AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

SUMMARY: With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics-Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically focused classification of germline sequence variants in a research setting. AVAILABILITY AND IMPLEMENTATION: AutoGVP is an open source dockerized workflow implemented in R and freely available on GitHub at https://github.com/diskin-lab-chop/AutoGVP.

Prospective Evaluation of a Tiered Opioid Prescribing Guideline for Inpatient Colorectal Operations.

OBJECTIVE: This study sought to prospectively validate an institutional prescribing guideline based on previously defined opioid consumption patterns following inpatient colorectal operations. BACKGROUND: In light of the opioid epidemic, reducing excess prescription quantities is key while still tailoring to patient needs. METHODS: This is a cohort study of elective colorectal operations (colectomies, proctectomies, and ostomy reversals) at a single tertiary care medical center. Opioid prescribing and consumption patterns [quantified as Equianalgesic 5 mg Oxycodone Pills (EOP)] were compared before and after adoption of a tiered opioid prescribing guideline. Tiers were divided based on opioid consumption in the 24 hours before discharge: Tier 1 (0 EOP), Tier 2 (0.1-3 EOP), and Tier 3 (>3 EOP). Our guideline recommended maximum prescriptions of 0 EOP for Tier 1, 12 EOP for Tier 2, and 30 EOP for Tier 3. Results: The study included 100 patients before and 101 after guideline adoption. Demographic and operative characteristics were similar between cohorts. Guideline adherence was 85%. Overall, there was a 41%reduction in mean prescription quantity and 53% reduction in excess pills per prescription. No change in opioid consumption or refill rates was observed. CONCLUSIONS: Adoption of a tiered opioid prescribing guideline significantly reduced opioid prescription quantity with no change in consumption or refill rates. Standardization of discharge prescriptions based on patient consumption in the 24 hours before discharge may be an important step toward minimizing excess prescribing.

We Built it, But Did They Come: Veterans' Use of VA Healthcare System-Provided Complementary and Integrative Health Approaches.

BACKGROUND: Interest in complementary and integrative health (CIH) approaches, such as meditation, yoga, and acupuncture, continues to grow. The evidence of effectiveness for some CIH approaches has increased in the last decade, especially for pain, with many being recommended in varying degrees in national guidelines. To offer nonpharmacological health management options and meet patient demand, the nation's largest integrated healthcare system, the Veterans Health Administration (VA), greatly expanded their provision of CIH approaches recently. OBJECTIVE: This paper addressed the questions of how many VA patients might use CIH approaches and chiropractic care if they were available at modest to no fee, and would patients with some health conditions or characteristics be more likely than others to use these therapies. DESIGN: Using electronic medical records, we conducted a national, three-year, retrospective analysis of VA patients' use of eleven VA-covered therapies: chiropractic care, acupuncture, Battlefield Acupuncture, biofeedback, clinical hypnosis, guided imagery, massage therapy, meditation, Tai Chi/Qigong, and yoga. PARTICIPANTS: We created a national cohort of veterans using VA healthcare from October 2016-September 2019. KEY RESULTS: Veterans' use of these approaches increased 70% in three years. By 2019, use was 5.7% among all VA patients, but highest among patients with chronic musculoskeletal pain (13.9%), post-traumatic stress disorder (PTSD; 10.6%), depression (10.4%), anxiety (10.2%), or obesity (7.8%). The approach used varied by age and race/ethnicity, with women being uniformly more likely than men to use each approach. Patients having chronic musculoskeletal pain, obesity, anxiety, depression, or PTSD were more likely than others to use each of the approaches. CONCLUSIONS: Veterans' use of some approaches rapidly grew recently and was robust, especially among patients most in need. This information might help shape federal/state health policy on the provision of evidence-based CIH approaches and guide other healthcare institutions considering providing them.

MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data.

