BioBricks.ai: a versioned data registry for life sciences data assets.

Introduction: Researchers in biomedicine and public health often spend weeks locating, cleansing, and integrating data from disparate sources before analysis can begin. This redundancy slows discovery and leads to inconsistent pipelines.

Methods: We created BioBricks.

Multiomic and clinical analysis of multiply recurrent meningiomas reveals risk factors, underlying biology, and insights into evolution.

An important subset of meningiomas behaves aggressively and is characterized by multiple recurrences. We identify clinical, genetic, and epigenetic predictors of multiply recurrent meningiomas (MRMs) and evaluate the evolution of these meningiomas in patient-matched samples. On multivariable binomial logistic regression, MRMs were significantly associated with male sex ( = 0.

Development of a polygenic score predicting drug resistance and patient outcome in breast cancer.

Gene expression profiles of hundreds of cancer cell-lines and the cell-lines' response to drug treatment were analyzed to identify genes whose expression correlated with drug resistance. In the GDSC dataset of 809 cancer cell lines, expression of 36 genes were associated with drug resistance (increased IC50) to many anti-cancer drugs. This was validated in the CTRP dataset of 860 cell lines.

BioBricks.ai: A Versioned Data Registry for Life Sciences Data Assets.

Researchers in biomedical research, public health and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and innovation. Instead of countless developers creating redundant and inconsistent data pipelines, BioBricks.ai offers a centralized data repository and a suite of developer-friendly tools to simplify access to scientific data.

Spinal calcifying pseudoneoplasms of the neuraxis: A case report and review of the literature.

Calcifying pseudoneoplasms of the neuraxis (CAPNON) are rare, non-neoplastic, slow-growing tumors that can present anywhere throughout the central nervous system. While the etiology of these lesions remains unknown, the mainstay of treatment is surgical excision. We describe a case of CAPNON at our institution in a 66 year-old female patient who presented with 5 months of pain and burning sensation in her thigh.

Impact of histopathological classification of non-functioning adenomas on long term outcomes: comparison of the 2004 and 2017 WHO classifications.

Purpose: Outcomes of patients with non-functioning pituitary adenomas categorized using the 2004 and 2017 WHO classification systems are understudied. We report outcomes from the University of Virginia of patients with non-functioning pituitary adenomas categorized using both systems.

Methods: We constructed a database from all 239 patients who underwent resection of a non-functioning pituitary adenoma between 2003 and 2015 and had at least 5 years of follow-up.

Primary Spinal Cord Astrocytomas: Two-Center Clinical Experience of Low- and High-Grade Lesions.

Objective: Primary spinal cord astrocytomas are rare, fatal, and poorly studied.

Methods: This study included a 2-center, retrospective analysis of primary spinal cord astrocytoma patients from 1997 to 2020. Patients with drop metastases or without at least one follow-up were excluded.

Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer.

Germline Variants (GVs) are effective in predicting cancer risk and may be relevant in predicting patient outcomes. Here we provide a bioinformatic pipeline to identify GVs from the TCGA lower grade glioma cohort in Genomics Data Commons. We integrate paired whole exome sequences from normal and tumor samples and RNA sequences from tumor samples to determine a patient's GV status.

Detecting molecular subtypes from multi-omics datasets using SUMO.

We present a data integration framework that uses non-negative matrix factorization of patient-similarity networks to integrate continuous multi-omics datasets for molecular subtyping. It is demonstrated to have the capability to handle missing data without using imputation and to be consistently among the best in detecting subtypes with differential prognosis and enrichment of clinical associations in a large number of cancers. When applying the approach to data from individuals with lower-grade gliomas, we identify a subtype with a significantly worse prognosis.

Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy.

High tumor mutational burden (TMB) is associated with response to checkpoint blockade in several cancers. We identify pathogenic germline variants associated with increased TMB (GVITMB). GVITMB were found in 7 genes using a pan-cancer approach (, , , , , and ) and 38 gene sets (e.

Stereotactic Radiosurgery for Atypical (World Health Organization II) and Anaplastic (World Health Organization III) Meningiomas: Results From a Multicenter, International Cohort Study.

Background: Atypical and anaplastic meningiomas have reduced progression-free/overall survival (PFS/OS) compared to benign meningiomas. Stereotactic radiosurgery (SRS) for atypical meningiomas (AMs) and anaplastic meningiomas (malignant meningiomas, MMs) has not been adequately described.

Objective: To define clinical/radiographic outcomes for patients undergoing SRS for AM/MMs.

Germline Variants That Affect Tumor Progression.

