Detection of NTRK Fusions and TRK Expression and Performance of pan-TRK Immunohistochemistry in Routine Diagnostics:Results from a Nationwide Community-Based Cohort

Gene fusions involving NTRK1, NTRK2, and NTRK3 are rare drivers of cancer that can be targeted with histology-agnostic inhibitors. This study aimed to determine the nationwide landscape of NTRK/TRK testing in the Netherlands and the usage of pan-TRK immunohistochemistry (IHC) as a preselection tool to detect NTRK fusions. All pathology reports in 2017–2020 containing the search term ‘TRK’ were retrieved from the Dutch Pathology Registry (PALGA). Patient characteristics, tumor histology, NTRK/TRK testing methods, and reported results were extracted. NTRK/TRK testing was reported for 7457 tumors. Absolute testing rates increased from 815 (2017) to 3380 (2020). Tumors were tested with DNA/RNA-based molecular assay(s) (48%), IHC (47%), or in combination (5%). A total of 69 fusions involving NTRK1 (n = 22), NTRK2 (n = 6) and NTRK3 (n = 41) were identified in tumors from adult (n = 51) and pediatric (n = 18) patients. In patients tested with both IHC and a molecular assay (n = 327, of which 29 NTRK fusion-positive), pan-TRK IHC had a sensitivity of 77% (95% confidence interval (CI), 56–91) and a specificity of 84% (95% CI, 78–88%). These results showed that pan-TRK IHC has a low sensitivity in current routine practice and warrants the introduction of quality guidelines regarding the implementation and interpretation of pan-TRK IHC

Prevalence of KRAS p.(G12C) in stage IV NSCLC patients in the Netherlands:a nation-wide retrospective cohort study

OBJECTIVES: The recent accelerated FDA approval of sotorasib, a highly selective KRAS G12C inhibitor, offers new opportunities for the treatment of KRAS p.(G12C)-mutated non-squamous non-small cell lung cancer (NSCLC). The objective of the current study was to the determine the prevalence of KRAS mutations in stage IV non-squamous NSCLC in The Netherlands to reveal the potential impact of upcoming KRAS targeted therapy. MATERIALS AND METHODS: All patients diagnosed with stage IV non-squamous NSCLC in 2013, 2015 and 2017 in the Netherlands were selected by linking the nation-wide Netherlands Cancer Registry (NCR) and the Dutch Pathology Registry (PALGA). Demographic and pathological variables were retrieved from the pathology reports including sex, age, KRAS mutation status, molecular test method used, and the mutation status of other genes. RESULTS: Prevalence for any KRAS mutations in codon 12/13/61/146 was 39.1%. KRAS p.(G12C) was detected in 15.5% of all non-squamous NSCLC cases representing 39.6% of all KRAS-mutant cases. National testing rate for KRAS mutations increased from 70% in 2013 to 82% in 2017. Testing techniques changed significantly over time with next generation sequencing as the main used method in 2017 (71.6%) but did not affect prevalence of KRAS mutations over time. When KRAS was tested as part of a larger panel, the KRAS p.(G12C) mutation was frequently reported with a concurrent mutation in TP53 (47.7%) or STK11 (10.3%). CONCLUSION: The high prevalence for KRAS p.(G12C) offers a promising new specific treatment option for 15% of all stage IV non-squamous NSCLC patients

Considerable interlaboratory variation in PD-L1 positivity in a nationwide cohort of non-small cell lung cancer patients

Objectives: Immunohistochemical expression of programmed death-ligand 1 (PD-L1) is used as a predictive biomarker for prescription of immunotherapy to non-small cell lung cancer (NSCLC) patients. Accurate assessment of PD-L1 expression is therefore crucial. In this study, the extent of interlaboratory variation in PD-L1 positivity in the Netherlands was assessed, using real-world clinical pathology data. Materials and Methods: Data on all NSCLC patients in the Netherlands with a mention of PD-L1 testing in their pathology report from July 2017 to December 2018 were extracted from PALGA, the nationwide network and registry of histo- and cytopathology in the Netherlands. PD-L1 positivity rates were determined for each laboratory that performed PD-L1 testing, with separate analyses for histological and cytological material. Two cutoffs (1% and 50%) were used to determine PD-L1 positivity. Differences between laboratories were assessed using funnel plots with 95% confidence limits around the overall mean. Results: 6,354 patients from 30 laboratories were included in the analysis of histology data. At the 1% cutoff, maximum interlaboratory variation was 39.1% (32.7%-71.8%) and ten laboratories (33.3%) differed significantly from the mean. Using the 50% cutoff, four laboratories (13.3%) differed significantly from the mean and maximum variation was 23.1% (17.2%-40.3%). In the analysis of cytology data, 1,868 patients from 23 laboratories were included. Eight laboratories (34.8%) differed significantly from the mean in the analyses of both cutoffs. Maximum variation was 41.2% (32.2%-73.4%) and 29.2% (14.7%-43.9%) using the 1% and 50% cutoffs, respectively. Conclusion: Considerable interlaboratory variation in PD-L1 positivity was observed. Variation was largest using the 1% cutoff. At the 50% cutoff, analysis of cytology data demonstrated a higher degree of variation than the analysis of histology data

