RNA-based Assays Research Articles

Laboratory detection of donors implicated in transfusion-transmitted malaria.

Transfusion-transmitted malaria (TTM) is rare in non-endemic areas (non-EAs) but can potentially be fatal. This review analyzes the laboratory results of donors causing TTM in non-EAs, to assess the detectability of their Plasmodium infection by molecular or antibody tests. TTM cases in the United States, Canada, and Europe since 2010 were identified through a literature review. Authors and laboratories were contacted for missing details about sample types and laboratory methods. Results of Plasmodium polymerase chain reaction (PCR) and antibody tests were summarized. Twelve cases of TTM and one bone marrow transplant transmission were identified. Of the 13 source donors, 12 were tested by PCR, 10 were positive on at least one sample; the 2 negative donors were tested only on retained segments of blood refrigerated for several weeks. All donors were PCR positive on a fresh sample except one who was positive on a retained but not a fresh sample. These PCRs targeted Plasmodium DNA with sensitivities in the range of 1000-10,000 parasites/mL. Antibody EIA was positive in only three of seven donors tested. This review found that antibody EIAs failed to detect four of the seven TTM donors tested. DNA-based PCRs were able to detect Plasmodium infection in all donors tested except for two tested only on samples likely to have deteriorated from prolonged storage. Recently developed ribosomal RNA-based molecular donor screening assays are approximately 1000 fold more sensitive than these DNA-based PCRs, holding promise as a potential method to further reduce TTM.

Multicenter validation of an RNA-based assay to predict anti-PD-1 disease control in patients with recurrent or metastatic head and neck squamous cell carcinoma: the PREDAPT study.

Despite advances in cancer care and detection, >65% of patients with squamous cell cancer of the head and neck (HNSCC) will develop recurrent and/or metastatic disease. The prognosis for these patients is poor with a 5-year overall survival of 39%. Recent treatment advances in immunotherapy, including immune checkpoint inhibitors like pembrolizumab and nivolumab, have resulted in clinical benefit in a subset of patients. There is a critical clinical need to identify patients who benefit from these antiprogrammed cell death protein 1 (anti-PD-1) immune checkpoint inhibitors. Here, we report findings from a multicenter observational study, PREDicting immunotherapy efficacy from Analysis of Pre-treatment Tumor biopsies (PREDAPT), conducted across 17 US healthcare systems. PREDAPT aimed to validate OncoPrism-HNSCC, a clinical biomarker assay predictive of disease control in patients with recurrent or metastatic HNSCC treated with anti-PD-1 immune checkpoint inhibitors as a single agent (monotherapy) and in combination with chemotherapy (chemo-immunotherapy). The test used RNA-sequencing data and machine learning models to score each patient and place them into groups of low, medium, or high. The OncoPrism-HNSCC prediction significantly correlated with disease control in both the monotherapy cohort (n=62, p=0.004) and the chemo-immunotherapy cohort (n=50, p=0.01). OncoPrism-HNSCC also significantly predicted progression-free survival in both cohorts (p=0.015 and p=0.037, respectively). OncoPrism-HNSCC had more than threefold higher specificity than programmed death-ligand 1 combined positive score and nearly fourfold higher sensitivity than tumor mutational burden for predicting disease control. Here, we demonstrate the clinical validity of the OncoPrism-HNSCC assay in identifying patients with disease control in response to anti-PD-1 immune checkpoint inhibitors. NCT04510129.

8109 Cancer-Associated Fibroblasts Correlate with Aggressive Thyroid Cancer Behavior: Insights from Four Large Patient Cohorts

