Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers

Spatially resolved characterization of the transcriptome and proteome promises to provide further clarity on cancer pathogenesis and etiology, which may inform future clinical practice through classifier development for clinical outcomes. However, batch effects may potentially obscure the ability of machine learning methods to derive complex associations within spatial omics data. Profiling thirty-five stage three colon cancer patients using the GeoMX Digital Spatial Profiler, we found that mixed-effects machine learning (MEML) methods† may provide utility for overcoming significant batch effects to communicate key and complex disease associations from spatial information. These results point to further exploration and application of MEML methods within the spatial omics algorithm development life cycle for clinical deployment.

Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing

This chapter details the use of gold nanorods conjugated with peptide nucleic acid probes for sequence-specific detection of circulating tumor DNA (ctDNA). ctDNA is gaining increased attention as a biomarker for liquid biopsy, the process of detecting molecules in the peripheral blood rather than a tissue sample. It has wide ranging applications as a diagnostic and prognostic biomarker with a similar mutational profile as the tumor. Plasmonic nanoparticles offer a relatively rapid, amplification-free method for detection of ctDNA through the use of sequence-specific peptide nucleic acid (PNA) probes. In this chapter, we discuss methods for probe design, conjugation to plasmonic particles, and ctDNA quantitation with the resulting sensor. This chapter is a resource for those looking to use plasmonic gold particles for sensing in a solution format for a range of applications.

Living the best of both worlds: A personal scientific journey

Opportunity is the essence of a career in science or medicine and this continues to be a major source of satisfaction for the many scientists and health care providers worldwide. Having trained as a PhD scientist, the world of clinical medicine seemed to be a galaxy away. I could not have been more wrong in that assumption. Here, I tell the story of my career trajectory so that those new to the sciences understand the potential and the opportunities afforded by a career in clinical laboratory medicine.

CRISPR-cas13 enzymology rapidly detects SARS-CoV-2 fragments in a clinical setting

Background

The well-recognized genome editing ability of the CRISPR-Cas system has triggered significant advances in CRISPR diagnostics. This has prompted an interest in developing new biosensing applications for nucleic acid detection. Recently, such applications have been engineered for detection of SARS-CoV-2. Increased demand for testing and consumables of RT-PCR assays has led to the use of alternate testing options. Here we evaluate the accuracy and performance of a novel fluorescence-based assay that received EUA authorization for detecting SARS-CoV-2 in clinical samples.

Methods

The Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) technology forms the basis of the Sherlock CRISPR SARS-CoV-2 kit using the CRISPR-Cas13a system. Our experimental strategy included selection of COVID-19 patient samples from previously validated RT-PCR assays. Positive samples were selected based on a broad range of cycle thresholds.

Results

A total of 60 COVID-19 patient samples were correctly diagnosed with 100% detection accuracy (relative fluorescence ratios: N gene 95% CI 29.9–43.8, ORF1ab gene 95% CI 30.1–46.3). All controls, including RNase P, showed expected findings. Overall ratios were robustly distinct between positive and negative cases relative to the pre-established 5-fold change in fluorescence.

Conclusions

We have evaluated the accuracy of detecting conserved targets of SARS-CoV-2 across a range of viral loads, including low titers, using SHERLOCK CRISPR collateral detection in a clinical setting. These findings demonstrate encouraging results, at a time when COVID-19 clinical diagnosis and screening protocols remain in demand; especially as new variants emerge and vaccine mandates evolve. This approach highlights new thinking in infectious disease identification and can be expanded to measure nucleic acids in other clinical isolates.

High-Throughput CRISPR-Cas13 SARS-CoV-2 Test

BACKGROUND

The ability to control the spread of COVID-19 continues to be hampered by a lack of rapid, scalable, and easily deployable diagnostic solutions.

METHODS

: We developed a diagnostic method based on CRISPR that can deliver sensitive, specific, and high-throughput detection of Sudden Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The assay utilizes SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the qualitative detection of SARS-CoV-2 RNA and may be performed directly on a swab or saliva sample without nucleic acid extraction. The assay uses a 384-well format and provides results in less than one hour.