The growing number of next-generation sequencing (NGS) data presents a unique opportunity to study the combined impact of mitochondrial and nuclear-encoded genetic variation in complex disease. Mitochondrial DNA variants and in particular, heteroplasmic variants, are critical for determining human disease severity. While there are approaches for obtaining mitochondrial DNA variants from NGS data, these software do not account for the unique characteristics of mitochondrial genetics and can be inaccurate even for homoplasmic variants. We introduce MitoScape, a novel, big-data, software for extracting mitochondrial DNA sequences from NGS. MitoScape adopts a novel departure from other algorithms by using machine learning to model the unique characteristics of mitochondrial genetics. We also employ a novel approach of using rho-zero (mitochondrial DNA-depleted) data to model nuclear-encoded mitochondrial sequences. We showed that MitoScape produces accurate heteroplasmy estimates using gold-standard mitochondrial DNA data. We provide a comprehensive comparison of the most common tools for obtaining mtDNA variants from NGS and showed that MitoScape had superior performance to compared tools in every statistically category we compared, including false positives and false negatives. By applying MitoScape to common disease examples, we illustrate how MitoScape facilitates important heteroplasmy-disease association discoveries by expanding upon a reported association between hypertrophic cardiomyopathy and mitochondrial haplogroup T in men (adjusted p-value = 0.003). The improved accuracy of mitochondrial DNA variants produced by MitoScape will be instrumental in diagnosing disease in the context of personalized medicine and clinical diagnostics.

The InsP7 phosphatase Siw14 regulates inositol pyrophosphate levels to control localization of the general stress response transcription factor Msn2.

The environmental stress response (ESR) is critical for cell survival. Yeast cells unable to synthesize inositol pyrophosphates (PP-InsPs) are unable to induce the ESR. We recently discovered a diphosphoinositol pentakisphosphate (PP-InsP5) phosphatase in Saccharomyces cerevisiae encoded by SIW14 Yeast strains deleted for SIW14 have increased levels of PP-InsPs. We hypothesized that strains with high inositol pyrophosphate levels will have an increased stress response. We examined the response of the siw14Δ mutant to heat shock, nutrient limitation, osmotic stress, and oxidative treatment using cell growth assays and found increased resistance to each. Transcriptional responses to oxidative and osmotic stresses were assessed using microarray and reverse transcriptase quantitative PCR. The ESR was partially induced in the siw14Δ mutant strain, consistent with the increased stress resistance, and the mutant strain further induced the ESR in response to oxidative and osmotic stresses. The levels of PP-InsPs increased in WT cells under oxidative stress but not under hyperosmotic stress, and they were high and unchanging in the mutant. Phosphatase activity of Siw14 was inhibited by oxidation that was reversible. To determine how altered PP-InsP levels affect the ESR, we performed epistasis experiments with mutations in rpd3 and msn2/4 combined with siw14Δ. We show that mutations in msn2Δ and msn4Δ, but not rpd3, are epistatic to siw14Δ by assessing growth under oxidative stress conditions and expression of CTT1 Msn2-GFP nuclear localization was increased in the siw14Δ. These data support a model in which the modulation of PP-InsPs influence the ESR through general stress response transcription factors Msn2/4.

Integrated molecular and clinical analysis of low-grade gliomas in children with neurofibromatosis type 1 (NF1).

Low-grade gliomas (LGGs) are the most common childhood brain tumor in the general population and in individuals with the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome. Surgical biopsy is rarely performed prior to treatment in the setting of NF1, resulting in a paucity of tumor genomic information. To define the molecular landscape of NF1-associated LGGs (NF1-LGG), we integrated clinical data, histological diagnoses, and multi-level genetic/genomic analyses on 70 individuals from 25 centers worldwide. Whereas, most tumors harbored bi-allelic NF1 inactivation as the only genetic abnormality, 11% had additional mutations. Moreover, tumors classified as non-pilocytic astrocytoma based on DNA methylation analysis were significantly more likely to harbor these additional mutations. The most common secondary alteration was FGFR1 mutation, which conferred an additional growth advantage in multiple complementary experimental murine Nf1 models. Taken together, this comprehensive characterization has important implications for the management of children with NF1-LGG, distinct from their sporadic counterparts.

A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.

