Implementing Next-Generation Sequencing Process Changes to Increase Capacity and Improve Timeliness of Molecular Biomarker Profiling for Lung Cancer Patients.

BACKGROUND: Faced with expansion of molecular tumor biomarker profiling, the molecular genetics laboratory at Kingston Health Science Centre experienced significant pressures to maintain the provincially mandated 2-week turnaround time (TAT) for lung cancer (LC) patients. We used quality improvement methodology to identify opportunities for improved efficiencies and report the impact of the initiative. METHODS: We set a target of reducing average TAT from accessioning to clinical molecular lab report for LC patients. Process measures included percentage of cases reaching TAT within target and number of cases. We developed a value stream map and used lean methodology to identify baseline inefficiencies. Plan-Do-Study-Act cycles were implemented to streamline, standardize, and automate laboratory workflows. Statistical process control (SPC) charts assessed for significance by special cause variation. RESULTS: A total of 257 LC cases were included (39 baseline January-May 2021; 218 post-expansion of testing June 2021). The average time for baseline TAT was 12.8 days, peaking at 23.4 days after expansion of testing, and improved to 13.9 days following improvement interventions, demonstrating statistical significance by special cause variation (nonrandom variation) on SPC charts. CONCLUSIONS: The implementation of standardized manual and automated laboratory processes improved timeliness of biomarker reporting despite the increasing volume of testing at our center.

Mold in Foam Pillows and Mattresses: A Novel Cause of Hypersensitivity Pneumonitis.

Hypersensitivity pneumonitis (HP) is an inflammatory and/or fibrotic disease affecting the lung parenchyma and small airways. It typically results from an immune-mediated reaction provoked by an overt or occult inhaled antigen in susceptible individuals. The chronic or fibrotic form of HP has a poor prognosis, especially when no inciting antigen is identified, which occurs in up to 60% of cases. We report two cases of HP associated with exposure to mold in foam pillows and a mattress, which has not previously been reported as a risk factor for HP. Given the high prevalence of foam in pillows and mattresses, mold in foam in bedding may explain many HP cases with a previously unrecognized cause. Early identification and avoidance of foam in bedding may prevent HP progression to end-stage pulmonary fibrosis and death.

Canadian Multicenter Project on Standardization of Programmed Death-Ligand 1 Immunohistochemistry 22C3 Laboratory-Developed Tests for Pembrolizumab Therapy in NSCLC.

INTRODUCTION: The programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) assay is used to select patients for first or second-line pembrolizumab monotherapy in NSCLC. The PD-L1 IHC 22C3 pharmDx assay requires an Autostainer Link 48 instrument. Laboratories without this stainer have the option to develop a highly accurate 22C3 IHC laboratory-developed test (LDT) on other instruments. The Canadian 22C3 IHC LDT validation project was initiated to harmonize the quality of PD-L1 22C3 IHC LDT protocols across 20 Canadian pathology laboratories. METHODS: Centrally optimized 22C3 LDT protocols were distributed to participating laboratories. The LDT results were assessed against results using reference PD-L1 IHC 22C3 pharmDx. Analytical sensitivity and specificity were assessed using cell lines with varying PD-L1 expression levels (phase 1) and IHC critical assay performance controls (phase 2B). Diagnostic sensitivity and specificity were assessed using whole sections of 50 NSCLC cases (phase 2A) and tissue microarrays with an additional 50 NSCLC cases (phase 2C). RESULTS: In phase 1, 80% of participants reached acceptance criteria for analytical performance in the first attempt with disseminated protocols. However, in phase 2A, only 40% of participants reached the desired diagnostic accuracy for both 1% and 50% tumor proportion score cutoff. In phase 2B, further protocol modifications were conducted, which increased the number of successful laboratories to 75% in phase 2C. CONCLUSIONS: It is possible to harmonize highly accurate 22C3 LDTs for both 1% and 50% tumor proportion score in NSCLC across many laboratories with different platforms. However, despite a centralized approach, diagnostic validation of predictive IHC LDTs can be challenging and not always successful.

Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study.

BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. METHODS: We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. RESULTS: Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies. CONCLUSION: This methodology enables simultaneous detection of multiple ALK, ROS1, RET, and NTRK1 gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods.

Correction to: Use of multicolor fluorescence in situ hybridization to detect deletions in clinical tissue sections.

Figure 2 is incorrect in the original version of this article. The correct figure 2 is provided below.

Use of multicolor fluorescence in situ hybridization to detect deletions in clinical tissue sections.

A variety of laboratory methods are available for the detection of deletions of tumor suppressor genes and losses of their proteins. The clinical utility of fluorescence in situ hybridization (FISH) for the identification of deletions of tumor suppressor genes has previously been limited by difficulties in the interpretation of FISH signal patterns. The first deletion FISH assays using formalin-fixed paraffin-embedded tissue sections had to deal with a significant background level of signal losses affecting nuclei that are truncated by the cutting process of slide preparation. Recently, more efficient probe designs, incorporating probes adjacent to the tumor suppressor gene of interest, have increased the accuracy of FISH deletion assays so that true chromosomal deletions can be readily distinguished from the false signal losses caused by sectioning artifacts. This mini-review discusses the importance of recurrent tumor suppressor gene deletions in human cancer and reviews the common FISH methods being used to detect the genomic losses encountered in clinical specimens. The use of new probe designs to recognize truncation artifacts is illustrated with a four-color PTEN FISH set optimized for prostate cancer tissue sections. Data are presented to show that when section thickness is reduced, the frequency of signal truncation losses is increased. We also provide some general guidelines that will help pathologists and cytogeneticists run routine deletion FISH assays and recognize sectioning artifacts. Finally, we summarize how recently developed sequence-based approaches are being used to identify recurrent deletions using small DNA samples from tumors.

Diagnostic Yield for Cancer and Diagnostic Accuracy of Computed Tomography-guided Core Needle Biopsy of Subsolid Pulmonary Lesions.

PURPOSE: We aimed to determine the diagnostic yield for cancer and diagnostic accuracy of computed tomography-guided core needle biopsy (CTNB) in subsolid pulmonary lesions. MATERIALS AND METHODS: Fifty-two biopsies of 52 subsolid lesions in 51 patients were identified from a database of 912 lung biopsies and analyzed for the diagnostic yield for cancer and diagnostic accuracy of core CTNB diagnosis as well as complication rates. RESULTS: When indeterminate biopsy results were included in the analysis, the diagnostic yield for cancer was 80.8% and the diagnostic accuracy of core needle biopsy was 84.6% (n=52). It was 85.7% and 91.7%, respectively, when indeterminate results were excluded (n=48) and 82.4% and 82.4%, respectively, for biopsies with surgical confirmation (n=17). Attenuation was statistically significant for diagnostic yield for cancer (P=0.028) and diagnostic accuracy of core needle biopsy (P=0.001) when the indeterminate results were excluded (n=48). Attenuation and size were not statistically significant for diagnostic yield for cancer and diagnostic accuracy of needle biopsy (n=52), and size was not statistically significant for either when the indeterminate results were excluded. These results were achieved without any major complications as per the Society of Interventional Radiology Standards of Practice. CONCLUSIONS: CTNB offers a high yield in establishing a histopathologic diagnosis of subsolid pulmonary lesions, with both ground-glass and solid-predominance. The pure ground-glass category of lesions requires further research to determine the true diagnostic yield and diagnostic accuracy of core needle biopsies.

The histology of human right atrial tissue in patients with high-risk Obstructive Sleep Apnea and underlying cardiovascular disease: A pilot study.

