ASPYRE-Lung: validation of a simple, fast, robust and novel method for multi-variant genomic analysis of actionable NSCLC variants in FFPE tissue.

Introduction: Genomic variant testing of tumors is a critical gateway for patients to access the full potential of personalized oncology therapeutics. Current methods such as next-generation sequencing are costly and challenging to interpret, while PCR assays are limited in the number of variants they can cover. We developed ASPYRE® (Allele-Specific PYrophosphorolysis REaction) technology to address the urgent need for rapid, accessible and affordable diagnostics informing actionable genomic target variants of a given cancer. The targeted ASPYRE-Lung panel for non-small cell carcinoma covers 114 variants in 11 genes (ALK, BRAF, EGFR, ERBB2, KRAS, RET, ROS1, MET & NTRK1/2/3) to robustly inform clinical management. The assay detects single nucleotide variants, insertions, deletions, and gene fusions from tissue-derived DNA and RNA simultaneously. Methods: We tested the limit of detection, specificity, analytical accuracy and analytical precision of ASPYRE-Lung using FFPE lung tissue samples from patients with non-small cell lung carcinoma, variant-negative FFPE tissue from healthy donors, and FFPE-based contrived samples with controllable variant allele fractions. Results: The sensitivity of ASPYRE-Lung was determined to be ≤ 3% variant allele fraction for single nucleotide variants and insertions or deletions, 100 copies for fusions, and 200 copies for MET exon 14 skipping. The specificity was 100% with no false positive results. The analytical accuracy test yielded no discordant calls between ASPYRE-Lung and expected results for clinical samples (via orthogonal testing) or contrived samples, and results were replicable across operators, reagent lots, runs, and real-time PCR instruments with a high degree of precision. Conclusions: The technology is simple and fast, requiring only four reagent transfer steps using standard laboratory equipment (PCR and qPCR instruments) with analysis via a cloud-based algorithm. The ASPYRE-Lung assay has the potential to be transformative in facilitating access to rapid, actionable molecular profiling of tissue for patients with non-small cell carcinoma.

FIT negative clinic as a safety net for low-risk patients with colorectal cancer: impact on endoscopy and radiology utilisation-a retrospective cohort study.

Background: Faecal immunochemical testing (FIT) is recommended by the National Institute for Health and Care Excellence to triage symptomatic primary care patients who have unexplained symptoms but do not meet the criteria for a suspected lower gastrointestinal cancer pathway. During the COVID-19 pandemic, FIT was used to triage patients referred with urgent 2-week wait (2ww) cancer referrals instead of a direct-to-test strategy. FIT-negative patients were assessed and safety netted in a FIT negative clinic. Methods: We reviewed case notes for 622 patients referred on a 2ww pathway and seen in a FIT negative clinic between June 2020 and April 2021 in a tertiary care hospital. We collected information on demographics, indication for referral, dates for referral, clinic visit, investigations and long-term outcomes. Results: The average age of the patients was 71.5 years with 54% female, and a median follow-up of 2.5 years. Indications for referrals included: anaemia (11%), iron deficiency (24%), weight loss (9%), bleeding per rectum (5%) and change in bowel habits (61%). Of the cases, 28% (95% CI 24% to 31%) had endoscopic (15%, 95% CI 12% to 18%) and/or radiological (20%, 95% CI 17% to 23%) investigations requested after clinic review, and among those investigated, malignancy rate was 1.7%, with rectosigmoid neuroendocrine tumour, oesophageal cancer and lung adenocarcinoma. Conclusion: A FIT negative clinic provides a safety net for patients with unexplained symptoms but low risk of colorectal cancer. These real-world data demonstrate significantly reduced demand on endoscopy and radiology services for FIT-negative patients referred via the 2ww pathway.

A Giant Parathyroid Adenoma Presenting as Nausea, Vomiting, and Headaches in an Adolescent Male.

