Technical Validation of a Next-Generation Sequencing Assay for Detecting Actionable Mutations in Patients with Gastrointestinal Cancer

Targeted next-generation sequencing is becoming increasingly common as a clinical diagnostic and prognostic test for patient- and tumor-specific genetic profiles as well as to optimally select targeted therapies. Here, we describe a custom-developed, next-generation sequencing test for detecting single-nucleotide variants (SNVs) and short insertions and deletions (indels) in 93 genes related to gastrointestinal cancer from routine formalin-fixed, paraffin-embedded clinical specimens. We implemented a validation strategy, based on the College of American Pathologists requirements, using reference DNA mixtures from cell lines with known genetic variants, which model a broad range of allele frequencies. Test sensitivity achieved >99% for both SNVs and indels, with allele frequencies >10%, with high specificity (97.4% for SNVs and 93.6% for indels). We further confirmed test accuracies using primary formalin-fixed, paraffin-embedded colorectal cancer specimens characterized by alternative and conventional clinical diagnostic technologies. Robust performance was observed on the formalin-fixed, paraffin-embedded specimens: sensitivity was 97.2% and specificity was 99.2%. We also observed high intrarun and inter-run reproducibility, as well as a low cross-contamination rate. Overall assessment using cell line samples and formalin-fixed, paraffin-embedded samples showed that our custom next-generation sequencing assay has consistent detection sensitivity down to 10% variant frequency.

Work-exacerbated asthma in a workers' compensation population

BACKGROUND

Asthma is becoming more prevalent with large numbers of individuals suffering from work-exacerbated asthma.

AIMS

To examine the characteristics of workplace exposures and working days lost in relation to work-exacerbated asthma (WEA) in a workers' compensation population.

METHODS

An analysis of accepted workers' compensation asthma claims in Ontario over a 5-year period. Claims among the top three industry groups were categorized based on working time lost of 1 day or less, 2-5 days and 6 days or more. Attributable agents were subdivided into dusts, smoke, chemicals and sensitizers.

RESULTS

Among the asthma claims, 72% (645) fulfilled criteria for WEA from their history. The commonest industry groups were services, education and health care, with 270 claims that met our analysis requirements. Within these industry groups, education had a lower proportion of workers with short exacerbations (missing 1 day or less: 27%) while the health care industry had a higher than expected proportion of short exacerbations (55%). The agents to which WEA was attributed differed across the groups, with dusts having the highest proportion in the education group (65%), smoke in the service industry (34%) and sensitizers in health care (41%). Those agents more commonly attributed to exacerbations tended to have lower rates of prolonged exacerbation compared with less commonly involved agents.

CONCLUSIONS

The morbidity of WEA and the type of agents to which it was attributed varied between industry groups.

Essence of Time in Construction Contracts

The building industry has in recent years seen huge costs incurreddue to disputes arising on notice requirement clauses. Theseclaims could have been averted if the parties had been diligent inproviding the necessary notices. This article sets out to explorethe law briefl y as interpreted by the courts in common law andequity and discuss the possibility of defence under the principle ofpromissory estoppel. More importantly it also shares the author’sview on how such pitfalls could have been prevented by givingthe proper notices within the timeline required by the contractconditions. It cannot be emphasised enough that contractorswould be wise to comply strictly with the notice provisions in thecontract instead of relying on the estoppel principle or waiver orunconscionability to save their day. Notice clauses essentiallyrequire a competent contracts administrator to follow the time lineprovided in the contract conditions and would be most effective ifthe project team worked closely with the contracts administratorto ensure that proper notices are given when directions orinstructions are received. Although it is common to see noticeclauses which make it a condition precedent for a contractor to beentitled to claim for an extension of time or loss and expense claimbeing interpreted restrictively, in any litigation or arbitration it isalways diffi cult to predict how the courts or tribunal would be willingto uphold such notice clause. It is therefore in the interest of theparties that notice clauses should be properly observed. Suffi ceto say, failure to comply with a notice clause and time bar may befatal to a claim.

PlasmaKinetic™ (bipolar) transurethral resection of prostate: a prospective trial to study pathological artefacts, surgical parameters and clinical outcomes

INTRODUCTION

The aims of the study were to compare the degree of cautery artefacts in prostatic chips between monopolar and PlasmaKinetic™ transurethral resection of prostate (TURP), and to determine if there is any difference in the intraoperative and post surgical parameters between them.

METHODS

After institutional review board approval, patients were prospectively enrolled to undergo PlasmaKinetic™ TURP. Their parameters were compared with those of the historical monopolar TURP controls. All histological specimens were reviewed by a single senior pathologist.

