Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

A Continuation Method of Parameter Inversion for Non-Equilibrium Convection-Dispersion Equation

Based on the homotopy mapping, a globally convergent method of parameter inversion for non-equilibrium convection-dispersion equations (CDEs) is developed. Moreover, in order to further improve the computational efficiency of the algorithm, a properly smooth function, which is derived from the sigmoid function, is employed to update the homotopy parameter during iteration. Numerical results show the feature of global convergence and high performance of this method. In addition, even the measurement quantities are heavily contaminated by noises, and a good solution can be found.

Three-Dimensional Network Model And Its Parameter Calibration

A material model, whose framework is parallel spring-bundles oriented in 3-D space, is proposed. Based on a discussion of the discrete schemes and optimum discretization of the solid angles, a 3-D network cell consisted of one-dimensional components is developed with its geometrical and physical parameters calibrated. It is proved that the 3-D network model is able to exactly simulate materials with arbitrary Poisson ratio from 0 to 1/2, breaking through the limit that the previous models in the literature are only suitable for materials with Poisson ratio from 0 to 1/3. A simplified model is also proposed to realize high computation accuracy within low computation cost. Examples demonstrate that the 3-D network model has particular superiority in the simulation of short-fiber reinforced composites.

Comparison of Various Adhesion Contact Theories and the Influence of Dimensionless Load Parameter

Three models, JKR (Johnson, Kendall and Roberts), DMT (Derjaguin, Muller, and Toporov) andMD (Maugis-Dugdale),are compared with the Hertz model in dealing with nano-contact problems. It has been shown that both the dimensionless load parameter, P D P=.1/4

The role of androgens in fetal growth: observational study in two genetic models of disordered androgen signalling.

OBJECTIVE: To examine the role of androgens on birth weight in genetic models of altered androgen signalling. SETTING: Cambridge Disorders of Sex Development (DSD) database and the Swedish national screening programme for congenital adrenal hyperplasia (CAH). PATIENTS: (1) 29 girls with XY karyotype and mutation positive complete androgen insensitivity syndrome (CAIS); (2) 43 girls and 30 boys with genotype confirmed CAH. MAIN OUTCOME MEASURES: Birth weight, birth weight-for-gestational-age (birth weight standard deviation score (SDS)) calculated by comparison with national references. RESULTS: Mean birth weight SDS in CAIS XY infants was higher than the reference for girls (mean, 95% CI: 0.4, 0.1 to 0.7; p=0.02) and was similar to the national reference for boys (0.1, -0.2 to 0.4). Birth weight SDS in CAH girls was similar to the national reference for girls (0.0, -0.2 to 0.2) and did not vary by severity of gene mutation. Birth weight SDS in CAH boys was also similar to the national reference for boys (0.2, -0.2 to 0.6). CONCLUSION: CAIS XY infants have a birth weight distribution similar to normal male infants and birth weight is not increased in infants with CAH. Alterations in androgen signalling have little impact on birth weight. Sex dimorphism in birth size is unrelated to prenatal androgen exposure.

A species conserving genetic algorithm for multimodal function optimization

This paper introduces a new technique called species conservation for evolving parallel subpopulations. The technique is based on the concept of dividing the population into several species according to their similarity. Each of these species is built around a dominating individual called the species seed. Species seeds found in the current generation are saved (conserved) by moving them into the next generation. Our technique has proved to be very effective in finding multiple solutions of multimodal optimization problems. We demonstrate this by applying it to a set of test problems, including some problems known to be deceptive to genetic algorithms.

Material parameter extraction in THz-TDS using a converging beam transfer function

We demonstrate a parameter extraction algorithm based on a theoretical transfer function, which takes into account a converging THz beam. Using this, we successfully extract material parameters from data obtained for a quartz sample with a THz time domain spectrometer. © 2010 IEEE.

Direct parameter extraction in capacitively transduced micromechanical resonators using the anti-resonance

This paper presents a method for the fast and direct extraction of model parameters for capacitive MEMS resonators from their measured transmission response such as quality factor, resonant frequency, and motional resistance. We show that these parameters may be extracted without having to first de-embed the resonator motional current from the feedthrough. The series and parallel resonances from the measured electrical transmission are used to determine the MEMS resonator circuit parameters. The theoretical basis for the method is elucidated by using both the Nyquist and susceptance frequency response plots, and applicable in the limit where CF > CmQ; commonly the case when characterizing MEMS resonators at RF. The method is then applied to the measured electrical transmission for capacitively transduced MEMS resonators, and compared against parameters obtained using a Lorentzian fit to the measured response. Close agreement between the two methods is reported herein. © 2010 IEEE.

Direct parameter extraction in feedthrough-embedded capacitive MEMS resonators

This paper presents a method for fast and accurate determination of parameters relevant to the characterization of capacitive MEMS resonators like quality factor (Q), resonant frequency (fn), and equivalent circuit parameters such as the motional capacitance (Cm). In the presence of a parasitic feedthrough capacitor (CF) appearing across the input and output ports, the transmission characteristic is marked by two resonances: series (S) and parallel (P). Close approximations of these circuit parameters are obtained without having to first de-embed the resonator motional current typically buried in feedthrough by using the series and parallel resonances. While previous methods with the same objective are well known, we show that these are limited to the condition where CF ≪ CmQ. In contrast, this work focuses on moderate capacitive feedthrough levels where CF > CmQ, which are more common in MEMS resonators. The method is applied to data obtained from the measured electrical transmission of fabricated SOI MEMS resonators. Parameter values deduced via direct extraction are then compared against those obtained by a full extraction procedure where de-embedding is first performed and followed by a Lorentzian fit to the data based on the classical transfer function associated with a generic LRC series resonant circuit. © 2011 Elsevier B.V. All rights reserved.