Abstract Disclosure: M.A. Loberg: None. X. George: None. P.J. Courtney: None. H.C. Eric: None. A. Golding: None. B. David: None. M. Alshalalfa: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc. Y. Hao: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc. J.P. Klopper: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc. R.T. Kloos: Employee; Self; Veracyte, Inc.. Stock Owner; Self; Veracyte, Inc.. V. Weiss: None. Thyroid tumor molecular analysis often utilizes fine-needle aspirate (FNA) samples to predict malignancy with high sensitivity. An outstanding question is if molecular sequencing can provide prognostic information to predict disease aggression, potentially informing management. Recently, the composition of the tumor microenvironment, in particular the presence of tumor-promoting fibroblasts, has been associated with aggressive thyroid cancer. However, fibroblast gene expression has not previously been analyzed in thyroid tumor FNA samples. In this work, we detect cancer-associated fibroblast (CAF) gene signatures across 4 distinct bulk RNA sequencing cohorts and confirm detection in FNA samples. Associations between CAF gene signatures and tumor characteristics were explored in: Afirma Genomic Sequencing Classifier (GSC) cohort from FNA (n=47,695), a Memorial Healthcare System (MHS) retrospective FNA cohort with pathology outcome data (n=318), TCGA papillary thyroid cancers (n=496), and a Vanderbilt University Medical Center-University of Washington (VUMC-UW) resection cohort (n=312). Published breast CAF gene sets were used to generate normal fibroblast and CAF subtype scores. Novel thyroid cancer specific CAF gene sets were generated from thyroid cancer single-cell RNA sequencing data. Scores for each gene set were calculated as the average Z-score. Across all cohorts, multiple CAF subsets were enriched in samples with BRAFV600E and papillary histology. The strongest enrichment was in an SFRP2+ CAF subset identified in thyroid cancer single-cell sequencing data. In Afirma GSC FNA samples, SFRP2+ CAFs were enriched in GSC-suspicious and Bethesda V/VI relative to GSC-benign nodules (Wilcoxon p value < 2e-[1]6 for all). In TCGA, SFRP2+ CAFs were associated with extrathyroidal extension, advanced disease stage, and aggressive histology. In the MHS cohort of 318 malignant FNA samples, SFRP2+ CAFs were significantly higher in patients with vascular invasion or lymph node metastasis (LNM) (OR:2.75 [95% CI 1.63-4.75], p=4e-5). In the VUMC-UW cohort, SFRP2+ CAFs were associated with shorter progression-free survival (PFS) (p=0.0033). In summary we created a novel thyroid cancer-specific CAF gene signature that is elevated in BRAFV600E+ and aggressive thyroid cancers across multiple large patient cohorts. We also demonstrated the ability to detect these CAF signatures in thyroid FNAs using the Afirma GSC molecular testing platform, with enrichment in suspicious and malignant samples. Amongst the CAF scores tested, thyroid-specific CAF subsets had the highest prognostic potential, and SFRP2+ CAFs, specifically, were associated with shorter PFS, tumor invasion and LNM. Together, these results highlight the potential of interrogating the thyroid tumor stroma in FNA using RNA-based assays to inform prognosis and possibly management. Presentation: 6/3/2024

The Next Chapter in Cancer Diagnostics: Advances in HPV-Positive Head and Neck Cancer.

Human papillomavirus (HPV)-associated head and neck squamous cell carcinoma (HNSCC), particularly oropharyngeal squamous cell carcinoma (OPSCC), is an increasingly prevalent pathology worldwide, especially in developed countries. For diagnosing HPV in HNSCC, the combination of p16 immunohistochemistry (IHC) and polymerase chain reaction (PCR) offers high sensitivity and specificity, with p16 IHC being a reliable initial screen and PCR confirming HPV presence. Advanced techniques like next-generation sequencing (NGS) and RNA-based assays provide detailed insights but are primarily used in research settings. Regardless of HPV status, standard oncological treatments currently include surgery, radiation, and/or chemotherapy. This conventional approach does not account for the typically better prognosis of HPV-positive HNSCC patients, leading to increased chemo/radiation-induced secondary morbidities and reduced quality of life. Therefore, it is crucial to identify and detect HPV positivity and other molecular characteristics of HNSCC to personalize treatment strategies. This comprehensive review aims to summarize current knowledge on various HPV detection techniques and evaluate their advantages and disadvantages, with a focus on developing methodologies to identify new biomarkers in HPV-positive HNSCC. The review discusses direct and indirect HPV examination in tumor tissue, DNA- and RNA-based detection techniques, protein-based markers, liquid biopsy potentials, immune-related markers, epigenetic markers, novel biomarkers, and emerging technologies, providing an overall insight into the current state of knowledge.

A molecular method to assess viability of Phytophthora in infected wood following heat treatment

International trade in wood products is an important component of the global economy. However, wood and wood products may have pests associated with them that could be introduced into importing countries, posing phytosanitary risks, and leading to the implementation of regulatory restrictions that affect wood trade. The application of heat to kill wood-associated pests has been a successful phytosanitary method to reduce their spread. To evaluate the efficacy of wood heat treatment to kill fungal and fungus-like pathogens, the method of choice has been to grow organisms in cultures for subsequent identification. However, some plant pathogens can be difficult or impossible to grow in axenic cultures and a molecular method can still be useful for assessing pathogen viability after heat-treatment. RNA is a single stranded molecule that is responsible for the transcription of genes. Since it becomes rapidly unstable after cell death, it provides a measure of viability. We therefore designed and tested RNA-based molecular diagnostic assays targeting essential genes and assessed their presence after heat treatment in wood colonized by four Phytophthora species of phytosanitary concern (P. xmultiformis, P. cinnamomi, P. lateralis and P. ramorum) through reverse transcription and real-time polymerase chain reaction (RT-qPCR). Our assays differentiate between genomic and mRNA as the TaqMan probes span exon-intron junctions. We validated these RT-qPCR assays to assess heat treatment efficacy of Phytophthora-inoculated wood. These assays can be very useful tools to assess effectiveness of current and emerging phytosanitary wood treatments.

