The Biomedical Research Hub: a federated platform for patient research data.

OBJECTIVE: The objective was to develop and operate a cloud-based federated system for managing, analyzing, and sharing patient data for research purposes, while allowing each resource sharing patient data to operate their component based upon their own governance rules. The federated system is called the Biomedical Research Hub (BRH). MATERIALS AND METHODS: The BRH is a cloud-based federated system built over a core set of software services called framework services. BRH framework services include authentication and authorization, services for generating and assessing findable, accessible, interoperable, and reusable (FAIR) data, and services for importing and exporting bulk clinical data. The BRH includes data resources providing data operated by different entities and workspaces that can access and analyze data from one or more of the data resources in the BRH. RESULTS: The BRH contains multiple data commons that in aggregate provide access to over 6 PB of research data from over 400 000 research participants. DISCUSSION AND CONCLUSION: With the growing acceptance of using public cloud computing platforms for biomedical research, and the growing use of opaque persistent digital identifiers for datasets, data objects, and other entities, there is now a foundation for systems that federate data from multiple independently operated data resources that expose FAIR application programming interfaces, each using a separate data model. Applications can be built that access data from one or more of the data resources.

Pigmented Ependymoma of the Fourth Ventricle-A Curious Entity: Report of a Rare Case With Review of Literature.

A 16-year-old boy presented with a tumor located in fourth ventricle, which showed histological features of an ependymoma replete with perivascular pseudorosettes and true ependymal rosettes. Interestingly, many of the tumor cells exhibited abundant cytoplasm stuffed with a grayish brown pigment. Histochemical stains showed the pigment to be acid fast and periodic acid-Schiff positive and negative for Masson-Fontana melanin stain. Additionally, the pigment displayed brilliant autofluorescence under ultraviolet light of a fluorescent microscope. Ultrastructure examination of the pigment revealed a non-membrane-bound biphasic structure with an electron-dense core and electron-lucent periphery. Only few similar case reports mention such pigmented ependymomas to contain a mixture of neuromelanin and lipofuscin while others mention it to be melanin itself. Our workup suggests the pigment to represent lipofuscin or its derivative. Generally known to be a pigment of wear and tear, the significance of finding it in a tumor with such abundance remains to be understood and explored.

Peripheral blood involvement in angioimmunoblastic T-cell lymphoma: a case report and review of the literature.

Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive variant of peripheral T-cell lymphoma, occurring in elderly patients without any gender predisposition. It accounts for 1-2% of all non-Hodgkin lymphoma. Although characterized by some peculiar histological features, diagnosis of AITL can sometimes be challenging and a definite diagnosis requires a complete immunophenotypic and molecular workup. Peripheral Blood (PB) involvement in AITL has not been studied in detail and there is a paucity of published data about leukemic presentation of AITL. We present a case of a 38-year-old female diagnosed as AITL with PB involvement. Flow cytometric (FCM) examination of PB showed 40% abnormal lymphoid cells which were CD45+, CD4+, CD2+, cCD3+, CD5+, CD10+, CD16+ and TCRγδ restricted. PB involvement by AITL appears to be more common and under-reported. Nevertheless, detection of these tumoral T lymphocytes needs to be assessed in large case studies for assessing the true incidence of PB involvement. FCM analysis is an effective and reliable approach in the identification of leukemic phase of AITL and can lead to timely and effective intervention.

A Real-world Perspective of CD123 Expression in Acute Leukemia as Promising Biomarker to Predict Treatment Outcome in B-ALL and AML.

INTRODUCTION: CD123 is overexpressed in many hematologic malignancies and found to be useful in characterizing leukemic blasts of both acute myeloid leukemia (AML) and B-acute lymphoblastic leukemia (B-ALL). CD123 has been recently found to be a marker of leukemic stem cells, and its utility to measure residual disease and potential role in disease relapse is under evaluation. MATERIALS AND METHODS: Herein, we have evaluated the expression of CD123 in 757 samples of acute leukemia including 479 treatment-naive and 278 follow-up samples and compared with post-induction morphologic complete remission and measurable residual disease (MRD) status. Multiparametric flow cytometry was used for assessment of CD123 expression and immunophenotypic characterization of leukemic blasts at diagnostic and MRD assessment time points. RESULTS: Using variable cutoffs of 5%, 10%, and 20% to define a case as CD123-positive, expression of CD123 was observed in 75.6%, 66.2%, and 50% of AML and 88.6%, 81.8%, and 75% of B-ALL, respectively. Of 11 patients, 7 (63.63%) had mixed phenotype acute leukemia, but none of the 12 patients with T-acute lymphoblastic leukemia showed positivity for CD123. CD123 expression at diagnosis was associated with post-induction MRD-positive status in both B-ALL (P < .001) and AML (P = .001). We also evaluated the utility of CD123 as a leukemia-associated aberrant immunophenotype and found it to be useful in both patients with AML (baseline, 50.6%; follow-up, 53%) and B-ALL (baseline, 75%; follow-up, 73.07%). CONCLUSIONS: In conclusion, CD123 may be considered as a cardinal marker for residual disease assessment and response evaluation in AML and B-ALL.