RESULTS

Assay performance was evaluated with 105 (55 negative, 50 positive) remnant SARS-CoV-2 specimens previously identified as positive using Food and Drug Administration emergency use authorized assays and re-tested with a modified version of the Centers for Disease Control and Prevention (CDC) RT-qPCR assay. When combined with magnetic bead-based extraction, the high throughput SHERLOCK SARS-CoV-2 assay was 100% concordant (n = 60) with the CDC RT-qPCR. When used with direct sample addition the high throughput assay was also 100% concordant with the CDC RT-qPCR direct method (n = 45). With direct saliva sample addition, the negative and positive percent agreements were 100% (15/15, 95% CI : 81.8-100%) and 88% (15/17, 95% CI : 63.6-98.5%), respectively, compared with results from a collaborating clinical laboratory.

CONCLUSIONS

This high throughput assay identifies SARS-CoV-2 from patient samples with or without nucleic acid extraction with high concordance to RT-qPCR methods. This test enables high complexity laboratories to rapidly increase their testing capacities with simple equipment.

Sustainability and clinical outcomes of routine screening for pathogenic DPYD gene variants prior to fluoropyrimidine (FP) chemotherapy for gastrointestinal (GI) cancer

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Background: Dihyropyrimidine dehydrogenase (DPD) deficiency is present in 3-5% of patients, and is associated with substantially increased risk of severe and/or fatal toxicity during standard-dose FP chemotherapy. Genotyping of pathogenic DPYD variants is a readily available screening test for DPD deficiency, and prospective studies show that dose-reduced FP chemotherapy can be used safely in heterozygous DPYD variant carriers. Methods: Following a sentinel toxicity event the GI medical oncology group at the Norris Cotton Cancer Center adopted a shared practice of routine screening for pathogenic DPYD gene variants prior to FP chemotherapy (5-FU or capecitabine). Screening procedures involved physicians, NP/PAs, nurses, pharmacists, and schedulers. Testing was completed at a send-out lab until late 2020, when an in-house test became available. The current test panel evaluates for 3 gene variants: c.1905+1G > A (*2A), c.1679T > G (*13), and c.2846A > T. We report on the sustainability and clinical outcomes of DPYD gene variant screening. We identified all patients starting new FP-containing intravenous chemotherapy regimens (e.g., FOLFOX, CAPOX) for treatment of GI cancer at two sites (LEB & STJ) between Jan. 2019 and May 2021. We used electronic medical records to evaluate for completion of DPYD genotyping, and we describe the prevalence and management of DPYD gene variant carriers. Results: We identified 333 patients starting FP-containing chemotherapy regimens during the study period, including 287 patients without prior history of FP chemotherapy. Screening with DPYD genotyping was completed in 228 of 287 eligible patients (79%). Screening rates increased from 34% in Q1 of 2019 to 90% in Jan-May 2021. Five GI oncology sub-specialists accounted for 89% of screen-eligible patients and 96% of completed tests, but 10 unique physicians ordered ≥1 test. Of 228 screened patients, six (2.6%) were heterozygous carriers of pathogenic DPYD gene variants (*2A [2 patients], *13 [1], and c.2846A > T [3]). Variant carriers started FP chemotherapy with a 33-50% reduction. Two of six patients required further dose reduction due to FP-related toxicity (grade 4 neutropenia, grade 3 diarrhea). All evaluable variant carriers completed planned initial treatment. Implementation challenges included variable insurance coverage of DPYD genotyping, site-specific test ordering and reporting processes, and inconsistent turn-around time for send-out testing (resolved with on-site testing). Conclusions: Routine screening for pathogenic DPYD gene variants prior to FP chemotherapy is feasible and sustainable in the U.S. DPYD genotyping coupled with chemotherapy dose reductions for DPYD variant carriers facilitates safe and timely completion of planned chemotherapy treatments.

Mammary-type Myofibroblastoma with Leiomyomatous Differentiation: A Rare Variant with Potential Pitfalls

Myofibroblastoma is a rare, benign stromal tumor with a diverse morphologic spectrum. Mammary-type myofibroblastoma (MTMF) is the extra-mammary counterpart of this neoplasm and its occurrence throughout the body has become increasingly recognized. Similar morphologic variations of MTMF have now been described which mirror those seen in the breast. We describe a case of intra-abdominal MTMF composed of short fascicles of eosinophilic spindle cells admixed with mature adipose tissue. The spindle cells stained diffusely positive for CD34, desmin, smooth muscle actin, and h-caldesmon by immunohistochemistry. Concurrent loss of RB1 (13q14) and 13q34 loci were confirmed by fluorescence in situ hybridization whereas anchored multiplex PCR and whole transcriptome sequencing did not reveal any pathognomonic fusions suggesting an alternative diagnosis. To the best of our knowledge this is the first documented case of leiomyomatous variant of MTMF.

