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Supplementary Tables 1-4, Figures 1-11 from miR-99 Family of MicroRNAs Suppresses the Expression of Prostate-Specific Antigen and Prostate Cancer Cell Proliferation

Professor Mary-Ellen O’Connell, in her new book, The Art of Law in the International Community, packs the tale of an extra-positive approach to law-making back at the centre of the stage. The book attempts to consider the of the community to explain the rise of two pillars of contemporary international law, namely the legal regulation of the use of force and the rules (or more precisely the meta-rules) on jus cogens. The book shifts steadily towards the intersection between natural law, jus cogens, and the ban of unilateral use of force. Methodologically speaking, the two regimes intersect since both are off springs of the UN Charter and the 1969 Vienna Convention. Perhaps not in the same trend of state practice, both principles formulate the general principle of international law. In sum, they add a small group of rules which feature the new world order in the aftermath of World War II.

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.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.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%).In conclusion, CD123 may be considered as a cardinal marker for residual disease assessment and response evaluation in AML and B-ALL.

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.

In the early 1930s, a Jewish man gleefully staring at Der Stürmer, a Nazi propaganda rag baffled his friends. His friends inquired: “Why are you enjoying it so much?” He answers, “if you read Jewish papers, the news is terrible. But, according to this, the news is all good. We control the banks, we control the country and we run the whole world!” Such has been the fate of the Jewish community and especially of the Rothschild Family. A fate which has been marred with hate and envy, which perpetuated itself as a point of discourse and corny theory. Deciphering and de-bunking these theories, Niall Ferguson, through his writings allows readers an alternative and academic perspective. One can string a common thread in the masterful writing of Nial Ferguson as he covers expansive ground citing examples to evidence that networks have existed ever since humanity has. From the structure of the brain to the food chain, from the family tree to freemasonry

On Saturday 20 March 2021, Turkey did the unthinkable. It was announced that Turkey had withdrawn from a human rights treaty. In a presidential decree, Turkey had declared that it had denounced its obligations from the (hereinafter Convention). The convention is a legally-binding Council of Europe treaty, covering domestic violence and seeking to end legal impunity for perpetrators. It covers 34 European countries and took effect in 2014. It bears the name of a famous Turkish city (Istanbul) which straddles Europe and Asia across the Bosphorus Strait. Sitting at the epicenter of trade and commerce, one expects the leader of the aforementioned Convention to lead by example.

States like its citizens and residents do not exist in silos. International relations catapulted by globalisation have created an increasingly interconnected global village. Irrespective of the populist backlash on globalisation, the importance of international relations has not vitiated, as a matter of fact, it has become even more relevant. However, one must understand the critical nuances of the international legal regime and especially the law which governs the actors/ agents of nations. States’ interaction is a double-edged sword. They seek the promotion of exports and also public relations (less euphemistically known as propaganda) while meandering over what must be done and what cannot be done. Since time immemorial, diplomats and other envoys have needed privileges and immunities for the effective performance of their functions in the receiving state. The preamble to the Vienna Convention recites that ‘the purpose of such privileges and immunities is not to benefit individuals but to ensure the efficient performance of the functions of diplomatic missions as representing states’.

Once Hugo Grotius said in his book that there are two types of an arbitrator, one who is acting in the capacity of a judge and allowing every rule of law with the procedure. The other kind of arbitrator is who follows the concept of equity principle and the same can be linked to the law of merchant which can be further connected to the arbitration by using the rules of custom as well as trade. The main reason to undergird the use of arbitration in the commercial transaction was to eradicate the absurdity of court rules, and there was no uniformity concerning the applicability of laws. Earlier, the hoary concept of law of merchant was also prevalent, which gave rise to formation and enforcement of its rules in arbitration. The idea of Lex Mercatorian gave rise to the use of usage and customs which merchants followed and were earlier prevalent in Europe.