Primary hyperparathyroidism is rare in the pediatric population and is typically caused by a single parathyroid adenoma. Parathyroid adenomas are almost always small and not palpable on exam but can be evaluated by neck ultrasonography or 99 m Tc-sestamibi scan. Surgical resection is the only curative treatment. In this case, a 16-year-old male presents with a 10-day history of nausea, vomiting, and headaches and is found to have a highly elevated calcium and parathyroid hormone level and a cerebral calcification in his frontal lobe noted on computed tomography. He had a palpable mass over the region of his left inferior parathyroid gland which was surgically resected with histopathology revealing a giant parathyroid adenoma. Giant parathyroid adenomas are exceptionally rare in children and adolescents and are more likely to present with severe hypercalcemic crisis than smaller adenomas. As early symptoms are often nonspecific, awareness of this clinical entity is important. There are several reports of basal ganglia calcifications in the setting of parathyroid adenoma, but, to our knowledge, this is the first report of a patient with frontal lobe calcification.

Early management of acute severe UC in the biologics era: development and international validation of a prognostic clinical index to predict steroid response.

OBJECTIVES: We aimed to determine whether changes in acute severe colitis (ASC) management have translated to improved outcomes and to develop a simple model predicting steroid non-response on admission. DESIGN: Outcomes of 131 adult ASC admissions (117 patients) in Oxford, UK between 2015 and 2019 were compared with data from 1992 to 1993. All patients received standard treatment with intravenous corticosteroids and endoscopic disease activity scoring (Ulcerative Colitis Endoscopic Index of Severity (UCEIS)). Steroid non-response was defined as receiving medical rescue therapy or surgery. A predictive model developed in the Oxford cohort was validated in Australia and India (Gold Coast University Hospital 2015-2020, n=110; All India Institute of Medical Sciences, New Delhi 2018-2020, n=62). RESULTS: In the 2015-2019 Oxford cohort, 15% required colectomy during admission vs 29% in 1992-1993 (p=0.033), while 71 (54%) patients received medical rescue therapy (27% ciclosporin, 27% anti-tumour necrosis factor, compared with 27% ciclosporin in 1992-1993 (p=0.0015). Admission C reactive protein (CRP) (false discovery rate, p=0.00066), albumin (0.0066) and UCEIS scores (0.015) predicted steroid non-response. A four-point model was developed involving CRP of ≥100 mg/L (one point), albumin of ≤25 g/L (one point), and UCEIS score of ≥4 (1 point) or ≥7 (2 points). Patients scoring 0, 1, 2, 3 and 4 in the validation cohorts had steroid response rates of 100, 75.0%, 54.9%, 18.2% and 0%, respectively. Scoring of ≥3 was 84% (95% CI 0.70 to 0.98) predictive of steroid failure (OR 11.9, 95% CI 10.8 to 13.0). Colectomy rates in the validation cohorts were were 8%-11%. CONCLUSIONS: Emergency colectomy rates for ASC have halved in 25 years to 8%-15% worldwide. Patients who will not respond to corticosteroids are readily identified on admission and may be prioritised for early intensification of therapy.

Ultra-sensitive molecular detection of gene fusions from RNA using ASPYRE.

BACKGROUND: RNA is a critical analyte for unambiguous detection of actionable mutations used to guide treatment decisions in oncology. Currently available methods for gene fusion detection include molecular or antibody-based assays, which suffer from either being limited to single-gene targeting, lack of sensitivity, or long turnaround time. The sensitivity and predictive value of next generation sequencing DNA-based assays to detect fusions by sequencing intronic regions is variable, due to the extensive size of introns. The required depth of sequencing and input nucleic acid required can be prohibitive; in addition it is not certain that predicted gene fusions are actually expressed. RESULTS: Herein we describe a method based on pyrophosphorolysis to include detection of gene fusions from RNA, with identical assay steps and conditions to detect somatic mutations in DNA [1], permitting concurrent assessment of DNA and RNA in a single instrument run. CONCLUSION: The limit of detection was under 6 molecules/ 6 µL target volume. The workflow and instrumentation required are akin to PCR assays, and the entire assay from extracted nucleic acid to sample analysis can be completed within a single day.

Patient-reported Outcomes: the ICHOM Standard Set for Inflammatory Bowel Disease in Real-life Practice Helps Quantify Deficits in Current Care.