FLI1 and MIC2 expression in precursor B-lymphoblastic leukemia with Burkitt-like morphology and extensive extramedullary involvement: A diagnostic challenge in pediatric small round cell tumor.

Pediatric small round cell tumors (PSRCTs) constitute a large proportion of childhood malignancies with overlapping diagnostic and clinical features but radically different therapies. Here, we report a case of 16-year-old male child presenting with diffuse abdominal and mediastinal mass, axillary lymphadenopathy, and pleural effusion. Bone marrow aspirate showed near total replacement by small round malignant cells. The bone marrow biopsy showed interstitial infiltration by malignant cells, which were CD45- CD3- CD20- MIC2+ FLI1+ and diagnosis of Ewing's sarcoma was established. In contrast, flowcytometric immunophenotyping of the bone marrow aspirate showed CD45- cells, which were CD19+ cytCD79a+ CD10+ CD81+ CD38+ HLA-DR+ CD22+ CD20- consistent with B-cell acute lymphoblastic leukemia (B-ALL). The extended immunostaining panel on bone marrow biopsy also showed positivity for cytCD79a, CD10, CD19, and BCL-2, whereas fluorescent in-situ hybridization for EWSR1 gene rearrangement was negative. Thus, a final diagnosis of CD45- FLI1+ MIC2+ B-ALL was established. Rare cases of CD45- B-ALL with immunoreactivity for MIC2 and Friend leukemia virus integration 1 (FLI1) have posed a diagnostic challenge for PSRCTs in the recent past. This case report highlights the role of multimodality approach in establishing a correct diagnosis in CD45- PSRCTs to ensure definitive therapy and better clinical outcome.

Tracking the Growth of Superparamagnetic Nanoparticles with an In-Situ Magnetic Particle Spectrometer (INSPECT).

Magnetic Particle Spectroscopy (MPS) is a measurement technique to determine the magnetic properties of superparamagnetic iron oxide nanoparticles (SPIONs) in an oscillating magnetic field as applied in Magnetic Particle Imaging (MPI). State of the art MPS devices are solely capable of measuring the magnetization response of the SPIONs to an oscillatory magnetic excitation retrospectively, i.e. after the synthesis process. In this contribution, a novel in-situ magnetic particle spectrometer (INSPECT) is presented, which can be used to monitor the entire synthesis process from particle genesis via growth to the stable colloidal suspension of the nanoparticles in real time. The device is suitable for the use in a biochemistry environment. It has a chamber size of 72 mm such that a 100 ml reaction flask can be used for synthesis. For an alkaline-based precipitation, the change of magnetic properties of SPIONs during the nucleation and growth phase of the synthesis is demonstrated. The device is able to record the changes in the amplitude and phase spectra, and, in turn, the hysteresis. Hence, it is a powerful tool for an in-depth understanding of the nanoparticle formation dynamics during the synthesis process.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.

Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance and merge callsets from an ensemble of SV-calling algorithms. It includes a fusion model built using analysis of 27 deep-coverage human genomes from the 1000 Genomes Project. We identify 843 novel SV calls that were not reported by the 1000 Genomes Project for these 27 samples. Experimental validation of a subset of these calls yields a validation rate of 86.7%. FusorSV is available at https://github.com/TheJacksonLaboratory/SVE .

A Bayesian Framework for Generalized Linear Mixed Modeling Identifies New Candidate Loci for Late-Onset Alzheimer's Disease.