Clinical Validation of a 106-SNV MALDI-ToF MS Pharmacogenomic Panel

BACKGROUND

Laboratorians have the opportunity to help minimize the frequency of adverse drug reactions by implementing pharmacogenomic testing and alerting care providers to possible patient/drug incompatibilities before drug treatment is initiated. Methods combining PCR with MALDI-ToF MS have allowed for sensitive, economical, and multiplexed pharmacogenomic testing results to be delivered in a timely fashion.

METHOD

This study evaluated the analytical performance of the Agena Biosciences iPLEX® PGx 74 panel and a custom iPLEX panel on a MassARRAY MALDI-TOF MS instrument in a clinical laboratory setting. Collectively, these panels evaluate 112 SNVs across 34 genes implicated in drug response. Using commercially available samples (Coriell Biorepository) and in-house extracted DNA, we determined ideal reaction conditions and assessed accuracy, precision, and robustness.

RESULTS

Following protocol optimization, the Agena PGx74 and custom panels demonstrated 100% concordance with the 1000 Genomes Project Database and clinically validated hydrolysis probe genotyping assays. 100% concordance was also observed in all assessments of assay precision when appropriate QC metrics were applied.

CONCLUSIONS

Significant development time was required to optimize sample preparation and instrumental analysis and 3 assays were removed due to inconsistent performance. Following modification of the manufacturer's protocol and instituting manual review of each assay plate, the Agena PGx74 and custom panel constitute a cost-effective, robust, and accurate method for clinical identification of 106 SNVs involved in drug response.

Abstract 631: Germline cancer predisposition results from the National Cancer Institute - Children's Oncology Group (NCI-COG) Pediatric MATCH Trial

Background: Although genomic changes identified by clinical tumor sequencing may be present in the germline, precision oncology trials have generally not incorporated germline testing and reporting. We describe our experience with clinical reporting of matched tumor and germline results from the NCI-COG Pediatric Molecular Analysis for Therapy Choice (MATCH) trial (NCT03155620).

Design/Method: Patients age 1 to 21 years old with treatment-refractory solid tumors, non-Hodgkin lymphomas, or histiocytic disorders were eligible. DNA and RNA extracted from FFPE tumors were sequenced using Oncomine Assay v.3 with reporting of potentially actionable fusions, amplifications, and mutations, including loss of function variants in tumor suppressor genes. Germline reporting focused on 36 genes from the same DNA panel that convey adult or pediatric cancer susceptibility but does not include all cancer susceptibility genes (e.g. APC, DICER1). Deletions and splice site variants were not reported.

Results: As of June 2020, 1009 patients had been enrolled from 132 COG sites, with tumor and germline testing complete for 868 patients to date. Overall, 62 (7.1%) germline reports included a pathogenic or likely pathogenic germline variant (termed germline findings) in 18 cancer susceptibility genes. This frequency was similar in patients with solid tumors (46/633, 7.3%), CNS tumors (14/204, 6.9%), and lymphomas/histiocytoses (2/31, 6.5%). Variant(s) of potential germline significance were identified in 25% of tumor reports; of these, 74% (163/221) had no germline findings. The proportion of germline findings for genes with >10 reported tumor variants varied: 32% (7/22) in NF1, 25% (3/12) in RB1, 16% (17/108) in TP53 and 0% in ALK (0/21) and PTEN (0/12). Of note, 82% (14/17) of tumor variants in breast cancer susceptibility genes (BRCA1/2, CHEK2 and PALB2) had germline findings. On study intake forms, 25% of patients with germline findings had a “known genetic disease” reported. Oncologists caring for patients with a germline finding were then queried about prior knowledge of a genetic diagnosis. Of 24 respondents, 13 (54%) reported no prior molecular diagnosis of the identified condition.