Coronavirus or COVID-19 not only overturned everyday life, but also forced us to remodel the very structure on which our civilization functions. The United Nations (hereinafter referred to as 'U.N.') and more particularly World Health Organisation (hereinafter referred to as 'WHO') have emerged as vital organisations dedicated towards curbing and preventing the spread of coronavirus and ensuring proper supply of medicines and other essential commodities during these critical times. The role of States has also become crucial in aspects of governance amid such an extraordinary situation that humanity finds itself in. Apart from general requirements of safety standards, many Conventions and Treaties provide for provisions which call for the role of the Government and global cooperation during an international health emergency. The UN Charter under Articles 1,2,55 and 56 and the 1970 Declaration on the Principles of International Law concerning Friendly Relations and Co-operation among States stresses States to cooperate during such extraordinary situations. Further, Article 25 of the 1948 Universal Declaration of Human Rights provides for the Right of People to have a healthy life and the duty on the State to protect this Right. In addition to it, the 1966 International Covenant on Economic, Social, and Cultural Rights under Article 12 lists duties of the participating States to ensure that the people should have the highest standards of health. Additionally, the Convention stresses upon the "prevention, treatment, and control of epidemic, endemic, occupational and other diseases”. Furthermore, the UN Committee on Economic, Social, and Cultural Rights under the 1966 Convention urged for "the creation of a system of urgent medical care in cases of epidemics and the provision of disaster relief and humanitarian assistance in emergencies.”

Sean Murphy, Professor of Law at the George Washington University and Member of the United Nations International Law Commission (ICL) pressed upon the requirement of “a global convention on crimes against humanity (as it) appears to be a key missing piece in the current framework of international humanitarian law, international criminal law, and human rights law”. While the consideration for this is well-founded and is the essence of the hour. One is compelled to consider crimes against humanity as formulated in the Rome Statute forming themselves as parts of customary international law thus vitiating the requirement of a Convention.

The immunity of Heads of State was challenged in the indictment of Omar Al-Bashir, Sudanese President by the International Criminal Court (hereinafter, ICC). While there remains a stunted doubt concerning the understanding that Bashir was guilty of all crimes such as crimes against humanity: murder, extermination, forcible transfer, torture, and rape; two counts of war crimes: intentionally directing attacks against a civilian population as such or against individual civilians not taking part in hostilities, and pillaging; three counts of genocide: by killing, by causing serious bodily or mental harm, and by deliberately inflicting on each target group conditions of life calculated to bring about the group's physical destruction there were questions about his immunity at the ICC. This article sheds light on the issues of immunity of heads of state and the arguments on the indictment of Bashir. The factual matrix and involvement of the United Nations Security Council are relevant because they aid in determining the scope of the ICC jurisdiction. In addition, they also highlight the discourse around the head of state immunity and the need to determine ICC’s role on state immunity when it conflicts with the public international law. As a response to this, the article will highlight the work of the International Law Commission (herein after ILC) around the discourse of immunity as a solution to this contemporary challenge to the jurisprudence of international criminal law.

While the American’s are famous for claiming themselves to be the torchbearers of democracy, they have often found themselves as abusers of the international rule of law. Well, international law is a little tricky. That is the case because, within a country, a law is based on governmentsanctioned rules. This, in short, is known as municipal or domestic law. However, there is no world government to dictate the world’s rules of engagement. As a substitute states consent and binds their consensual states to international treaties and agreements. But the United States has refrained itself from ratifying the Rome Statute, the Vienna Convention, and several nuclear weapons and landmine bans. Thus, beckons the question, how does one country prosecute another country for violating a treaty it never signed to it?

The ‘common heritage of mankind’ (Legal Concept) principle within international law provides for a general framework of universal responsibility of sustained legal and environmental protection. It establishes a close link of space law to the law governing other areas beyond national jurisdiction, such as the high seas, the deep seafloor, and some might even argue Antarctica.

