Implementing evidence-based assertions of clinical actionability in the context of secondary findings: Updates from the ClinGen Actionability Working Group.

PURPOSE: The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions. METHODS: Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs. RESULTS: The resulting rubric has a 4-point scale (limited, moderate, strong, and definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, predefined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs. CONCLUSION: The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.

Functional analysis of a putative type III polyketide synthase from deep-sea sediment metagenome.

Type III polyketide synthases (type III PKSs) are single homodimeric enzymes that produce diverse products such as phloroglucinol, pyrones, resorcinols and chalcones which are biotechnologically important molecules. In an attempt to identify new type III PKS from extreme environments, the deep-sea sediment metagenome from Bay of Bengal was screened for type III PKS genes. BLASTX analyses of Nanopore sequence derived metagenome with the in-house created PKS database revealed a full length type III PKS from a 5 kb fragment. The annotated full length type III PKS, S9PKS showed 25-30 % sequence identity towards previously characterized enzymes. To functionally characterize the gene, it was synthesized, cloned into pET28a and pColdI vectors under T7 and csp promoters, respectively, and expressed in Escherichia coli Rosetta(DE3) pLysS. The optimized PKS (OptiPKS) was expressed as inclusion bodies under both promoters. The inclusion bodies were successfully solubilised using low concentration of urea, refolded and purified using Ni-NTA Agarose resin. The purified OptiPKS was tested for functionality using fatty acyl-CoA substrates at various temperatures. High performance liquid chromatography (HPLC) analyses revealed that OptiPKS produced tri and tetraketide pyrones using C4 to C10 acyl-CoA starter substrates. Further characterization and mutation of the enzyme would reveal its functional significance. Thus, the study could be a lead for the annotation and functional characterization of putative type III PKS from environmental metagenome data.

Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications.

Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.

Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance.

Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.

PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery.

We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols and training materials for processing PDX data. Currently, the portal contains PDXNet model information and data resources from 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCI's Patient-Derived Model Repository (PDMR) for public access. These models have 2134 associated sequencing files from 873 samples across 308 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal includes results from freely available, robust, validated and standardized analysis workflows on PDXNet sequencing files and PDMR data (3857 samples from 629 patients across 85 disease types). The PDXNet portal is continuously updated with new data and is of significant utility to the cancer research community as it provides a centralized location for PDXNet resources, which support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials.

ClinGen's Pediatric Actionability Working Group: Clinical actionability of secondary findings from genome-scale sequencing in children and adolescents.

PURPOSE: Synthesis and curation of evidence regarding the clinical actionability of secondary findings (SFs) from genome-scale sequencing are needed to support decision-making on reporting of these findings. To assess actionability of SFs in children and adolescents, the Clinical Genome Resource established the Pediatric Actionability Working Group (AWG). METHODS: The Pediatric AWG modified the framework of the existing Adult AWG, which included production of summary reports of actionability for genes and associated conditions and consensus actionability scores for specific outcome-intervention pairs. Modification of the adult framework for the pediatric setting included accounting for special considerations for reporting presymptomatic or predictive genetic findings in the pediatric context, such as maintaining future autonomy by not disclosing conditions not actionable until adulthood. The Pediatric AWG then applied this new framework to genes and associated conditions with putative actionability. RESULTS: As of September 2021, the Pediatric AWG applied the new framework to 70 actionability topics representing 143 genes. Reports and scores are publicly available at www.clinicalgenome.org. CONCLUSION: The Pediatric AWG continues to curate gene-condition topics and build an evidence-based resource, supporting clinical communities and decision-makers with policy development on the return of SFs in pediatric populations.

ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.

BACKGROUND: Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking. RESULTS: Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications. CONCLUSIONS: The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.

Geometrically Interlocking Space-Filling Tiling Based on Fabric Weaves.

In this article, we introduce a framework for the geometric design and fabrication of a family of geometrically interlocking space-filling shapes, which we call woven tiles. Our framework is based on a unique combination of (1) Voronoi partitioning of space using curve segments as the Voronoi sites and (2) the design of these curve segments based on weave patterns closed under symmetry operations. The underlying weave geometry provides an interlocking property to the tiles and the closure property under symmetry operations ensure single tile can fill space. In order to demonstrate this general framework, we focus on specific symmetry operations induced by fabric weaving patterns. We specifically showcase the design and fabrication of woven tiles on flat and curved domains by using the most common 2-fold fabrics, namely, plain, twill, and satin weaves. We further evaluate and compare the mechanical behavior of the so created woven tiles through finite element analysis.