Recent technical and methodological advances have greatly enhanced genome-wide association studies (GWAS). The advent of low-cost, whole-genome sequencing facilitates high-resolution variant identification, and the development of linear mixed models (LMM) allows improved identification of putatively causal variants. While essential for correcting false positive associations due to sample relatedness and population stratification, LMMs have commonly been restricted to quantitative variables. However, phenotypic traits in association studies are often categorical, coded as binary case-control or ordered variables describing disease stages. To address these issues, we have devised a method for genomic association studies that implements a generalized LMM (GLMM) in a Bayesian framework, called Bayes-GLMM Bayes-GLMM has four major features: (1) support of categorical, binary, and quantitative variables; (2) cohesive integration of previous GWAS results for related traits; (3) correction for sample relatedness by mixed modeling; and (4) model estimation by both Markov chain Monte Carlo sampling and maximal likelihood estimation. We applied Bayes-GLMM to the whole-genome sequencing cohort of the Alzheimer's Disease Sequencing Project. This study contains 570 individuals from 111 families, each with Alzheimer's disease diagnosed at one of four confidence levels. Using Bayes-GLMM we identified four variants in three loci significantly associated with Alzheimer's disease. Two variants, rs140233081 and rs149372995, lie between PRKAR1B and PDGFA The coded proteins are localized to the glial-vascular unit, and PDGFA transcript levels are associated with Alzheimer's disease-related neuropathology. In summary, this work provides implementation of a flexible, generalized mixed-model approach in a Bayesian framework for association studies.

Computational inference of a genomic pluripotency signature in human and mouse stem cells.

UNLABELLED: Recent analyses of next-generation sequencing datasets have shown that cell-specific regulatory elements in stem cells are marked with distinguishable patterns of transcription factor (TF) binding and epigenetic marks. For example, we recently demonstrated that promoters of cell-specific genes are covered with expanded trimethylation of histone H3 at lysine 4 (H3K4me3) marks (i.e., broad H3K4me3 domains). Moreover, binding of specific TFs, such as OCT4, NANOG, and SOX2, have been shown to play a critical role in maintaining the pluripotency of stem cells. Despite these observations, a systematic exploration of genomic and epigenomic features of stem-cell-specific gene promoters has not been conducted. Advanced machine-learning models can capture distinguishable genomic and epigenomic characteristics of stem-cell-specific promoters by taking advantage of the wealth of publicly available datasets. Here, we propose a three-step framework to discover novel data characteristics of high-throughput next generation sequencing datasets that distinguish pluripotency genes in human and mouse embryonic stem cells (ESCs). Our framework involves: i) feature extraction to identify novel features of genomic datasets; ii) feature selection using a logistic regression model combined with the Least Absolute Shrinkage and Selection Operator (LASSO) method to find the most critical datasets and features; and iii) cross validation with features selected using LASSO method to assess the predictive power of selected data features in distinguishing pluripotency genes. We show that specific epigenetic marks, and specific features of these marks, are enriched at pluripotency gene promoters. Moreover, we also assess both the individual and combined effect of TF binding, epigenetic mark deposition, gene expression datasets for marking pluripotency genes. Our findings are consistent with the existence of a conserved, complex and integrative genomic signature in ESCs that can be exploited to flag important candidate pluripotency genes. They also validate our computational framework for fostering a deeper understanding of genomic datasets in stem cells, in the future, could be extended to study cell-type-specific genomic landscapes in other cell types. REVIEWERS: This article was reviewed by Zoltan Gaspari and Piotr Zielenkiewicz.

The tandem duplicator phenotype as a distinct genomic configuration in cancer.

Next-generation sequencing studies have revealed genome-wide structural variation patterns in cancer, such as chromothripsis and chromoplexy, that do not engage a single discernable driver mutation, and whose clinical relevance is unclear. We devised a robust genomic metric able to identify cancers with a chromotype called tandem duplicator phenotype (TDP) characterized by frequent and distributed tandem duplications (TDs). Enriched only in triple-negative breast cancer (TNBC) and in ovarian, endometrial, and liver cancers, TDP tumors conjointly exhibit tumor protein p53 (TP53) mutations, disruption of breast cancer 1 (BRCA1), and increased expression of DNA replication genes pointing at rereplication in a defective checkpoint environment as a plausible causal mechanism. The resultant TDs in TDP augment global oncogene expression and disrupt tumor suppressor genes. Importantly, the TDP strongly correlates with cisplatin sensitivity in both TNBC cell lines and primary patient-derived xenografts. We conclude that the TDP is a common cancer chromotype that coordinately alters oncogene/tumor suppressor expression with potential as a marker for chemotherapeutic response.

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.

An integrated map of structural variation in 2,504 human genomes.

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Efficient CRISPR/Cas9-Mediated Genome Editing in Mice by Zygote Electroporation of Nuclease.