The efficacy of electrocoalescence is critically dependent upon the interfacial tension of the crude–water interface. This study demonstrates the effect of interfacial tension on the electrocoalescence efficiency in crudes with high acidity. The interfacial tension is estimated using spinning drop tensiometer (SDT) and electrocoalescence experiments are performed at an electric field = 1.15 kVrms/cm at a frequency of 50 Hz. It is observed that separation of water from the crude is hindered at high pH for two very different reasons depending upon the source of alkalinity. Calcium hydroxide induced alkalinity leads to more rigid interface, resulting in delayed electrocoalescence. On the other hand, sodium hydroxide based alkalinity leads to ultra-low tension of crude–water interface, thereby causing oil-in-water emulsion. Increase in the pH also leads to poor quality of brine resolution, in case of sodium hydroxide based alkalinity (pH = 10) we get unresolved turbid emulsion.

Magnetic particle imaging (MPI) is a novel tomographic imaging modality which uses static and dynamic magnetic fields to measure the magnetic response generated by superparamagnetic iron oxide nanoparticles (SPIONs). For the characterization of the SPIONs magnetic particle spectroscopy (MPS) is used. In the current research, a low noise amplifier (LNA) suitable for MPI and MPS is presented. LNA plays a significant role in the receive chain of MPI and MPS by amplifying the signals from the nanoparticles while keeping the noise induced through its own circuitry minimal. The LNA is based on the summing configuration and fabricated on a printed circuit board (PCB). Moreover, the prototyped LNA is compared with a commercially available pre-amplifier. The input voltage noise of the prototyped LNA with a receiving coil of series resistance of 0.551 mΩ and an inductance of 130 μH is 561 pV/√Hz with a noise figure (NF) of 11.57 dB.

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.

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. Electronic supplementary material The online version of this article (10.1186/s13059-018-1404-6) contains supplementary material, which is available to authorized users.

Magnetic particle spectrometry (MPS) is a novel technique used to measure the magnetization response of superparamagnetic iron oxide nanoparticles (SPIONs). Therefore, it is one of the most important tools for the characterization of the SPIONs for imaging modalities such as magnetic particle imaging (MPI) and Magnetic Resonance Imaging (MRI). In MPS, change in the particle magnetization induces a voltage in a dedicated receive coil. The amplitude of the signal can be very low (ranging from a few nV to 100 μV) depending upon the concentration of the nanoparticles. Hence, the received signal needs to be amplified with a low noise amplifier (LNA). LNA’s paramount task is to amplify the received signal while keeping the noise induced by its own circuitry minimum. In the current research, we purpose modeling, design, and development of a prototyped LNA for MPS. The designed prototype LNA is based on the parallelization technique of Op-amps. The prototyped LNA consists of 16 Op-amps in parallel and is manufactured on a printed circuit board (PCB), with a size of 110.38 mm × 59.46 mm and 234 components. The input noise of the amplifier is approx. 546 pV/√Hz with a noise figure (NF) of approx. 1.4 dB with a receive coil termination. Furthermore, a comparison between the prototyped LNA and a commercially available amplifier is shown.

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 (, Structural variants (SVs) in human genomes contribute diversity and diseases. Here, the authors use a multi-platform strategy to generate haplotype-resolved SVs for three human parent–child trios.

There are various methods to synthesize superparamagnetic nanoparticles (SPIONs) useful for MPI (magnetic particle imaging) and in therapy (Hypothermia) such as co-precipitation, hydrothermal reactions etc. In this research, the focus is to analyse the effects of crucial parameters such as effect of molecular mass of dextran and temperature of the co-precipitation. These parameters play a crucial role in the inherent magnetic properties of the resulting SPIONs. The amplitude spectrum and hysteresis curve of the SPIONs is analysed with MPS (magnetic particle spectrometer). PCCS (photon cross-correlation spectroscopy) measurements are done to analyse the size distribution of hydrodynamic diameter the resulting SPIONs.