Conclusions: Coordinated germline and tumor testing revealed clinically relevant cancer susceptibility variants across a spectrum of genes in 7% of pediatric patients with treatment-refractory cancers. This is likely an underestimate of germline findings given test limitations. The parallel tumor/normal reporting approach minimized the need for targeted reflex genetic testing in 19% of study participants and provided new information on cancer susceptibility in germline positive patients to half of the responding oncologists. The NCI-COG Pediatric MATCH trial reporting process can serve as a model for precision oncology trials and clinical tumor profiling.

Citation Format: Sarah Scollon, Sharon E. Plon, Steven Joffe, Jaclyn A. Biegel, Shashikant Kulkarni, George Miles, David Patton, Brent Coffey, Paul M. Williams, Gregory J. Tsongalis, Mark J. Routbort, Julie M. Gastier-Foster, Lauren Saguilig, Jin Piao, Todd A. Alonzo, Katherine A. Janeway, Peter C. Adamson, Margaret Mooney, James V. Tricoli, Nita L. Seibel, Donald W. Parsons. Germline cancer predisposition results from the National Cancer Institute - Children's Oncology Group (NCI-COG) Pediatric MATCH Trial [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 631.

Factors impacting enrollment on NCI-COG Pediatric MATCH trial treatment protocols

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Background: The NCI-Children’s Oncology Group (COG) Pediatric Molecular Analysis for Therapy Choice (MATCH) trial assigns patients age 1 to 21 years with relapsed or refractory solid tumors, lymphomas, and histiocytic disorders to phase 2 treatment arms of molecularly-targeted therapies based on the genetic alterations detected in their tumor. Treatment arm assignments and enrollment decisions have now been made for 1000 study participants: we report here match and enrollment data and factors affecting treatment protocol enrollment. Methods: Patients enrolled in the Pediatric MATCH screening protocol were assigned to an open treatment protocol if an actionable mutation (aMOI) was detected by tumor DNA and RNA-based cancer gene panel sequencing. After a match, treatment protocol enrollment must occur within 8-12 weeks. Patient demographic data, reasons for not enrolling on treatment protocol (if applicable), and prior history of molecular testing were reported by study sites. The Fisher exact test was used to compare protocol enrollment rates between groups. Results: Results were analyzed for the first 1000 patients with testing completed (enrolled between July 2017 and October 2020). At least one tumor aMOI was detected in 310 (31%) patients and treatment protocol slots were available for 284 patients (28%). A total of 131 patients (46% of those matched) enrolled on a treatment arm. No difference in treatment protocol match or enrollment rate was observed for gender, race, or ethnicity. Both treatment protocol match rate (105/275, 38% vs 86/394, 22%) and enrollment rate (56/275, 20% vs 33/394, 8%) were significantly more frequent in patients with a reported history of prior molecular testing (p<0.0001). The most common reasons provided for not enrolling on a treatment protocol were: patient receiving other treatment (32% of responses), poor clinical status (16%), lack of measurable disease (11%), or ineligible diagnosis for that treatment arm (10%). Ineligibility due to history of excluded prior targeted therapy (6%) or inability to swallow capsules (4%) was less frequent. Conclusions: The rate of Pediatric MATCH treatment protocol enrollment has exceeded pre-study projections, due to more frequent actionable mutation detection and treatment assignment than anticipated (28% observed, 10% projected). This may in part reflect an increased number of targetable events in recurrent or refractory pediatric cancers. Correlative studies analyzing pre-treatment tumors from MATCH study patients are underway and will address this hypothesis. Prior history of molecular testing was associated with higher match and enrollment rate and poor clinical status was a common reason for not enrolling on a treatment protocol, suggesting that early molecular screening of children with solid malignancies may facilitate enrollment to biomarker-selected trials of targeted therapies. Clinical trial information: NCT03155620.