Associations of Immune Checkpoint Predictive Biomarkers (MHC-I and MHC-II) with Clinical and Molecular Features in a Diverse Breast Cancer Cohort.

Immunotherapy (IO) in triple-negative breast cancer (TNBC) has improved survival outcomes, with promising improvements in pCR rates among early high-risk hormone receptor (HR)+/HER2- breast cancers. However, biomarkers are needed to select patients likely to benefit from IO. MHC-I and tumor-specific MHC-II (tsMHC-II) expression are candidate biomarkers for PD-(L)1 checkpoint inhibition but existing data from clinical trials included limited racial/ethnic diversity. We performed multiplexed immunofluorescence assays in the Carolina Breast Cancer Study (CBCS; n = 1,628, 48% Black, 52% non-Black). Intrinsic subtype and P53 mutant-like status were identified using RNA-based multigene assays. We ranked participants based on tumoral MHC-I intensity (top 33% categorized as "MHC-Ihigh") and MHC-II+ (≥5% of tumor cells as tsMHC-II+). MHC-I/II were evaluated in association with clinicopathological features by race. Black participants had higher frequency of TNBC (25% vs. 12.5%, P ≤ 0.001) and basal-like (30% vs. 14%, P ≤ 0.001) tumors overall, and higher frequency of basal-like (11% vs. 5.5%, P = 0.002) and TP53 mutant tumors (26% vs. 17%, P = 0.002) among HR+/HER2-. The frequency of tsMHC-II+ was higher in HR+/HER2- Black participants (7.9% vs. 4.9%, P = 0.04). Black participants also had higher frequency of MHC-Ihigh (38.7% vs. 28.2%, P < 0.001), which was significant among HR+/HER2- (28.2% vs. 22.1%, P = 0.02). In this diverse study population, MHC-I and MHC-II tumor cell expression were more highly expressed in HR+/HER2- tumors from Black women, underscoring the importance of diverse and equitable enrollment in future IO trials.

Differences in 21-Gene and PAM50 Recurrence Scores in Younger and Black Women With Breast Cancer.

Genomic tests, such as the Oncotype Dx 21-gene and Prosigna risk of recurrence (ROR-P) assay, are commonly used for breast cancer prognostication. Emerging data suggest variability between assays, but this has not been compared in diverse populations. RNA sequencing was performed on 647 previously untreated stage I-III estrogen receptor-positive/human epidermal growth factor receptor 2-negative tumors in the Carolina Breast Cancer Study, which oversampled Black and younger women (age <50 years at diagnosis), using research versions of two common RNA-based prognostic assays: ROR-PR and the 21-gene recurrence score (RSR). Relative frequency differences and 95% CIs were estimated for associations with race and age, and hazards of 5-year local or distant recurrence were modeled with Cox regression. Proliferation and estrogen module scores from each assay, representing broad activity of genes in those pathways, were examined to guide interpretation of differences between tests. Among both younger and older individuals, Black women had higher frequency of intermediate and high ROR-PR scores than non-Black women. Race was not significantly associated with RSR in either age group. High (hazard ratio [HR], 4.67 [95% CI, 1.73 to 12.70]) and intermediate (HR, 2.12 [95% CI, 0.98 to 4.62]) ROR-PR scores were associated with greater risk of recurrence, but RSR did not predict recurrence. RSR emphasized estrogen over proliferation modules, whereas ROR-PR emphasized proliferation. Higher proliferation scores were associated with younger age and Black race in both assays. Modifications to the RSR algorithm that increased emphasis on proliferation improved prognostication in this diverse population. ROR-PR and the 21-gene RSR differentially emphasize estrogen-related and proliferative biology. The emphasis of 21-gene RS on estrogen-related biology and lower endocrine therapy initiation among Black women may contribute to poorer prognostic ability in heterogeneously treated populations.

Associations of predictive biomarkers, MHC-I and MHC-II, with clinical and molecular features in a diverse breast cancer cohort.

