Molecular Diagnostic Data Research Articles

Present Understanding of Biodiversity of Anoxygenic Phototrophic Bacteria in the Relic Lake Mogilnoe (Kildin Island, Murmansk oblast, Russia)

The relic Lake Mogilnoe, separated from the Barents Sea by a sand and pebble dam, is located in the high Arctic on the Kildin island (Murmansk region). This lake is a classic example of a meromictic basin of marine origin. The data obtained during the 2018 expedition showed changes in the hydrochemical regime of the lake that have occurred over the past 20 years. Sulfide concentration in the monimolimnion of the lake was as high as 140 mg/L. A tendency for salinization of the surface waters to 7 g/L has been noted. The Lake Mogilnoe is characterized by a discrepancy between the halocline and thermocline levels. The chemocline zone in the lake is below the halocline level. In a narrow oxygen-containing layer between 3 and 7.5 m, aerobic microflora of the marine type and marine fauna were present. The bacterial plate was formed at the boundary of the sulfide layer at ~8 m and mainly consisted of green sulfur bacteria (GSB). Brown-colored GSB species containing bacteriochlorophyll e were predominant. The previously formed concept of anaerobic phototrophic bacteria (APB) biodiversity based on morphological characteristics was modified using metagenomic data obtained by analyzing DNA from two samples of lake water in the chemocline zone, and was also supplemented by identifying new GSB species. Molecular diagnostic data confirmed the absolute dominance of the brackish species of GSB Chlorobium phaeovibrioides. This is the first on isolation and identification of brown- and green-colored Prosthecochloris aestuarii morphotypes from Lake Mogilnoe and identified, as well as of bacteriochlorophyll c-containing Prosthecochloris sp. The taxonomic position of Pelodyction phaem, which was constantly present in the Lake Mogilnoe, is discussed in detail. Despite the partial isolation of the ecosystem of Lake Mogilnoe from the Barents Sea, the main properties of the dominant GSB species of GSB and Prosthecochloris aestuarii turned out to be similar to those of the phylotypes living in lakes on the White Sea coast of the, which remained connected with the Barents Sea.

Circulating monocytes decrease significantly following disease-directed therapy and may reflect disease expansion in Langerhans Cell Histiocytosis.

We aimed to examine the association between relative monocytosis and the recurrence of pulmonary Langerhans Cell Histiocytosis. Clinical, laboratory, radiographic and treatment data for 86 patients with a histopathological diagnosis of Langerhans Cell Histiocytosis over a 20-year duration. Parameters such as biological sex, age at diagnosis, time to diagnosis, molecular diagnostic data and imaging were collected. Treatment responses were assessed predominantly through radiography, with RECIST 1.1 criteria applied to MRI or CT scans and PERCIST utilized for serial PET imaging. Investigators also assessed peripheral blood absolute monocyte count at various time points, including initial diagnosis and the most recently available value. While peripheral blood absolute monocyte count between the earliest assessed timepoint and latest value did not differ, the mean value on progression (0.94K/µL), however, was significantly higher than that following re-institution of therapy (0.31, p = 0.000794. Our observation of relative monocytosis on LCH disease progression may be related to an increase in circulating LCH on disease progression or from increased monocyte production for later differentiation into mature dendritic cells that participate in MHC Class 1 upregulation. This trend is especially evident in pulmonary LCH which is incited by tissue trauma and irritation by environmental factors. The phenomena observed in our study parallel other non-LCH cohorts, specifically in published findings from our own group in patients with Rosai Dorfman and Erdheim Chester Disease. To further elucidate the molecular underpinnings of LCH and explore the etiology of this monocyte trend, expanded integrated genomic-transcriptomic sequencing analyses to evaluate the molecular character of LCH and ultimately clarify the origin of this monocyte trend are in progress. These studies are poised to offer invaluable insight to the molecular mechanisms underlying LCH, specifically as they pertain to monocyte signaling and differentiation.

Parvovirus B19 Outbreak in Israel: Retrospective Molecular Analysis from 2010 to 2023.

This study presents an analysis of the epidemiological trends of parvovirus B19 (B19V) in Israel from 2010 to 2023, with particular emphasis on the outbreak in 2023. The analysis utilized molecular diagnostic data from individual patients obtained at the Central Virology Laboratory. Between 2010 and 2022, 8.5% of PCR-tested samples were positive for B19V, whereas in 2023, this percentage surged to 31% of PCR-tested samples. Throughout the study period, annual cycles consistently peaked in early spring/summer, with the most recent prominent outbreak occurring in 2016. Predominantly, diagnoses were made in children and women aged 20-39. Despite the notable surge in 2023, over 80% of positive cases continued to be observed in children and young women, with a decrease in cases during winter months. Furthermore, genotype 1a of the virus remained the predominant strain circulating during the outbreak. In light of these circumstances, consideration should be given to implementing screening measures, particularly among high-risk groups such as pregnant women.