Biomarker testing in non-small cell lung cancer (NSCLC): An assessment of current practices in precision oncology in the community setting—A trial of the ECOG-ACRIN cancer research group (EAQ161CD)

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Background: Molecular biomarker testing is integral to NSCLC cancer care, but adoption and testing practices in the community are varied and often suboptimal. Testing practices, such as standard testing protocols and results turnaround time (TAT), impact timely treatment decisions. We examined adoption and testing practices for guideline recommended NSCLC biomarkers among National Cancer Institute Community Research Program (NCORP) sites. The study was conducted in collaboration with Wake Forest NCORP Research Base. Methods: An online survey was administered to onsite labs affiliated with NCORP sites April 2019 – June 2020. We assessed testing practices for 7 NCCN recommended biomarkers, including 3 with category 1 recommendation (EGFR, ALK, PD-L1) and 4 with category 2 recommendations (BRAF, ROS1, MET, RET). Guideline concordant result TAT was defined as return of EGFR and ALK results in ≤ 10 days (Lindeman 2018) (see Table for other outcomes). We used proportions, including two-sided Fischer exact tests, to compare outcomes by site characteristics (safety net, practice size). Results: The survey response rate was 69% (58/85). All responding labs offered testing for category 1 biomarkers (EGFR, ALK and PD-L1); only 10% conducted these tests in-house (Table). The majority of labs also tested for category 2 biomarkers (67%). TAT varied, with most labs returning results in ≤ 10 days for EGFR and ALK (69%, but only a minority meet this TAT for all biomarkers. Larger practice size (> 1400 new cancer cases a year) was associated with in-house testing of EGFR, ALK, PD-L1 (p=0.03) and having standard testing protocols (p<0.001). Safety net affiliation did not significantly impact practices. Conclusions: We found universal adoption of NCCN category 1 biomarkers among the labs affiliated with NCORP sites, with the majority meeting guideline concordant results TAT. There is opportunity for improvement in adoption of category 2 biomarkers and result TAT, for example, by using standard testing protocols. Reassuringly, no difference in testing practices was detected by safety net affiliation.[Table: see text]

Reducing dermal exposure to agrochemical carcinogens using a fluorescent dye-based intervention among subsistence farmers in rural Honduras

BACKGROUND

Occupational exposure to agrochemicals, some of which are known or suspected carcinogens, is a major health hazard for subsistence agricultural workers and their families. These impacts are more prevalent in low-and-middle income countries (LMIC) due to weak regulations, lack of awareness of the risks of contamination, predominant use of handheld backpack style spraying equipment, general lack of personal protective equipment (PPE), and low literacy about proper agrochemical application techniques. Reducing exposure to agrochemicals was identified as a paramount concern by rural Hondurans working with a community-engaged research initiative. Fluorescent tracer dyes have been described as a means of visualizing and quantifying dermal exposure to agricultural chemicals, and exposure models adapted for LMIC have been developed previously. Tracer dyes have also been used in educational simulations to promote pesticide safety. However, studies evaluating the effectiveness of these educational dye interventions in reducing future exposure have been lacking.

AIM

To evaluate whether observing one's own chemical contamination after applying agrochemicals changed the amount of occupational dermal exposure during a subsequent chemical application.

METHODS

We employed a multi-modal community intervention in a rural village in Honduras that incorporated chemical safety education and use of a fluorescent tracer dye during pesticide application on two consecutive occasions, and compared dermal exposure between the intervention group (previous dye experience and safety education, n = 6) and the control group (safety education only, n = 7).

RESULTS

Mean total visual score (TVS) of the tracer dye, which accounts for both extent and intensity of whole-body contamination, was lower among those who had previously experienced the dye intervention (mean TVS = 41.3) than among participants who were dye-naïve (mean TVS = 78.4), with a difference between means of -37.10 (95% CI [-66.26, -7.95], p = 0.02). Stratifying by body part, contamination was significantly lower for the anterior left lower extremity and bilateral feet for the dye-experienced group vs. dye-naïve, with most other segments showing a trend toward decreased contamination as well.

CONCLUSION

Participants who had previously experienced the dye intervention were significantly less contaminated than the dye-naïve control group during a subsequent spraying event. The findings of this small pilot study suggest that a multi-modal, community-based approach that utilizes fluorescence-augmented contamination for individualized learning (FACIL) may be effective in reducing dermal exposure to carcinogenic agrochemicals among subsistence farmers in Honduras and other LMIC.