Medulloblastoma is a highly heterogeneous pediatric brain tumor with five molecular subtypes, Sonic Hedgehog TP53-mutant, Sonic Hedgehog TP53-wildtype, WNT, Group 3, and Group 4, defined by the World Health Organization. The current mechanism for classification into these molecular subtypes is through the use of immunostaining, methylation, and/or genetics. We surveyed the literature and identified a number of RNA-Seq and microarray datasets in order to develop, train, test, and validate a robust classifier to identify medulloblastoma molecular subtypes through the use of transcriptomic profiling data. We have developed a GPL-3 licensed R package and a Shiny Application to enable users to quickly and robustly classify medulloblastoma samples using transcriptomic data. The classifier utilizes a large composite microarray dataset (15 individual datasets), an individual microarray study, and an RNA-Seq dataset, using gene ratios instead of gene expression measures as features for the model. Discriminating features were identified using the limma R package and samples were classified using an unweighted mean of normalized scores. We utilized two training datasets and applied the classifier in 15 separate datasets. We observed a minimum accuracy of 85.71% in the smallest dataset and a maximum of 100% accuracy in four datasets with an overall median accuracy of 97.8% across the 15 datasets, with the majority of misclassification occurring between the heterogeneous Group 3 and Group 4 subtypes. We anticipate this medulloblastoma transcriptomic subtype classifier will be broadly applicable to the cancer research and clinical communities.

Development of a Practice Guideline for Discharge Opioid Prescribing After Major Colorectal Surgery.

BACKGROUND: Better alignment of opioid prescription quantities with patient need could help reduce excessive prescribing. OBJECTIVE: The study sought to develop an institutional prescribing guideline based on defined opioid consumption patterns after inpatient colorectal operations. DESIGN: This was a retrospective cohort study. SETTINGS: The study was conducted at a single tertiary care center. PATIENTS: Patients who underwent elective major colorectal procedures between July 2018 and January 2019 were included. MAIN OUTCOME MEASURES: The study measured prescription and consumption quantities measured as equianalgesic oxycodone 5-mg pills. RESULTS: Patients were categorized into 3 groups based on consumption in the 24-hour period before discharge: tier 1 consumed 0 equianalgesic oxycodone 5-mg pills (n = 53), tier 2 consumed 0.1 to 3.0 equianalgesic oxycodone 5-mg pills (n = 25), and tier 3 consumed >3.0 equianalgesic oxycodone 5-mg pills (n = 22). Average prescription quantity was 17.5 ± 10.5 equianalgesic oxycodone 5-mg pills (range, 0-78). Patients consumed a mean of 6.7 ± 10.9 equianalgesic oxycodone 5-mg pills after discharge and had 10.8 ± 10.2 equianalgesic oxycodone 5-mg pill excess, whereas 51% of patients consumed no pills. Opioid consumption was significantly different between each tier (p < 0.001). A prescribing guideline was developed to satisfy the majority of patients: 0 equianalgesic oxycodone 5-mg pills if tier 1, 12 pills if tier 2, and 30 pills if tier 3. Tiered guideline adoption could reduce prescribed pills by 45% and excess pills per prescription by 73%. Patient history of IBD was independently associated with increased odds of exceeding the guideline (adjusted OR = 7.2 (95% CI, 1.6-32.6)). LIMITATIONS: The study was limited by its single-center, retrospective design and that outpatient opioid consumption was self-reported. CONCLUSIONS: Following hospital discharge after major colorectal surgery, more than half of patients consumed no opioid pills, and 62% of prescribed opioids were in excess. Outpatient opioid consumption was highly associated with inpatient opioid use in the 24 hours before discharge. Prospective validation of this prescribing guideline is needed, but adoption could reduce excessive prescribing. See Video Abstract at http://links.lww.com/DCR/B575. DESARROLLO DE UNA GUA PRCTICA PARA LA PRESCRIPCIN DE OPIOIDES AL EGRESO DESPUS DE UNA CIRUGA COLORRECTAL MAYOR: ANTECEDENTES:Una mejor alineación de las cantidades de prescripción de opioides con las necesidades del paciente podría ayudar a reducir la prescripción excesiva.OBJETIVO:El estudio buscó desarrollar una guía institucional de prescripción basada en patrones definidos de consumo de opioides luego de cirugías colorrectales hospitalarias.DISEÑO:Estudio de cohorte retrospectivo.ENTORNO CLÍNICO:El estudio se llevó a cabo en un solo centro de atención terciaria.PACIENTES:Pacientes que se sometieron a procedimientos colorrectales mayores electivos entre julio de 2018 y enero de 2019.PRINCIPALES MEDIDAS DE RESULTADO:El estudio midió las cantidades de prescripción y consumo medidas como píldoras de 5 mg de oxicodona equianalgésica (EOP).RESULTADOS:Los pacientes se clasificaron en tres grupos según el consumo en el período de 24 horas antes del egreso: el nivel 1 consumió 0 EOP (n = 53), el nivel 2 consumió 0,1-3 EOP (n = 25) y el nivel 3 consumió más de 3 EOP (n = 22). La cantidad promedio de prescripción fue 17,5 (± 10,5) EOP (rango: 0-78). Los pacientes consumieron una media de 6,7 (± 10,9) EOP posterior al egreso y tuvieron un exceso de 10,8 (± 10,2) EOP, mientras que el 51% de los pacientes no consumieron píldoras. El consumo de opioides fue significativamente diferente entre cada nivel (p <0,001). Se desarrolló una guía de prescripción para satisfacer a la mayoría de los pacientes: 0 EOP del nivel 1, 12 EOP del nivel 2 y 30 EOP del nivel 3. La adquisición de una guía escalonada podría reducir las píldoras recetadas en un 45% y el exceso de píldoras por receta en un 73%. El historial del paciente de enfermedad inflamatoria intestinal se asoció de forma independiente con un aumento de las probabilidades de superar la guía (ORa 7,2; IC del 95%: 1,6-32,6).LIMITACIONES:El estudio estuvo limitado por su diseño retrospectivo de un solo centro y por el consumo de opioides del paciente ambulatorio el cual fue autoinformado.CONCLUSIONES:Tras el egreso hospitalario de una cirugía colorrectal mayor, más de la mitad de los pacientes no consumieron pastillas opioides y el 62% de los opioides prescritos estaban en exceso. El consumo de opioides como paciente ambulatorio estuvo altamente asociado con el uso de opioides como paciente hospitalizado en las 24 horas previas al egreso. Se necesita una validación prospectiva de esta guía de prescripción, pero la adopción podría reducir la prescripción excesiva. Consulte Video Resumen en http://links.lww.com/DCR/B575.

