Deterministic evolution and stringent selection during preneoplasia.

The earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours.

Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals.

DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids.

Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.

Molecular classification of metastatic and recurrent endometrial endometrioid carcinoma: prognostic relevance among low- and high-stage tumours.

AIMS: Molecular classification according to The Cancer Genome Atlas (TCGA) improves endometrial endometrioid carcinoma (EEC) prognostication and has specific treatment implications; however, original data were skewed towards low-grade and low-stage tumours. Herein, we molecularly classify EECs metastatic at the time of diagnosis or with subsequently documented recurrent/metastatic disease to examine correlation with clinical outcomes. METHODS: TCGA categories include POLE-mutated, microsatellite instability (MSI), p53 abnormal (p53 abnl) and no specific molecular profile (NSMP). POLE targeted sequencing at exons 9, 11, 13 and 14 and immunohistochemistry (IHC) for PMS2, MSH6 and p53 were performed to establish molecular classification. RESULTS: The distribution in our cohort of 141 EECs was similar to that generally reported in EEC, with nine POLE-mutated (6%), 45 MSI (32%), 16 p53 abnl (11%) and 71 NSMP (50%), with similar distributions between low- and high-stage cohorts. We demonstrate that when stratified by molecular subtype, disease-specific survival from the time of high-stage (stages III-IV) presentation or time of recurrence in low-stage (stages I-II) disease among metastatic and/or recurrent EEC is strongly associated with TCGA classification (high-stage P = 0.02, low-stage P = 0.017). Discordant molecular classification between primary and metastatic/recurrent tumours occurred in four of 105 (3.8%) patients, two related to PMS2/MSH6 IHC and two related to p53 IHC. CONCLUSIONS: We demonstrate that molecular classification is prognostically relevant not only at the time of diagnosis, but also at the time of recurrence and in the metastatic setting. Rare subclonal alterations occur and suggest a role for confirming TCGA classification in recurrent/metastatic tumours.

Exact confidence intervals for population growth rate, longevity and generation time.

By quantifying key life history parameters in populations, such as growth rate, longevity, and generation time, researchers and administrators can obtain valuable insights into its dynamics. Although point estimates of demographic parameters have been available since the inception of demography as a scientific discipline, the construction of confidence intervals has typically relied on approximations through series expansions or computationally intensive techniques. This study introduces the first mathematical expression for calculating confidence intervals for the aforementioned life history traits when individuals are unidentifiable and data are presented as a life table. The key finding is the accurate estimation of the confidence interval for r, the instantaneous growth rate, which is tested using Monte Carlo simulations with four arbitrary discrete distributions. In comparison to the bootstrap method, the proposed interval construction method proves more efficient, particularly for experiments with a total offspring size below 400. We discuss handling cases where data are organized in extended life tables or as a matrix of vital rates. We have developed and provided accompanying code to facilitate these computations.

Time to diagnosis in rapid exome/genome sequencing in the clinical inpatient setting.

Exome and genome sequencing are clinically available, with many laboratories offering expedited testing (e.g., "rapid" and "ultra-rapid"). With the increase in uptake of expedited testing, there is a need for the development of inpatient protocols for best practices based on real-life data. A retrospective 2-year review (October 2019-November 2021) of the utilization of rapid exome and genome sequencing for inpatient cases at a tertiary care center using a utilization management tracking database with subsequent chart review was performed. Thirty-three expedited "rapid/priority" exome/genome tests were performed clinically. The average total turnaround time (TAT) was 17.88 days (5-43 days) with an average TAT of 13.97 days (3-41 days) for the performing laboratory. There were 5 positive diagnostic results (15.2%), 3 likely positive diagnostic results (9%), 2 noncontributory results (6%), and 26 nondiagnostic results (69.7%). Real-life data suggest that there is an approximately 3.91-day lag in getting samples to the performing laboratory. Although laboratories may advertise their expected TAT, a number of factors can potentially impact the actual time from test order placement to communication of the results for clinical use. Understanding the points of delay will enable the development of internal protocols and policies to improve time to diagnosis.