BACKGROUND: Patient-reported outcome measures [PROMs] are key to documenting outcomes that matter most to patients and are increasingly important to commissioners of health care seeking value. We report the first series of the ICHOM Standard Set for Inflammatory Bowel Disease [IBD]. METHODS: Patients treated for ulcerative colitis [UC] or Crohn's disease [CD] in our centre were offered enrolment into the web-based TrueColours-IBD programme. Through this programme, e-mail prompts linking to validated questionnaires were sent for symptoms, quality of life, and ICHOM IBD outcomes. RESULTS: The first 1299 consecutive patients enrolled [779 UC, 520 CD] were studied with median 270 days of follow-up (interquartile range [IQR] 116, 504). 671 [52%] were female, mean age 42 years (standard deviation [sd] 16), mean body mass index [BMI] 26 [sd 5.3]. At registration, 483 [37%] were using advanced therapies. Median adherence to fortnightly quality of life reporting and quarterly outcomes was 100% [IQR 48, 100%] and 100% [IQR 75, 100%], respectively. In the previous 12 months, prednisolone use was reported by 229 [29%] patients with UC vs 81 [16%] with CD, p <0.001; 202 [16%] for <3 months; and 108 [8%] for >3 months. An IBD-related intervention was reported by 174 [13%] patients, and 80 [6%] reported an unplanned hospital admission. There were high rates of fatigue [50%] and mood disturbance [23%]. CONCLUSIONS: Outcomes reported by patients illustrate the scale of the therapeutic deficit in current care. Proof of principle is demonstrated that PROM data can be collected continuously with little burden on health care professionals. This may become a metric for quality improvement programmes or to compare outcomes.

Impact of Artificial Intelligence on Miss Rate of Colorectal Neoplasia.

BACKGROUND & AIMS: Artificial intelligence (AI) may detect colorectal polyps that have been missed due to perceptual pitfalls. By reducing such miss rate, AI may increase the detection of colorectal neoplasia leading to a higher degree of colorectal cancer (CRC) prevention. METHODS: Patients undergoing CRC screening or surveillance were enrolled in 8 centers (Italy, UK, US), and randomized (1:1) to undergo 2 same-day, back-to-back colonoscopies with or without AI (deep learning computer aided diagnosis endoscopy) in 2 different arms, namely AI followed by colonoscopy without AI or vice-versa. Adenoma miss rate (AMR) was calculated as the number of histologically verified lesions detected at second colonoscopy divided by the total number of lesions detected at first and second colonoscopy. Mean number of lesions detected in the second colonoscopy and proportion of false negative subjects (no lesion at first colonoscopy and at least 1 at second) were calculated. Odds ratios (ORs) and 95% confidence intervals (CIs) were adjusted by endoscopist, age, sex, and indication for colonoscopy. Adverse events were also measured. RESULTS: A total of 230 subjects (116 AI first, 114 standard colonoscopy first) were included in the study analysis. AMR was 15.5% (38 of 246) and 32.4% (80 of 247) in the arm with AI and non-AI colonoscopy first, respectively (adjusted OR, 0.38; 95% CI, 0.23-0.62). In detail, AMR was lower for AI first for the ≤5 mm (15.9% vs 35.8%; OR, 0.34; 95% CI, 0.21-0.55) and nonpolypoid lesions (16.8% vs 45.8%; OR, 0.24; 95% CI, 0.13-0.43), and it was lower both in the proximal (18.3% vs 32.5%; OR, 0.46; 95% CI, 0.26-0.78) and distal colon (10.8% vs 32.1%; OR, 0.25; 95% CI, 0.11-0.57). Mean number of adenomas at second colonoscopy was lower in the AI-first group as compared with non-AI colonoscopy first (0.33 ± 0.63 vs 0.70 ± 0.97, P < .001). False negative rates were 6.8% (3 of 44 patients) and 29.6% (13 of 44) in the AI and non-AI first arms, respectively (OR, 0.17; 95% CI, 0.05-0.67). No difference in the rate of adverse events was found between the 2 groups. CONCLUSIONS: AI resulted in an approximately 2-fold reduction in miss rate of colorectal neoplasia, supporting AI-benefit in reducing perceptual errors for small and subtle lesions at standard colonoscopy. CLINICALTRIALS: gov, Number: NCT03954548.