BRAF fusions in pediatric histiocytic neoplasms define distinct therapeutic responsiveness to RAF paradox breakers.

Pediatric histiocytic neoplasms are hematopoietic disorders frequently driven by the BRAF-V600E mutation. Here, we identified two BRAF gene fusions (novel MTAP-BRAF and MS4A6A-BRAF) in two aggressive histiocytic neoplasms. In contrast to previously described BRAF fusions, MTAP-BRAF and MS4A6A-BRAF do not respond to the paradox breaker RAF inhibitor (RAFi) PLX8394 due to stable fusion dimerization mediated by the N-terminal fusion partners. This highlights a significant and clinically relevant shift from the current dogma that BRAF-fusions respond similarly to BRAF-inhibitors. As an alternative, we show suppression of fusion-driven oncogenic growth with the pan-RAFi LY3009120 and MEK inhibition.

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.

BACKGROUND: Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion prediction algorithms makes therapeutic prioritization difficult. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require informed filtering, making it difficult for researchers and clinicians to rapidly discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy. RESULTS: We developed annoFuse, an R package, and shinyFuse, a companion web application, to annotate, prioritize, and explore biologically-relevant expressed gene fusions, downstream of fusion calling. We validated annoFuse using a random cohort of TCGA RNA-Seq samples (N = 160) and achieved a 96% sensitivity for retention of high-confidence fusions (N = 603). annoFuse uses FusionAnnotator annotations to filter non-oncogenic and/or artifactual fusions. Then, fusions are prioritized if previously reported in TCGA and/or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, and/or transcription factors. We applied annoFuse to fusion calls from pediatric brain tumor RNA-Seq samples (N = 1028) provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project to determine recurrent fusions and recurrently-fused genes within different brain tumor histologies. annoFuse annotates protein domains using the PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention. As a standard function, reportFuse enables generation of a reproducible R Markdown report to summarize filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusions within cohorts. Finally, we created shinyFuse for algorithm-agnostic interactive exploration and plotting of gene fusions. CONCLUSIONS: annoFuse provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Arriba by merging, filtering, and prioritizing putative oncogenic fusions across large cancer datasets, as demonstrated here with data from the OpenPBTA project. We are expanding the package to be widely-applicable to other fusion algorithms and expect annoFuse to provide researchers a method for rapidly evaluating, prioritizing, and translating fusion findings in patient tumors.