BACKGROUND: Obstructive Sleep Apnea (OSA) results in intermittent hypoxia leading to atrial remodeling, which, among other things, facilitates development of atrial fibrillation. While much data exists on the macrostructural changes in cardiac physiology induced by OSA, there is a lack of studies looking for histologic changes in human atrial tissue induced by OSA which might lead to the observed macrostructural changes. METHODS: A case control study was performed. Patients undergoing coronary artery bypass grafting (CABG) were evaluated for OSA and categorized as high-risk or low-risk. The right atrial tissue samples were obtained during CABG and both microscopic histological analysis and Sirius Red staining were performed. RESULTS: 18 patients undergoing CABG were included; 10 high-risk OSA and 8 low-risk OSA in evenly matched populations. No statistically significant difference between the two groups was observed in amount of myocytolysis (p = 0.181), nuclear hypertrophy (p = 0.671), myocardial inflammation (p = n/a), amyloid deposition (p = n/a), or presence of thrombi (p = n/a), as measured through routine H&E staining. As well, no statistically significant difference in interstitial and epicardial collagen was observed, as measured by Sirius Red staining (for total tissue: p = 0.619: for myocardium: p = 0.776). CONCLUSIONS: In this pilot study there were no observable histological differences in human right atrial tissue from individuals at high- and low-risk for OSA. Further investigation would be required for more definitive results.

Extraction and analysis of discrete synoptic pathology report data using R.

BACKGROUND: Synoptic pathology reports can serve as a rich source of cancer information, particularly when the content is available as discrete electronic data fields. Our institution generates such reports as part of a province wide program in Ontario but the resulting data is not easily extracted and analyzed at the local level. METHODS: A low cost system was developed using the open sourced and freely available R scripting/data analysis environment to parse synoptic report results into a dataframe and perform basic summary statistics. RESULTS: As a pilot project text reports from 427 prostate needle biopsies were successfully read into R and the data elements split out and converted into appropriated data classes for analysis. CONCLUSION: This approach provides a simple solution at minimal cost that can make discrete synoptic report data readily available for quality assurance and research activities.

Isolated anterior urethral recurrence of prostatic adenocarcinoma.

Isolated anterior urethral metastases from prostate cancer are rare. The pathogenesis of this form of loco-regional recurrence may be related to spread by instrumentation-induced implantation and could potentially then be associated with a better prognosis than metastatic disease secondary to a more malignant phenotype. We report a case of a 68-year-old man with high-risk prostate cancer, diagnosed at transurethral resection of prostate, who was originally treated with combination external beam radiotherapy and hormonal therapy. He re-presented 4 years after his original diagnosis with recurrent gross hematuria and cystourethroscopic biopsies of anterior urethral polyps revealing isolated recurrent prostatic adenocarcinoma. We present our this case and review the literature.

Fer protein-tyrosine kinase promotes lung adenocarcinoma cell invasion and tumor metastasis.

UNLABELLED: Epidermal growth factor receptor (EGFR) is frequently amplified or mutated in non-small cell lung cancer (NSCLC). Although Fer protein-tyrosine kinase signals downstream of EGFR, its role in NSCLC tumor progression has not been reported. Here, Fer kinase was elevated in NSCLC tumors compared to normal lung epithelium. EGFR signaling in NSCLC cells fosters rapid Fer activation and increased localization to lamellipodia. Stable silencing of Fer in H1299 lung adenocarcinoma cells (Fer KD) caused impaired EGFR-induced lamellipodia formation compared to control cells. Fer KD NSCLC cells showed reduced Vav2 tyrosine phosphorylation that was correlated with direct Fer-mediated phosphorylation of Vav2 on tyrosine-172, which was previously reported to increase the guanine nucleotide exchange factor activity of Vav2. Indeed, Fer KD cells displayed defects in Rac-GTP localization to lamellipodia, cell migration, and cell invasion in vitro. To test the role of Fer in NSCLC progression and metastasis, control and Fer KD cells were grown as subcutaneous tumors in mice. Although Fer was not required for tumor growth, Fer KD tumor-bearing mice had significantly fewer numbers of spontaneous metastases. Combined, these data demonstrate that Fer kinase is elevated in NSCLC tumors and is important for cellular invasion and metastasis. IMPLICATIONS: Fer protein-tyrosine kinase is a potential therapeutic target in metastatic lung cancer. Mol Cancer Res; 11(8); 952-63. ©2013 AACR.