Harmonizing the post-analytical phase: focus on the laboratory report.

The final, post-analytical, phase of laboratory testing is increasingly recognized as a fundamental step in maximizing quality and effectiveness of laboratory information. There is a need to close the loop of the total testing cycle by improving upon the laboratory report, and its notification to users. The harmonization of the post-analytical phase is somewhat complicated, mainly because it calls for communication that involves parties speaking different languages, including laboratorians, physicians, information technology specialists, and patients. Recently, increasing interest has been expressed in integrated diagnostics, defined as convergence of imaging, pathology, and laboratory tests with advanced information technology (IT). In particular, a common laboratory, radiology and pathology diagnostic reporting system that integrates text, sentinel images and molecular diagnostic data to an integrated, coherent interpretation enhances management decisions and improves quality of care.

Relative Monocytosis Is Predictive of Disease Progression and Confirmatory of Response Assessment in Langerhans Cell Histiocytosis

Introduction Langerhans cell histiocytosis (LCH) is a clonal histiocytic neoplasm, which arises when myeloid precursors expressing CD207 (Langerin) and CD1a expand and circulate as mature dendritic cells, clinically manifesting in multisystemic eosinophilic granulomas at osseous sites (notably the cranium), lungs, cutaneous tissue, and visceral structures (pituitary gland, liver, spleen). Molecular alterations in MAP kinase signaling are common, specifically in BRAFV600E, which is identified in greater than 50% of patients. Limited LCH is commonly managed with local therapies, such as surgery and radiation, while disseminated disease is managed with systemic therapies, including multi-agent chemotherapy or targeted agents, such as BRAF inhibitors. While diagnostic and management paradigms are well-established in LCH, clinical studies evaluating indicators of disease progression are lacking. Methods Clinical, laboratory, radiographic and treatment data for 49 patients with a histopathologic diagnosis of Langerhans Cell Histiocytosis treated at a single institution over a 20-year period was reviewed by multiple study investigators. Specific parameters reviewed included biological sex, age at and time to diagnosis, molecular diagnostic data by immunohistochemistry and/or next generation sequencing, diagnostic imaging utilized, treatment rendered, clinical and/or radiographic response. Radiography in all but 1/49 patients was used to assess treatment responses, by RECIST 1.1 where MRI, or CT was utilized and PERCIST for serial PET imaging. The peripheral blood absolute monocyte count (in K/µL) was also assessed in each patient at various timepoints, including at initial diagnosis and the most recent value. We also performed a more focused assessment of absolute monocytes at the time of disease progression (when applicable) and again following reinstitution of therapy. Statistical analyses to compare sets of data were conducted using unpaired two-sided t-tests. Results Of the 49 patients included in this analysis, 28 were female and 21 male, with an average age at diagnosis of approximately 38 years; time between symptom onset and diagnosis varied widely across the cohort but was generally less than 12 months. Molecular diagnostics were employed in only 8/49 patients, 3 by IHC, 4 by NGS and 1 by both; BRAFV600E was assessed in 6 patients and was positive in 2. Approach to imaging at diagnosis and throughout treatment varied but most commonly included conventional CT (25), followed by MRI (17) and PET (16). LCH was observed as a primary pulmonary disease in 18 patients (36.7%), as involvement of skull/CNS/ocular structures in 10 and as localized cutaneous involvement in 5. Complete responses were observed in 17 of 49 patients, 11/17 of whom underwent local therapy (radiation and/or surgery) at ≥1 point in his or her treatment course. On the other end of the spectrum, 5 patients never achieved any response and always had progressive/persistent disease, all of whom had been diagnosed with pulmonary LCH in the setting of chronic tobacco use. Peripheral blood absolute monocyte count between the earliest-assessed timepoint and latest value, lastly, did not differ. The mean value on progression (0.94 K/µL), however, was significantly higher than that following re-institution of therapy (0.31, p=0.0005) as depicted in Figure 1. Discussion The identification of relative monocytosis at the time of LCH progression was an unexpected finding in this study. LCH pathogenesis has been felt to berelated to dysregulated hematopoiesis and acquisition of somatic mutations during monocyte differentiation, ultimately driving clonal expansion of CD1a+/CD207+ histiocytes. Within this working model of disruption to monocyte differentiation, one explanation of our observed findings is a simple expansion in circulating monocytes as a manifestation of disease progressing throughout various tissues. Another possibility is that circulating monocytes are upregulated and later differentiate into mature dendritic cells for MHC Class I presentation. Similar observations have been made at our institution in cohorts of non-LCH histiocytosis, specifically Rosai Dorfman and Erdheim Chester Disease. Expanded integrated genomic-transcriptomic sequencing analyses to evaluate the molecular character of LCH and ultimately clarify the origin of this monocyte trend are currently underway.