517 Background: The addition of immunotherapy (IO) to chemotherapy in triple negative breast cancer (TNBC) has improved survival outcomes and recent studies have also shown improvements in pCR rates in early high-risk HR+/HER2- breast cancer. However, these improvements are not without toxicities and thus there is a critical need for biomarkers to select patients that are most likely to benefit from immunotherapy. MHC-I and tumor-specific MHC-II (tsMHC-II) expression are candidate biomarkers for predicting PD-(L)1 checkpoint inhibition benefit and have previously shown potential for predicting treatment response in multiple tumor types, including breast cancer. However, the existing data were generated from clinical trials with limited racial/ethnic diversity. Here we report associations between MHC-I and MHC-II expression and clinicopathological features in a large, racially and ethnically diverse breast cancer cohort. Methods: We performed multiplexed immunofluorescent tissue-based analysis of participants in the Carolina Breast Cancer Study (CBCS). Intrinsic subtype and P53 mutant-like status were identified using RNA-based multigene assays. To evaluate MHC-I we ranked all participants based on tumoral MHC-I intensity, with the top 33% categorized as "MHC-IHigh"; MHC-II+ expression on tumor cells was defined as ≥5% of tumor cells. Association between MHC-I/II and clinicopathological features by race was tested using Chi-square test or fisher-exact test and relative frequency difference (RFD) was calculated. Results: This study included 1630 participants (48% Black and 52% non-Black) with Stage I-III breast cancer. Black participants had a higher incidence of TNBC (25% vs. 12.5%, p=&lt;0.001) and Basal-like (29% vs. 14%, p=&lt;0.001) tumors. Basal-like and TP53 mutant tumors were more frequently observed among Black participants with HR+/HER2- tumors (11% vs. 5.5%, p=0.006 for Basal-like; 26% vs. 17%, p=0.003 for p53 mutant-like). While there was a similar distribution of tsMHC-II+ tumors between Black and non-Black participants, the relative frequency of tsMHC-II+ tumors was significantly more common in Black participants with HR+/HER2- breast cancer compared to non-Black participants (7.9% vs. 5%, p=0.04). Moreover, Black participants also were significantly more likely to have MHC-Ihigh tumors (38.9% vs. 28.4%, p=0.01), which, after IHC subtype stratification, was only significant among participants with HR+/HER2- breast cancer (28.2% vs. 22.3%, p=0.02). Conclusions: In this diverse breast cancer cohort, MHC-I and MHC-II expression, candidate predictive biomarkers of IO benefit, were more prevalent in tumors from Black women with HR+/HER2- breast cancer. These results underscore the importance of diverse and equitable clinical trial enrollment in future IO trials, especially in HR+/HER2- breast cancer.

Phase 2 study of neoadjuvant enzalutamide and paclitaxel for luminal androgen receptor-enriched TNBC: Trial results and insights into “ARness”

Luminal androgen receptor (LAR)-enriched triple-negative breast cancer (TNBC) is a distinct subtype. The efficacy of AR inhibitors and the relevant biomarkers in neoadjuvant therapy (NAT) are yet to be determined. We tested the combination of the AR inhibitor enzalutamide (120mg daily by mouth) and paclitaxel (80mg/m2 weekly intravenously) (ZT) for 12weeks as NAT for LAR-enriched TNBC. Eligibility criteria included a percentage of cells expressing nuclear AR by immunohistochemistry (iAR) of at least 10% and a reduction in sonographic volume of less than 70% after four cycles of doxorubicin and cyclophosphamide. Twenty-four patients were enrolled. Ten achieved a pathologic complete response or residual cancer burden-I. ZT was safe, with no unexpected side effects. An iAR of at least 70% had a positive predictive value of 0.92 and a negative predictive value of 0.97 in predicting LAR-enriched TNBC according to RNA-based assays. Our data support future trials of AR blockade in early-stage LAR-enriched TNBC.

Acute Promyelocytic Leukemia With Torque Teno Mini Virus::RARA Fusion: An Approach to Screening and Diagnosis

Acute promyelocytic leukemia (APL) with variant RARA translocation is linked to over 15 partner genes. Recent publications encompassing 6 cases have expanded the spectrum of RARA partners to torque teno mini virus (TTMV). This entity is likely underrecognized due to the lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide the necessary tools to screen and diagnose APL with TTMV::RARA using existing clinical DNA- or RNA-based NGS assays, which led to the identification of 4 cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and 3 retrospectively, including 2 from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including 1 with multiple relapses after acute myeloid leukemia-type chemotherapy and hematopoietic stem cell transplant. Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon reinduction (including all-trans retinoic acid in 1 case) and subsequent hematopoietic stem cell transplant. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression. RARA rearrangement was not detected by karyotype or fluorescent in situ hybridization. Custom analysis of NGS fusion panel data identified TTMV::RARA rearrangements and, in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARA is a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectable RARA fusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of all-trans retinoic acid may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.