Targeted mutational profiling of Epstein Barr virus-positive mucocutaneous ulcer: Implications for differential diagnosis with EBV-positive diffuse large B-cell lymphoma.

Epstein Barr Virus-positive mucocutaneous ulcer (EBVMCU) can be difficult to distinguish from EBV-positive diffuse large B cell lymphoma (DLBCL). We used targeted next-generation sequencing (NGS) to explore genetic alterations in EBVMCU to aid in this diagnostic challenge. Ten cases of EBVMCU were evaluated by a targeted NGS panel of 164 genes. Targeted NGS identified 18 variants in 15 genes in eight cases of EBVMCU. Loss of function TET2 variants were most frequently identified (3 of 10 cases, 30 %). One TET2 variant occurred at low variant allele frequency (VAF) of 3 %, which may be suggestive of clonal hematopoiesis of indeterminate potential. One case harbored a loss of function DNMT3A variant at low VAF. Two cases demonstrated missense variants in the IRF8 gene. Both variants occurred at a VAF close to 50 % and with an estimated high burden of disease (75 %). Two cases of mucosal gastrointestinal involvement had no reportable variants. Mutational profiling of EBVMCU identified TET2 loss of function variants at an elevated frequency in our cohort; however, the findings are not specific and its clinical significance cannot be completely elucidated. Further studies are needed to confirm the findings in an independent and larger cohort of EBVMCU, to determine the cell of origin of the variants, and to further assess their significance in the pathogenesis of this disorder.

Color stability of dual-cured and light-cured resin cements: A systematic review and meta-analysis of in vitro studies.

PURPOSE: This systematic review and meta-analysis aimed to evaluate the difference in the color stability of light-cured and dual-cured resin cements. MATERIALS AND METHODS: Two separate reviewers used the PubMed, Scopus, Web of Science, Embase, and Scielo databases to execute the systematic review. For the analysis, studies that evaluated the color stability of dual-cured and light-cured resin cements over time were used. The random effects model was used in the meta-analysis. Analyses of subgroups were carried out based on the aging technique. The methodological quality of each in vitro study was evaluated in accordance with the parameters of a prior systematic review. RESULTS: From all databases, a total of 2223 articles were retrieved. Following the screening of titles and abstracts, 44 studies were selected for full text review, and a total of 27 articles were used for the qualitative analysis. Finally, 23 articles remained for the qualitative analysis. The majority of studies were labeled as having a medium risk of bias. The global analysis showed that the dual-cure resin cements had considerably greater differences in the color change (p = 0.006). A high heterogeneity index (86%) was found in the analysis. CONCLUSIONS: The best available in vitro evidence suggests that dual-polymerizing cement has higher color variation than light-polymerized materials. To reduce the likelihood of color change after the luting of thin ceramic restorations, clinicians should employ light-polymerizable resin cements.

In situ study of the effect of endogenous and exogenous agents on color stability, hardness, and surface roughness of an elastomer for facial prostheses.

PURPOSE: To evaluate in situ the influence of sweat, oil, sunscreen, and disinfectant solution on the color stability, hardness, and roughness of elastomer for facial prostheses. MATERIALS AND METHODS: Standardized and intrinsically pigmented specimens remained in contact with human skin from the same person for 30 days, considering exposures (n = 36 per group), absent of exposition (Control, C); sweat and oiliness contact (SO); sweat and oiliness associated with sunscreen (SOS); 0.12% chlorhexidine digluconate immersion (CD0.12%); and all agents exposed (SOSCD). The main variables were color change (CIELab and National Standard Bureau system, NBS), Shore A hardness, and surface roughness, measured at baseline and 30 days. Qualitative analyses were performed by atomic force microscopy (AFM) and scanning electron microscopy (SEM). The data were analyzed by Kruskal-Wallis tests (color) and two-way ANOVA (hardness and roughness) with Sidak post-test (α = 0.05). RESULTS: CD0.12% (1.54 ± 0.49) and SOSCD (2.10 ± 1.03) had similar effects and caused the smallest color changes, considered mild and noticeable (NBS), respectively. SOS promoted the greatest color change (6.99 ± 1.43, NBS: large) and hardness (17.97 ± 0.56); SOS promoted intermediate roughness (3.48 ± 1.05) between SOSCD (2.25 ± 0.53), and two similar groups: C (4.46 ± 0.95), and CD0.12% (4.39 ± 1.26). The qualitative analysis showed an irregular, dense, dry, and whitish layer on the surface of the specimens exposed to sunscreen, which was reduced when in contact with 0.12% chlorhexidine digluconate. CONCLUSIONS: Endogenous and exogenous factors are capable of altering elastomer properties. The 0.12% chlorhexidine digluconate minimized the changes caused by sweat, oil, and sunscreen.

MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models.

Experimentally estimating peptide-major histocompatibility complex (pMHC) binding affinity has been quite challenging due to the many receptors and the many potential ligands implicated in it. We have thus proposed a straightforward computational methodology considering the different mechanisms involved in pMHC binding to facilitate studying such receptor-ligand interactions. We have developed a pipeline using semi-empirical quantum mechanical methods for calculating pMHC class I and II molecules' binding energy (BE). This pipeline can systematize the methodology for calculating pMHC system BE, enabling the rational design of T-cell epitopes to be used as pharmaceuticals and vaccines.

Endovascular Closure of an Acquired Vascular Fistula, an Uncommon Complication of a Tunneled Hemodialysis Catheter: A Case Report.

PURPOSE: The objective of this case is to report an endovascular occlusion of an acquired vascular fistula using an Amplatzer Vascular Plug II. Also, it is to review the available literature on risk factors, pathophysiology, and related management strategies about complications of the tunneled central venous catheter (TCVC). CASE REPORT: The case was a 40-year-old man with a chronic kidney disease (CKD) on dialysis and with a history of several previous TCVC placements, along with recurrent infections. The last TCVC developed a fistula between the superior vena cava and the right pulmonary artery, shown by computed tomography (CT). We decided to remove a long-term TCVC and occluded the fistula applying an endovascular embolic device, an Amplatzer Vascular Plug II, subsequently. The patient was given parenteral treatment during 10 days of hospitalization. Over 9 months of follow-up, the device was appropriately positioned and did not obstruct the vascular flow. CONCLUSION: Tunneled central venous catheters are frequently used for hemodialysis in patients in the last stage of CKD who do not have an arteriovenous fistula. Occasionally, delayed complications such as adherence or catheter migration occur. This case illustrates an endovascular treatment with excellent results and low risk of morbidity and mortality. CLINICAL IMPACT: The purpose of this work is to present an endovascular occlusion by means of an Amplatzer® Vascular Plug II in a residual fistula. The endovascular way is decided in situations, for instance, once the cardiothoracic surgeons argue that the patient is not in general conditions to tolerate surgery, the surgical procedure would be complex, or, in a surgical approach with a difficult-to-resolve hemorrhage. We explain the technique and the materials we used for an excellent result and a low risk of complications. This case is intended to serve as an aid in the treatment of similar events.

Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus.

Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the CF transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, there are many other pathogenic mutations throughout the CF gene. An autologous airway stem cell therapy in which the CFTR cDNA is precisely inserted into the CFTR locus may enable the development of a durable cure for almost all CF patients, irrespective of the causal mutation. Here, we use CRISPR-Cas9 and two adeno-associated viruses (AAVs) carrying the two halves of the CFTR cDNA to sequentially insert the full CFTR cDNA along with a truncated CD19 (tCD19) enrichment tag in upper airway basal stem cells (UABCs) and human bronchial epithelial cells (HBECs). The modified cells were enriched to obtain 60%-80% tCD19+ UABCs and HBECs from 11 different CF donors with a variety of mutations. Differentiated epithelial monolayers cultured at air-liquid interface showed restored CFTR function that was >70% of the CFTR function in non-CF controls. Thus, our study enables the development of a therapy for almost all CF patients, including patients who cannot be treated using recently approved modulator therapies.