Analysis of Different Illuminance of the Room Lighting Condition on the Accuracy (Trueness and Precision) of An Intraoral Scanner.

PURPOSE: To measure the influence of illuminance of the ambient light between 1000 lux (room light) and 10 000 lux (chair light) on the accuracy of an intraoral scanner (IOS). MATERIAL AND METHODS: A typodont was digitized using an extraoral scanner to obtain a reference standard tessellation language (STL) file. Ten groups were created based on the different illuminance of the ambient light conditions tested starting from 1000 lux (no chair light) to 10000 lux (chair light) in increments of 1000 lux by increasing the distance between the chair light and the mannequin, with the room light turned on. Ten digital scans per group were obtained (n = 10) using an IOS (Trios 3; 3Shape). The accuracy of the digital scans was evaluated with respect to the reference mesh of the typodont using a 3D mesh processing software. Kruskal-Wallis and pair-wise comparison tests were used to analyze the data (α = 0.05). RESULTS: Significant difference for trueness and precision values were found among the groups (p < 0.001). The 1000-lux group exhibited the lowest discrepancy values with a median of 26.33 µm and an interquartile range (IQR) of 40.04 µm (11.97-52.00) (p < 0.001); while the 5000-lux group obtained the highest discrepancy values with a median of 46.38 µm and an IQR of 99.94 µm (19.05-118.98) (p < 0.001). The pair-wise multi-comparison showed no difference between the 8000- and 4000-lux groups (p = 0.287). In all groups, the IQR was higher than the mean errors from the control mesh, suggesting that the relative precision was low. CONCLUSIONS: A 1000-lux illumination lighting condition is recommended to maximize the scanning accuracy of the IOS tested; the chair light should be avoided. Furthermore, the scanning accuracy response under the illuminance range tested presented a lack of monotonicity.

Clinical Study of the Influence of Ambient Lighting Conditions on the Mesh Quality of an Intraoral Scanner.

PURPOSE: To compute the effect of ambient light illuminance settings on the mesh quality of the digital scans accomplished in a subject. MATERIAL AND METHODS: A subject was recruited. The maxillary dentition did not present any dental restoration. A prosthodontist recorded different complete-arch maxillary digital scans by using an IOS (TRIOS 3; 3Shape) under 4 different illuminance light conditions namely chair light at 10,000-lux illuminance (CL group), room light at 1000-lux illuminance (RL group), natural light at 500-lux illuminance (NL group), and no light at 0-lux luminosity (ZL group). Ten digital scans for each group were consecutively obtained. Mesh quality was examined using the iso2mesh MATLAB package. Shapiro-Wilk test revealed a nonnormally distributed data. Kruskal-Wallis one-way ANOVA, and pair-wise comparison were selected to evaluate the data (α = 0.05). RESULTS: Significant differences in mesh quality values were measured among the groups (p < 0.001). Pair-wise comparisons revealed that significant difference was found across all pairs of lighting groups, except for the RL-NL comparison (p = 0.279). However, the CL condition obtained the highest mean values, followed by RL and NL groups, and the lowest mean values were obtained on the ZL lighting condition. CONCLUSIONS: Chair light at 10,000-lux illuminance condition is recommended to maximize the quality mesh values of the IOS system tested (TRIOS 3; 3Shape).

Distinct DNA repair pathways cause genomic instability at alternative DNA structures.

Alternative DNA structure-forming sequences can stimulate mutagenesis and are enriched at mutation hotspots in human cancer genomes, implicating them in disease etiology. However, the mechanisms involved are not well characterized. Here, we discover that Z-DNA is mutagenic in yeast as well as human cells, and that the nucleotide excision repair complex, Rad10-Rad1(ERCC1-XPF), and the mismatch repair complex, Msh2-Msh3, are required for Z-DNA-induced genetic instability in yeast and human cells. Both ERCC1-XPF and MSH2-MSH3 bind to Z-DNA-forming sequences, though ERCC1-XPF recruitment to Z-DNA is dependent on MSH2-MSH3. Moreover, ERCC1-XPF-dependent DNA strand-breaks occur near the Z-DNA-forming region in human cell extracts, and we model these interactions at the sub-molecular level. We propose a relationship in which these complexes recognize and process Z-DNA in eukaryotes, representing a mechanism of Z-DNA-induced genomic instability.

Clinical Study of the Influence of Ambient Light Scanning Conditions on the Accuracy (Trueness and Precision) of an Intraoral Scanner.