Abstract PO4-16-02: Can high progesterone receptor (PgR) expression identify tumours with low-risk tumour gene expression scores?

Abstract Background Strong PgR expression predicts favorable outcomes for ER+ve HER2-ve breast cancer and has been proposed as a surrogate marker to distinguish between IHC-defined luminal A and luminal B subtypes. It is therefore possible that strong PgR expression may be able to predict tumor gene expression test results and independently identify tumors that are unlikely to be chemotherapy sensitive. PgR expression is traditionally determined by immunohistochemistry (IHC). Several validated RNA-based PGR expression tests have been developed that may outperform IHC. Methods We compared Oncotype DX RS with Oncotype DX reported PGR in 4 independent datasets which included 407 cases from the OPTIMA prelim trial. We further analyzed 251 OPTIMA prelim cases which had additional tumor gene expression data. All gene expression assays were performed by the test vendor, including PGR gene expression determined using the Mammatyper assay. PgR IHC was determined in a single laboratory on triplicate tissue micro-arrays using quantitative image analysis including a 10% manual quality control check. We analyzed PGR expression using cutoffs that correspond to approximately 20% staining; the standard Oncotype DX PGR assay is reported as positive if the score is &amp;gt;5.4, corresponding to approximately 1% staining by IHC. We used Spearman’s rank correlation coefficient to compare PGR data. Results The four Oncotype DX datasets consistently demonstrated that high Oncotype PGR expression was associated with a low RS (table). Combining the 3 validation data sets consisting of 633 cases, 70.9% had high PGR expression of which 92.7% had a an Oncotype RS ≤25. Approximately 50% of cases with low Oncotype PGR expression had an Oncotype RS &amp;gt;25. Mammatyper and Oncotype PGR were highly correlated (Rs = 0.9258, P&amp;lt; 0.001) in the OPTIMA prelim dataset (n=251), with only 8.4% of tumors having discordant high/low Mammatyper and Oncotype PGR scores. 93.2% of 176 Mammatyper high PGR expression cases had an RS ≤25. The Mammatyper PGR and PgR IHC correlation was weaker (Rs=0.763, P&amp;lt; 0.001); 87.2% of 211 cases with &amp;gt;20% staining had RS ≤25. PgR IHC staining had a bimodal distribution and there was little effect on the prediction of low RS score up to a 67% cut-off. Mammatyper and Oncotype PGR scores both appear to have a normal distribution. We took advantage of this to perform an exploratory analysis using a higher Mammatyper PGR cutoff. We were able to show superior prediction of a low RS (96.8%) but with a reduced proportion (50.2%) of high PGR score tumors. High PGR gene expression was weakly associated with low (≤60) Prosigna ROR_PT score and MammaPrint low risk (72.2% and 65.9% respectively) and with Prosigna and MammaPrint luminal A subtype (both 64.8%). Conclusion High progesterone receptor gene expression measured using locally performed RNA-based assays may allow the reliable prediction of Oncotype DX low-risk tumours. This analysis provides additional information for the clinical utility of PGR measurement. Additional data will be presented on the optimal PGR cutoff. OPTIMA prelim is registered as ISRCTN42400492 and funded by the UK NIHR Health Technology Assessment Programme, award number 10/34/01. Views expressed are those of the authors and not those of the HTA Programme, NIHR, NHS or the Department of Health. Table. Oncotype DX RS and PGR in 4 datasets Distribution of RS according to %cases with high or low PGR Citation Format: Robert Stein, Ralph Wirtz, Andrea Marshall, Jane Bayani, Sebastian Eidt, Claudia Schumacher, Hans-Peter Sinn, Andreas Schneeweiss, Andreas Makris, Iain Macpherson, Luke Hughes-Davies, Tammy Piper, Monika Sobol, Georgina Dotchin, Helen Higgins, Sarah Pinder, Abeer Shaaban, Janet Dunn, John MS Bartlett. Can high progesterone receptor (PgR) expression identify tumours with low-risk tumour gene expression scores? [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-16-02.