Clinicopathological and molecular diagnostic features of early-onset gastric cancer: a study based on data from a single-center dedicated gastric cancer database

Objective: To clarify the clinicopathological, especially molecular, features of early-onset gastric cancer with the aim of informing analysis of treatment strategies. Methods: In this retrospective case-control study, we examined data from a dedicated gastric cancer database in Zhongshan Hospital affiliated to Fudan University. The original cohort comprised 2506 patients with gastric cancer who had undergone gastrectomy in Zhongshan Hospital Fudan University from July 2020 to October 2021, including 198 with early-onset gastric cancer (aged ≤45 years) and 2,308 with non-early gastric cancer. We used a simple random sampling method to select 396 of the 2,308 patients aged >45 years (ratio of 1:2) as the control group and then compared molecular diagnostic data and clinicopathological features of the two groups. Results: The median age was 39 years in the early-onset gastric cancer group, while 66 years in the control group. The clinicopathological features of early-onset gastric cancer included female predominance (59.1% [117/198] vs. 27.8% [110/396], χ2=54.816, P<0.001), less comorbidity (32.3% [64/198] vs. 57.1% [226/396], χ2=32.355, P<0.001), poorer differentiation (93.9% [186/198] vs. 74.5% [295/396], χ2=30.777, P<0.001) and higher proportion of diffuse type (40.4% [80/198] vs. 15.9% [63/396], χ2=69.639, P<0.001), distant metastasis (7.1% [14/198] vs. 2.8% [11/396], χ2=6.034, P=0.014). Regarding treatment, distal gastrectomy was more commonly performed than proximal gastrectomy (55.1% [109/198] vs. 47.0% [186/396], 1.5% [3/198] vs. 8.3% [33/396], χ2=11.644, P=0.003). Family history of gastric cancer, TNM stage, tumor size, lymph node dissection, nerve invasion, nodes harboring metastases, range of lymph node dissection, digestive tract reconstruction procedure, implementation of laparoscopic surgery, combined resection, and preoperative treatment did not differ significantly between the two groups (all P>0.05). Molecular diagnosis showed there was a smaller percentage of mismatch repair deficiency in the early-onset gastric cancer than in the control group (1.0% [2/198] vs. 10.1% [40/396], χ2=16.301, P<0.001), and a higher rate of positivity for Claudin 18.2 (77.8% [154/198] vs. 53.0% [210/396], χ2=5.442,P<0.001). HER-2 and Epstein-Barr virus positivity rates did not differ significantly between the two groups. Conclusion: Early-onset gastric cancer is a distinct type of gastric cancer with a high degree of malignancy, and treatment targeting Claudin 18.2 may be effective.

External validation of the Molecular International Prognostic Scoring System (IPSS-M) for myelodysplastic syndromes.

7056 Background: Myelodysplastic Syndromes (MDS) comprise of a group of clonal diseases characterized by dysplastic hematopoietic progenitor cells, leading to cytopenias and in select cases transformation to acute myeloid leukemia (AML). In June 2022 the Molecular International Prognostic Scoring System (IPSS-M) was developed to build on the traditional IPSS-R and is reported to be prognostic even with incomplete molecular data. We aimed to validate this scoring system with an external dataset, and utilize a patient population which typically does not contain complete molecular testing at diagnosis. Methods: This single center study at a tertiary medical center in New York, NY was conducted as an external validation of the IPSS-M. Patients with MDS who had documented peripheral blood counts, bone marrow biopsies, and cytogenetic data were identified in the institutional tissue bank. After eliminating repetitive patient samples, 405 patient entries, collected between July 7, 2010 and March 29, 2022 were included in this study. 392 patients had previously been categorized by IPSS-R score. 332 patients had at least one subsequent follow-up event. 94 patients had bone marrow biopsies that were peri-diagnostic (within 12 months of diagnosis). Results: Patients in the entire cohort had a median age of 74 years (range, 30-96). The median follow-up duration was 1.5 years (range 0.0-9.9 years). Nearly all patients had at least partial molecular diagnostic data. Other than PRPF8 mutations (0%), all other mutations included in the IPSS-M scoring system were tested in a subset of the study population. The most common mutations in the patient population were SF3B1 (20.4%), ASXL1 (17.6%), and SRSF2 (15.9%); 12.2% of patients had the del5q cytogenetic abnormality, and 5.6% were found to have at least one TP53 mutation; 2.7% were TP53 (multi-hit). 29% of all patients were up-staged from IPSS-R to IPSS-M score, while 12% were down-staged. At the time of study evaluation, there were 84 events; 61.3% of patients were alive at the time of analysis. The median overall survival was 3.6 years (25-75% range: 2.75-5.50 years). When limited to patients with peri-diagnostic bone marrow biopsies, there were statistically significant differences in overall survival between IPSS-M categories (p&lt;0.000001) as well as IPSS-R categories (p&lt;0.00001). There was no statistical difference in survival between IPSS-M categories (p=0.6) or IPSS-R categories (p = 0.2) if scores were calculated at any time point in the patient’s disease course. Conclusions: This study validates the utility of both the IPSS-M and the IPSS-R scoring systems, and notably retains important risk stratification with incomplete diagnostic data. Importantly, the scoring systems are not effectively prognostic as the disease progresses, and thus should only be utilized at or near the time of diagnosis.

