Performance comparison: exome sequencing as a single test replacing Sanger sequencing.

Next generation sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome sequencing as a single test replacing Sanger sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-sequencing results of 258 genes to those obtained from next generation sequencing (NGS) using two exome-sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different sequencing methods and DNA sources). Sanger sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger sequencing and 97-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger sequencing or NGS.

Factors associated with utilization of neoadjuvant chemotherapy in charlson comorbidity zero non-metastatic muscle-invasive bladder cancer patients.

BACKGROUND: Guideline-based best practice treatment for muscle invasive bladder cancer (MIBC) involves neoadjuvant chemotherapy followed by radical cystectomy (NACRC). Prior studies have shown that a minority of patients receive NACRC and older age and renal function are drivers of non-receipt of NACRC. This study investigates treatment rates and factors associated with not receiving NACRC in MIBC patients with lower comorbidity status most likely to be candidates for NACRC. MATERIALS AND METHODS: Retrospective United States National Cancer Database analysis from 2006 to 2015 of MIBC patients with Charlson comorbidity index (CCI) of zero. Analysis of NACRC treatment trends in higher CCI patients was also performed. RESULTS: 15.561 MIBC patients met inclusion criteria. 1.507 (9.7%) received NACRC within 9 months of diagnosis. NACRC increased over time (15.0% in 2015 compared to 3.6% in 2006). Higher NACRC was noted in females, cT3 or cT4 cancer, later year of diagnosis, and academic facility treatment. Lower utilization was noted for blacks and NACRC decreased with increasing age and CCI. Only 16.9% of patients aged 23-62 in the lowest age quartile with muscle invasive bladder cancer and CCI of 0 received NACRC. CONCLUSIONS: Although utilization is increasing, receipt of NACRC remains low even in populations most likely to be candidates. Further study should continue to elucidate barriers to utilization of NACRC.

Evaluating Financial Toxicity in Urologic Practice.

OBJECTIVE: To evaluate financial toxicity in Urologic surgery using the Comprehensive Score for financial Toxicity (COST) as well as validate a single item measure of toxicity. METHODS: A cross-sectional study of 182 patients undergoing oncologic and benign urologic procedures at a single academic medical center. Oncologic procedures included robotic assisted laparoscopic prostatectomy, transurethral resection of bladder tumor, and radical cystectomy. Benign procedures included holmium laser enucleation of the prostate, intravesical chemodenervation, ureteroscopy laser lithotripsy, and ureteral stent exchange. Retrospective review, patient interviews, and the previously validated COST survey, as well as a novel single item measure of toxicity were used pre and post-op. Descriptive statistics and logistic regression models compared COST scores by type of urologic procedure. RESULTS: Eighty (44%) patients underwent oncologic procedures and 102 (56%) benign procedures. Benign patients were most likely to have lower income and be younger than oncologic patients, with a median age of 56.7 vs 64.9. One in 4 patients undergoing urologic procedures experienced moderate to severe financial toxicity, without a statistically significant difference between the benign and the oncology groups pre- or post-operatively. Single item measure strongly correlated with COST (r = -0.80) pre- and post-operative. CONCLUSION: The COST survey and a single-item financial toxicity measure are both valid tools that can be used to measure financial toxicity in urology. Further research is needed to elicit the exact cause of financial toxicity in the heterogenous urologic patient population.

National Trends in the Utilization of Androgen Deprivation Therapy for Very Low Risk Prostate Cancer.

OBJECTIVE: To analyze national trends using the National Cancer Database (NCDB) in use of androgen deprivation therapy (ADT), outside of standard of care, in patients with very low risk prostate cancer. METHODS: We identified 52,797 men in the NCDB from 2010 to 2015 diagnosed with very low risk prostate cancer as defined (cT1cM0, PSA <10, Gleason ≤6, <3 biopsy cores positive). We evaluated the treatment trends and the proportion of men treated with ADT based on race, income, insurance status, treatment facility volume, and Charlson comorbidity. RESULTS: From 2010 to 2015, prevalence of primary ADT use in patients with very low risk prostate cancer remained 0.7%. Patients treated at low-volume facilities were more likely to receive primary ADT (hazard ratio [HR] 1.29, P <.001) as were black patients (HR 1.47, P <.001). When evaluated over time, the proportion of men treated with primary ADT who were white decreased while the proportion of men who were black increased. CONCLUSION: The use of primary ADT in men with very low risk prostate cancer has not changed over time, and may be over utilized, particularly among black men and those treated at low-volume facilities.

Cell birth and death in the developing retina of the Brazilian opossum, Monodelphis domestica.

The purpose of this study was to characterize cytogenesis and apoptosis in the developing retina of the Brazilian opossum, Monodelphis domestica. Monodelphis is a small pouchless marsupial whose young undergo a protracted period of postnatal development. Moreover, the Monodelphis retina represents a unique in vivo compartment for investigating cellular interactions that occur during early neural development and is an important system to study plasticity of neural stem cells following transplantation. Using bromodeoxyuridine (BrdU) labeling of newly generated cells, double-labeling immunohistochemistry and TUNEL labeling of apoptotic cells we have performed a detailed analysis of cell birth and death in the Monodelphis retina from fetal development through early postnatal life. Pregnant opossums or pups received a single injection of BrdU between gestational day 12 and postnatal day 35 (35PN), eyes were collected two hours after injection or on day 15, 30, or 60 of postnatal life. BrdU-labeled cells were visualized immunohistochemically. Cells were classified according to their morphology, location and immunoreactivity for cell-type specific antibodies. Cell genesis in the opossum retina begins at E13 and was near completion by 25PN. Apoptotic retinal cells were identified using the TUNEL technique for labeling of fragmented DNA. Apoptosis covered a relatively broad period of postnatal development, beginning around 10PN, peaking at 30PN, and concluding before 60PN. These results demonstrate that the retina of Monodelphis, a polyprotodont marsupial, is generated in a similar pattern to the wallaby, a diprotodont marsupial, and to eutherian species.

Factors associated with utilization of neoadjuvant chemotherapy in charlson comorbidity zero non-metastatic muscle-invasive bladder cancer patients

ABSTRACT Background: Guideline-based best practice treatment for muscle invasive bladder cancer (MIBC) involves neoadjuvant chemotherapy followed by radical cystectomy (NACRC). Prior studies have shown that a minority of patients receive NACRC and older age and renal function are drivers of non-receipt of NACRC. This study investigates treatment rates and factors associated with not receiving NACRC in MIBC patients with lower comorbidity status most likely to be candidates for NACRC. Materials and Methods: Retrospective United States National Cancer Database analysis from 2006 to 2015 of MIBC patients with Charlson comorbidity index (CCI) of zero. Analysis of NACRC treatment trends in higher CCI patients was also performed. Results: 15.561 MIBC patients met inclusion criteria. 1.507 (9.7%) received NACRC within 9 months of diagnosis. NACRC increased over time (15.0% in 2015 compared to 3.6% in 2006). Higher NACRC was noted in females, cT3 or cT4 cancer, later year of diagnosis, and academic facility treatment. Lower utilization was noted for blacks and NACRC decreased with increasing age and CCI. Only 16.9% of patients aged 23-62 in the lowest age quartile with muscle invasive bladder cancer and CCI of 0 received NACRC. Conclusions: Although utilization is increasing, receipt of NACRC remains low even in populations most likely to be candidates. Further study should continue to elucidate barriers to utilization of NACRC.