Pulse wave measurements provide vital information in medical diagnosis. For this reason, a measurement system is developed for determining the transient time of the pulse wave between the heart and the ear. To detect pressure variations in the sealed ear canal, caused by the arriving pulse wave, an in-ear sensor is developed which uses heart sounds as time reference. Furthermore, for extracting the heart sounds from the pressure measurements and calculating the pulse wave transient time, a MATLAB-based algorithm is described. An embedded microcontroller based measurement board is presented, which realizes an interface between the sensor and the computer for signal processing.

Electrical impedance tomography (EIT) is an imaging method that is able to estimate the electrical conductivity distribution of living tissue. This work presents a field programmable gate array (FPGA)-based multi-frequency EIT system for complex, time-resolved bioimpedance measurements. The system has the capability to work with measurement setups with up to 16 current electrodes and 16 voltage electrodes. The excitation current has a range of about 10 $\mu$A to 5 mA, whereas the sinusoidal signal used for excitation can have a frequency of up to 500 kHz. Additionally, the usage of a chirp or rectangular signal excitation is possible. Furthermore, the described system has a sample rate of up to 3480 impedance spectra per second (ISPS). The performance of the EIT system is demonstrated with a resistor-based phantom and tank phantoms. Additionally, first measurements taken from the human thorax during a breathing cycle are presented.

The present research work highlighted the possibility of exploiting marine microbes for the biosynthesis of copper nanoparticles and further investigated thermodynamic changes during the biomineralization of copper in a microbial system by isothermal titration calorimetry. A bacterial strain (M-7) isolated from Kanyakumari coast, India was found capable of synthesizing these nanoparticles. Based on phylogenetic relationship, the strain M-7 was identified as Kocuria flava. The nanoparticles produced were characterized using UV-vis spectrophotometry, Transmission electron microscopy (TEM) and Dynamic light scattering (DLS). Data revealed the formation of spherical and quasi-spherical shaped nanoparticles with an average particle size ranging between 5 and 30 nm. Additionally, a study on the effect of different media components indicated that media containing higher amount of casein enzymic hydrolysate and yeast extract supported the formation of stable colloidal suspension of nanoparticles. Finally, isothermal titration calorimetry (ITC) was carried out to understand the change in heat energy during the formation of nanoparticles in different media. Combinatorial observations of all these studies may open up new strategies to develop tailor made copper nanoparticles via green route.

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, and strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three human parent–child trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (

This paper includes a flexible algorithm for traversing a directed and an undirected graph. Graph traversal is defined as the problem of visiting all the nodes in a graph in a particular manner, updating and/or checking their values along the way. The Breadth first search along with Depth first search are the most widely used algorithms for traversing a graph. In this article, an algorithm is proposed for traversing a graph taking in consideration the vertex with the maximum outgoing edges. Instead of beginning from the root node and then gaining access to visit the neighbors of the currently visited node, the algorithms looks for the vertex with the maximum edges and then continue traversing all the neighboring vertices of that vertex. This paper presents an algorithm to traverse an undirected or a directed graph and calculates the time and space complexity of the algorithm. The work proposed here intends to find a new algorithm that can be universally applied to all types of graphs General Terms Your general terms must be any term which can be used for general classification of the submitted material such as Pattern Recognition, Security, Algorithms.

Bioimpedance measurements are useful tools in biomedical engineering and life science. Bioimpedance is the electrical impedance of living tissue and can be used in the analysis of various physiological parameters. Bioimpedance is commonly measured by injecting a small well known alternating current via surface electrodes into an object under test and measuring the resultant surface voltages. It is non-invasive, painless and has no known hazards. This work presents a field programmable gate array based high accuracy broadband bioimpedance measurement system for time resolved bioimpedance measurements. The system is able to measure magnitude and phase of complex impedances under test in a frequency range of about 10-500 kHz with excitation currents from 10 µA to 5 mA. The overall measurement uncertainties stay below 1% for the impedance magnitude and below 0.5° for the phase in most measurement ranges. Furthermore, the described system has a sample rate of up to 3840 impedance spectra per second. The performance of the bioimpedance measurement system is demonstrated with a resistor based system calibration and with measurements on biological samples.