Ancestry and frequency of genetic variants in the general population are confounders in the characterization of germline variants linked to cancer.

BACKGROUND: Pediatric high-grade gliomas (pHGGs) are incurable malignant brain cancers. Clear somatic genetic drivers are difficult to identify in the majority of cases. We hypothesized that this may be due to the existence of germline variants that influence tumor etiology and/or progression and are filtered out using traditional pipelines for somatic mutation calling. METHODS: In this study, we analyzed whole-genome sequencing (WGS) datasets of matched germlines and tumor tissues to identify recurrent germline variants in pHGG patients. RESULTS: We identified two structural variants that were highly recurrent in a discovery cohort of 8 pHGG patients. One was a ~ 40 kb deletion immediately upstream of the NEGR1 locus and predicted to remove the promoter region of this gene. This copy number variant (CNV) was present in all patients in our discovery cohort (n = 8) and in 86.3% of patients in our validation cohort (n = 73 cases). We also identified a second recurrent deletion 55.7 kb in size affecting the BTNL3 and BTNL8 loci. This BTNL3-8 deletion was observed in 62.5% patients in our discovery cohort, and in 17.8% of the patients in the validation cohort. Our single-cell RNA sequencing (scRNA-seq) data showed that both deletions result in disruption of transcription of the affected genes. However, analysis of genomic information from multiple non-cancer cohorts showed that both the NEGR1 promoter deletion and the BTNL3-8 deletion were CNVs occurring at high frequencies in the general population. Intriguingly, the upstream NEGR1 CNV deletion was homozygous in ~ 40% of individuals in the non-cancer population. This finding was immediately relevant because the affected genes have important physiological functions, and our analyses showed that NEGR1 expression levels have prognostic value for pHGG patient survival. We also found that these deletions occurred at different frequencies among different ethnic groups. CONCLUSIONS: Our study highlights the need to integrate cancer genomic analyses and genomic data from large control populations. Failure to do so may lead to spurious association of genes with cancer etiology. Importantly, our results showcase the need for careful evaluation of differences in the frequency of genetic variants among different ethnic groups.

Does Offering Battlefield Acupuncture Lead to Subsequent Use of Traditional Acupuncture?

OBJECTIVES: Veterans Health Administration encourages auricular acupuncture (Battlefield Acupuncture/BFA) as a nonpharmacologic approach to pain management. Qualitative reports highlighted a "gateway hypothesis": providing BFA can lead to additional nonpharmacologic treatments. This analysis examines subsequent use of traditional acupuncture. RESEARCH DESIGN: Cohort study of Veterans treated with BFA and a propensity score matched comparison group with a 3-month follow-up period to identify subsequent use of traditional acupuncture. Matching variables included pain, comorbidity, and demographics, with further adjustment in multivariate regression analysis. SUBJECTS: We identified 41,234 patients who used BFA across 130 Veterans Health Administration medical facilities between October 1, 2016 and March 31, 2019. These patients were matched 2:1 on Veterans who used VA care but not BFA during the same period resulting in a population of 24,037 BFA users and a comparison cohort of 40,358 non-BFA users. Patients with prior use of traditional acupuncture were excluded. RESULTS: Among Veterans receiving BFA, 9.5% subsequently used traditional acupuncture compared with 0.9% of non-BFA users (P<0.001). In adjusted analysis, accounting for patient characteristics and regional availability of traditional acupuncture, patients who used BFA had 10.9 times greater odds (95% confidence interval, 8.67-12.24) of subsequent traditional acupuncture use. CONCLUSIONS: Providing BFA, which is easy to administer during a patient visit and does not require providers be formally certified, led to a substantial increase in use of traditional acupuncture. These findings suggest that the value of offering BFA may not only be its immediate potential for pain relief but also subsequent engagement in additional therapies.

Data Accuracy and Predictors of High Ratings of Colon and Rectal Surgeons on an Online Physician Rating Website.