Antibacterial activity and physicochemical properties of a sealer containing copaiba oil.

This study aimed to evaluate the antimicrobial activity and physicochemical properties of a novel dual-cure endodontic sealer containing copaiba oil. The copaiba oil was obtained and characterized by gas chromatography (GC), and the minimum inhibitory concentration (MIC) was performed. The experimental sealers were formulated with copaiba oil concentrations of 0, 0.5, 1, and 2%, and the RealSeal™ (Sybron endo, Orange, USA) and AH Plus (Dentsply De Trey Gmbh, Konstanz, Germany) were used as the commercial references. The antimicrobial activity of the sealers was evaluated by the direct contact test for 1h and 24h. To evaluate the physicochemical properties of the sealers, the degree of conversion, setting time, film thickness, dimensional stability, and radiopacity tests were performed. The data were statistically analyzed by one-way ANOVA and Tukey's test (α = 0.05). Concerning the results, the sealers containing copaiba oil showed antimicrobial activity without harming the physicochemical properties.

Complications related to the Cook-Swartz implantable Doppler probe use in head and neck microvascular reconstruction: a systematic review.

PURPOSE: Vascular perfusion research has been dedicated to identify inexpensive, effective, and easy to use methods to assess free flap perfusion for both buried and non-buried flaps. METHODS: Systematic review of complications in patients underwent Head and Neck microsurgical reconstruction and vascular implantable Doppler monitoring. RESULTS: Sixteen articles were included for qualitative analysis. 2535 (92.2%) patients received IDP monitorization. Venous thrombosis was the most common vascular complication effecting 28 (1.1%). Regarding complications potentially related to the use of the IDP, just one study described the presence of granuloma formation along the suture line in 2 (0.07%) patients. CONCLUSIONS: Our findings indicated that Cook-Swartz IDP will represents a safe and effective device for FF monitoring in HN reconstructive micro-surgery. A detailed prospective registration of the results and complications related to the use of IDP remains mandatory to precisely estimate results, cost, and complications.

Synthesis and characterization of calcium-releasing elastomeric resin-based endodontic sealers.

OBJECTIVES: To evaluate the incorporation of halloysite nanotubes (HNTs) loaded with one of two calcium sources (i.e., calcium hydroxide/CaOH2 or beta-tricalcium phosphate/ß-TCP) on the physicochemical and biological properties of an experimental resin-based dual-cured endodontic sealer. MATERIALS AND METHODS: HNTs were encapsulated with CaOH2 or ß-TCP at 10 wt.%. HNTs containing CaOH2 or ß-TCP were added into the experimental sealers at 50 wt.%. The control sealers were the calcium-free HNT-modified resin-based experimental sealer and AH Plus™, a commercially available endodontic sealer. Degree of conversion, setting time, flow, film thickness, radiopacity, dimensional stability, and calcium ions release were determined. Antibiofilm properties and cytocompatibility of the formulated sealers and commercial control were also evaluated. One and two-way ANOVA analysis followed by Tukey's post hoc test was conducted to evaluate the effect of the independent variable on the evaluated properties. RESULTS: FTIR confirmed the encapsulation of calcium sources into HNTs. Regarding flow and film thickness, the values obtained from these sealers were in accordance with the specifications provided by ISO 6876. For radiopacity, AH Plus™ achieved the highest radiopacity (p<0.05). Among the experimental formulations, all experimental HNT-containing compositions exhibited values below 3 mm Al. The experimental sealers showed greater dimensional changes when compared to the commercial (AH Plus™) control. The release of calcium ions was observed for the HNT_CaOH2 and HNT_ß-TCP sealers without statistical differences. Experimental sealers containing HNT_CaOH2 and HNT_ß-TCP significantly reduced the CFU/mL count and showed cell compatibility. CONCLUSIONS: The findings of this study demonstrate that the incorporation of HNT_CaOH2 or HNT_ß-TCP into resin-based experimental sealers promoted antimicrobial effects and gradual calcium release without impairing cytocompatibility or physicochemical properties of the sealers. Still, an adjustment to reach the minimal radiopacity established by ISO 6876 is needed. CLINICAL RELEVANCE: The experimental resin-based sealers seemed to be an alternative for endodontics. The incorporation of calcium sources exerts promising antimicrobial effects while displaying low cell toxicity.