Detection of Mycoplasma hyopneumoniae viability using a PCR-based assay

Mycoplasma hyopneumoniae detection in clinical specimens is accomplished by PCR targeting bacterial DNA. However, the high stability of DNA and the lack of relationship between bacterial viability and DNA detection by PCR can lead to diagnostic interpretation issues. Bacterial messenger RNA is rapidly degraded after cell death, and consequently, assays targeting mRNA detection can be used for the exclusive detection of viable bacterial cells. Therefore, this study aimed at developing a PCR-based assay for the detection of M. hyopneumoniae mRNA and at validating its applicability to differentiate viable from inert bacteria. Development of the RNA-based PCR encompassed studies to determine its analytical sensitivity, specificity, and repeatability, as well as its diagnostic accuracy. Comparisons between DNA and mRNA detection for the same target gene were performed to evaluate the ability of the RNA-based PCR to detect exclusively viable M. hyopneumoniae after bacterial inactivation using various methods. The RNA-based PCR was also compared to the DNA-based PCR as a tool to monitor the growth of M. hyopneumoniae in vitro. Under the conditions of this study, the developed RNA-based PCR assay detected only viable or very recently inactivated M. hyopneumoniae, while the DNA-based PCR consistently detected cells irrespective of their viability status. Changes in growth activity over time were only observable via RNA-based PCR. This viability PCR assay could be directly applied to evaluate the clearance of M. hyopneumoniae or to determine the viability of the bacterium at late stages of eradication programs.

Multicenter evaluation of an automated, multiplex, RNA-based molecular assay for detection of ALK, ROS1, RET fusions and MET exon 14 skipping in NSCLC.

The current study assessed the performance of the fully automated RT-PCR-based Idylla™ GeneFusion Assay, which simultaneously covers the advanced non-small cell lung carcinoma (aNSCLC) actionable ALK, ROS1, RET, and MET exon 14 rearrangements, in a routine clinical setting involving 12 European clinical centers. The Idylla™ GeneFusion Assay detects fusions using fusion-specific as well as expression imbalance detection, the latter enabling detection of uncommon fusions not covered by fusion-specific assays. In total, 326 archival aNSCLC formalin-fixed paraffin-embedded (FFPE) samples were included of which 44% were resected specimen, 46% tissue biopsies, and 9% cytological specimen. With a total of 179 biomarker-positive cases (i.e., 85 ALK, 33 ROS1, 20 RET fusions and 41 MET exon 14 skipping), this is one of the largest fusion-positive datasets ever tested. The results of the Idylla™ GeneFusion Assay were compared with earlier results of routine reference technologies including fluorescence in situ hybridization, immunohistochemistry, reverse-transcription polymerase chain reaction, and next-generation sequencing, establishing a high sensitivity/specificity of 96.1%/99.6% for ALK, 96.7%/99.0% for ROS1, 100%/99.3% for RET fusion, and 92.5%/99.6% for MET exon 14 skipping, and a low failure rate (0.9%). The Idylla™ GeneFusion Assay was found to be a reliable, sensitive, and specific tool for routine detection of ALK, ROS1, RET fusions and MET exon 14 skipping. Given its short turnaround time of about 3 h, it is a time-efficient upfront screening tool in FFPE samples, supporting rapid clinical decision making. Moreover, expression-imbalance-based detection of potentially novel fusions may be easily verified with other routine technologies without delaying treatment initiation.

Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer.

Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.

Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non-small cell lung cancer cytology specimens: A single-center experience with comparison to fluorescence insitu hybridization.

Genomic profiling is needed to identify actionable alterations in non-small cell lung cancer (NSCLC). Panel-based testing such as next-generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA-based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing. A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA-based NGS and ALK, RET, and/or ROS1 by FISH. Genomic alterations were detected in 29 cases by NGS, including ALK, RET, ROS1, NTRK, NUTM1, and FGFR3 fusions and MET exon 14 skipping alterations. Of the 20 cases with ALK, RET, and ROS1 fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where EML4::ALK (n=2) and SLC34A2::ROS1 (n=1) fusions were not detected by the corresponding FISH assay; one case with EZR::ROS1 was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting ALK, RET, and ROS1 fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively. RNA-based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA-based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.

Tyrosine kinase alterations in colorectal cancer with emphasis on the distinct clinicopathological characteristics.

Tyrosine kinase (TK) alterations, such as anaplastic lymphoma kinase (ALK) fusion, neurotrophic tyrosine receptor kinase (NTRK) fusion, c-ros oncogene 1 (ROS1) fusion and mesenchymal-epithelial transition factor (MET) exon 14 skipping, have been reported in colorectal cancers (CRC). We have previously reported CRCs with NTRK fusion among our cohort. However, their clinicopathological features have not been fully elucidated. Tissue microarray (TMA)-based immunohistochemistry (IHC) was performed on 951 CRC lesions from 944 patients. IHC was evaluated as positive or negative for ALK and ROS1 and 0 to 3+ for c-MET. For ALK and ROS1 IHC-positive cases, RNA-based imbalanced gene expression assays, Archer FusionPlex assays and reverse transcription-polymerase chain reaction (RT-PCR) followed by Sanger sequencing were performed. For c-MET IHC 3+ cases, RT-PCR followed by Sanger sequencing were performed. ALK IHC was positive in three cases (0.2%) and all showed imbalanced ALK gene expression. The following ALK fusions were confirmed: EML4 (exon 21)::ALK (exon 20), EML4 (exon 6)::ALK (exon 19) and HMBOX1 (exon 6)::ALK (exon 20). Two showed microsatellite instability-high/mismatch repair (MMR)-deficient, and all were located in the right colon. ROS1 IHC was positive in one case; however, imbalanced expression and ROS1 fusion was negative. Forty-two cases (4.4%) showed c-MET IHC3+. MET exon 14 skipping was confirmed in nine cases. All cases were microsatellite stable/MMR-proficient, and eight were located in the left colon and rectum. CRCs with these TK alterations had distinct clinicopathological features. Together with our previous study, 15 cases (1.6%) harboured targetable TK alterations (three NTRK fusion, three ALK fusion, nine MET exon 14 skipping).