BACKGROUND: Online physician rating Web sites are used by over half of consumers to select doctors. No studies have examined physician rating Web sites for colon and rectal surgeons. OBJECTIVE: The purpose of this study was to evaluate the accuracy and rating patterns of colon and rectal surgeons on the largest physician rating Web site. DESIGN: Physician characteristics and ratings were collected from a randomly selected sample of 500 from 3043 Healthgrades "colon and rectal surgery specialists." Board certifications were verified with the American Board of Surgery and American Board of Colon and Rectal Surgery Web sites. SETTINGS: Data acquisition was completed on July 18, 2018. PATIENTS: Patients were not directly studied. MAIN OUTCOME MEASURES: The primary outcome was to assess the accuracy of Healthgrades in reporting American Board of Surgery and American Board of Colon and Rectal Surgery certification. The secondary outcome was to identify factors associated with high star ratings. RESULTS: A total of 48 (9.6%) of the 500 sampled were incorrectly identified as practicing US surgeons and excluded from subsequent analysis. Healthgrades showed 80.1% agreement with verified board certifications for American Board of Surgery and 85.4% for American Board of Colon and Rectal Surgery. The mean star rating was 4.2 of 5.0 (SD = 0.9), and 77 (21.6%) had 5-star ratings. In a multivariable logistic model (p < 0.001), 5-star rating was associated with 1 to 9 years (OR = 2.76; p = 0.04) or >40 years in practice (OR = 3.35; p = 0.04) and fewer reviews (OR = 0.88; p < 0.001). There were no significant associations with surgeon sex, age, geographic region, or board certification. LIMITATIONS: Data were limited to a single physician rating Web site. CONCLUSIONS: In the modern age of healthcare consumerism, physician rating Web sites should be used with caution given inaccuracies. More accurate online resources are needed to inform patient decisions in the selection of specialized colon and rectal surgical care. See Video Abstract at http://links.lww.com/DCR/B91. PRECISIÓN DE DATOS Y PREDICTORES DE ALTAS CALIFICACIONES DE CIRUJANOS DE COLON Y RECTO EN UN SITIO WEB DE CALIFICACIÓN MÉDICA EN LÍNEA: Más de la mitad de los consumidores utilizan los sitios web de calificación de médicos en línea para seleccionar médicos. Ningún estudio ha examinado los sitios web de calificación de médicos para cirujanos de colon y recto.Evaluar la precisión y los patrones de calificación de los cirujanos de colon y recto en el sitio web más grande de calificación de médicos.Las características y calificaciones de los médicos se obtuvieron de una muestra seleccionada al azar de 500 de 3,043 "especialistas en cirugía de colon y recto" de Healthgrades. Las certificaciones del Consejo se verificaron en los sitios web del Consejo Americano de Cirugía y del Consejo Americano de Cirugía de Colon y Recto.La adquisición de datos se completó el 18 de julio de 2018.Los pacientes no fueron estudiados directamente.El resultado primario fue evaluar la precisión de Healthgrades al informar la certificación por el Consejo Americano de Cirugía y por el Consejo Americano de Cirugía de Colon y Recto. El resultado secundario fue identificar factores asociados con altas calificaciones en estrellas.Un total de 48 (9.6%) de la muestra de 500 fueron identificados incorrectamente como cirujanos practicantes de EE. UU. y excluidos del análisis subsecuente. Healthgrades mostró un 80.1% de concordancia con las certificaciones verificadas del Consejo Americano de Cirugía y el 85.4% con el Consejo Americano de Cirugía de Colon y Recto. La calificación promedio de estrellas fue 4.2 / 5 (SD 0.9), y 77 (21.6%) tuvieron calificaciones de 5 estrellas. En un modelo logístico multivariable (p <0.001), la calificación de 5 estrellas se asoció con 1-9 años (OR 2.76, p = 0.04) o más de 40 años en la práctica (OR 3.35, p = 0.04) y menos evaluaciones (OR 0.88, p <0.001). No hubo asociaciones significativas con el género, edad, región geográfica o certificación por los Consejos del cirujano.Los datos se limitaron a un solo sitio web de calificación de médicos.En la era moderna del consumismo en atención médica, los sitios web de calificación de los médicos deben usarse con precaución debido a imprecisiones. Se necesitan recursos en línea más precisos para que las decisiones de los pacientes sean informadas en la selección de atención quirúrgica especializada de colon y recto. Consulte Video Resumen en http://links.lww.com/DCR/B91. (Traducción-Dr. Jorge Silva-Velazco).

A pilot precision medicine trial for children with diffuse intrinsic pontine glioma-PNOC003: A report from the Pacific Pediatric Neuro-Oncology Consortium.