Prostate cancer is the second highest cause of male cancer deaths in the United States. A significant number of tumors advance to a highly invasive and metastatic stage, which is typically resistant to traditional cancer therapeutics. In order to identify chromosomal structural variants that may contribute to prostate cancer progression we sequenced the genomes of a HPV-18 immortalized nonmalignant human prostate epithelial cell line, RWPE1, and compared it to its malignant, metastatic derivative, WPE1-NB26. There were a total of 34 large (>1 Mbp) and 38 small copy number variants (

The present study aims at exploiting marine microbial diversity for biosynthesis of metal nanoparticles and also investigates role of microbial proteins in the process of bio-mineralization of gold and silver. This is the first report for concurrent production of gold and silver nanoparticles (AuNPs and AgNPs) by extracellular secretion of a novel strain of Stenotrophomonas, isolated from Indian marine origin. This novel strain has faster rate kinetics for AgNPs synthesis than any other organism reported earlier. The nanoparticles were further characterized using UV-vis spectrophotometer, TEM, DLS and EDAX confirming their size ranging from 10-50 nm and 40-60 nm in dimensions for AuNPs and AgNPs, respectively. TEM analysis indicated formation of multi-shaped nanoparticles with heterogeneous size distribution in both the cases. Finally, the SDS-PAGE analysis of extracellular media supernatant suggested a potential involvement of certain low molecular weight secretory proteins in AuNPs and AgNPs biosynthesis.

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. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0148-z) contains supplementary material, which is available to authorized users.

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.

As of this writing, next generation sequencing (NGS) is an unparalleled source of clinically useful information on sequence variants at the scale of single nucleotides, whereas microarray-based comparative genomic hybridization techniques along with cytogenetic techniques such as G banding, fluorescence in situ hybridization, spectral karyotyping, etc., remain the mainstay of analysis aimed at detection of structural variants (i.e., variants from >1000 bp to those involving megabases of DNA). However, given its potential to provide the total of genetic information NGS is increasingly applied also in structural variant detection. The challenges in this field are mainly related to short read lengths generated by current NGS platforms and widespread use of approaches selectively targeting for analysis only a fraction of the genome. In this chapter we discuss the approach taken by several groups to take NGS data and identify disease-related genetic evidence focusing on copy number variations and other structural variations. Particular focus is on studies in cancer in which the impact of structural variation both for basic biology and for clinical use is highest.

MicroRNAs (miRNA) have been globally profiled in cancers but there tends to be poor agreement between studies including in the same cancers. In addition, few putative miRNA targets have been validated. To overcome the lack of reproducibility, we profiled miRNAs by next generation sequencing and locked nucleic acid miRNA microarrays and verified concordant changes by quantitative RT-PCR. Notably, miR-125b and the miR-99 family members miR-99a, -99b, and -100 were downregulated in all assays in advanced prostate cancer cell lines relative to the parental cell lines from which they were derived. All four miRNAs were also downregulated in human prostate tumor tissue compared with normal prostate. Transfection of miR-99a, -99b, or -100 inhibited the growth of prostate cancer cells and decreased the expression of prostate-specific antigen (PSA), suggesting potential roles as tumor suppressors in this setting. To identify targets of these miRNAs, we combined computational prediction of potential targets with experimental validation by microarray and polyribosomal loading analysis. Three direct targets of the miR-99 family that were validated in this manner were the chromatin-remodeling factors SMARCA5 and SMARCD1 and the growth regulatory kinase mTOR. We determined that PSA is posttranscriptionally regulated by the miR-99 family members, at least partially, by repression of SMARCA5. Together, our findings suggest key functions and targets of miR-99 family members in prostate cancer suppression and prognosis. Cancer Res; 71(4); 1313–24. ©2011 AACR.