Evaluation of a Next-Generation Sequencing Metagenomics Assay to Detect and Quantify DNA Viruses in Plasma from Transplant Recipients

Viral infections are major causes of morbidity and mortality in solid-organ and hematopoietic stem cell transplant recipients. This study evaluated the performance of the Galileo Pathogen Solution metagenomics Next-Generation sequencing assay to detect and quantify 11 DNA viruses (cytomegalovirus, Epstein-Barr virus, BK virus, human adenovirus, JC virus, herpes simplex virus 1 and 2, varicella zoster virus, human herpesvirus 6A and 6B, and parvovirus B19) and to qualitatively detect torque teno virus. DNA extracted from 47 plasma samples of viremic transplant recipients were subjected to DNA library preparation with pathogen enrichment/human background depletion, sequencing, and automated data analysis. The viral loads were determined with the Galileo assay using a standard curve generated from a calibration panel. All of the samples tested had a 100% agreement with the real-time quantitative PCR (qPCR) assays in detecting the primary virus targets and the majority of the quantified samples had a viral load difference within 0.46 log₁₀ IU/mL or copies/mL. The mean difference for cytomegalovirus between the Galileo and qPCR assays was 0.21 log₁₀ IU/mL (SD, ±0.43 log₁₀ IU/mL). The mean difference for BK virus between the Galileo and qPCR assays was 0.17 log₁₀ cp/mL (SD, ±0.67 log₁₀ cp/mL). Additionally, 75 co-infections were detected in 31 samples by the Galileo assay. The study findings show that the Galileo assay can simultaneously detect and quantify multiple viruses in transplant recipients with results that are comparable with standard-of-care qPCR assays.

Comparison of Tissue Molecular Biomarker Testing Turnaround Times and Concordance Between Standard of Care and the Biocartis Idylla Platform in Patients With Colorectal Cancer

OBJECTIVES

Management of colorectal cancer warrants mutational analysis of KRAS/NRAS when considering anti-epidermal growth factor receptor therapy and BRAF testing for prognostic stratification. In this multicenter study, we compared a fully integrated, cartridge-based system to standard-of-care assays used by participating laboratories.

METHODS

Twenty laboratories enrolled 874 colorectal cancer cases between November 2017 and December 2018. Testing was performed on the Idylla automated system (Biocartis) using the KRAS and NRAS-BRAF cartridges (research use only) and results compared with in-house standard-of-care testing methods.

RESULTS

There were sufficient data on 780 cases to measure turnaround time compared with standard assays. In-house polymerase chain reaction (PCR) had an average testing turnaround time of 5.6 days, send-out PCR of 22.5 days, in-house Sanger sequencing of 14.7 days, send-out Sanger of 17.8 days, in-house next-generation sequencing (NGS) of 12.5 days, and send-out NGS of 20.0 days. Standard testing had an average turnaround time of 11 days. Idylla average time to results was 4.9 days with a range of 0.4 to 13.5 days.

CONCLUSIONS

The described cartridge-based system offers rapid and reliable testing of clinically actionable mutation in colorectal cancer specimens directly from formalin-fixed, paraffin-embedded tissue sections. Its simplicity and ease of use compared with other molecular techniques make it suitable for routine clinical laboratory testing.

Molecular genetic profiling reveals novel association between FLT3 mutation and survival in glioma

INTRODUCTION

Recent molecular characterization of gliomas has uncovered somatic gene variation and DNA methylation changes that are associated with etiology, prognosis, and therapeutic response. Here we describe genomic profiling of gliomas assessed for associations between genetic mutations and patient outcomes, including overall survival (OS) and recurrence-free survival (RFS).

METHODS

Mutations in a 50-gene cancer panel, 1p19q co-deletion, and MGMT promoter methylation (MGMT methylation) status were obtained from tumor tissue of 293 glioma patients. Multivariable regression models for overall survival (OS) and recurrence-free survival (RFS) were constructed for MGMT methylation, 1p19q co-deletion, and gene mutations controlling for age, treatment status, and WHO grade.