Detection of Hybrid Fusion Transcripts, Aberrant Transcript Expression, and Specific Single Nucleotide Variants in Acute Leukemia and Myeloid Disorders with Recurrent Gene Rearrangements

Introduction: A variety of gene rearrangements and molecular alterations are key drivers in the pathobiology of acute leukemia and myeloid disorders; current classification systems increasingly incorporate these findings in diagnostic algorithms. Therefore, clinical laboratories require versatile tools, which can detect an increasing number and variety of molecular and cytogenetic alterations of clinical significance. Methods: We validated an RNA-based next-generation sequencing (NGS) assay that enables the detection of: (i) numerous hybrid fusion transcripts (including rare/novel gene partners), (ii) aberrantly expressed EVI1 (MECOM) and IKZF1 (Del exons 4–7) transcripts, and (iii) hotspot variants in KIT, ABL1, NPM1 (relevant in the context of gene rearrangement status). Results: For hybrid fusion transcripts, the assay showed 98–100% concordance for known positive and negative samples, with an analytical sensitivity (i.e., limit of detection) of approximately 0.8% cells. Samples with underlying EVI1 (MECOM) translocations demonstrated increased EVI1 (MECOM) expression. Aberrant IKZF1 (Del exons 4–7) transcripts detectable with the assay were also present on orthogonal reverse transcription PCR. Specific hotspot mutations in KIT, ABL1, and NPM1 detected with the assay showed 100% concordance with orthogonal testing. Lastly, several illustrative samples are included to highlight the assay’s clinically relevant contributions to patient workup. Conclusion: Through its ability to simultaneously detect various gene rearrangements, aberrantly expressed transcripts, and hotspot mutations, this RNA-based NGS assay is a valuable tool for clinical laboratories to supplement other molecular and cytogenetic methods used in the diagnostic workup and in clinical research for patients with acute leukemia and myeloid disorders.

Smaller panel, similar results: genomic profiling and molecularly informed therapy in pancreatic cancer

Pancreatic cancer has a dismal prognosis. One reason is resistance to cytotoxic drugs. Molecularly matched therapies might overcome this resistance but the best approach to identify those patients who may benefit is unknown. Therefore, we sought to evaluate a molecularly guided treatment approach. We retrospectively analyzed the clinical outcome and mutational status of patients with pancreatic cancer who received molecular profiling at the West German Cancer Center Essen from 2016 to 2021. We carried out a 47-gene DNA next-generation sequencing (NGS) panel. Furthermore, we assessed microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) status and, sequentially and only in case of KRAS wild-type, gene fusions via RNA-based NGS. Patient data and treatment were retrieved from the electronic medical records. Of 190 included patients, 171 had pancreatic ductal adenocarcinoma (90%). One hundred and three patients had stage IV pancreatic cancer at diagnosis (54%). MMR analysis in 94 patients (94/190, 49.5%) identified 3 patients with dMMR (3/94, 3.2%). Notably, we identified 32 patients with KRAS wild-type status (16.8%). To identify driver alterations in these patients, we conducted an RNA-based fusion assay on 13 assessable samples and identified 5 potentially actionable fusions (5/13, 38.5%). Overall, we identified 34 patients with potentially actionable alterations (34/190, 17.9%). Of these 34 patients, 10 patients (10/34, 29.4%) finally received at least one molecularly targeted treatment and 4 patients had an exceptional response (>9 months on treatment). Here, we show that a small-sized gene panel can suffice to identify relevant therapeutic options for pancreatic cancer patients. Informally comparing with previous large-scale studies, this approach yields a similar detection rate of actionable targets. We propose molecular sequencing of pancreatic cancer as standard of care to identify KRAS wild-type and rare molecular subsets for targeted treatment strategies.

