Genetic sex validation for sample tracking in next-generation sequencing clinical testing.

OBJECTIVE: Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. RESULTS: Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors (49.09%), samples from transgender participants (3.64%) and stem cell or bone marrow transplant patients (7.27%) along with undetermined sample mix-ups (40%) for which sample swaps occurred prior to arrival at genome centers, however the exact cause of the events at the sampling sites resulting in the mix-ups were not able to be determined.

Trends in Opioid and Nonsteroidal Anti-Inflammatory Drug Use for Patients with Kidney Stones in United States Emergency Departments from 2015 to 2021.

Introduction: Renal colic is frequently treated with opioids; however, narcotic analgesic use can lead to dependence and abuse. We evaluated use trends of opioids and nonsteroidal anti-inflammatory drugs (NSAIDs) for pain management of kidney stones in United States emergency departments (EDs) from 2015 to 2021. Methods: Kidney stone encounters were identified using National Hospital Ambulatory Medical Care Survey data. We applied a multistage survey weighting procedure to account for selection probability, nonresponse, and population weights. Medication use trends were estimated through logistic regressions on the timing of the encounter, adjusted for selected demographic and clinical characteristics. Results: Between 2015 and 2021, there were an estimated 9,433,291 kidney stone encounters in United States EDs. Opioid use decreased significantly (annual odds ratio [OR]: 0.87, p = 0.003), and there was no significant trend in NSAID use. At discharge, male patients were more likely than females (OR: 1.93, p = 0.001) to receive opioids, and Black patients were less likely than White patients (OR: 0.34, p = 0.010) to receive opioids. Regional variation was also observed, with higher odds of discharge prescriptions in the West (OR: 3.15, p = 0.003) and Midwest (OR: 2.49, p = 0.010), compared with the Northeast. Thirty-five percent of patients received opioids that were stronger than morphine. Conclusion: These results suggest improved opioid stewardship from ED physicians in response to the national opioid epidemic. However, regional variation as well as disparities in discharge prescriptions for Black and female patients underscore opportunities for continued efforts.

Genetic Sex Validation for Sample Tracking in Clinical Testing.

Objective: Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. Results: Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients along with undetermined sample mix-ups.

Breathing in danger: how particulate matter pollution is putting the public at risk of lung cancer†.

We are constantly exposed to chemicals and other agents in our environment that can influence our risk of tumorigenesis, but exactly how these factors contribute to cancer development is largely unknown. Fine particulate matter measuring ≤2.5 µm (PM2.5 ) from air pollution can accumulate in alveoli, contributing to inflammation and tissue damage. Despite prior correlative studies highlighting the mortality risk, there has been a historical reluctance to lower national standards for safe PM2.5 exposure. A recent publication further highlights the attributable risk of PM2.5 exposure with lung cancer - particularly in 'never-smokers' with EGFR-driven non-small cell lung cancer. Importantly, it also elucidates a mechanistic link between PM2.5 exposure and tumorigenesis using in vivo models of EGFR non-small cell lung cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Color Doppler ultrasound imaging in varicoceles: Is the difference in venous diameter encountered during Valsalva predictive of palpable varicocele grade?

Objective: The clinical grading system for varicoceles is subjective and dependent on clinician experience. Color Doppler ultrasound (US) has not been standardized in the diagnosis of varicoceles. We aimed to determine if US measurement of varicocele could be predictive of World Health Organization (WHO) varicocele grade. Methods: Men who presented for either scrotal pain or infertility to a tertiary men's health clinic underwent physical examination, and varicoceles were graded following WHO criteria (0=subclinical, 1, 2, 3). US was used to measure largest venous diameter in the pampiniform plexus bilaterally at rest and during Valsalva maneuver. Receiver operator characteristic curve analysis was used to determine if resting diameter, diameter during Valsalva, or change in diameter between at rest and during Valsalva provided the highest sensitivity and specificity for determining clinical grade. Threshold values for diameter were determined from these receiver operator characteristic curves. Results: A total of 102 men (50 with clinical varicocele and 52 with subclinical varicocele) were included. Diameter at rest was the best ultrasonographic discriminator between subclinical and clinical varicoceles (area under the curve [AUC]=0.67) with a diameter threshold of 3.0 mm (sensitivity 79%, specificity 42%). Diameter during Valsalva had the greatest AUC for determining clinical Grades 1 versus 2 (AUC=0.57) with diameter threshold of 5.7 mm (sensitivity 71%, specificity 33%). For differentiating between Grades 2 and 3, diameter at rest had the greatest AUC of 0.65 with a threshold of 3.6 mm (sensitivity 71%, specificity 58%). Conclusion: Our results corroborate other studies that have shown a weak correlation between US and clinical grading. The use of diameter during Valsalva was less predictive than diameter at rest and was only clinically significant in differentiating between Grade 1 and 2 varicocele. A standardized method for determining clinically relevant varicoceles on US would allow for improved patient counseling and clinical decision-making.