RESULTS

46 patients were recruited to undergo PlasmaKinetic™ TURP. The resection time was significantly longer for the bipolar group compared to the monopolar group (50.2 versus 36.7 min, p-value is 0.001). The speed of resection (resection weight/time) was lower for the bipolar group (0.45 versus 0.56 g/min, p-value is 0.017). More irrigant was used for the bipolar group (21.2 versus 15.6 litres, p-value is 0.001) intraoperatively. There was no statistically significant difference in terms of intraoperative drop in haemoglobin and serum sodium change between the two groups. There seems to be a lesser degree of cautery artefacts in the PlasmaKinetic™ group than the monopolar group (42.17 versus 45.07 microns); however, this was not statistically significant (p-value is 0.452).

CONCLUSION

Bipolar TURP seems to result in a lesser degree of cautery artefacts when compared to conventional monopolar TURP, albeit statistically insignificant, compared to monopolar TURP. TURP also resulted in a longer resection time and increased irrigant use, but no difference in blood loss and serum sodium levels.

Updated survival results of the randomized phase II study comparing cisplatin/capecitabine (CX) with epirubicin plus CX (ECX) in advanced gastric cancer (AGC)

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Background: We previously reported results of a randomized study showing that CX is equally active to ECX in terms of progression-free survival (PFS) (Yun et al. Eur J Cancer. 2010). Here we report updated overall survival (OS) results with an additional 12 months' follow-up.

Methods: Ninety-one chemotherapy-naïve patients with histologically-confirmed, measurable AGC were randomized to receive CX (cisplatin 75 mg/m2 iv on day 1 and capecitabine 1,000 mg/m2 bid po on days 1-14, n=45) or ECX (epirubicin 50 mg/m2 plus CX, n=44) every 3 weeks. After CX or ECX had failed, second-line chemotherapy (SLC) was recommended for all patients if their performance status was preserved.

Results: Treatment duration was similar for both arms (4.4 for CX v 4.2 months for ECX). There was no relevant difference in the occurrence of overall grade 3 or 4 toxicities between the CX and ECX arms (80% v 78%, respectively; p=0.516). However, none in the CX and 12% in the ECX arm discontinued treatment because of toxicity. There were no significant differences in therapeutic efficacy between CX and ECX with respect to the response rate (38% v 37%, respectively), PFS (6.4 v 6.5 months), as well as OS (12.7 v 13.8 months; p=0.51). After failure, 60% of patients (26 CX and 28 ECX patients) received SLC. However, OS was not differed whether a patient was treated with SLC or not (13.1 v 11.2 months; p=0.94).

Conclusions: The present analysis confirms previous findings that both CX and ECX appear to be comparatively active as first-line chemotherapy for AGC. Furthermore, the role of SLC in AGC warrants further evaluation.

No significant financial relationships to disclose.

Elevated LDH and paranasal sinus involvement are risk factors for central nervous system involvement in patients with peripheral T-cell lymphoma

Background: The incidence and risk factors of central nervous system (CNS) involvement in peripheral T-cell lymphomas (PTCLs) are still unclear.

Patients and methods: We analyzed 228 patients with PTCLs, excluding cases of extranodal natural killer/T-cell lymphoma and primary cutaneous T-cell lymphoma, by retrospectively collecting the clinical features and outcomes of the patients.

Results: Twenty events (8.77%, 20/228) of CNS involvement were observed during a median follow-up period of 13.9 months (range 0.03–159.43). Based on univariate analysis, elevated serum lactate dehydrogenase (LDH) level [P = 0.019, relative risk (RR) 5.904, 95% confidence interval (CI) 1.334–26.123] and involvement of the paranasal sinus (P = 0.032, RR 3.137, 95% CI 1.105–8.908) adversely affect CNS involvement. In multivariate analysis, both were independently poor prognostic factors for CNS relapse [elevated LDH level: P = 0.011, hazard ratio (HR) 6.716, 95% CI 1.548–29.131; involvement of the paranasal sinus: P = 0.008, HR 3.784, 95% CI 1.420–10.083]. The survival duration of patients with CNS involvement was significantly shorter than that of the patients without CNS involvement (P = 0.009), with median overall survival of 7.60 months (95% CI of 4.92–10.28) versus 27.43 months (95% CI of 0.00–57.38), respectively.

Conclusions: Elevated LDH level and involvement of the paranasal sinus are two risk factors for CNS involvement in patients with PTCLs. Considering the poor prognoses after CNS relapse, prophylaxis should be considered with the presence of any risk factor.