Abstract 5452: Complimentary use of DNA- and RNA-based NGS assays optimizes detection of clinically relevant translocations for comprehensive genomic profiling

Abstract Introduction: Detection of gene translocations is a key component of clinical diagnostics to enable precision medicine in oncology. Several methods such as fluorescence in situ hybridization or RT-PCR have historically been employed, however, next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) including DNA and RNA sequencing approaches have been validated for this purpose. Here we explore the complimentary nature of these methods to enable detection of clinically relevant translocations to guide patient care. Methods: We utilized Endeavor, a 505 gene DNA-based CGP assay developed by Personal Genome Diagnostics, to assess single nucleotide variants, insertion/deletions, amplifications, translocations, microsatellite instability, and tumor mutation burden as well as a 53 gene RNA-based Invitae NGS FusionPlex Solid Tumor v1 assay. 151 patients with advanced or metastatic solid tumors, including lung, colorectal, esophageal, breast, brain, bladder, and prostate cancers, were consecutively enrolled and only overlapping target regions were evaluated to compare performance. Results: Of the 151 cases selected for the study, failure rates were 2.0% and 9.9% for Endeavor and FusionPlex, respectively. Translocations were detected in 21/151 (13.9%) cases by Endeavor and 17/105 (11.3%) cases by FusionPlex. For the 133 cases where data was available from both assays, 12 (9.0%) concordant translocation positive cases were detected involving ALK, RET, NTRK1, NTRK3, MET exon 14 skipping, EGFRvIII, and EWSR1 with 109 (82.0%) cases translocation negative by both assays achieving a concordance rate of 91%. For 7 (5.3%) cases, Endeavor detected translocations events in FGFR1, FGFR2, ETV4, ETV6, MYC, and NTRK3 that were not detected by FusionPlex. Conversely, FusionPlex identified 5 (3.8%) cases with translocations in ROS1, NTRK2, and EGFRvIII that were not detected by Endeavor (Table 1). Discrepancies in translocation detection were attributed to variability in assay failure rates, panel design, and underlying biological differences in detectability associated with DNA- and RNA-based methods. Conclusions: In this study, comparison of translocation detection using DNA and RNA-based NGS approaches revealed a high concordance between the two assays and were equally valuable for identifying actionable targets. These findings provide confirmatory support for the complimentary use of DNA- and RNA-based NGS approaches to most accurately identify clinically relevant translocations thereby providing more comprehensive results to help guide cancer treatment strategies. Citation Format: Rongqin Ren, Jennifer Jackson, Jacob Kames, David Riles, Christopher Coldren, Scott Wheeler, Pranil Chandra, Michelle Shiller. Complimentary use of DNA- and RNA-based NGS assays optimizes detection of clinically relevant translocations for comprehensive genomic profiling. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5452.

NTRK Fusion in a Cohort of BRAF p. V600E Wild-Type Papillary Thyroid Carcinomas

Owing to the availability of a potent tropomyosin receptor kinase (TRK) inhibitor, it is necessary to develop an effective strategy to identify an enriched population of NTRK fusions in papillary thyroid carcinoma (PTC) in routine diagnostic practice. The reported prevalence of NTRK fusion in a large cohort of PTC is ∼3%. We performed an analysis to refine the characteristic histologic features of PTCs harboring NTRK fusions and further validate the diagnostic utility of pan-TRK immunohistochemistry as a screening tool. In this study, 450 PTCs known to harbor no BRAF p. V600E mutations were screened by pan-TRK immunohistochemistry, and the cases with TRK expression were confirmed by RNA-based next-generation sequencing assay. Eleven NTRK fusion cases were detected (2.4%), and all PTCs were classical subtypes. NTRK1 and NTRK3 were involved in the fusion with 9 different partner genes. Most cases showed similar characteristic histologic findings. Nodular permeative border, multinodular growth with a predominantly follicular pattern, extensive lymphatic invasion, and prominent internodular and intratumoral fibrosis were the characteristic histologic features of NTRK-rearranged PTCs. The ill-defined margins in the ultrasonography findings, which could not be clearly distinguished from the adjacent nontumorous thyroid tissue, were nodular permeative margins in histologic findings. Therefore, preoperative ultrasonographic findings in nodule margins were consistent with the final histologic findings. NTRK1/3 fusion in PTCs showed an overall sensitivity of 100% (95% CI, 71.51%-100%) and specificity of 100% (95% CI, 71.51%-100%) in the 22 cases examined, as confirmed with next-generation sequencing. Our study provides an integrative report of the preoperative ultrasonographic, histologic, immunohistochemical, and molecular features of NTRK-rearranged PTCs. Based on these findings, we propose an algorithmic approach for the stepwise assessment of NTRK fusions in PTCs.