Racial and socioeconomic disparities in glioblastoma outcomes: A single-center, retrospective cohort study.

Glioblastoma (GBM) is the most common malignant primary brain tumor. Emerging reports have suggested that racial and socioeconomic disparities influence the outcomes of patients with GBM. No studies to date have investigated these disparities controlling for isocitrate dehydrogenase (IDH) mutation and O-6-methylguanine-DNA methyltransferase (MGMT) status. Adult patients with GBM were retrospectively reviewed at a single institution from 2008 to 2019. Univariable and multivariable complete survival analyses were performed. A Cox proportional hazards model was used to assess the effect of race and socioeconomic status controlling for a priori selected variables with known relevance to survival. In total, 995 patients met inclusion criteria. Of these, 117 patients (11.7%) were African American (AA). The median overall survival for the entire cohort was 14.23months. In the multivariable model, AA patients had better survival compared with White patients (hazard ratio [HR], 0.37; 95% confidence interval [CI], 0.2-0.69). The observed survival difference was significant in both a complete case analysis model and a multiple imputations model accounting for missing molecular data and controlling for treatment and socioeconomic status. AA patients with low income (HR, 2.17; 95% CI, 1.04-4.50), public insurance (HR, 2.25; 95% CI, 1.04-4.87), or no insurance (HR, 15.63; 95% CI, 2.72-89.67) had worse survival compared with White patients with low income, public insurance, or no insurance, respectively. Significant racial and socioeconomic disparities were identified after controlling for treatment, GBM genetic profile, and other variables associated with survival. Overall, AA patients demonstrated better survival. These findings may suggest the possibility of a protective genetic advantage in AA patients. To best personalize treatment for and understand the causes of glioblastoma, racial and socioeconomic influences must be examined. The authors report their experience at the O'Neal Comprehensive Cancer Center in the deep south. In this report, contemporary molecular diagnostic data are included. The authors conclude that there are significant racial and socioeconomic disparities that influence glioblastoma outcome and that African American patients do better.

Real-world performance analysis of a novel computational method in the precision oncology of pediatric tumors.

The utility of routine extensive molecular profiling of pediatric tumors is a matter of debate due to the high number of genetic alterations of unknown significance or low evidence and the lack of standardized and personalized decision support methods. Digital drug assignment (DDA) is a novel computational method to prioritize treatment options by aggregating numerous evidence-based associations between multiple drivers, targets, and targeted agents. DDA has been validated to improve personalized treatment decisions based on the outcome data of adult patients treated in the SHIVA01 clinical trial. The aim of this study was to evaluate the utility of DDA in pediatric oncology. Between 2017 and 2020, 103 high-risk pediatric cancer patients (< 21years) were involved in our precision oncology program, and samples from 100 patients were eligible for further analysis. Tissue or blood samples were analyzed by whole-exome (WES) or targeted panel sequencing and other molecular diagnostic modalities and processed by a software system using the DDA algorithm for therapeutic decision support. Finally, a molecular tumor board (MTB) evaluated the results to provide therapy recommendations. Of the 100 cases with comprehensive molecular diagnostic data, 88 yielded WES and 12 panel sequencing results. DDA identified matching off-label targeted treatment options (actionability) in 72/100 cases (72%), while 57/100 (57%) showed potential drug resistance. Actionability reached 88% (29/33) by 2020 due to the continuous updates of the evidence database. MTB approved the clinical use of a DDA-top-listed treatment in 56 of 72 actionable cases (78%). The approved therapies had significantly higher aggregated evidence levels (AELs) than dismissed therapies. Filtering of WES results for targeted panels missed important mutations affecting therapy selection. DDA is a promising approach to overcome challenges associated with the interpretation of extensive molecular profiling in the routine care of high-risk pediatric cancers. Knowledgebase updates enable automatic interpretation of a continuously expanding gene set, a "virtual" panel, filtered out from genome-wide analysis to always maximize the performance of precision treatment planning.