Effect of contamination and decontamination methods on the bond strength of adhesive systems to dentin: A systematic review.

INTRODUCTION: In a suitable condition, it is important to perform any dental restorative procedure using an operatory field isolated. Then, the aim of this study was to compare the bond strength of composite restorations to dentin affected by any contamination agent through a systematic review. METHODS: This systematic review was performed following the PRISMA 2020 guidelines. The literature search was conducted until September 2022 by scanning the following databases: Embase, PubMed, Scielo, Scopus, and Web of Science. Manuscripts evaluated the bond strength of resin-based materials to permanent human dentin contaminated with blood or saliva were selected for full-text review. The risk of bias was assessed by the RoBDEMAT tool. RESULTS: A total of 3750 papers resulted from the search from all databases. After the full-text reading, a total of 62 articles remained for the qualitative analysis. The contamination agents used were blood, saliva, and hemostatic agents. A great variety of protocols were used to contaminate the dentin surface, and the contamination process occurred in several steps of the bonding process, including before and after the etching process, after the primer application and after the adhesive application. Also, several decontamination procedures were tested, including reapplication of the etching material, rinsing with water, chlorhexidine or sodium hypochlorite and reapplication of the adhesive system. CONCLUSION: Any contamination with blood or saliva impaired the bond strength of resin-based materials to dentin. Decontamination procedures including water-spray and reapplication of the bonding system could revert the impairment produced by the saliva or blood contamination. The use of hemostatic agents as a method of blood decontamination is not recommended. CLINICAL SIGNIFICANCE: Clinicians should avoid contamination during a bonding procedure, otherwise, a reduction in the bond quality is expected.

Triple scan evaluation of internal and marginal adaptation of overlays using different restorative materials.

OBJECTIVE: Problems in the confection of indirect restorations may increase the marginal and internal gap. This study aimed to quantify the marginal and the internal fit of overlays fabricated with three different materials. MATERIALS AND METHODS: Standardized cavities were prepared on endodontically treated human third molars and digital impressions were done using an intraoral camera (Trios 3). Restorations were designed (n = 15) and fabricated with three materials: Hybrid ceramic (Cerasmart; GC Corp, EUROPE), high-strength lithium disilicate (GC Initial® LiSi Press; GC Corp, Tokyo, Japan), and zirconia reinforced Lithium Silicate Glass Ceramic (Vita Suprinity; Vita, Germany). Axial, marginal, pulpal, and gingival gaps were calculated by measuring the distance between the restoration and the tooth at several reference points. Two-Way analysis of variance was used for statistical analysis. The significance level was set at α = 0.05. RESULTS: Mean gap was significantly influenced by the material (p < 0.001), gap localization (p < 0.001), and interaction between the factors (p = 0.002). For all materials, the highest gap was observed at gingival and pulpal surfaces (p ≤ 0.015). LiSi Press achieved the overall lowest values at axial values measurements (p ≤ 0.003). CONCLUSIONS: The performance of a CAD/CAM system relative to marginal adaptation is influenced by the restorative material used. High-strength lithium disilicate seems to be showed the best marginal adaptation. CLINICAL SIGNIFICANCE: Marginal and internal adaptation of CAD/CAM restorations could be influenced by the type of material chosen.

Prospective molecular classification of endometrial carcinomas: institutional implementation, practice, and clinical experience.

