Whole exome sequencing (WES) is used to identify mutations in a patient's tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES ...has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth.
Despite our understanding that social media and online healthcare communities can help to eliminate health information asymmetry and improve patients’ self‐care engagement, we have yet to understand ...what happens when patients have access to others’ health data and how patients’ access to these shared experiences and opinions influence their health knowledge and perceived treatment outcome. In this study, we apply social information processing theory and incorporate (1) uncertainty of a treatment, (2) information exposure, and (3) credibility of the information source into patients’ information evaluation function to assess how patients utilize shared health information and experiences. An empirical model, which combines various aspects of patients’ firsthand experiences about treatments into a single construct, yields empirical evidence that patients’ perceived treatment outcome is prone to social influence from other patients’ shared experiences. By disaggregating the sources of social influence, we find that social influence created by generalized others in the community outweighs that by familiar others of one's intimate social group. In addition, we find that other factors, such as positive sentiment in comments and patients’ prior experiences, also affect patients’ perceived treatment outcome. Based on our findings, implications for health promotion and health behaviors are presented.
Aggregation of amyloid-beta protein (Aβ) is a key pathogenic event in Alzheimer’s disease (AD). Curcumin, a constituent of the Indian spice Turmeric is structurally similar to Congo Red and has been ...demonstrated to bind Aβ amyloid and prevent further oligomerization of Aβ monomers onto growing amyloid β-sheets. Reasoning that oligomerization kinetics and mechanism of amyloid formation are similar in Parkinson’s disease (PD) and AD, we investigated the effect of curcumin on α-synuclein (AS) protein aggregation. In vitro model of AS aggregation was developed by treatment of purified AS protein (wild-type) with 1 mM Fe
3+
(Fenton reaction). It was observed that the addition of curcumin inhibited aggregation in a dose-dependent manner and increased AS solubility. The aggregation-inhibiting effect of curcumin was next investigated in cell culture utilizing catecholaminergic SH-SY5Y cell line. A model system was developed in which the red fluorescent protein (DsRed2) was fused with A53T mutant of AS and its aggregation examined under different concentrations of curcumin. To estimate aggregation in an unbiased manner, a protocol was developed in which the images were captured automatically through a high-throughput cell-based screening microscope. The obtained images were processed automatically for aggregates within a defined dimension of 1–6 μm. Greater than 32% decrease in mutant α-synuclein aggregation was observed within 48 h subsequent to curcumin addition. Our data suggest that curcumin inhibits AS oligomerization into higher molecular weight aggregates and therefore should be further explored as a potential therapeutic compound for PD and related disorders.
Locally advanced non-small cell lung cancer (NSCLC) is highly resistant to chemoradiotherapy, and many cancer patients experience chronic stress. Studies that suggest stimulation of β-adrenergic ...receptors (β-AR) promotes tumor invasion and therapy resistance. We investigated whether β-AR inhibition with beta-blockers acts as a chemotherapy and radiation sensitizer in vitro and in patients treated with chemoradiation for locally advanced NSCLC.
We investigated the effects of the non-selective beta-blocker propranolol on two human lung adenocarcinoma cell lines (PC9, A549) treated with radiation or cisplatin. We retrospectively evaluated 77 patients with Stage IIIA NSCLC who received induction chemoradiation followed by surgery. Pathological and imaging response, metastatic rate, and survival were analyzed using SPSS v22.0 and PrismGraphpad6.
Propranolol combined with radiation or cisplatin decreased clonogenic survival of PC9 and A549 cells in vitro (
< 0.05). Furthermore, propranolol decreased expression of phospho-protein kinase A (p-PKA), a β-adrenergic pathway downstream activation target, in both cell lines compared to irradiation or cisplatin alone (
< 0.05). In patients treated for Stage IIIA NSCLC, 16 took beta-blockers, and 61 did not. Beta-blockade is associated with a trend to improved overall survival (OS) at 1 year (81.3% vs 57.4%,
= 0.08) and distant metastasis-free survival (DMFS) (2.6 years vs. 1.3 years,
= 0.16). Although beta-blocker use was associated with decreased distant metastases (risk ratio (RR) 0.19;
= 0.03), it did not affect primary tumor pathological response (
= 0.40) or imaging response (
= 0.36).