Flock worker's lung disease: natural history of cases and exposed workers in Kingston, Ontario.

BACKGROUND: The natural history of flock worker's lung (FWL) and longitudinal lung function changes in nylon flock-exposed workers have not been well characterized. METHODS: Symptoms, pulmonary function testing, and chest radiographs from five index cases, subsequent case referrals, and screened employees of a flocking plant in Kingston, Ontario, Canada, were compared and analyzed for changes over time (variable follow-up intervals between 1991 and 2011). RESULTS: Nine cases and 30 flock-exposed workers without FWL were identified. Four cases had persistent interstitial lung disease despite three having left the workplace. Two developed hypoxemic respiratory failure and secondary pulmonary hypertension and died of complications 18 and 20 years after diagnosis, respectively. Five cases resolved after leaving the workplace. Compared with resolved cases, persistent cases had lower diffusing capacity of the lung for carbon monoxide at presentation (P < .05) and follow-up (P < .05). Among exposed workers employed for 14.5 ± 4.7 years, five had abnormal chest radiographs vs none at baseline (P = .001) over 14.8 ± 4.6 years of follow-up. The prevalence of wheeze increased (P = .001), and FEV1/FVC decreased (P < .001). FEV1% predicted was significantly lower at follow-up (P = .05). Average FEV1 decline was 46 mL/year (range, -27 to 151 mL/y). Seventy-seven percent of exposed workers were current or former smokers. CONCLUSIONS: The natural history of FWL includes the following patterns: complete resolution of symptoms; radiographic and pulmonary function abnormalities; permanent, but stable symptoms and restrictive pulmonary function deficits; and progressive decline in pulmonary function, causing death from respiratory failure and secondary pulmonary hypertension. A low baseline diffusing capacity of the lung for carbon monoxide is associated with the persistence and progression of FWL.

Separation of benign and malignant glands in prostatic adenocarcinoma.

This paper presents an analysis of the high resolution histopathology images of the prostate with a focus on the evolution of morphological gland features in prostatic adenocarcinoma. Here we propose a novel technique of labeling individual glands as malignant or benign. In the first step, the gland and nuclei objects of the images are automatically segmented. Individual gland units are segmented out by consolidating their lumina with the surrounding layers of epithelium and nuclei. The nuclei objects are segmented by using a marker controlled watershed algorithm. Two new features, Number of Nuclei Layer (N(NL)) and Ratio of Epithelial layer area to Lumen area (R(EL)) have been extracted from the segmented units. The main advantage of this approach is that it can detect individual malignant gland units, irrespective of neighboring histology and/or the spatial extent of the cancer. The proposed algorithm has been tested on 40 histopathology scenes taken from 10 high resolution whole mount images and achieved a sensitivity of 0.83 and specificity of 0.81 in a leave-75%-out cross-validation.

High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models.

In this paper we present a high-throughput system for detecting regions of carcinoma of the prostate (CaP) in HSs from radical prostatectomies (RPs) using probabilistic pairwise Markov models (PPMMs), a novel type of Markov random field (MRF). At diagnostic resolution a digitized HS can contain 80Kx70K pixels - far too many for current automated Gleason grading algorithms to process. However, grading can be separated into two distinct steps: (1) detecting cancerous regions and (2) then grading these regions. The detection step does not require diagnostic resolution and can be performed much more quickly. Thus, we introduce a CaP detection system capable of analyzing an entire digitized whole-mount HS (2x1.75cm(2)) in under three minutes (on a desktop computer) while achieving a CaP detection sensitivity and specificity of 0.87 and 0.90, respectively. We obtain this high-throughput by tailoring the system to analyze the HSs at low resolution (8microm per pixel). This motivates the following algorithm: (Step 1) glands are segmented, (Step 2) the segmented glands are classified as malignant or benign, and (Step 3) the malignant glands are consolidated into continuous regions. The classification of individual glands leverages two features: gland size and the tendency for proximate glands to share the same class. The latter feature describes a spatial dependency which we model using a Markov prior. Typically, Markov priors are expressed as the product of potential functions. Unfortunately, potential functions are mathematical abstractions, and constructing priors through their selection becomes an ad hoc procedure, resulting in simplistic models such as the Potts. Addressing this problem, we introduce PPMMs which formulate priors in terms of probability density functions, allowing the creation of more sophisticated models. To demonstrate the efficacy of our CaP detection system and assess the advantages of using a PPMM prior instead of the Potts, we alternately incorporate both priors into our algorithm and rigorously evaluate system performance, extracting statistics from over 6000 simulations run across 40 RP specimens. Perhaps the most indicative result is as follows: at a CaP sensitivity of 0.87 the accompanying false positive rates of the system when alternately employing the PPMM and Potts priors are 0.10 and 0.20, respectively.