PURPOSE: To quantify the impact of ambient lighting conditions on the accuracy (trueness and precision) of an intraoral scanner (IOS) when maxillary complete-arch and maxillary right quadrant digital scans were performed in a patient. MATERIAL AND METHODS: One complete dentate patient was selected. A complete maxillary arch vinyl polysiloxane impression was obtained and poured using Type IV dental stone. The working cast was digitized using a laboratory scanner (E4 Dental Scanner; 3Shape) and the reference standard tessellation language (STL file) was obtained. Two groups were created based on the extension of the maxillary digital scans performed namely complete-arch (CA group) and right quadrant (RQ) groups. The CA and RQ digital scans of the patient were performed using an IOS (TRIOS 3; 3Shape) with 4 lighting conditions chair light (CL), 10 000 lux, room light (RL), 1003 lux, natural light (NL), 500 lux, and no light (ZL), 0 lux. Ten digital scans per group at each ambient light settings (CL, RL, NL, and ZL) were consecutively obtained (n = 10). The STLR file was used to analyze the discrepancy between the digitized working cast and digital scans using MeshLab software. Kruskal-Wallis, one-way ANOVA, and pair-wise comparison were used to analyze the data. RESULTS: Significant difference in the trueness and precision values were found across different lighting conditions where RL condition obtained the lowest absolute error compared with the other lighting conditions tested followed by CL, NL, and ZL. On the CA group, RL condition also obtained the best accuracy values, CL and NL conditions performed closely and under ZL condition the mean error presented the highest values. On the RQ group, CL condition presented the lowest absolute error when compared with the other lighting conditions evaluated. A pair-wise multicomparison showed no significant difference between NL and ZL conditions. In all groups, the standard deviation was higher than the mean errors from the control mesh, indicating that the relative precision was low. CONCLUSIONS: Light conditions significantly influenced on the scanning accuracy of the IOS evaluated. RL condition obtained the lowest absolute error value of the digital scans performed. The extension of the digital scan was a scanning accuracy influencing factor. The higher the extension of the digital scan performed, the lower the accuracy values obtained. Furthermore, ambient light scanning conditions influenced differently depending on the extension of the digital scans made.

RemeDB: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets.

Environmental pollution has emerged to be a major hazard in today's world. Pollutants from varied sources cause harmful effects to the ecosystem. The major pollutants across marine and terrestrial regions are hydrocarbons, plastics, and dyes. Conventional methods for remediation have their own limitations and shortcomings to deal with these environmental pollutants. Bio-based remediation techniques using microbes have gained momentum in the recent past, primarily ascribed to their eco-friendly approach. The role of microbial enzymes in remediating the pollutants are well reported, and further exploration of microbial resources could lead to discovery of novel pollutant degrading enzymes (PDEs). Recent advances in next-generation sequencing technologies and metagenomics have provided the impetus to explore environmental microbes for potentially novel bioremediation enzymes. In this study, a tool, RemeDB, was developed for identifying bioremediation enzymes sequences from metagenomes. RemeDB aims at identifying hydrocarbon, dye, and plastic degrading enzymes from various metagenomic libraries. A sequence database consisting of >30,000 sequences proven to degrade the major pollutants was curated from various literature sources and this constituted the PDEs' database. Programs such as HMMER and RAPSearch were incorporated to scan across large metagenomic sequences libraries to identify PDEs. The tool was tested with metagenome data sets from varied sources and the outputs were validated. RemeDB was efficient to classify and identify the signature patterns of PDEs in the input data sets.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one's confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

Extending gene ontology in the context of extracellular RNA and vesicle communication.

BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO. In addition, we have initiated an ongoing process of extractions of gene product annotations associated with these terms from Vesiclepedia and ExoCarta, conversion of the extracted annotations to Gene Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium. As a use case, we have incorporated some of the GO terms into annotations of samples from the exRNA Atlas and implemented a faceted search interface based on such annotations. RESULTS: We have added 7 new terms and modified 9 existing terms (along with their synonyms and relationships) to GO. Additionally, 18,695 unique coding gene products (mRNAs and proteins) and 963 unique non-coding gene products (ncRNAs) which are associated with the terms: "extracellular vesicle", "extracellular exosome", "apoptotic body", and "microvesicle" were extracted from ExoCarta and Vesiclepedia. These annotations are currently being processed for submission to GO. CONCLUSIONS: As an inter-community effort, we have made a substantial update to GO in the exRNA context. We have also demonstrated the utility of some of the new GO terms for sample annotation and metadata search.

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.