Combinations of Single-Gene Biomarkers Can Precisely Stratify 1,028 Adult Gliomas for Prognostication.

Advanced genomic techniques have now been incorporated into diagnostic practice in neuro-oncology in the literature. However, these assays are expensive and time-consuming and demand bioinformatics expertise for data interpretation. In contrast, single-gene tests can be run much more cheaply, with a short turnaround time, and are available in general pathology laboratories. The objective of this study was to establish a molecular grading scheme for adult gliomas using combinations of commonly available single-gene tests. We retrospectively evaluated molecular diagnostic data of 1,275 cases of adult diffuse gliomas from three institutions where we were testing for IDH1/2 mutation, TERTp mutation, 1p19q codeletion, EGFR amplification, 10q deletion, BRAF V600E, and H3 mutations liberally in our regular diagnostic workup. We found that a molecular grading scheme of Group 1 (1p19q codeleted, IDH mutant), Group 2 (IDH mutant, 1p19q non-deleted, TERT mutant), Group 3 (IDH mutant, 1p19q non-deleted, TERT wild type), Group 4 (IDH wild type, BRAF mutant), Group 5 (IDH wild type, BRAF wild type and not possessing the criteria of Group 6), and Group 6 (IDH wild type, and any one of TERT mutant, EGFR amplification, 10q deletion, or H3 mutant) could significantly stratify this large cohort of gliomas for risk. A total of 1,028 (80.6%) cases were thus classifiable with sufficient molecular data. There were 270 cases of molecular Group 1, 59 cases of molecular Group 2, 248 cases of molecular Group 3, 27 cases of molecular Group 4, 117 cases of molecular Group 5, and 307 cases of molecular Group 6. The molecular groups were independent prognosticators by multivariate analyses and in specific instances, superseded conventional histological grades. We were also able to validate the usefulness of the Groups with a cohort retrieved from The Cancer Genome Atlas (TCGA) where similar molecular tests were liberally available. We conclude that a single-gene molecular stratification system, useful for fine prognostication, is feasible and can be adopted by a general pathology laboratory.

Taxonomic and identification review of adventive Fiorinia Targioni Tozzetti (Hemiptera, Coccomorpha, Diaspididae) of the United States.

This work provides general descriptions, illustrations, molecular diagnostic data, taxonomic keys, slide mounting recommendations, and Florida distribution records for Fiorinia Targioni Tozzetti species occurring in the USA. Species treated are F.externa Ferris, F.fioriniae (Targioni Tozzetti), F.japonica Kuwana, F.pinicola Maskell, F.phantasma Cockerell & Robinson, F.proboscidaria Green, and F.theae Green. New descriptions of second-instar males and females of all seven species in addition to first-instar nymphs and adult females of F.phantasma and F.proboscidaria are presented. Taxonomic keys to second-instar males and females are developed for the first time and previously available taxonomic keys to first-instar nymphs and adult females are improved. DNA sequences were used to further evaluate the monophyly of Fiorinia and provide additional diagnostic tools for Fiorinia species. Multigene phylogenetic analyses, COI barcoding methods, and examination of type material indicate that F.yongxingensis Liu, Cai & Feng, 2020, syn. nov. is a junior synonym of F.phantasma. A morphological survey of the genus demonstrates, for the first time, the utility of second-instar males for diagnostics. This study will help inform regulatory and pest management decisions by facilitating morphological and molecular identification of adventive Fiorinia species occurring in the USA.

Precision Medicine Approaches for Infantile-Onset Developmental and Epileptic Encephalopathies.

Epilepsy is an etiologically heterogeneous condition; however, genetic factors are thought to play a role in most patients. For those with infantile-onset developmental and epileptic encephalopathy (DEE), a genetic diagnosis is now obtained in more than 50% of patients. There is considerable motivation to utilize these molecular diagnostic data to help guide treatment, as children with DEEs often have drug-resistant seizures as well as developmental impairment related to cerebral epileptiform activity. Precision medicine approaches have the potential to dramatically improve the quality of life for these children and their families. At present, treatment can be targeted for patients with diagnoses in many genetic causes of infantile-onset DEE, including genes encoding sodium or potassium channel subunits, tuberous sclerosis, and congenital metabolic diseases. Precision medicine may refer to more intelligent choices of conventional antiseizure medications, repurposed agents previously used for other indications, novel compounds, enzyme replacement, or gene therapy approaches.

Twenty Years of Equine Piroplasmosis Research: Global Distribution, Molecular Diagnosis, and Phylogeny.