Composite paraganglioma-ganglioneuroma of the urinary bladder: a rare neoplasm causing hemodynamic crisis at tumour resection.

A 64-year-old man presented with gross painless hematuria. Cystoscopy revealed a submucosal bladder neck mass covered by normal urothelium. During transurethral resection, the patient developed hemodynamic crisis including sinus bradycardia. Histopathologic examination revealed a primary bladder composite paraganglioma-ganglioneuroma (CPG). The patient underwent partial cystectomy and is symptom-free after one year. Bladder CPGs are extremely rare neoplasms that may result in life-threatening catecholamine secretion, especially during tumour manipulation. These tumours require complete surgical excision and should be included in the differential diagnosis of any solitary bladder mass covered by normal urothelium, especially when there is a history of hypertension or micturition attacks.

Synchronous ipsilateral renal cell carcinoma and urothelial carcinoma of the renal pelvis.

Renal cell carcinoma (RCC) and urothelial carcinoma of the upper urinary tract are not uncommon urological malignancies. Their simultaneous occurrence in a patient is, however, extraordinarily rare. We report the case of a patient who underwent laparoscopic nephrectomy for suspected RCC. Preoperative imaging was suspicious for renal pelvic involvement, which was confirmed upon bivalving the fresh specimen at the time of surgery, with the discovery of a separate urothelium-based lesion. We discuss this rare occurrence and our management approach.

Augmenting detection of prostate cancer in transrectal ultrasound images using SVM and RF time series.

We propose a novel and accurate method based on ultrasound RF time series analysis and an extended version of support vector machine classification for generating probabilistic cancer maps that can augment ultrasound images of prostate and enhance the biopsy process. To form the RF time series, we record sequential ultrasound RF echoes backscattered from tissue while the imaging probe and the tissue are stationary in position. We show that RF time series acquired from agar-gelatin-based tissue mimicking phantoms, with difference only in the size of cell-mimicking microscopic glass beads, are distinguishable with statistically reliable accuracies up to 80.5%. This fact indicates that the differences in tissue microstructures affect the ultrasound RF time series features. Based on this phenomenon, in an ex vivo study involving 35 prostate specimens, we show that the features extracted from RF time series are significantly more accurate and sensitive compared to two other established categories of ultrasound-based tissue typing methods. We report an area under receiver operating characteristic curve of 0.95 in tenfold cross validation and 0.82 in leave-one-patient-out cross validation for detection of prostate cancer.

Prostate cancer probability maps based on ultrasound RF time series and SVM classifiers.

We describe a very efficient method based on ultrasound RF time series analysis and support vector machine classification for generating probabilistic prostate cancer colormaps to augment the biopsy process. To form the RF time series, we continuously record ultrasound RF echoes backscattered from tissue while the imaging probe and the tissue are stationary in position. In an in-vitro study involving 30 prostate specimens, we show that the features extracted from RF time series are significantly more accurate and sensitive compared to two other established categories of ultrasound-based tissue typing methods. The method results in an area under ROC curve of 0.95 in 10-fold cross-validation.