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Incidental findings in the bowel cancer population screening program: other polyps and malignancies – A nationwide study

The introduction of bowel cancer population screening programs has had a profound impact on gastrointestinal pathology. While the focus is mainly on quality assurance of diagnoses relevant for the outcome of these programs (colorectal cancer and its precursors), incidental findings are increasingly diagnosed. The incidence of such findings is largely unknown. Therefore, we investigated the incidence of incidental findings within the national screening program of the Netherlands. From the Dutch nationwide pathology databank (PALGA), we retrieved all histological diagnoses of patients participating in the national bowel cancer screening program from the start in 2014 until 1/1/2021. Descriptive statistics were used. During these 7 years, in total 9407 other polyps and malignancies (262 per 10,000 colonoscopies) were diagnosed. The majority (65%) were classified as inflammatory polyps. The most common malignancies were neuroendocrine tumours (n = 198, 6 per 10,000 colonoscopies); less common were lymphomas (n = 64) and metastases (n = 33). Mesenchymal polyps, such as leiomyomas and lipomas, were relatively common (27 and 16 per 10,000 colonoscopies, respectively), in comparison with neural polyps such as perineuriomas, ganglioneuromas, and neurofibromas (respectively 3, 2, and 1 per 10,000 colonoscopies). This is the largest study into the incidence of nonconventional colorectal polyps and malignancies in a homogeneous cohort of asymptomatic patients. Several of these diagnoses may have consequences for treatment and follow-up, in particular the malignancies and detection of patients with hereditary cancer syndromes

Improved quality of patient care through routine second review of histopathology specimens prior to multidisciplinary meetings

Aim Double reading may be a valuable tool for improving quality of patient care by identifying diagnostic errors before final sign-out, but standard double reading would significantly increase costs of pathology. We assessed the added value of intradepartmental routine double reading of histopathology specimens prior to multidisciplinary meetings. Methods Diagnoses, treatment plans and prognoses of patients are often discussed at multidisciplinary meetings. As part of the daily routine, all pathology specimens to be discussed at upcoming multidisciplinary meetings undergo prior intradepartmental double reading. We identified all histopathology specimens from 2013 that underwent such double reading and determined major and minor discordance rates based on clinical relevance between the initial and consensus sign-out diagnoses. Results We included 6796 histopathology specimens that underwent double reading, representing approximately 8% of all histopathology cases at our institution in 2013. Double reading diagnoses were concordant in 6566 specimens (96.6%). Major and minor discordances were observed in 60 (0.9%) and 170 (2.5%) specimens, respectively. Urology specimens had significantly more discordances than other tissues of origin, Gleason grading of prostate cancer biopsies being the most frequent diagnostic problem. Furthermore, premalignant and malignant cases showed significantly higher discordance rates than the rest. The vast majority (90%) of discordances represented changes within the same diagnostic category (eg, malignant to malignant). Conclusions Routine double reading of histopathology specimens prior to multidisciplinary meetings prevents diagnostic errors. It resulted in about 1% discordant diagnoses of potential clinical significance, indicating that second review is worthwhile in terms of patient safety and quality of patient care

Improved quality of patient care through routine second review of histopathology specimens prior to multidisciplinary meetings

Aim Double reading may be a valuable tool for improving quality of patient care by identifying diagnostic errors before final sign-out, but standard double reading would significantly increase costs of pathology. We assessed the added value of intradepartmental routine double reading of histopathology specimens prior to multidisciplinary meetings. Methods Diagnoses, treatment plans and prognoses of patients are often discussed at multidisciplinary meetings. As part of the daily routine, all pathology specimens to be discussed at upcoming multidisciplinary meetings undergo prior intradepartmental double reading. We identified all histopathology specimens from 2013 that underwent such double reading and determined major and minor discordance rates based on clinical relevance between the initial and consensus sign-out diagnoses. Results We included 6796 histopathology specimens that underwent double reading, representing approximately 8% of all histopathology cases at our institution in 2013. Double reading diagnoses were concordant in 6566 specimens (96.6%). Major and minor discordances were observed in 60 (0.9%) and 170 (2.5%) specimens, respectively. Urology specimens had significantly more discordances than other tissues of origin, Gleason grading of prostate cancer biopsies being the most frequent diagnostic problem. Furthermore, premalignant and malignant cases showed significantly higher discordance rates than the rest. The vast majority (90%) of discordances represented changes within the same diagnostic category (eg, malignant to malignant). Conclusions Routine double reading of histopathology specimens prior to multidisciplinary meetings prevents diagnostic errors. It resulted in about 1% discordant diagnoses of potential clinical significance, indicating that second review is worthwhile in terms of patient safety and quality of patient care