Poor correlation between preclinical and patient efficacy data for tumor targeted monotherapies in glioblastoma: the results of a systematic review.

PURPOSE: Limited progress has been made in treating glioblastoma, and we hypothesise that poor concordance between preclinical and clinical efficacy in this disease is a major barrier to drug development. We undertook a systematic review to quantify this issue. METHODS: We identified phase I trials (P1Ts) of tumor targeted drugs, subsequent trial results and preceding relevant preclinical data published in adult glioblastoma patients between 2006-2019 via structured searches of EMBASE/MEDLINE/PUBMED. Detailed clinical/preclinical information was extracted. Associations between preclinical and clinical efficacy metrics were determined using appropriate non-parametric statistical tests. RESULTS: A total of 28 eligible P1Ts were identified, with median ORR of 2.9% (range 0.0-33.3%). Twenty-three (82%) had published relevant preclinical data available. Five (18%) had relevant later phase clinical trial data available. There was overall poor correlation between preclinical and clinical efficacy metrics on univariate testing. However, drugs that had undergone in vivo testing had significantly longer median overall survival (7.9 vs 5.6mo, p = 0.02). Additionally, drugs tested in ≥ 2 biologically-distinct in vivo models ('multiple models') had a significantly better median response rate than those tested using only one ('single model') or those lacking in vivo data (6.8% vs 1.2% vs. 0.0% respectively, p = 0.027). CONCLUSION: Currently used preclinical models poorly predict subsequent activity in P1Ts, and generally over-estimate the anti-tumor activity of these drugs. This underscores the need for better preclinical models to aid the development of novel anti-glioblastoma drugs. Until these become widely available and used, the use of multiple biologically-distinct in vivo models should be strongly encouraged.

Regulation of the antigen presentation machinery in cancer and its implication for immune surveillance.

Evading immune destruction is one of the hallmarks of cancer. A key mechanism of immune evasion deployed by tumour cells is to reduce neoantigen presentation through down-regulation of the antigen presentation machinery. MHC-I and MHC-II proteins are key components of the antigen presentation machinery responsible for neoantigen presentation to CD8+ and CD4+ T lymphocytes, respectively. Their expression in tumour cells is modulated by a complex interplay of genomic, transcriptomic and post translational factors involving multiple intracellular antigen processing pathways. Ongoing research investigates mechanisms invoked by cancer cells to abrogate MHC-I expression and attenuate anti-tumour CD8+ cytotoxic T cell response. The discovery of MHC-II on tumour cells has been less characterized. However, this finding has triggered further interest in utilising tumour-specific MHC-II to harness sustained anti-tumour immunity through the activation of CD4+ T helper cells. Tumour-specific expression of MHC-I and MHC-II has been associated with improved patient survival in most clinical studies. Thus, their reactivation represents an attractive way to unleash anti-tumour immunity. This review provides a comprehensive overview of physiologically conserved or novel mechanisms utilised by tumour cells to reduce MHC-I or MHC-II expression. It outlines current approaches employed at the preclinical and clinical trial interface towards reversing these processes in order to improve response to immunotherapy and survival outcomes for patients with cancer.

The systemic management of central nervous system metastases and leptomeningeal disease from advanced lung, melanoma, and breast cancer with molecular drivers: An Australian perspective.

The advent of systemic therapies with high intracranial efficacy in recent years is changing the therapeutic paradigm and renewing interest in the management of central nervous system (CNS) and leptomeningeal metastases from solid organ tumors. CNS metastases have traditionally heralded a dismal prognosis with median survival of 3-10 months, and were primarily treated with local therapeutic modalities, such as surgery or radiation therapy. Although these modalities still have a role in the management of CNS disease, newer agents, such as small molecule tyrosine kinase inhibitors and immune-checkpoint inhibitors, are now paving the way as an alternative therapeutic option for those with oligometastatic or low-volume intracranial disease, potentially eliminating or delaying the need for local treatment modalities in this setting. Herein, we summarize the systemic treatments with proven intracranial efficacy, currently approved for use in Australia for advanced mutation-driven non-small cell lung cancer, melanoma, and breast cancer, as well as novel agents in preclinical and clinical trial development.