Equine piroplasmosis (EP), caused by the hemoparasites Theileria equi, Theileria haneyi, and Babesia caballi, is an important tick-borne disease of equines that is prevalent in most parts of the world. Infection may affect animal welfare and has economic impacts related to limitations in horse transport between endemic and non-endemic regions, reduced performance of sport horses and treatment costs. Here, we analyzed the epidemiological, serological, and molecular diagnostic data published in the last 20 years, and all DNA sequences submitted to GenBank database, to describe the current global prevalence of these parasites. We demonstrate that EP is endemic in most parts of the world, and that it is spreading into more temperate climates. We emphasize the importance of using DNA sequencing and genotyping to monitor the spread of parasites, and point to the necessity of further studies to improve genotypic characterization of newly recognized parasite species and strains, and their linkage to virulence.

Abstract 3215: ClinGen somatic cancer working group: Disseminating standardized cancer molecular diagnostic data and evidence through global collaboration and expert curation

Abstract The Clinical Genome (ClinGen) Resource is a US National Human Genome Research Institute (NHGRI)-funded program dedicated to building an expert curated and freely available central resource that defines the clinical relevance of genes and variants for use in precision medicine. Teams of experts in various clinical domains come together as working groups within ClinGen to facilitate the interpretation, annotation and utilization of genes-variants for clinical application. Somatic Cancer is one such ClinGen Clinical Domain Working Group (CDWG) that consists of over 90 members worldwide, including clinicians, clinical laboratory diagnosticians, genomic scientists and bioinformaticians. Members of this CDWG identify high priority somatic variants in different cancer types that require expert curation and consensus in their clinical interpretation. In order to accurately implement practice guidelines/standards for variant interpretation, the Somatic Cancer CDWG recently established a somatic Variant Curation Expert Panel (VCEP) approval process. Based on their interest and clinical domain expertise, a subset of the CDWG members formed somatic VCEPs to perform authoritative curation on the shortlisted genes-somatic variants within the context of a disease, therapeutic indication or biological pathway. Expert curation within these VCEPs is performed by utilizing guidelines such as those recommended by AMP/ASCO/CAP (Li et al. 2017) and the Somatic Cancer CDWG (Ritter et al. 2016). Wherever necessary, the somatic VCEPs will develop: 1) gene- and disease-specific modifications to address gaps in existing variant assessment guidelines, 2) quantitative approaches for variant interpretation, and 3) implement standardized protocols for annotating somatic variants in genes for a specific disease, drug or biological pathway. Furthermore, ClinGen recently formed the Cancer Variant Interpretation (CVI) committee to provide support, review and feedback on the provisional somatic variant interpretation proposals developed by the VCEPs. The CVI provides somatic VCEPs with a preliminary approval before the final approval by the ClinGen CDWG oversight committee and ultimately ‘expert panel' status in ClinVar, an NCBI-maintained database of clinically relevant gene variants. NTRK fusions in cancer is the first Somatic VCEP going through the ClinGen Somatic Expert Panel approval process. Alterations in the FGFR pathway in GU cancers is the second somatic VCEP under consideration. The Somatic CDWG uses the CIViC (Clinical Interpretation of Variants in Cancer) platform for curation of somatic variants. To date, the CDWG has curated 268 evidence items relating to cancer variants in CIViC, 6 assertions, and 33 evidence source suggestions. The ultimate goal of the Somatic CDWG is to enhance the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource and other cancer variant knowledgebases. Citation Format: Shruti Rao, Deborah Ritter, Arpad Danos, Gordana Raca, Angshumoy Roy, Kilannin Krysiak, Wan-Hsin Lin, Erica Barnell, Matthew McCoy, Beth Pitel, Dmitriy Sonkin, Jue Wang, Seyed Ali Hosseini, Shamini Selvarajah, Ian King, Rashmi Kanagal-Shamana, Xinjie Xu, Jeremy L. Warner, Funda Meric-Bernstam, Jason D. Merker, Marilyn Li, Alex H. Wagner, Malachi Griffith, Obi L. Griffith, Shashikant Kulkarni, Subha Madhavan. ClinGen somatic cancer working group: Disseminating standardized cancer molecular diagnostic data and evidence through global collaboration and expert curation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3215.