Research priorities to improve the health of children and adults with dysphagia: a National Institute of Health Research and Royal College of Speech and Language Therapists research priority setting partnership.

OBJECTIVE: To conduct the first UK-wide research priority setting project informing researchers and funders of critical knowledge gaps requiring investigation to improve the health and well-being of patients with eating, drinking and swallowing disorders (dysphagia) and their carers. DESIGN: A priority setting partnership between the National Institute of Health Research (NIHR) and the Royal College of Speech and Language Therapists using a modified nominal group technique. A steering group and NIHR representatives oversaw four project phases: (1) survey gathering research suggestions, (2) verification and aggregation of suggestions with systematic review research recommendations, (3) multistakeholder workshop to develop research questions, (4) interim priority setting via an online ranking survey and (5) final priority setting. SETTING: UK health services and community. PARTICIPANTS: Patients with dysphagia, carers and professionals who work with children and adults with dysphagia from the UK. RESULTS: One hundred and fifty-six speech and language therapists submitted 332 research suggestions related to dysphagia. These were mapped to 88 research recommendations from systematic reviews to form 24 'uncertainty topics' (knowledge gaps that are answerable by research). Four patients, 1 carer and 30 healthcare professionals collaboratively produced 77 research questions in relation to these topics. Thereafter, 387 patients, carers and professionals with experience of dysphagia prioritised 10 research questions using an interim prioritisation survey. Votes and feedback for each question were collated and reviewed by the steering and dysphagia reference groups. Nine further questions were added to the long-list and top 10 lists of priority questions were agreed. CONCLUSION: Three top 10 lists of topics grouped as adults, neonates and children, and all ages, and a further long list of questions were identified by patients, carers and healthcare professionals as research priorities to improve the lives of those with dysphagia.

Single-copy detection of somatic variants from solid and liquid biopsy.

Accurate detection of somatic variants, against a background of wild-type molecules, is essential for clinical decision making in oncology. Existing approaches, such as allele-specific real-time PCR, are typically limited to a single target gene and lack sensitivity. Alternatively, next-generation sequencing methods suffer from slow turnaround time, high costs, and are complex to implement, typically limiting them to single-site use. Here, we report a method, which we term Allele-Specific PYrophosphorolysis Reaction (ASPYRE), for high sensitivity detection of panels of somatic variants. ASPYRE has a simple workflow and is compatible with standard molecular biology reagents and real-time PCR instruments. We show that ASPYRE has single molecule sensitivity and is tolerant of DNA extracted from plasma and formalin fixed paraffin embedded (FFPE) samples. We also demonstrate two multiplex panels, including one for detection of 47 EGFR variants. ASPYRE presents an effective and accessible method that simplifies highly sensitive and multiplexed detection of somatic variants.

Using quality improvement to implement consensus guidelines for postnatal steroid treatment of preterm infants with developing bronchopulmonary dysplasia.

OBJECTIVE: Achieve over 90% adherence to consensus guidelines on use of postnatal steroids (PNS) in preterm infants for bronchopulmonary dysplasia (BPD) within 6 months. METHODS: A multidisciplinary team formulated and implemented consensus guidelines using the Plan-Do-Study-Act method of quality improvement. Outcome measure was rate of compliance to guidelines, process measure was age of starting PNS treatment, and balancing measure was rate of repeat steroid courses. RESULTS: Retrospective application of guidelines to preceding 10 months showed mean baseline compliance rate of 71% (n = 42). After implementation, compliance escalated to a mean rate of 96% within 6 months. Rate of PNS treatment ≤ 30 days of life increased from 50 to 80%, while rate of repeat PNS was unchanged. CONCLUSIONS: Compliance with new guidelines for PNS treatment of BPD was quickly attained using simple quality improvement interventions. Further study is needed to evaluate effects of these guidelines on clinical outcomes.

Nickel-Carbon-Zirconium Material Derived from Nickel-Oxide Clusters Installed in a Metal-Organic Framework Scaffold by Atomic Layer Deposition.

