Evaluation of two new highly multiplexed PCR assays as an alternative to next‐generation sequencing for IDH1/2 mutation detection

IDH1 and IDH2 somatic mutations have been identified in solid tumors and blood malignancies. The development of inhibitors of mutant IDH1 and IDH2 in the past few years has prompted the development of a fast and sensitive assay to detect IDH1 ^R132 , IDH2 ^R140 and IDH2 ^R172 mutations to identify patients eligible for these targeted therapies. This study aimed to compare two new multiplexed PCR assays – an automated quantitative PCR (qPCR) on the PGX platform and a droplet digital PCR (ddPCR) with next‐generation sequencing (NGS) for IDH1/2 mutation detection. These assays were evaluated on 102 DNA extracted from patient peripheral blood, bone marrow and formalin‐fixed paraffin‐embedded tissue samples with mutation allelic frequency ranging from 0.6% to 45.6%. The ddPCR assay had better analytical performances than the PGX assay with 100% specificity, 100% sensitivity and a detection limit down to 0.5% on IDH1 ^R132 , IDH2 ^R140 and IDH2 ^R172 codons, and a high correlation with NGS results. Therefore, the new highly multiplexed ddPCR is a fast and cost‐effective assay that meets most clinical needs to identify and follow cancer patients in the era of anti‐IDH1/2‐targeted therapies.     

Reliable or not? An automated classification of webpages about early childhood vaccination using supervised machine learning

ObjectiveTo investigate the applicability of supervised machine learning (SML) to classify health-related webpages as ‘reliable’ or ‘unreliable’ in an automated way.MethodsWe collected the textual content of 468 different Dutch webpages about early childhood vaccination. Webpages were manually coded as ‘reliable’ or ‘unreliable’ based on their alignment with evidence-based vaccination guidelines. Four SML models were trained on part of the data, whereas the remaining data was used for model testing.ResultsAll models appeared to be successful in the automated identification of unreliable (F1 scores: 0.54–0.86) and reliable information (F1 scores: 0.82–0.91). Typical words for unreliable information are ‘dr’, ‘immune system’, and ‘vaccine damage’, whereas ‘measles’, ‘child’, and ‘immunization rate’, were frequent in reliable information. Our best performing model was also successful in terms of out-of-sample prediction, tested on a dataset about HPV vaccination.ConclusionAutomated classification of online content in terms of reliability, using basic classifiers, performs well and is particularly useful to identify reliable information.Practice implicationsThe classifiers can be used as a starting point to develop more complex classifiers, but also warning tools which can help people evaluate the content they encounter online.     

Detection of circulating tumour DNA after neoadjuvant chemoradiotherapy in patients with locally advanced oesophageal cancer

Active surveillance instead of standard surgery after neoadjuvant chemoradiotherapy (nCRT) has been proposed for patients with oesophageal cancer. Circulating tumour DNA (ctDNA) may be used to facilitate selection of patients for surgery. We show that detection of ctDNA after nCRT seems highly suggestive of major residual disease. Tumour biopsies and blood samples were taken before, and 6 and 12 weeks after, nCRT. Biopsies were analysed with regular targeted next-generation sequencing (NGS). Circulating cell-free DNA (cfDNA) was analysed using targeted NGS with unique molecular identifiers and digital polymerase chain reaction. cfDNA mutations matching pre-treatment biopsy mutations confirmed the presence of ctDNA. In total, 31 patients were included, of whom 24 had a biopsy mutation that was potentially detectable in cfDNA (77%). Pre-treatment ctDNA was detected in nine of 24 patients (38%), four of whom had incurable disease progression before surgery. Pre-treatment ctDNA detection had a sensitivity of 47% (95% CI 24–71) (8/17), specificity of 85% (95% CI 42–99) (6/7), positive predictive value (PPV) of 89% (95% CI 51–99) (8/9), and negative predictive value (NPV) of 40% (95% CI 17–67) (6/15) for detecting major residual disease (>10% residue in the resection specimen or progression before surgery). After nCRT, ctDNA was detected in three patients, two of whom had disease progression. Post-nCRT ctDNA detection had a sensitivity of 21% (95% CI 6–51) (3/14), specificity of 100% (95% CI 56–100) (7/7), PPV of 100% (95% CI 31–100) (3/3), and NPV of 39% (95% CI 18–64) (7/18) for detecting major residual disease. The addition of ctDNA to the current set of diagnostics did not lead to more patients being clinically identified with residual disease. These results indicate that pre-treatment and post-nCRT ctDNA detection may be useful in identifying patients at high risk of disease progression. The addition of ctDNA analysis to the current set of diagnostic modalities may not improve detection of residual disease after nCRT. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.     

An Indonesian slimming drug with undeclared ingredients causing harm

This paper reports the presence of undeclared drugs in the herbal slimming supplement Sulami®. The four cases of the adverse drug reactions related to Sulami® were reported to the Dutch Pharmacovigilance Centre (Lareb) or the Dutch Poisons Information Centre (DPIC). The analysis of all four collected samples revealed adulteration with sibutramine and canrenone. Both drugs can cause serious adverse drug reactions. From a legal point of view, it is clear that Sulami® does not meet the legal requirement for safety. As defined in the European General Food Law Regulation, food business operators are responsible for food safety. This also applies to online store owners who sell herbal preparations. Thus, it is clear that it is forbidden to sell Sulami® on the European and Dutch market. Collaboration between involved national authorities makes it possible to identify risky products. This allows the nationally responsible regulators to take targeted action. They can call on users to report sell points what makes it possible to arrest the sellers and confiscate the dangerous products. Beyond the national, also, the European enforcement organizations should take legal measures where possible, to protect public health. The Heads of Food Safety Agencies Working Group on Food Supplements “an Initiative on European level” is a good example of efforts to improve consumer safety.