Rapid Detection of Airway Pathogens in Lung Transplant Recipients

Airway infections may necessitate prompt treatment in lung transplant recipients, given their immunosuppressed status, but maybe difficult to distinguish clinically from acute rejection, a potential antecedent of chronic lung allograft dysfunction and death. Traditional culture techniques can delay the time to diagnosis particularly for bacterial infections. We hypothesized that a rapid multiplex molecular assay could improve time to diagnosis and appropriate clinical decision making in lung transplant recipients. We performed a prospective observational clinical trial (NCT03933878) investigating the efficiency and accuracy of the BioFire Pneumonia Panel in the context of post-transplant bronchoscopy. This molecular assay tests the presence and/or quantity for 26 common airway bacterial and viral pathogens in under 2 hours. Prospectively enrolled lung transplant recipients had molecular and standard of care (SOC) diagnostics in parallel. Research clinicians performed shadow clinical decision making in real time using molecular diagnostic data in addition to clinical records. Time to report and interpretation were reported as median and interquartile ranges and compared by Wilcox rank-sum test. Agreement between methods, limited to pathogens on the molecular panel, was calculated by Gwet's AC1 statistic, which is robust despite skewed distributions. For the 148 enrolled subjects, molecular results were available at 3.8 [2.8-5.1] hours following bronchoscopy, which was 12.7 [6.3-30] hours prior to SOC viral results (P <0.001) and 1.8 [1.7-2.7] days prior to SOC bacterial culture results (P <0.001). Positive molecular results were interpreted 10.2 [7.9-23] hours following bronchoscopy, which was 2.4 [0.8-3.3] days less than SOC. Agreement between assays was 0.96 (95%CI 0.93-0.99) for bacteria and 0.92 (95% CI 0.86-0.97) for viruses. Of 24 positive molecular results, 5 resulted in a shadow antibiotic recommendation, whereas SOC results lead to antimicrobial initiation for 43. Notable molecular panel deficiencies included fungal pathogens and H. parainfluenzae, accounting for 17 and 13 of the 43 actionable SOC results, respectively. This molecular diagnostic could allow more rapid initiation of antibiotics in select cases and comparable viral detection versus SOC. However, as common lung transplant pathogens are not included in this panel, it cannot replace SOC microbial cultures.

A neuropathology-based approach to epilepsy surgery in brain tumors and proposal for a new terminology use for long-term epilepsy-associated brain tumors

Every fourth patient submitted to epilepsy surgery suffers from a brain tumor. Microscopically, these neoplasms present with a wide-ranging spectrum of glial or glio-neuronal tumor subtypes. Gangliogliomas (GG) and dysembryoplastic neuroepithelial tumors (DNTs) are the most frequently recognized entities accounting for 65 % of 1,551 tumors collected at the European Epilepsy Brain Bank (n = 5,842 epilepsy surgery samples). These tumors often present with early seizure onset at a mean age of 16.5 years, with 77 % of neoplasms affecting the temporal lobe. Relapse and malignant progression are rare events in this particular group of brain tumors. Surgical resection should be regarded, therefore, also as important treatment strategy to prevent epilepsy progression as well as seizure- and medication-related comorbidities. The characteristic clinical presentation and broad histopathological spectrum of these highly epileptogenic brain tumors will herein be classified as “long-term epilepsy associated tumors—LEATs”. LEATs differ from most other brain tumors by early onset of spontaneous seizures, and conceptually are regarded as developmental tumors to explain their pleomorphic microscopic appearance and frequent association with Focal Cortical Dysplasia Type IIIb. However, the broad neuropathologic spectrum and lack of reliable histopathological signatures make these tumors difficult to classify using the WHO system of brain tumors. As another consequence from poor agreement in published LEAT series, molecular diagnostic data remain ambiguous. Availability of surgical tissue specimens from patients which have been well characterized during their presurgical evaluation should open the possibility to systematically address the origin and epileptogenicity of LEATs, and will be further discussed herein. As a conclusion, the authors propose a novel A–B–C terminology of epileptogenic brain tumors (“epileptomas”) which hopefully promote the discussion between neuropathologists, neurooncologists and epileptologists. It must be our future mission to achieve international consensus for the clinico-pathological classification of LEATs that would also involve World Health Organization (WHO) and the International League against Epilepsy (ILAE).

A Population-Based Cohort Study of Mycobacterium tuberculosis Beijing Strains: An Emerging Public Health Threat in an Immigrant-Receiving Country?