Atomic layer deposition is employed to install nickel oxide into NU-1000. Upon heating to 900 °C under nitrogen, a carbon material containing ZrO2 and Ni is formed. In notable contrast to the parent metal-organic framework, the pyrolyzed material is: (a) stable in highly alkaline solutions (typical conditions for water electro-oxidation) and (b) electrically conductive and thus able to deliver oxidizing equivalents (holes) to catalytic sites located far from the underlying conductive-glass electrode. The pyrolysis-derived material was characterized and its electrocatalytic activity for oxygen evolution was investigated.

Endoscopic Disease Activity in Inflammatory Bowel Disease.

Endoscopic scoring systems in Crohn's disease and ulcerative colitis aim to translate the assessment of mucosal disease activity into a quantified value. This value seeks to provide a clear, objective record of the endoscopic mucosal severity, which can then be used to guide medical management decisions. The primary driver of all endoscopic indices, however, is to define a scale of responsiveness for therapeutic endpoints in clinical trials. Mucosal healing now has widespread acceptance as a therapeutic and clinical endpoint, but despite the development of multiple endoscopic scoring systems, the endoscopic definition has yet to be resolved. This review describes recent advances in endoscopic scoring systems for ulcerative colitis (Mayo Clinic endoscopy subscore, UCEIS, and UCCIS among others) and for Crohn's disease.

New and emerging endoscopic haemostasis techniques.

Endoscopic treatment has been accepted as first-line treatment of upper gastrointestinal bleeding, both for variceal as well as for non-variceal haemorrhage. Dual modality treatment including injection therapy with mechanical or thermal haemostatic techniques has shown superior outcome compared with injection monotherapy in non-variceal bleeding. During recent years, new endoscopic devices have been developed and existing endoscopic techniques have been adapted to facilitate primary control of bleeding or achieve haemostasis in refractory haemorrhage. For mechanical haemostasis, larger, rotatable and repositionable clips have been developed; multiple-preloaded clips are also available now. Over the scope clips allow to ligate larger vessels and can close ulcer defects up to 20 mm. Topical, easily applied substances withdraw fluid from the blood and thereby initiate blood clotting. This can be helpful in diffuse oozing bleeding, for example, from tumour or hypertensive gastropathy and has also shown promising results in variceal and arterial bleeding as bridging before definitive treatment is available. Radiofrequency ablation and multiband ligation have emerged as new tools in the endoscopic management of gastric antral vascular ectasia. In acute refractory variceal bleeding, a covered and removable oesophagus stent can provide tamponade and gain time for transport to an interventional endoscopic centre or for radiological intervention such as TIPS.

Mucosal healing as a target of therapy for colonic inflammatory bowel disease and methods to score disease activity.

Mucosal healing is an important therapeutic end point in clinical trials and clinical practice. There is no validated definition of mucosal healing in patients with inflammatory bowel disease, although the benefits of achieving mucosal healing include decreased need for corticosteroids, sustained clinical remission, decreased colectomy, and bowel resection. The Ulcerative Colitis Endoscopic Index of Severity is the only validated endoscopic index in ulcerative colitis. The Crohn's Disease Endoscopic Index of Severity and the Simple Endoscopic Score for Crohn's Disease are validated for Crohn disease, and the Rutgeerts Postoperative Endoscopic Index is used to predict recurrence after an ileocolic resection.

Cdx genes, inflammation and the pathogenesis of Barrett's metaplasia.

Metaplasia is the conversion of one cell or tissue type to another and can predispose patients to neoplasia. Perhaps one of the best-known examples of metaplasia is Barrett's metaplasia (BM), a pathological condition in which the distal oesophageal epithelium switches from stratified squamous to intestinal-type columnar epithelium. BM predisposes to oesophageal adenocarcinoma and is the consequence of long-term acid bile reflux. The incidence of BM and oesophageal adenocarcinoma has risen dramatically in recent years. A key event in the pathogenesis of BM is the induction of oesophageal CDX2 expression. Importantly, recent data reveal the molecular mechanisms that link inflammation in the development of Barrett's metaplasia, CDX2 and the progression to cancer. This review highlights the relationship between inflammation, metaplasia and carcinogenesis.