β-AR blockade enhanced radiation and cisplatin sensitivity of human lung cancer cells in vitro. Use of beta-blockers is associated with decreased distant metastases and potentially improved OS and DMFS. Additional studies are warranted to evaluate the role of beta-blockers as a chemoradiation sensitizer in locally advanced NSCLC.
The aim of this study was to determine if change in stage after neoadjuvant chemoradiation (CRT) was associated with improved survival in esophageal cancer using a national database.
Using the ...National Cancer Database, patients with non-metastatic, resectable esophageal cancer who received neoadjuvant CRT and surgery were identified. Comparing clinical to the pathologic stage, change in stage was classified as pathologic complete response (pCR), downstaged, same-staged, or upstaged. Univariable and multivariable Cox regression models were used to identify factors associated with survival.
A total of 7745 patients were identified. The median overall survival (OS) was 34.9 months. Median OS was 60.3 months if pCR, 39.1 months if downstaged, 28.3 months if same-staged, and 23.4 months if upstaged (p < 0.0001). On multivariable analysis, pCR was associated with improved OS compared to the other groups (downstaged: hazard ratio HR: 1.32 95% confidence interval CI: 1.18-1.46; same-staged: HR: 1.89 95% CI: 1.68-2.13; upstaged: HR: 2.54 95% CI: 2.25-2.86; all p < 0.0001).
In this large database study, change in stage after neoadjuvant CRT was strongly associated with survival for patients with non-metastatic, resectable esophageal cancer. There was a significant stepwise decline in survival, in descending order of pCR, downstaged tumor, same-staged tumor, and upstaged tumor.
•SBRT is infrequently used to treat Stage II NSCLC according to NCDB.•Median overall survival was 23.7 months in patients treated with SBRT.•Most common SBRT prescriptions were 50 Gy in 5 fractions ...and 48 Gy in 4 fractions.•BED10 was associated with improved survival, particularly in node-negative patients.
The role of stereotactic body radiation therapy (SBRT) in treating stage II non-small cell lung cancer (NSCLC) remains unclear. This study evaluates SBRT dose prescription patterns and survival outcomes in Stage II NSCLC using the National Cancer Database (NCDB).
Patients diagnosed with Stage II NSCLC and treated with SBRT between 2004–2013 were identified in NCDB. The biologically effective dose with α/β = 10 Gy (BED10) was calculated. Overall survival (OS) was analyzed using the Kaplan-Meier method and Cox regression models.
Of 56,543 patients with Stage II NSCLC, 451 (0.8%) received SBRT. There were 360 patients (79.8%) with node-negative and 91 patients (20.2%) with node-positive disease. The most common prescriptions were 10 Gy x 5 (35.9%) and 12 Gy x 4 (19.3%). The mean and median BED10 were 114.9 Gy and 105.6 Gy, respectively. With median follow-up of 19.3 months, overall median survival was 23.7 months. Median survival was 22.4 months for those treated with BED10 < 114.9 Gy versus 31.5 months for BED10 ≥ 114.9 Gy (p = 0.036). On multivariate analysis, BED10 as a continuous variable (hazard ratio HR 0.991, p = 0.009) and ≥ 114.9 Gy (HR 0.63, p = 0.015) were associated with improved survival in node-negative patients. BED10 as a continuous variable (HR 0.997, p = 0.465) and ≥ 114.9 Gy (HR 0.81, p = 0.546) were not significant factors for predicting survival in node-positive patients.
SBRT is infrequently utilized to treat Stage II NSCLC in the United States. Treatment with higher BED10 was associated with improved survival, and the benefit was limited to patients with node-negative disease.
Here we demonstrate a facile method by which to deliver complex spatiotemporal stimulation to neural networks in fast patterns, to trigger interesting forms of circuit-level plasticity in cortical ...areas. We present a complete platform by which patterns of electricity can be arbitrarily defined and distributed across a brain circuit, either simultaneously, asynchronously, or in complex patterns that can be easily designed and orchestrated with precise timing. Interfacing with acute slices of mouse cortex, we show that our system can be used to activate neurons at many locations and drive synaptic transmission in distributed patterns, and that this elicits new forms of plasticity that may not be observable via traditional methods, including interesting measurements of associational and sequence plasticity. Finally, we introduce an automated "network assay" for imaging activation and plasticity across a circuit. Spatiotemporal stimulation opens the door for high-throughput explorations of plasticity at the circuit level, and may provide a basis for new types of adaptive neural prosthetics.
DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier ...barcodes can detect mutations with a variant-allele frequency (VAF) as low as 0.1% using next-generation sequencing (NGS), sequencing depths of over 25,000× are required, thus hampering the detection of mutations at high sensitivity in patient samples and in most samples used in research. Here we show that low-frequency DNA variants can be detected via low-depth multiplexed NGS after their amplification, by a median of 300-fold, using polymerase chain reaction and rationally designed 'blocker' oligonucleotides that bind to the variants. Using an 80-plex NGS panel and a sequencing depth of 250×, we detected single nucleotide polymorphisms with a VAF of 0.019% and contamination in human cell lines at a VAF as low as 0.07%. With a 16-plex NGS panel covering 145 mutations across 9 genes involved in melanoma, we detected low-VAF mutations (0.2-5%) in 7 out of the 19 samples of freshly frozen tumour biopsies, suggesting that tumour heterogeneity could be notably higher than previously recognized.
Adenoma detection rate (ADR) is an accepted benchmark for screening colonoscopy. Factors driving ADR and its relationship with sessile serrated lesions detection rate (SSLDR) over time remain ...unclear. We aim to explore patient, physician, and procedural influences on ADR and SSLDR trends.
Using a large healthcare system in northern California from January 2010 to December 2020, a total of 146,818 screening colonoscopies performed by 33 endoscopists were included. ADR and SSLDR were calculated over time using natural language processing. Logistic regression was used to calculate the odd ratios of patient demographics, physician attributes, and procedural details over time.
Between 2010 and 2020, ADR rose from 19.4% to 44.4%, whereas SSLDR increased from 1.6% to 11.6%. ADR increased by 2.7% per year (95% confidence interval 1.9%-3.4%), and SSLDR increased by 1.0% per year (95% confidence interval 0.8%-1.2%). Higher ADR was associated with older age, male sex, higher body mass index, current smoker, higher comorbidities, and high-risk colonoscopy. By contrast, SSLDR was associated with younger age, female sex, white race, and fewer comorbidities. Patient and procedure characteristics did not significantly change over time ( P -interaction >0.05). Longer years in practice and male physician were associated with lower ADR and SSLDR in 2010, but significantly attenuated over time ( P -interaction <0.05).
Both ADR and SSLDR have increased over time. Patient and procedure factors did not significantly change over time. Male endoscopist and longer years in practice had lower initial ADR and SSLDR, but significantly lessened over time.
Abstract Purpose Radiology instruction is based on the principle that grouped (or massed) repetition of an intellectual activity leads to expertise. The aim of this study was to test the hypothesis ...that the spaced (or interleaved) method of teaching chest x-ray interpretation is more effective than the massed method. Methods After institutional review board approval was obtained, 40 first- and second-year medical students were randomized into two groups matched by age, gender, and education experience. Both groups saw six examples of 12 common chest radiographic patterns, one grouped, the other scrambled randomly without repeating strings. After a distraction, participants took a multiple-choice test consisting of two cases in each radiographic pattern, one previously shown, one new. Results were analyzed using two-tailed Student’s t test of proportion. Results Comparing interleaved and massed groups, the average overall score was 57% versus 43% ( P = .03), the recollection score was 61% versus 47% ( P = .03), and the induction score was 53% versus 40% ( P = 0.10), respectively. Comparing second- and first-year students, average scores were 67% and 39%, respectively ( P < .01). First-year students in the interleaved and massed groups scored 55% and 36% ( P = .02) in recall and 40% and 28% ( P = .10) in induction. Second-year students in the interleaved and massed groups scored 71% and 63% ( P = .36) in recall and 74% and 59% ( P = .03) in induction. Conclusions The interleaved method of instruction leads to better results than the massed method across all levels of education. A higher level of medical education improves performance independent of method of instruction.
PDF