Introduction Mycobacterium tuberculosis Beijing strains are frequently associated with tuberculosis outbreaks and drug resistance. However, contradictory evidence and limited study generalizability make it difficult to foresee if the emergence of Beijing strains in high-income immigrant-receiving countries poses an increased public health threat. The purpose of this study was to determine if Beijing strains are associated with high risk disease presentations relative to other strains within Canada.MethodsThis was a retrospective population-based study of culture-confirmed active TB cases in a major immigrant-receiving province of Canada in 1991 through 2007. Of 1,852 eligible cases, 1,826 (99%) were successfully genotyped. Demographic, clinical, and mycobacteriologic surveillance data were combined with molecular diagnostic data. The main outcome measures were site of disease, lung cavitation, sputum smear positivity, bacillary load, and first-line antituberculosis drug resistance.ResultsA total of 350 (19%) patients had Beijing strains; 298 (85%) of these were born in the Western Pacific. Compared to non-Beijing strains, Beijing strains were significantly more likely to be associated with polyresistance (aOR 1.8; 95% CI 1.0–3.3; p = 0.046) and multidrug-resistance (aOR 3.4; 1.0–11.3; p = 0.049). Conversely, Beijing strains were no more likely than non-Beijing strains to be associated with respiratory disease (aOR 1.3; 1.0–1.8; p = 0.053), high bacillary load (aOR 1.2; 0.6–2.7), lung cavitation (aOR 1.0; 0.7–1.5), immediately life-threatening forms of tuberculosis (aOR 0.8; 0.5–1.6), and monoresistance (aOR 0.9; 0.6–1.3). In subgroup analyses, Beijing strains only had a significant association with multidrug-resistant tuberculosis (aOR 6.1; 1.2–30.4), and an association of borderline significance with polyresistant tuberculosis (aOR 1.8; 1.0–3.5; p = 0.062), among individuals born in the Western Pacific.ConclusionOther than an increased risk of polyresistant or multidrug-resistant tuberculosis, Beijing strains appear to pose no more of a public health threat than non-Beijing strains within a high-income immigrant-receiving country.

Myelodysplastic Syndromes Arising in Patients With Germline TP53 Mutation and Li-Fraumeni Syndrome

Li-Fraumeni syndrome (LFS), characterized by predisposition to early onset of a variety of malignancies, is usually associated with germline mutation of the tumor-suppressor gene, TP53. Mutation carriers are at increased risk of multiple primary tumors, many of which arise in previous radiation-therapy sites. In patients with LFS, acute myeloid leukemia is uncommon and myelodysplastic syndrome (MDS) is rare. To evaluate the morphologic, cytogenetic, and molecular diagnostic findings of 3 unique cases of MDS arising in patients with germline TP53 mutation, 2 with classic LFS. We searched the Li-Fraumeni Syndrome Registry in the Department of Genetics at the University of Texas M. D. Anderson Cancer Center (Houston, Texas) and identified 3 patients with documented germline TP53 mutations or LFS who had developed MDS during a period of 6 years (2000-2005). The clinical, cytogenetic, and molecular diagnostic data and bone marrow aspirate smears and biopsies on all patients were reviewed. Immunohistochemical staining with antibody to p53 was also performed. Two patients met the criteria for classic LFS; one had no history of malignancy in first-degree relatives. The MDS followed chemotherapy and radiation therapy and progressed to acute myeloid leukemia in 2 patients. Cytogenetic analysis demonstrated chromosome 5 abnormalities in a complex karyotype in all cases. Two patients died, one of acute myeloid leukemia and one with glioblastoma multiforme, MDS, and persistent pancytopenia. Patients with LFS may develop MDS, which is most likely therapy-related and is associated with cytogenetic markers of poor prognosis.

Typing database for noroviruses

The FBVE (Food-borne Viruses in Europe) network was initiated during a research project funded by the European Commission (contract QLK1-1999-00594). The aim of the network is to establish a framework for rapid, (pre-publication) exchange of epidemiological, virological and molecular diagnostic data on outbreaks of viral gastroenteritis and acute hepatitis due to hepatitis A and E viruses for both surveillance and research purposes.

A comparison of the Berlin and Gent Nosologies in the diagnosis of Marfan syndrome: the NIH experience

We reviewed clinical and radiographic data on 73 patients evaluated for possible Marfan syndrome (MFS) at the National Institutes of Health for the purpose of comparing the 1987 Berlin and 1996 Gent diagnostic criteria. All patients had a physical examination, all had echocardiograms or known aortic root dilatation, 64 (88%) had ophthalmologic exams or known ectopia lentis, and 35 (48%) have had MRI scans to screen for dural ectasia. Thirty-one had a first degree relative who had been diagnosed with MFS, and we directly confirmed this diagnosis in 22 cases. Forty-eight patients met diagnostic criteria under the Berlin criteria and 39 under the Gent criteria (kappa correlation coefficient K=0.75). No patient who met diagnostic criteria under the Gent criteria failed to meet the Berlin criteria. Of patients diagnosed under the Berlin criteria, all had skeletal features of MFS, 40 (83%) had aortic root dilatation, 19 of 27 examined (70%) had dural ectasia, 27 (56%) had an affected first degree relative, and 12 of 44 examined (27%) had ectopia lentis. Determination of dural ectasia established the diagnosis for 9 patients under the Gent criteria but had no effect on diagnoses made under the Berlin criteria (K=0.53 comparing Berlin to Gent without dural ectasia data). In summary, approximately 20 percent of patients diagnosed with Marfan syndrome using the Berlin criteria do not meet the Gent diagnostic standard. Long term follow-up or molecular diagnostic data are necessary to establish the relative sensitivity and specificity of these diagnostic tools.