Search

Background PD1/PDL1 inhibitors have significantly improved overall survival in non-small cell lung cancer (NSCLC). PDL1 is now a standard biomarker along with molecular testing for therapy selection. Checkpoint therapy is given front-line for patients with high PDL1 and no actionable mutations or fusions, or after progression with any PDL1 expression. Studies comparing PDL1 status in the context of actionable mutations or fusions in NSCLC are sparse. Design All patients undergoing molecular testing for a next-generation sequencing (NGS) lung cancer panel at our institution in a 7-month period were reviewed. This included an NGS DNA panel for actionable/driver genes: EGFR, ERBB2, BRAF, K/NRAS, PIK3CA, and IDH1/2; and a NGS RNA fusion panel for ALK, ROS1, RET, NTRK1/3, NRG1, and MET e14 skipping. PDL1 expression by IHC was scored for tumor proportion score (TPS). Statistical comparison was performed using Fisher’s Exact test. Results 186 patients with NSCLC were included (126 adenocarcinoma, 33 squamous/adeno-squamous, 19 poorly differentiated, and 8 NSCLC-NOS); 162 of those had concurrent PDL1 IHC. 121 (65%) patients had a genomic alteration, most commonly RAS [28%], EGFR [24%], ALK [8%], MET [7%], and BRAF [5%]. Cases with genomic alterations were classified into those with and without RAS mutation/s. The prevalence of high PDL1 expression was greater in RAS-driven tumors: 47% vs 22% with non-RAS bearing genomic alterations (p=0.0173). There was no significant difference in the PDL1 expression between the genomically negative tumors and those with non-RAS bearing mutations. Recently, the FDA granted approval to sotorasib, a KRAS G12C inhibitor, in patients with locally advanced or metastatic NSCLC. However, there was no significant difference in the PDL1 expression between the tumors with RAS G12C mutation and those with other RAS mutations. Conclusion Our data indicate that close to half of RAS-driven NSCLC have high PDL1 expression, an important consideration for front-line therapy selection. The majority of genomically-actionable tumors have at least low-positive expression of PDL1, highlighting the potential importance of immune checkpoint therapy in the resistant-progression setting. In comparison, only about one third of genomically-negative cases have high PDL1 expression, and a significant percent are completely negative. When the actionable KRAS G12C mutation bearing cases were compared to those with other RAS mutations, no significant difference was noted in the PDL1 expression between these two subsets; further investigations and a larger cohort of patients may be helpful in this case to determine whether PDL1 levels are affected by a specific RAS mutation.

Although nasopharyngeal samples have been considered the gold standard for COVID-19 testing, variability in viral load across different anatomical sites could cause nasopharyngeal samples to be less sensitive than saliva or nasal samples in certain cases. Self-collected samples have logistical advantages over nasopharyngeal samples, making them amenable to population-scale screening. To evaluate sampling alternatives for population screening, we collected nasopharyngeal, saliva, and nasal samples from two cohorts with varied levels and types of symptoms. In a mixed cohort of 60 symptomatic and asymptomatic participants, we found that saliva had 88% concordance with nasopharyngeal samples when tested in the same testing lab (n = 41) and 68% concordance when tested in different testing labs (n = 19). In a second cohort of 20 participants hospitalized for COVID-19, saliva had 74% concordance with nasopharyngeal samples tested in the same testing lab but detected virus in two participants that tested negative with nasopharyngeal samples on the same day. Medical record review showed that the saliva-based testing sensitivity was related to the timing of symptom onset and disease stage. We find that no sample site will be perfectly sensitive for COVID-19 testing in all situations, and the significance of negative results will always need to be determined in the context of clinical signs and symptoms. Saliva retained high clinical sensitivity for early-stage and presymptomatic COVID-19 while allowing easier collection, minimizing the exposure of health care workers, and need for personal protective equipment and making it a viable option for population-scale testing. IMPORTANCE Methods for COVID-19 detection are necessary for public health efforts to monitor the spread of disease. Nasopharyngeal samples have been considered the best approach for COVID-19 testing. However, alternative samples like self-collected saliva offer advantages for population-scale screening. Meta-analyses of recent studies suggest that saliva is useful for detecting SARS-CoV-2; however, differences in disease prevalence, sample collection, and analysis methods still confound strong conclusions on the utility of saliva compared to nasopharyngeal samples. Here, we find that the sensitivity of saliva testing is related to both the timing of the sample collection relative to symptom onset and the disease stage. Importantly, several clinical vignettes in our cohorts highlight the challenges of medical decision making with limited knowledge of the associations between laboratory test data and the natural biology of infection.