This clinical trial evaluated whether whole exome sequencing (WES) and RNA sequencing (RNAseq) of paired normal and tumor tissues could be incorporated into a personalized treatment plan for newly diagnosed patients (<25 years of age) with diffuse intrinsic pontine glioma (DIPG). Additionally, whole genome sequencing (WGS) was compared to WES to determine if WGS would further inform treatment decisions, and whether circulating tumor DNA (ctDNA) could detect the H3K27M mutation to allow assessment of therapy response. Patients were selected across three Pacific Pediatric Neuro-Oncology Consortium member institutions between September 2014 and January 2016. WES and RNAseq were performed at diagnosis and recurrence when possible in a CLIA-certified laboratory. Patient-derived cell line development was attempted for each subject. Collection of blood for ctDNA was done prior to treatment and with each MRI. A specialized tumor board generated a treatment recommendation including up to four FDA-approved agents based upon the genomic alterations detected. A treatment plan was successfully issued within 21 business days from tissue collection for all 15 subjects, with 14 of the 15 subjects fulfilling the feasibility criteria. WGS results did not significantly deviate from WES-based therapy recommendations; however, WGS data provided further insight into tumor evolution and fidelity of patient-derived cell models. Detection of the H3F3A or HIST1H3B K27M (H3K27M) mutation using ctDNA was successful in 92% of H3K27M mutant cases. A personalized treatment recommendation for DIPG can be rendered within a multicenter setting using comprehensive next-generation sequencing technology in a clinically relevant timeframe.

Sclerosing Epithelioid Fibrosarcoma of the Bone With Rare EWSR1-CREB3L3 Translocation Driving Upregulation of the PI3K/mTOR Signaling Pathway.

Sclerosing epithelioid fibrosarcoma (SEF) is an uncommon neoplasm that rarely presents in bone. It is characterized by epithelioid cells arranged in nests and single-file cords within a sclerotic stromal background which may mimic neoplastic bone. SEF harbors an EWSR1 translocation, which may complicate its distinction from Ewing sarcoma in cases with histomorphologic overlap. We present a diagnostically challenging case of SEF in the mandible of a 16-year-old girl. Our experience highlights the lack of specificity of traditional morphology and EWSR1 break-apart fluorescent in situ hybridization. Open-ended RNA-based fusion gene testing coupled with MUC4 immunohistochemistry aided the eventual diagnosis in this case. Herein, we report the third case of SEF with EWSR1-CREB3L3 translocation and show that this fusion leads to aberrant upregulation of the phosphoinositide 3-kinase/mammalian target of rapamycin signaling pathway in heterologous cell models.

Inositol polyphosphates intersect with signaling and metabolic networks via two distinct mechanisms.

Inositol-based signaling molecules are central eukaryotic messengers and include the highly phosphorylated, diffusible inositol polyphosphates (InsPs) and inositol pyrophosphates (PP-InsPs). Despite the essential cellular regulatory functions of InsPs and PP-InsPs (including telomere maintenance, phosphate sensing, cell migration, and insulin secretion), the majority of their protein targets remain unknown. Here, the development of InsP and PP-InsP affinity reagents is described to comprehensively annotate the interactome of these messenger molecules. By using the reagents as bait, >150 putative protein targets were discovered from a eukaryotic cell lysate (Saccharomyces cerevisiae). Gene Ontology analysis of the binding partners revealed a significant overrepresentation of proteins involved in nucleotide metabolism, glucose metabolism, ribosome biogenesis, and phosphorylation-based signal transduction pathways. Notably, we isolated and characterized additional substrates of protein pyrophosphorylation, a unique posttranslational modification mediated by the PP-InsPs. Our findings not only demonstrate that the PP-InsPs provide a central line of communication between signaling and metabolic networks, but also highlight the unusual ability of these molecules to access two distinct modes of action.

A Novel Inositol Pyrophosphate Phosphatase in Saccharomyces cerevisiae: Siw14 PROTEIN SELECTIVELY CLEAVES THE ß-PHOSPHATE FROM 5-DIPHOSPHOINOSITOL PENTAKISPHOSPHATE (5PP-IP5).