Planning and Dosimetric Study of Volumetric Modulated Arc Based Hypofractionated Stereotactic Radiotherapy for Acoustic Schwannoma--6MV Flattening Filter Free Photon Beam.

BACKGROUND: The purpose of this study was to assess the dosimetric and clinical feasibility of volumetric modulated arc based hypofractionated stereotactic radiotherapy (RapidArc) treatment for large acoustic schwannoma (AS>10 cc). MATERIALS AND METHODS: Ten AS patients were immobilized using BrainLab mask. They were subject to multimodality imaging (magnetic resonance and computed tomography) to contour target and organs at risk (brainstem and cochlea). Volumetric modulated arc therapy (VMAT) based stereotactic plans were optimized in Eclipse (V11) treatment planning system (TPS) using progressive resolution optimizer-III and final dose calculations were performed using analytical anisotropic algorithm with 1.5 mm grid resolution. All AS presented in this study were treated with VMAT based HSRT to a total dose of 25 Gy in 5 fractions (5 fractions/ week). VMAT plan contains 2-4 non-coplanar arcs. Treatment planning was performed to achieve at least 99% of PTV volume (D99) receives 100% of prescription dose (25 Gy), while dose to OAR's were kept below the tolerance limits. Dose-volume histograms (DVH) were analyzed to assess plan quality. Treatments were delivered using upgraded 6 MV un-flattened photon beam (FFF) from Clinac-iX machine. Extensive pretreatment quality assurance measurements were carried out to report on quality of delivery. Point dosimetry was performed using three different detectors, which includes CC13 ion-chamber, Exradin A14 ion-chamber and Exradin W1 plastic scintillator detector (PSD) which have measuring volume of 0.13 cm3, 0.009 cm3 and 0.002 cm3 respectively. RESULTS: Average PTV volume of AS was 11.3 cc (±4.8), and located in eloquent areas. VMAT plans provided complete PTV coverage with average conformity index of 1.06 (±0.05). OAR's dose were kept below tolerance limit recommend by American Association of Physicist in Medicine task group-101(brainstem V0.5 cc<23 Gy, cochlea maximum<25 Gy and Optic pathway<25 Gy). PSD resulted in superior dosimetric accuracy compared with other two detectors (p=0.021 for PSD.

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.

Volumetric modulated arc-based hypofractionated stereotactic radiotherapy for the treatment of selected intracranial arteriovenous malformations: dosimetric report and early clinical experience.

PURPOSE: To evaluate, with a dosimetric and clinical feasibility study, RapidArc (a volumetric modulated arc technique) for hypofractionated stereotactic radiotherapy treatment of large arteriovenous malformations (AVMs). METHODS AND MATERIALS: Nine patients were subject to multimodality imaging (magnetic resonance, computed tomography, and digital subtraction angiography) to determine nidus and target volumes, as well as involved organs at risk (optical structures, inner ear, brain stem). Plans for multiple intensity-modulated arcs with a single isocenter were optimized for a fractionation of 25 Gy in 5 fractions. All plans were optimized for 6-MV photon beams. Dose-volume histograms were analyzed to assess plan quality. Delivery parameters were reported to appraise technical features of RapidArc, and pretreatment quality assurance measurements were carried out to report on quality of delivery. RESULTS: Average size of AVM nidus was 26.2 cm(3), and RapidArc plans provided complete target coverage with minimal overdosage (V(100%) = 100% and V(110%) < 1%) and excellent homogeneity (<6%). Organs at risk were highly spared. The D(1%) to chiasm, eyes, lenses, optic nerves, and brainstem (mean ± SD) was 6.4 ± 8.3, 1.9 ± 3.8, 2.3 ± 2.2, 0.7 ± 0.9, 4.4 ± 7.2, 12.2 ± 9.6 Gy, respectively. Conformity index (CI(95%)) was 2.2 ± 0.1. The number of monitor units per gray was 277 ± 45, total beam-on time was 2.5 ± 0.3 min. Planning vs. delivery γ pass rate was 98.3% ± 0.9%. None of the patients developed acute toxicity. With a median follow-up of 9 months, 3 patients presented with deterioration of symptoms and were found to have postradiation changes but responded symptomatically to steroids. These patients continue to do well on follow-up. One patient developed headache and seizures, which was attributed to intracranial bleed, confirmed on imaging. CONCLUSION: Hypofractionated stereotactic radiotherapy can be successfully delivered using the RapidArc form of volumetric arc technology for intracranial AVMs. The quality of delivery and calculated parameters are in agreement with each other and are in line with published reports for other sites.