The COVID-19 global pandemic is an unprecedented health emergency. Insufficient access to testing has hampered effective public health interventions and patient care management in a number of countries. Furthermore, the availability of regulatory-cleared reagents has challenged widespread implementation of testing. We rapidly developed a qRT-PCR SARS-CoV-2 detection assay using a 384-well format and tested its analytic performance across multiple nucleic acid extraction kits. Our data shows robust analytic accuracy on residual clinical biospecimens. Limit of detection sensitivity and specificity was confirmed with currently available commercial reagents. Our methods and results provide valuable information for other high-complexity laboratories seeking to develop effective, local, laboratory-developed procedures with high-throughput capability to detect SARS-CoV-2.

Intra-tumoral genomic heterogeneity is a well-established biologic property of human malignancies with emerging roles in cancer progression and therapy resistance. However, its impact on the clinical utility of genomic testing in patient management remains unclear. Furthermore, best practices to account for heterogeneity in the provision of highly accurate, clinically valid molecular testing have yet to be firmly established. Genomic biomarkers for the management of colorectal carcinoma are both well-established (ie, KRAS, NRAS) and emerging (BRAF, PIK3CA, and others) in respect to therapy selection and clinical trial eligibility. Critically, standard colorectal carcinoma management requires the exclusion of KRAS and NRAS mutations; thus optimal procedures to control for potential intra-tumoral heterogeneity are clinically important. Here, we assessed heterogeneity among three intra-tumoral sites within 99 colorectal carcinomas cases on a CLIA-validated oncology next generation sequencing assay and examined whether a pooling strategy overcame any discordant results. Overall, 11% of cases demonstrated discordant mutation results between sites; 2% of cases were discrepant for mutations within RAS genes while the remainder was discrepant in PIK3CA. Half of the discrepant cases were associated with borderline tumor cellularity assessment. Further, a sample pooling strategy across all three sites successfully detected the relevant mutation in all but one case. Our results indicate that intra-tumoral genomic heterogeneity of clinically relevant genes within colorectal carcinoma is a relatively infrequent occurrence and that a simple strategy to pool DNA from several tumor sites with adequate cellularity minimizes the risk of false negative results even further to ensure optimal patient management.

Background: Massively parallel, or next-generation, sequencing is a powerful technique for the assessment of somatic genomic alterations in cancer samples. Numerous gene targets can be interrogated simultaneously with a high degree of sensitivity. The clinical standard of care for many advanced solid and hematologic malignancies currently requires mutation analysis of several genes in the front-line setting, making focused next generation sequencing (NGS) assays an effective tool for clinical molecular diagnostic laboratories. Methods: We have utilized an integrated microfluidics circuit (IFC) technology for multiplex PCR-based library preparation coupled with a bioinformatic method designed to enhance indel detection. A parallel low input PCR-based library preparation method was developed for challenging specimens with low DNA yield. Computational data filters were written to optimize analytic sensitivity and specificity for clinically relevant variants. Results: Minimum sequencing coverage and precision of variant calls were the two primary criteria used to establish minimum DNA mass input onto the IFC. Wet-bench and bioinformatics protocols were modified based on data from the optimization and familiarization process to improve assay performance. The NGS platform was then clinically validated for single nucleotide and indel (up to 93 base pair) variant detection with overall analytic accuracy of 98% (97% sensitivity; 100% specificity) using as little as 3 ng of formalin-fixed, paraffin-embedded DNA or 0.3 ng of unfixed DNA. Conclusions: We created a targeted clinical NGS assay for common solid and hematologic cancers with high sensitivity, high specificity, and the flexibility to test very limited tissue samples often encountered in routine clinical practice.