Adjuvant therapies for non-muscle-invasive bladder cancer: advances during BCG shortage.

Non-muscle-invasive bladder cancer (NMIBC) represents a significant global therapeutic challenge, particularly in the era of Bacillus Calmette-Guérin (BCG) shortage. High-risk NMIBC can progress to muscle invasive or metastatic disease in 25% of patients. Optimal treatment selection, according to risk stratification, is imperative. International guidelines slightly differ in their categorisation of low, intermediate and high-risk NMIBC. Nonetheless, a single post-operative instillation of chemotherapy with Mitomycin C (MMC) or Gemcitabine improves relapse-free survival (RFS) in low-risk NMIBC. Induction and maintenance intravesical BCG remains the historical gold standard for patients with intermediate or high-risk NMIBC. However, clinicians may be forced to consider alternatives given the current BCG shortage. Both intravesical MMC and Gemcitabine have been associated with similar efficacy to BCG, albeit in smaller studies. MMC may also be manipulated using a variety of methods to potentiate its effects. BCG treatment delivery may also be modified without affecting efficacy through dose reduction and abbreviation or omission of maintenance therapy. Preliminary data also highlight that directly proceeding to radical cystectomy may not adversely affect long-term quality of life measures. Access to new systemic and intravesical therapies must be prioritised for patients with BCG recurrent or unresponsive disease. When used in conjunction with molecularly defined biomarkers, these agents herald the potential for improved survival outcomes and alleviation of the current BCG shortage.

Changes in prescribing habits for the treatment of metastatic renal clear cell carcinoma (mRCC) in Australia.

The availability of efficacious systemic therapies for metastatic clear cell renal cell carcinoma has heralded improved survival for Australians. The Pharmaceutical Benefits Schedule registry was interrogated to assess nation-wide prescribing patterns. Sunitinib remained the most commonly prescribed agent. Prescribing rates were significantly lower in Northern Territory than in other states, raising questions of disparities in access to care.

Analysing online Twitter discussions of bedwetting via a condition-specific hashtag (#Bedwetting).

AIM: Bedwetting is a common paediatric condition. #Bedwetting has been established as the official hashtag to structure Twitter discussions about the condition. We analysed online Twitter discussions for #Bedwetting. METHODS: Symplur, a Twitter analytics service was employed to aggregate Twitter activity, users and content including #Bedwetting, between October 2013 and November 2018. Activity was analysed via tweet volume and user adoption. Users were assorted using geographic location, occupation and affiliation data. Content in #Bedwetting Tweets was undertaken by retrieving information about retweets, links, frequently used words and hashtags. RESULTS: A total of 101 412 tweets and 9957 users utilising #Bedwetting were identified. Most tweets were sent with links (93%). The average ± SD number of tweets using #Bedwetting per month increased from 96 ± 87 in 2013 to 2935 ± 1644 in 2015. Tweet volume decreased to 1960 ± 257 in 2016 and subsequently increased to 2901 ± 1110 in 2017. New users increased from 4 in 2013 to 9957 users in 2018. Users tweeted from 69 countries. Advocacy organisations comprised 35% of the top 100 influencers. Common words in #Bedwetting tweets were 'potty', 'best' and 'training'. Popular associated hashtags were #Pottytraining, #Solutions and #Moms. Hyperlinks in #Bedwetting tweets included advocacy, academic and commercial websites. CONCLUSIONS: Our analysis of #Bedwetting highlights that Twitter is frequently used to discuss the condition's diagnosis and management. Various stakeholders in health care are utilising the platform to build awareness about bedwetting. We identified that Twitter is being employed to drive web traffic to other internet websites.

Inefficiencies in phase II to phase III transition impeding successful drug development in glioblastoma.