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system is an adaptive immune system in bacteria and archaea that has recently been exploited for genome engineering. Mutant mice can be generated in one step through direct delivery of the CRISPR/Cas9 components into a mouse zygote. Although the technology is robust, delivery remains a bottleneck, as it involves manual injection of the components into the pronuclei or the cytoplasm of mouse zygotes, which is technically demanding and inherently low throughput. To overcome this limitation, we employed electroporation as a means to deliver the CRISPR/Cas9 components, including Cas9 messenger RNA, single-guide RNA, and donor oligonucleotide, into mouse zygotes and recovered live mice with targeted nonhomologous end joining and homology-directed repair mutations with high efficiency. Our results demonstrate that mice carrying CRISPR/Cas9-mediated targeted mutations can be obtained with high efficiency by zygote electroporation.

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations.

Human cancers are frequently polyploid, containing multiple aneuploid subpopulations that differ in total DNA content. In this study we exploit this property to reconstruct evolutionary histories, by assuming that mutational complexity increases with time. We developed an experimental method called Ploidy-Seq that uses flow-sorting to isolate and enrich subpopulations with different ploidy prior to next-generation genome sequencing. We applied Ploidy-Seq to a patient with a triple-negative (ER-/PR-/HER2-) ductal carcinoma and performed whole-genome sequencing to trace the evolution of point mutations, indels, copy number aberrations, and structural variants in three clonal subpopulations during tumor growth. Our data show that few mutations (8% to 22%) were shared between all three subpopulations, and that the most aggressive clones comprised a minority of the tumor mass. We expect that Ploidy-Seq will have broad applications for delineating clonal diversity and investigating genome evolution in many human cancers.

Systems consequences of amplicon formation in human breast cancer.

Chromosomal structural variations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome profiling. We found that tandem duplications appear to be early events in tumor evolution, especially in the genesis of amplicons. In a detailed reconstruction of events on chromosome 17, we found large unpaired inversions and deletions connect a tandemly duplicated ERBB2 with neighboring 17q21.3 amplicons while simultaneously deleting the intervening BRCA1 tumor suppressor locus. This series of events appeared to be unusually common when examined in larger genomic data sets of breast cancers albeit using approaches with lesser resolution. Using siRNAs in breast cancer cell lines, we showed that the 17q21.3 amplicon harbored a significant number of weak oncogenes that appeared consistently coamplified in primary tumors. Down-regulation of BRCA1 expression augmented the cell proliferation in ERBB2-transfected human normal mammary epithelial cells. Coamplification of other functionally tested oncogenic elements in other breast tumors examined, such as RIPK2 and MYC on chromosome 8, also parallel these findings. Our analyses suggest that structural variations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously and that such oncogenic cassettes are favored during the evolution of a cancer.

Facile and rapid thermo-regulated biomineralization of gold by pullulan and study of its thermodynamic parameters.

A novel method for the production of gold nanoparticles (AuNPs) using pullulan as reducing and stabilizing agent has been developed. Quasi-spherical shaped AuNPs in the range of 50-100 nm were produced at three different temperature regimes 80°C, 90°C and 100°C as characterized using UV-vis spectrophotometer, TEM and DLS. Study of reaction kinetics and thermodynamic parameters indicated that the reaction between pullulan and chloroauric acid for AuNPs formation followed first order reaction kinetics and higher temperature was favorable for the synthesis of smaller sized AuNPs. FT-IR data analyses, provided an insight towards the mechanism of gold nanoparticle formation which suggested that, the free CH2OH groups of pullulan molecule were oxidized to carboxylate ions resulted in formation of AuNPs whereas the basic skeletal structure of pullulan remained unaltered. This study may open up new avenues for synthesis of tailor made biogenic AuNPs with possible application in biomedical field.

Abberantly placed impacted mandibular canine.

Pre-eruptive migration of a tooth across the midline is termed as transmigration. It is believed that transmigration is rare and unique to the mandibular permanent canines, and even more rarely reported for others. Transmigration is a phenomenon of yet unknown etiology. It follows the direction of its long axis, with the crown leading the migration. The tendency of a canine to cross the barrier of mandibular midline suture is a more important consideration than the distance of migration after crossing the midline. Here we present one new case of aberrantly positioned right mandibular canine which has undergone migration and was accidently found on radiological examination before orthodontic treatment. Once diagnosed an aberrantly positioned impacted canine requires surgical removal.