Germline variants have a rich history of being studied in the context of cancer risk. Emerging studies now suggest that germline variants contribute not only to cancer risk but to tumor progression as well. In this opinion article, we discuss the initial discoveries associating germline variants with patient outcome and the mechanisms by which germline variants affect molecular pathways.

Genomic and molecular characterization of pituitary adenoma pathogenesis: review and translational opportunities.

Objective: Innovations in genomics, epigenomics, and transcriptomics now lay the groundwork for therapeutic interventions against neoplastic disease. In the past 30 years, the molecular pathogenesis of pituitary adenomas has been characterized. This enhanced understanding of the biology of pituitary tumors has potential to impact current treatment paradigms, and there exists significant translational potential for these results.

ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines.

Extrachromosomal circular DNAs (eccDNAs) are somatically mosaic and contribute to intercellular heterogeneity in normal and tumor cells. Because short eccDNAs are poorly chromatinized, we hypothesized that they are sequenced by tagmentation in ATAC-seq experiments without any enrichment of circular DNA. Indeed, ATAC-seq identified thousands of eccDNAs in cell lines that were validated by inverse PCR and by metaphase FISH.

Cerebrospinal fluid area and syringogenesis in Chiari malformation type I.

Objective: Syringogenesis in Chiari malformation type I (CM-I) is thought to occur secondary to impaction of the cerebellar tonsils within the foramen magnum (FM). However, the correlation between the CSF area and syringogenesis has yet to be elucidated. The authors sought to determine whether the diminution in subarachnoid space is associated with syringogenesis.

The pan-cancer landscape of prognostic germline variants in 10,582 patients.

Background: While clinical factors such as age, grade, stage, and histological subtype provide physicians with information about patient prognosis, genomic data can further improve these predictions. Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no study has systematically analyzed multiple cancers in an unbiased way to identify genetic loci that can improve patient outcome predictions made using clinical factors.

Methods: We analyzed sequencing data from the over 10,000 cancer patients available through The Cancer Genome Atlas to identify germline variants associated with patient outcome using multivariate Cox regression models.

Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation.

DRAIC is a 1.7 kb spliced long noncoding RNA downregulated in castration-resistant advanced prostate cancer. Decreased DRAIC expression predicts poor patient outcome in prostate and seven other cancers, while increased DRAIC represses growth of xenografted tumors.

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance.

Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families.

Chiari I malformation in children-the natural history.

Purpose: To review the natural history of asymptomatic and symptomatic pediatric Chiari I malformations with and without syringomyelia.

Materials And Methods: We reviewed the literature for case reports and case series describing the natural history of asymptomatic and symptomatic children with Chiari I malformations with and without syringomyelia. Our review included approximately 700 asymptomatic children without syringomyelia, 100 symptomatic children without syringomyelia, 22 asymptomatic children with syringomyelia, and 11 symptomatic children with syringomyelia.

The biophysical role of hemodynamics in the pathogenesis of cerebral aneurysm formation and rupture.

The pathogenesis of intracranial aneurysms remains complex and multifactorial. While vascular, genetic, and epidemiological factors play a role, nascent aneurysm formation is believed to be induced by hemodynamic forces. Hemodynamic stresses and vascular insults lead to additional aneurysm and vessel remodeling.

Tumor to Cerebellar Peduncle T2-Weighted Imaging Intensity Ratio Fails to Predict Pituitary Adenoma Consistency.

 The consistency of pituitary macroadenomas affects the complexity of surgical resection. On T2-weighted (T2W) imaging, the intensity ratio of the tumor to the cerebellar peduncle (tumor to cerebellar peduncle T2-weighted imaging intensity [TCTI] ratio) correlates with meningioma consistency. We aimed to determine the correlation of this radiographic finding with pituitary macroadenoma consistency and to determine whether it can be used for preoperative planning.

The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients.

Lower grade gliomas are invasive brain tumors that are difficult to completely resect neurosurgically. They often recur following resection and progress, resulting in death. Although previous studies have shown that specific germline variants increase the risk of tumor formation, no previous study has screened many germline variants to identify variants predictive of survival in patients with glioma.

Ganglioglioma Arising from the Septum Pellucidum: Case Report and Review of the Literature.

Background: Gangliogliomas are low-grade neoplasms that typically affect patients under the age of 30 and present with epilepsy and symptoms of mass effect. Here, we report a case of an intraventricular ganglioglioma involving the septum pellucidum in a pediatric patient with history of optic glioma. Only one other pediatric intraventricular ganglioglioma arising from the septum pellucidum has been reported previously.