The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Digital Exposure of English Place-names (DEEP)

Place-names are a fundamental concept in all academic collections: everything happens somewhere. Contemporary place-names are comprehensively represented in digital gazetteer and geospatial web services such as GeoNames. However, despite millions of pounds of investment by JISC and other agencies in historical online resources in recent years, there is currently no equivalent for historic place-names. This project will digitize the entire 86 volume corpus of the Survey of English Place-Names (SEPN), the ultimate authority on historic place-names in England, and make its 4 million forms available.

Ultrasound biomicroscopy in deep sclerectomy

Purpose: To evaluate by ultrasound biomicroscopy (UBM) the anatomical characteristics and the intraocular pressure (IOP) lowering mechanisms of deep sclerectomy after long-term follow-up. Methods: In all, 22 eyes of 21 consecutive patients who had deep sclerectomy were examined by UBM. Several UBM variables were prospectively evaluated, including the presence and maximum length and height of the intrascleral space, the minimum thickness of residual trabeculo-Descemet membrane (TDM), the presence and type of subconjunctival filtering bleb, and the presence of other possible drainage sites, for example suprachoroidal. Surgical success was considered to be achieved when the IOP was

Control of intraocular pressure after deep sclerectomy

Aim: To study the long-term outcome of deep sclerectomy in patients with open angle glaucoma. Methods: Prospective consecutive series of 43 eyes (38 patients) with medically uncontrolled open-angle glaucoma undergoing deep sclerectomy. All patients underwent clinical assessment before and after surgery at day 7 and at months 1, 3, 6, 12, 18, 24, 36. Surgical success was considered if the patient's intraocular pressure (IOP)>22 mmHg and the IOP was lowered by more than 20% without the use of any medication. Kaplan-Meier survival curves were used to evaluate the success rate. Results: The mean follow-up time was 28.1±8.2 months. Mean IOP decreased significantly from a preoperative value of 24.6±5.5 mmHg to a postoperative value of 18.5±4.6 mmHg at 36 months (P>0.001). Microperforation of TDM occurred in three cases (7.0%) and ciliary body prolapse in one case (2.3%) but did not prevent completion of the operation. Postoperatively, hyphaema was detected in one case and shallow anterior chamber in another case and both were treated conservatively. Bleb encapsulation with elevation of IOP occurred in two cases (4.7%) and was treated with 5-fluorouracil subconjunctival injection. Goniopuncture with neodymium : YAG laser was performed in two cases (4.7%). There were no other late complications with the exception of failure of the operation. On the life-table analysis the success rate at 12, 24, and 30 months were 61.4, 36.6, and 18.9%, respectively. Conclusion: Deep sclerectomy reduced the IOP temporarily while minimising the risk of postoperative complications commonly encountered with standard trabeculectomy. However, after long-term follow-up surgery failed to maintain a low IOP. © 2006 Nature Publishing Group. All rights reserved.

Physical properties of a new Deep Eutectic Solvent based on lithium bis[(trifluoromethyl)sulfonyl]imide and N-methylacetamide as superionic suitable electrolyte for lithium ion batteries and electric double layer capacitors

Herein we present a study on the physical/chemical properties of a new Deep Eutectic Solvent (DES) based on N-methylacetamide (MAc) and lithium bis[(trifluoromethyl)sulfonyl]imide (LiTFSI). Due to its interesting properties, such as wide liquid-phase range from -60°C to 280°C, low vapor pressure, and high ionic conductivity up to 28.4mScm at 150°C and at x=1/4, this solution can be practically used as electrolyte for electrochemical storage systems such as electric double-layer capacitors (EDLCs) and/or lithium ion batteries (LiBs). Firstly, relationships between its transport properties (conductivity and viscosity) as a function of composition and temperature were discussed through Arrhenius' Law and Vogel-Tamman-Fulcher (VTF) equations, as well as by using the Walden classification. From this investigation, it appears that this complex electrolyte possesses a number of excellent transport properties, like a superionic character for example. Based on which, we then evaluated its electrochemical performances as electrolyte for EDLCs and LiBs applications by using activated carbon (AC) and lithium iron phosphate (LiFePO) electrodes, respectively. These results demonstrate that this electrolyte has a good compatibility with both electrodes (AC and LiFePO) in each testing cell driven also by excellent electrochemical properties in specific capacitance, rate and cycling performances, indicating that the LiTFSI/MAc DES can be a promising electrolyte for EDLCs and LiBs applications especially for those requiring high safety and stability. © 2013 Elsevier Ltd.

An Evidential Approach to Query Interface Matching on the Deep Web

Matching query interfaces is a crucial step in data integration across multiple Web databases. The problem is closely related to schema matching that typically exploits different features of schemas. Relying on a particular feature of schemas is not suffcient. We propose an evidential approach to combining multiple matchers using Dempster-Shafer theory of evidence. First, our approach views the match results of an individual matcher as a source of evidence that provides a level of confidence on the validity of each candidate attribute correspondence. Second, it combines multiple sources of evidence to get a combined mass function that represents the overall level of confidence, taking into account the match results of different matchers. Our combination mechanism does not require use of weighing parameters, hence no setting and tuning of them is needed. Third, it selects the top k attribute correspondences of each source attribute from the target schema based on the combined mass function. Finally it uses some heuristics to resolve any conflicts between the attribute correspondences of different source attributes. Our experimental results show that our approach is highly accurate and effective.

Visually extracting data records from the deep web

Web sites that rely on databases for their content are now ubiquitous. Query result pages are dynamically generated from these databases in response to user-submitted queries. Automatically extracting structured data from query result pages is a challenging problem, as the structure of the data is not explicitly represented. While humans have shown good intuition in visually understanding data records on a query result page as displayed by a web browser, no existing approach to data record extraction has made full use of this intuition. We propose a novel approach, in which we make use of the common sources of evidence that humans use to understand data records on a displayed query result page. These include structural regularity, and visual and content similarity between data records displayed on a query result page. Based on these observations we propose new techniques that can identify each data record individually, while ignoring noise items, such as navigation bars and adverts. We have implemented these techniques in a software prototype, rExtractor, and tested it using two datasets. Our experimental results show that our approach achieves significantly higher accuracy than previous approaches. Furthermore, it establishes the case for use of vision-based algorithms in the context of data extraction from web sites.