RESULTS

Mutational profiles of gliomas significantly differed based on WHO Grade, such as high prevalence of BRAF V600E, IDH1, and PTEN mutations in WHO Grade I, II/III, and IV tumors, respectively. In multivariate regression analysis, MGMT methylation and IDH1 mutations were significantly associated with improved OS (HR = 0.44, p = 0.0004 and HR = 0.21, p = 0.007, respectively), while FLT3 and TP53 mutations were significantly associated with poorer OS (HR = 19.46, p < 0.0001 and HR = 1.67, p = 0.014, respectively). MGMT methylation and IDH1 mutations were the only significant alterations associated with improved RFS in the model (HR = 0.42, p < 0.0001 and HR = 0.37, p = 0.002, respectively). These factors were then included in a combined model, which significantly exceeded the predictive value of the base model alone (age, surgery, radiation, chemo, grade) (likelihood ratio test OS p = 1.64 × 10^-8 and RFS p = 3.80 × 10^-7).

CONCLUSIONS

This study highlights the genomic landscape of gliomas in a single-institution cohort and identifies a novel association between FLT3 mutation and OS in gliomas.

Abstract C116: High-risk HPV screening and typing shows high co-infection rate and potential for low vaccine coverage in a low- and middle-income country

Introduction. Cervical cancer is almost always a result of infection with a high risk human papillomavirus (hrHPV) of which there are 14 different types. This type of cancer is prevalent in low- and middle-income countries (LMICs) where screening programs for pre- or invasive cervical cancer by Pap test or visual inspection with ascetic acid are limited in scope as is local expertise in evaluating Pap smears. Since 2006, a HPV vaccine protecting against hrHPV types 16 and 18 has been recommended by the WHO, and through the GAVI Alliance, is provided to some fractions of populations in more than 70 countries. A newer and more expensive vaccine protects again 9 types of HPV A broader spectrum 9-valent vaccine released in 2014 protects against HPV types 6, 11, 16, 18, 31, 33, 45, 52, and 58. Preventing cervical cancer by vaccination against HPV is considered to be a promising strategy. Materials and Methods. In three separate studies, we implemented molecular screening for hrHPV from cervical swab specimens, providing access to pre-cancer testing for women from several regions of Honduras, which is ranked the poorest country in the northern hemisphere. We screened 2,645 women from two rural regions and an urban region of Honduras. In the final study of 1725 Honduran factory workers, we substituted a large-capacity rice cooker for a standard laboratory hotplate to accelerate laboratory throughput for DNA extraction. A DNA-based multi-color melt curve analysis by PCR followed, and we were able to rapidly screen for all 14 hrHPV types. Results. Across all three studies, there was an average hrHPV positivity prevalence of 22%. The most common types of hrHPV found in each study were as follows: Study 1 hrHPV types 16, 31, 58, 59, and 68; Study 2 hrHPV types 16, 39, 52, 58, and 68; and Study 3 were hrHPV types 16, 35, 58, 63, and 64 were the most common. Among those infected with a hrHPV type, 18% had co-infections with multiple hrHPV types. Based on these results, the vast majority of infected women would not have been protected by the divalent HPV vaccine and a significant proportion of women would still not be protected by the multivalent vaccine, which does not cover the hrHPV types 35, 39, 52, 59, 63, 64, 88 found in these samples. Conclusions. Cervical cancer remains a prevalent and deadly disease in LMICs. Our studies examining the prevalence of hrHPV types in several different regions of Honduras identified high prevalence rates of viral types not targeted by commercially available vaccines. These findings suggest that vaccination programs alone should not be considered complete coverage against cervical cancer-causing high-risk HPV, and that further location-specific testing of cervical tissue for hrHPV typing is warranted.

Citation Format: Aaron E Atkinson, Carlos Alberto Matute Mandujano, Suyapa Bejarano, Linda S Kennedy, Gregory J Tsongalis. High-risk HPV screening and typing shows high co-infection rate and potential for low vaccine coverage in a low- and middle-income country [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr C116.

Implementation of an Emergency Use Authorization Test During an Impending National Crisis

The laboratory response to the current severe acute respiratory syndrome coronavirus 2 pandemic may be termed heroic. From the identification of the novel coronavirus to implementation of routine laboratory testing around the world to the development of potential vaccines, laboratories have played a critical role in the efforts to curtail this pandemic. In this brief report, we review our own effort at a midsized, rural, academic medical center to implement a molecular test for the virus; and we share insights and lessons learned from that process, which might be helpful in similar situations in the future.