BACKGROUND: Improving outcomes of patients with glioblastoma (GBM) represents a significant challenge in neuro-oncology. We undertook a systematic review of key parameters of phase II and III trials in GBM to identify and quantify the impact of trial design on this phenomenon. METHODS: Studies between 2005 and 2019 inclusive were identified though MEDLINE search and manual bibliography searches. Phase II studies (P2T) were restricted to those referenced by the corresponding phase III trials (P3T). Clinical and statistical characteristics were extracted. For each P3T, corresponding P2T data was "optimally matched," where same drug was used in similar schedule and similar population; "suboptimally matched" if dis-similar schedule and/or treatment setting; or "lacking." Phase II/III transition data were compared by Pearson Correlation, Fisher's exact or chi-square testing. RESULTS: Of 20 P3Ts identified, 6 (30%) lacked phase II data. Of the remaining 14 P3T, 9 had 1 prior P2T, 4 had 2 P2T, and 1 had 3 P2T, for a total of 20 P3T-P2T pairs (called dyads). The 13 "optimally matched" dyads showed strong concordance for mPFS (r 2 = 0.95, P < .01) and mOS (r 2 = 0.84, P < .01), while 7 "suboptimally matched" dyads did not (P > .05). Overall, 7 P3Ts underwent an ideal transition from P2T to P3T. "Newly diagnosed" P2Ts with mPFS < 14 months and/or mOS< 22 months had subsequent negative P3Ts. "Recurrent" P2Ts with mPFS < 6 months and mOS< 12 months also had negative P3Ts. CONCLUSION: Our findings highlight the critical role of optimally designed phase II trials in informing drug development for GBM.

Immune Checkpoint Inhibition With Chemoradiotherapy in Stage III Non-small-cell Lung Cancer: A Systematic Review and Meta-analysis of Safety Results.

The role of immune checkpoint inhibitors (ICIs) administered concurrently with or after definitive chemoradiation (CRT) in stage III non-small-cell lung cancer (NSCLC) has been detailed in several studies. We performed a systematic review to determine pneumonitis rates using ICIs with CRT. MEDLINE and EMBASE databases were searched using keywords and MeSH terms. Studies using anti-programmed cell death protein 1 (PD-1) or anti-programmed death-ligand 1 (PD-L1) therapy, either sequentially or concurrently with CRT, for patients with stage III NSCLC were included. A meta-analysis of pneumonitis rates was performed based on weighted pooled proportion, using random-effects models. Weighting was performed by the inverse variance or standard error of event rates. Comparative analysis between groups was performed. Odds ratios (OR) were used as the primary summary statistics. A total of 13 studies were identified (6 prospective clinical trials and 7 real-world reports). Rates of grade ≥ 3 pneumonitis were significantly higher in clinical trials using anti-PD-1 therapy compared with PD-L1 inhibitors (8.6%; 95% confidence interval [CI], 6.2%-11.9% vs. 4.4%; 95% CI, 3.0%-6.6%; OR, 2.0; P = .01). Clinical trials using concurrent ICI therapy with CRT had greater rates of grade 2 pneumonitis compared with sequential administration (23.0%; 95% CI, 15.8%-32.3% vs. 11.0%; 95% CI, 6.6%-17.8%; OR, 0.42; P = .02). Higher rates of grade ≥ 3 pneumonitis were observed in real-world studies compared with clinical trials involving sequential PD-L1 therapy (9.9%; 95% CI, 5.3%-17.9% vs. 4.4%; 95% CI, 2.9%-6.7%; OR, 0.43; P < .01). The suggestion of increased pneumonitis with a concurrent ICI strategy and using anti-PD-1 therapies warrants further consideration in future comparative studies.

A systematic evaluation of youtube as an information source for male infertility.

This study evaluates YouTube videos (YTVs) focused on male infertility to assess information quality and identify high-quality content that can reliably facilitate care. Top 50 YTVs based on relevance were identified using the keyword "male infertility." A checklist, adapted from American Urological Association guidelines addressing male infertility, was developed to assess YTV content. Two investigators extracted YTV features (including duration, likes, views, upload date), classified creators and ranked YTVs based on checklist scores. YTVs were then assigned grades A-D based on checklist scores. Kruskal-Wallis test and ANOVA were employed to draw associations between grades, content creator, and YTV features. Higher grades were associated with shorter video duration (p = 0.0305). Most YTVs (23/42) were created by healthcare-related organizations. Of the 42 YTVs included in the final analysis, 31% (13/42) explicitly defined infertility as an inability to conceive after 12 months of unprotected intercourse. Ninety percent (38/42) discussed male infertility evaluation methods, while 71% (30/42) discussed various interventions. Various content creators have adopted YouTube to discuss male infertility, and healthcare practitioners should be aware of YouTube's potential influence on patient understanding of male infertility. Knowledge gaps identified in YTVs can help improve patient counseling and enable practitioners to direct patients to reliable content.