The comprehensive genomic analysis of endometrial carcinoma (EC) by The Cancer Genome Atlas (TCGA) led to the discovery of four distinct and prognostically significant molecular subgroups. Molecular classification has the potential to improve risk-stratification when integrated with clinicopathologic features and has recently been included in national and international patient management EC guidelines. Thus, the adoption of molecular classification into routine pathologic and clinical practice is likely to grow significantly in the upcoming years. Establishing an efficient and standardized workflow for performing molecular classification on ECs, and reporting both the molecular and histologic findings in an integrative manner, is imperative. Here we describe our effort to implement rapid and routine molecular classification on all ECs diagnosed at our institution. To this effect, we performed immunohistochemistry as a surrogate marker for identifying genetic and/or epigenetic alterations in DNA mismatch repair (e.g., MLH1, PMS2, MSH6, MSH2), and TP53 genes. In addition, we have developed and employed a single-gene POLE SNaPshot assay, which is a rapid and analytically sensitive method for detecting select POLE exonuclease domain mutations (EDMs). We report our molecular testing workflow and integrative reporting system as well as the clinicopathologic and molecular features of 310 ECs that underwent routine molecular classification at our institution. The 310 ECs were molecularly classified as follows: 15 (5%) POLE mutant (POLEmut), 79 (25%) mismatch repair-deficient (MMRd), 135 (44%) no specific molecular profile (NSMP), and 81 (26%) p53 abnormal (p53abnl). This work provides an initial framework for implementing routine molecular classification of ECs.

Factors associated with the time to complete clinical exome sequencing in a pediatric patient population.

PURPOSE: Exome sequencing (ES) is becoming increasingly important for diagnosing rare genetic disorders. Patients and clinicians face several barriers when attempting to obtain ES. This study is aimed to describe factors associated with a longer time interval between provider recommendation of testing and sample collection for ES. METHODS: A retrospective chart review was conducted for insurance-authorized, completed pediatric ES in which initial requests were reviewed by Stanford's Genetic Testing Optimization Service between November 2018 and December 2019. Regression analysis was used to determine the association between the geocoded median household income and 3 different time point intervals defined as time to test, insurance decision, and scheduling/consent. RESULTS: Of the 281 charts reviewed, 115 cases were included in the final cohort. The average time from provider preauthorization request to sample collection took 104.4 days, and income was negatively correlated with the length of the insurance decision interval. CONCLUSION: Pediatric patients undergo a lengthy, uncertain process when attempting to obtain ES, some of which is associated with income. More research and clinician interventions are required to clarify specific socioeconomic factors that influence the ability to obtain timely ES and develop optimal protocols.

Circulating tumor DNA monitoring for early recurrence detection in epithelial ovarian cancer.

OBJECTIVE: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. We examined the utility of circulating tumor DNA (ctDNA) as a prognostic biomarker for EOC by assessing its relationship with patient outcome and CA-125, pre-surgically and during post-treatment surveillance. METHODS: Plasma samples were collected from patients with stage I-IV EOC. Cohort A included patients with pre-surgical samples (N = 44, median follow-up: 2.7 years), cohort B and C included: patients with serially collected post-surgically (N = 12) and, during surveillance (N = 13), respectively (median follow-up: 2 years). Plasma samples were analyzed using a tumor-informed, personalized multiplex-PCR NGS assay; ctDNA status and CA-125 levels were correlated with clinical features and outcomes. RESULTS: Genomic profiling was performed on the entire cohort and was consistent with that seen in TCGA. In cohort A, ctDNA-positivity was observed in 73% (32/44) of presurgical samples and was higher in high nuclear grade disease. In cohort B and C, ctDNA was only detected in patients who relapsed (100% sensitivity and specificity) and preceded radiological findings by an average of 10 months. The presence of ctDNA at a single timepoint after completion of surgery +/- adjuvant chemotherapy and serially during surveillance was a strong predictor of relapse (HR:17.6, p = 0.001 and p < 0.0001, respectively), while CA-125 positivity was not (p = 0.113 and p = 0.056). CONCLUSIONS: The presence of ctDNA post-surgically is highly prognostic of reduced recurrence-free survival. CtDNA outperformed CA-125 in identifying patients at highest risk of recurrence. These results suggest that monitoring ctDNA could be beneficial in clinical decision-making for EOC patients.