.7% concordance with IHC in detecting PTEN loss (80% sensitivity, 100% specificity, and 100% PPV). The copy number loss was further confirmed by low-pass whole-genome sequencing of cfDNA samples. When the assay was applied to profile mCRPC patients, copy number loss of PTEN was detected at the prevalence rate of 19.2% (10/52) and 35.9% (23/64) respectively. Notably, patients harboring PTEN copy number loss showed significantly worse overall survival in the two cohorts independently (log-rank P = 0.0001 and 0.0004 respectively). Conclusion: We have developed PredicineCARE for clinical use, a highly sensitive cfDNA-based assay to detect gene copy number variants in addition to gene mutations and fusions. Its ability to detect gene copy number loss in low fraction of tumor contents as a valuable molecular biomarker holds great potential for clinical applications and patient selections in personalized precision oncology, particularly for investigational drugs targeting the AKT-PI3K-PTEN pathway. Citation Format: Xiaoxi Dong, Minghua Zhang, Tiantian Zheng, Lu Tan, Feng Xie, Amy Xiaohong Wang, Pan Du, Shidong Jia, Chris Lu, Jianjun Yu. Clinical utility of cell-free DNA based PTEN copy number loss in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 551.

Modified sorbents based on walnut shell for sorption of toxic gases

In this article, low-cost carbon-based nanoporous materials were synthesized and impregnated in order to offer a sufficient protection for a wide range of toxic chemicals. The microstructure analysis of the samples reveals that the activation promotes the formation of a higher number of small pores and the development of a spongy texture of the sorbents leading thus to an increase in carbon content. The activated samples have apparent micro-mesoporosity confirmed by the corresponding isotherms of low-temperature adsorption of nitrogen. Furthermore, it has been shown that the activation procedure leads to samples with different acidity and this surface property has a marked influence on the performance of the materials. The results of a breakthrough time study for vapors of inorganic and organic substances indicate that the impregnations with Cu and Co are the most suitable for obtaining a universal sorbent. In this regard, an activated carbon impregnated with cobalt that can outperform commercial reference materials intended for this specific application has been developed in this work.

Single-Cell Isotope Dilution Analysis with LA-ICP-MS: A New Approach for Quantification of Nanoparticles in Single Cells.

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is an emerging method for the analysis of metal nanoparticles (NPs) in single cells. However, two main obstacles, low analytical throughput and lack of commercial reference materials, need to be overcome. In this work, we demonstrated the principles of a new approach termed "single-cell isotope dilution analysis" (SCIDA) to remove the two obstacles. For a proof of concept, macrophage cells were chosen as a model to study the uptake of silver NPs (AgNPs) at a single-cell level. Single cells exposed to AgNPs were placed in an array by a microfluidic technique; each cell in the array was precisely dispensed with a known picoliter droplet of an enriched isotope solution with a commercial inkjet printer; accurate quantification of AgNPs in single cells was done by using isotope dilution LA-ICP-MS. The average Ag mass of 1100 single cells, 396 ± 219 fg Ag per cell, was in good accord with the average of the population of cells determined by solution ICP-MS analysis. The detection limit was 0.2 fg Ag per cell. The SCIDA approach is expected to be widely applied for the study of cell-NP interactions and biological effects of NPs at the single-cell level.

Melatonin nanogel promotes skin healing response in burn wounds of rats.

Aim: Development of a melatonin nanogel intended for wound healing (WH) application. Materials & methods: The main components of the nanogel were poloxamer 407, chitosan and hyaluronic acid. The nanogel was characterized by the assessment of physical interactions, swelling, wettability, rheological properties and internal structure. The drug release, antimicrobial efficacy against different strains and biocompatibility with human keratinocytes were also tested. Finally, the WHefficacy was evaluated in rats. Results: The nanogel showed optimal physicochemical properties and an internal network of interconnected channels from which melatonin was released following first order kinetics. Antimicrobial activity was similar to commercial reference material and it promoted epidermis growth with evident wound contraction. Conclusion: Melatonin nanogel can be proposed as a promising system for WH.