Inositol pyrophosphates are high energy signaling molecules involved in cellular processes, such as energetic metabolism, telomere maintenance, stress responses, and vesicle trafficking, and can mediate protein phosphorylation. Although the inositol kinases underlying inositol pyrophosphate biosynthesis are well characterized, the phosphatases that selectively regulate their cellular pools are not fully described. The diphosphoinositol phosphate phosphohydrolase enzymes of the Nudix protein family have been demonstrated to dephosphorylate inositol pyrophosphates; however, theSaccharomyces cerevisiaehomolog Ddp1 prefers inorganic polyphosphate over inositol pyrophosphates. We identified a novel phosphatase of the recently discovered atypical dual specificity phosphatase family as a physiological inositol pyrophosphate phosphatase. Purified recombinant Siw14 hydrolyzes the ß-phosphate from 5-diphosphoinositol pentakisphosphate (5PP-IP5or IP7)in vitro. In vivo,siw14Δ yeast mutants possess increased IP7levels, whereas heterologousSIW14overexpression eliminates IP7from cells. IP7levels increased proportionately whensiw14Δ was combined withddp1Δ orvip1Δ, indicating independent activity by the enzymes encoded by these genes. We conclude that Siw14 is a physiological phosphatase that modulates inositol pyrophosphate metabolism by dephosphorylating the IP7isoform 5PP-IP5to IP6.

The biorepository portal toolkit: an honest brokered, modular service oriented software tool set for biospecimen-driven translational research.

BACKGROUND: High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of the clinical, specimen and genomic data collected for biorepository resources. METHODS: We introduce an electronic Honest Broker (eHB) and Biorepository Portal (BRP) open source project that, in tandem, allow for data integration while protecting patient privacy. This modular approach allows data and specimens to be associated with a biorepository subject at any time point asynchronously. This lowers the bar to develop new research projects based on scientific merit without institutional review for a proposal. RESULTS: By facilitating the automated de-identification of specimen and associated clinical and genomic data we create a future proofed specimen set that can withstand new workflows and be connected to new associated information over time. Thus facilitating collaborative advanced genomic and tissue research. CONCLUSIONS: As of Janurary of 2016 there are 23 unique protocols/patient cohorts being managed in the Biorepository Portal (BRP). There are over 4000 unique subject records in the electronic honest broker (eHB), over 30,000 specimens accessioned and 8 institutions participating in various biobanking activities using this tool kit. We specifically set out to build rich annotation of biospecimens with longitudinal clinical data; BRP/REDCap integration for multi-institutional repositories; EMR integration; further annotated specimens with genomic data specific to a domain; build application hooks for experiments at the specimen level integrated with analytic software; while protecting privacy per the Office of Civil Rights (OCR) and HIPAA.

Paradoxical activation and RAF inhibitor resistance of BRAF protein kinase fusions characterizing pediatric astrocytomas.

Astrocytomas are the most common type of brain tumors in children. Activated BRAF protein kinase mutations are characteristic of pediatric astrocytomas with KIAA1549-BRAF fusion genes typifying low-grade astrocytomas and (V600E)BRAF alterations characterizing distinct or higher-grade tumors. Recently, BRAF-targeted therapies, such as vemurafenib, have shown great promise in treating V600E-dependent melanomas. Like (V600E)BRAF, BRAF fusion kinases activate MAPK signaling and are sufficient for malignant transformation; however, here we characterized the distinct mechanisms of action of KIAA1549-BRAF and its differential responsiveness to PLX4720, a first-generation BRAF inhibitor and research analog of vemurafenib. We found that in cells expressing KIAA1549-BRAF, the fusion kinase functions as a homodimer that is resistant to PLX4720 and accordingly is associated with CRAF-independent paradoxical activation of MAPK signaling. Mutagenesis studies demonstrated that KIAA1549-BRAF fusion-mediated signaling is diminished with disruption of the BRAF kinase dimer interface. In addition, the KIAA1549-BRAF fusion displays increased binding affinity to kinase suppressor of RAS (KSR), an RAF relative recently demonstrated to facilitate MEK phosphorylation by BRAF. Despite its resistance to PLX4720, the KIAA1549-BRAF fusion is responsive to a second-generation selective BRAF inhibitor that, unlike vemurafenib, does not induce activation of wild-type BRAF. Our data support the development of targeted treatment paradigms for BRAF-altered pediatric astrocytomas and also demonstrate that therapies must be tailored to the specific mutational context and distinct mechanisms of action of the mutant kinase.