A case of molecularly confirmed BAP1 inactivated melanocytic tumor with retention of immunohistochemical expression: A confounding factor

BRCA1-associated Protein 1 (BAP1)-inactivated melanocytic nevi/tumors (BIMT) have distinct morphologic features. A typical case exhibits a biphasic population of cytologically bland conventional melanocytes and a second proliferation of larger epithelioid melanocytes with abundant eosinophilic cytoplasm. The vast majority of cases harbor BRAF V600E in both components with bi-allelic inactivation of BAP1 in the epithelioid component by various molecular mechanisms resulting in loss of nuclear protein expression, which can be demonstrated by immunohistochemistry. We present a case of BIMT with histopathologic features highly suggestive of this entity but unexpected retention of nuclear expression of the BAP1 protein. Subsequent molecular tests showed heterozygous loss of the BAP1 locus on the short arm of chromosome 3 (3p21.1) by chromosomal microarray analysis (CMA) and a suspected c.505C>T p.H169Y pathogenic variant identified by DNA sequencing that was subsequently confirmed by primer-specific SNaPshot mini-sequencing. In light of the heterozygous deletion of BAP1, this variant in the remaining allele encodes a catalytically inactive BAP1 mutant protein as shown in functional studies. The presence of a nonfunctional allele within the nucleus combined with a heterozygous deletion of BAP1 explains the clear and characteristic BIMT morphology observed by histopathology. This case underlines the potential importance of molecular diagnostics when protein expression studies do not correlate with morphology.

Feasibility of Brigade-Style, Multiphasic Cancer Screening in Rural Honduras

PURPOSE

To evaluate the feasibility of brigade-style, multiphasic cancer screening in Honduras, exploring data from 3 screening events that each tested for multiple cancers on single occasions.

METHODS

This series of 3 studies each used a single-arm, post-test-only design to explore the feasibility of implementing multiphasic, community-based cancer screening at the same rural location in 2013, 2016, and 2017. The 2013 event for women screened for 2 cancers (breast and cervix), and the 2016 event for women screened for 3 cancers (breast, cervix, and thyroid). The 2017 event for men screened for 5 cancers (skin, prostate, colorectal, oropharynx, and testes).

RESULTS

Totals of 473 and 401 women participated in the 2013 and 2016 events, respectively, and 301 men participated in the 2017 event. Staffing for each event varied from 33 to 44 people and relied primarily on in-country medical students and local community members. High rates (mean, 88%) of compliance with referral for follow-up testing at clinics and primary care facilities were observed after the screening events.

CONCLUSION

The multiphasic, community-based approach proved feasible for both women and men and resulted in high rates of compliance with follow-up testing. This approach appears highly replicable: it was conducted multiple times across the years with different screening targets, which could be further scaled elsewhere using the same technique.

Rapid EGFR mutation testing in lung cancer tissue samples using a fully automated system and single-use cartridge

Introduction

Activating mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene in non-small cell lung cancer (NSCLC) patients predicts response to EGFR tyrosine kinase inhibitors (TKIs). The Idylla™ system (Biocartis, Mechelen, Belgium) is a fully integrated, cartridge-based platform that provides automated sample processing and real-time PCR-based mutation detection in a single-use cartridge. This study evaluated the Idylla™ EGFR Mutation Assay cartridges against next-generation sequencing (NGS) using formalin fixed, paraffin embedded (FFPE) lung cancer tissue samples.

Methods

Thirty-four FFPE lung adenocarcinoma tissue samples were tested on the Idylla™ system. 21 had at least one mutation in EGFR and 13 had no EGFR mutation as determined by NGS analysis using the Ion AmpliSeq 50-gene Cancer Hotspot Panel v2 (Thermo Fisher Scientific). One 10 ​μm FFPE tissue section was used for each Idylla™ test and all cases met the Idylla™ minimum tumor content requirement (≥10%).

Results

Idylla™ results were in complete agreement with those obtained by NGS for EGFR mutations targeted by the Idylla™. NGS identified two additional EGFR mutations that are not targeted by the Idylla™ in two samples (E709V and V774M). No EGFR mutations were detected by the Idylla™ in samples determined by NGS as having wild-type EGFR.

Conclusion

The fully automated Idylla™ system offers rapid and reliable testing for clinically actionable mutations in EGFR directly from FFPE tissue sections. Its simplicity and ease of use compared to other available molecular techniques make it suitable for routine clinical use in a variety of settings.

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.