Abstract 182: A comprehensive genomic profiling approach to interrogate hematologic malignancies using a novel multimodal next generation sequencing assay in a single-tube

Abstract Background: Many new guidelines require a comprehensive genomic profiling approach for diagnosis, risk stratification and therapy decisions. Limitations in sample quantity and throughput may limit the number of single biomarker tests (FISH, karyotyping, sequencing, qRT-PCR, etc.) that can be performed for the patient. There are currently multiple commercial NGS assay options for total nucleic acid, however they involve independent parallel workflows and twice the amount of sample and effort. Here we developed a novel consolidated DNA/RNA workflow in a single-tube assay utilizing custom QIAseq multimodal chemistry. This simplified workflow enables a discovery approach of all critical DNA/RNA abnormalities in hematologic malignancies, extending our NGS capabilities to large structural changes, RNA fusions and expression. Methods: 297 Heme-focused genes and 14 chromosomes were targeted in the genome, along with 213 RNA genes targeting 712 exons involved in known fusions in the transcriptome using a custom QIAseq workflow. Captured DNA/RNA targets from 135 patients were sequenced with unique dual indices on an Illumina's NovaSeq 6000. Coverage and variant allele frequency from all gene and chromosomal targets in 25 disease free patients was compared to the same genomic targets in 76 patients that were referred for a suspected hematological malignancy (e.g. MDS, CML, AML, ALL, etc.). We compared results from our custom algorithm to karyotyping and FISH. In addition, we assessed the relationship between structural changes and the average mutation load for each indication. Positives gene fusions were confirmed by qRT-PCR or Sanger sequencing. Results: Cytogenetic abnormalities in 30/32 patients were confirmed by karyotyping and FISH; two cases with abnormalities were missed by NGS. NGS detected additional abnormalities not detected by cytogenetics, including a case of loss of chr17 including deletion of driver genes, NF1 and SUZ12. No significant relationship between chromosome abnormalities and tumor mutation burden was observed. However, patients referred for myeloid disorders with structural abnormalities had a significantly higher mutational burden (p<9.12x10−7). Mutational load in these patients was significantly associated with chromosome 17 abnormalities, primarily loss (p<0.013). qRT-PCR confirmed 100% of BCR-ABL fusions (p210, p190) in all patients (59/59) with International Scale (IS) percentages ranging from 2.4-100%. Notably, we confirmed two clinically significant fusions, SET-NUP214 and RUNX1-RUNX1T1 in two patients not previously interrogated by qRT-PCR. The SET-NUP214 fusion is normally associated with acute lymphoblastic leukemia (ALL) was identified in a patient with suspected CML. We also confirmed PCALM-MLLT10 gene fusion was detected in a commercial universal human RNA reference material, commonly used in expression profiling studies. Conclusions: This study confirms the validity and utility of simple but efficient comprehensive genomic profiling for use in hematologic malignancies. Coupled with FISH and cytogenetics tests, NGS can offer a better diagnostic and prognostic testing service for patients with hematologic disease to assist in treatment selection as well as precise patient care. Citation Format: Segun C. Jung, YongXin Yu, Yanglong Mou, Hyunjun Nam, Cynthie Wong, Samuel Koo, Brad Thomas, Forrest Blocker, Derek Lyle, Ryan Bender, Sally Agersborg, Lawrence M. Weiss, Vincent A. Funari. A comprehensive genomic profiling approach to interrogate hematologic malignancies using a novel multimodal next generation sequencing assay in a single-tube [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 182.

Adventures with Oxides: Utilizing Commercial and Internal Reference Materials for Geological and Materials Science Samples

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling.

Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter- and intra-assay as well as intra- and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.

Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential.

Because next-generation sequencing (NGS) for detecting somatic mutations has been adopted in clinical fields, both qualitative and quantitative QC of the somatic variants through whole coding regions detected by NGS is crucial. However, specific applications or guidelines, especially for quantitative QC, are currently insufficient. Our goal was to devise a practical approach for both quantitative and qualitative QC using an example of detecting clonal hematopoiesis of indeterminate potential (CHIP). We applied the QC scheme using commercial reference materials and in-house QC materials (IQCM) composed of haplotype map and cancer cell lines for monitoring CHIP. This approach efficiently validated a customized CHIP NGS assay. Accuracy, analytical sensitivity, analytical specificity, qualitative precision (concordance), and limit of detection achieved were 99.87%, 98.53%, 100.00%, 100.00%, and 1.00%, respectively. The quantitative precision analysis also had a higher CV percentage at a lower alternative read depth (R2 = 0.749∼0.858). Use of IQCM ensured more than 100-fold reduction in the cost per run compared with that achieved using commercial reference materials. Our approach determined the general analytical performance of NGS for detecting CHIP and recognized limitations such as lower precision at a lower level of variant burden. This approach could also be theoretically expanded to a general NGS assay for detecting somatic variants. Considering the reliable NGS results and cost-effectiveness, we propose the use of IQCM for QC of NGS assays at clinical laboratories.