SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data

BACKGROUND: Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles. RESULTS: We have developed a visualization tool for displaying whole genome array CGH data in the context of chromosomal location. SeeGH is an application that translates spot signal ratio data from array CGH experiments to displays of high resolution chromosome profiles. Data is imported from a simple tab delimited text file obtained from standard microarray image analysis software. SeeGH processes the signal ratio data and graphically displays it in a conventional CGH karyotype diagram with the added features of magnification and DNA segment annotation. In this process, SeeGH imports the data into a database, calculates the average ratio and standard deviation for each replicate spot, and links them to chromosome regions for graphical display. Once the data is displayed, users have the option of hiding or flagging DNA segments based on user defined criteria, and retrieve annotation information such as clone name, NCBI sequence accession number, ratio, base pair position on the chromosome, and standard deviation. CONCLUSIONS: SeeGH represents a novel software tool used to view and analyze array CGH data. The software gives users the ability to view the data in an overall genomic view as well as magnify specific chromosomal regions facilitating the precise localization of genetic alterations. SeeGH is easily installed and runs on Microsoft Windows 2000 or later environments

The bright-end galaxy candidates at z ~ 9 from 79 independent HST fields

We present a full data analysis of the pure-parallel Hubble Space Telescope (HST) imaging observations in the Brightest of Reionizing Galaxies Survey (BoRG[z9]) in Cycle 22. The medium-deep exposures with five HST/WFC3IR+UVIS filter bands from 79 independent sightlines (~370 arcmin^2) provide the least biased determination of number density for z>9 bright galaxies against cosmic variance. After a strict two-step selection for candidate galaxies, including dropout color and photometric redshift analyses, and revision of previous BoRG candidates, we identify one source at z~10 and two sources at z~9. The z~10 candidate shows evidence of line-of-sight lens magnification (mu~1.5), yet it appears surprisingly luminous (MUV ~ -22.6\pm0.3 mag), making it one of the brightest candidates at z > 8 known (~ 0.3 mag brighter than the z = 8.68 galaxy EGSY8p7, spectroscopically confirmed by Zitrin and collaborators). For z ~ 9 candidates, we include previous data points at fainter magnitudes and find that the data are well fitted by a Schechter luminosity function with alpha ~ -2.1, MUV ~ -21.5 mag, and log phi ~ -4.5 Mpc^-3mag^-1, for the first time without fixing any parameters. The inferred cosmic star formation rate density is consistent with unaccelerated evolution from lower redshift.Comment: 18pages, 7figures, 6tables. accepted to the Astrophysical Journa

Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues

BACKGROUND: Formalin-fixed paraffin-embedded (FFPE) tissues represent the largest source of archival biological material available for genomic studies of human cancer. Therefore, it is desirable to develop methods that enable whole genome amplification (WGA) using DNA extracted from FFPE tissues. Multiple-strand Displacement Amplification (MDA) is an isothermal method for WGA that uses the large fragment of Bst DNA polymerase. To date, MDA has been feasible only for genomic DNA isolated from fresh or snap-frozen tissue, and yields a representational distortion of less than threefold. RESULTS: We amplified genomic DNA of five FFPE samples of normal human lung tissue with the large fragment of Bst DNA polymerase. Using quantitative PCR, the copy number of 7 genes was evaluated in both amplified and original DNA samples. Four neuroblastoma xenograft samples derived from cell lines with known N-myc gene copy number were also evaluated, as were 7 samples of non-small cell lung cancer (NSCLC) tumors with known Skp2 gene amplification. In addition, we compared the array comparative genomic hybridization (CGH)-based genome profiles of two NSCLC samples before and after Bst MDA. A median 990-fold amplification of DNA was achieved. The DNA amplification products had a very high molecular weight (> 23 Kb). When the gene content of the amplified samples was compared to that of the original samples, the representational distortion was limited to threefold. Array CGH genome profiles of amplified and non-amplified FFPE DNA were similar. CONCLUSION: Large fragment Bst DNA polymerase is suitable for WGA of DNA extracted from FFPE tissues, with an expected maximal representational distortion of threefold. Amplified DNA may be used for the detection of gene copy number changes by quantitative realtime PCR and genome profiling by array CGH

The Bright End of the z~9 and z~10 UV Luminosity Functions using all five CANDELS Fields

The deep, wide-area (~800-900 arcmin**2) near-infrared/WFC3/IR + Spitzer/IRAC observations over the CANDELS fields have been a remarkable resource for constraining the bright end of high redshift UV luminosity functions (LFs). However, the lack of HST 1.05-micron observations over the CANDELS fields has made it difficult to identify z~9-10 sources robustly, since such data are needed to confirm the presence of an abrupt Lyman break at 1.2 microns. We report here on the successful identification of many such z~9-10 sources from a new HST program (z9-CANDELS) that targets the highest-probability z~9-10 galaxy candidates with observations at 1.05 microns, to search for a robust Lyman-break at 1.2 microns. The potential z~9-10 candidates are preselected from the full HST, Spitzer/IRAC S-CANDELS observations, and the deepest-available ground-based optical+near-infrared observations. We identified 15 credible z~9-10 galaxies over the CANDELS fields. Nine of these galaxies lie at z~9 and 5 are new identifications. Our targeted follow-up strategy has proven to be very efficient in making use of scarce HST time to secure a reliable sample of z~9-10 galaxies. Through extensive simulations, we replicate the selection process for our sample (both the preselection and follow-up) and use it to improve current estimates for the volume density of bright z~9 and z~10 galaxies. The volume densities we find are 5(-2)(+3)x and 8(-3)(+9)x lower, respectively, than found at z~8. When compared with the best-fit evolution (i.e., dlog_{10} rho(UV)/dz=-0.29+/-0.02) in the UV luminosities densities from z~8 to z~4 integrated to 0.3L*(z=3) (-20 mag), these luminosity densities are 2.6(-0.9)(+1.5)x and 2.2(-1.1)(+2.0)x lower, respectively, than the extrapolated trends. Our new results are broadly consistent with the "accelerated evolution" scenario at z>8, as seen in many theoretical models.Comment: 23 pages, 15 figures, 7 tables, updated to match the version in press, including some minor textual corrections identified at the proof stag

Instrumenter l’activité des élèves pour orienter la cognition et la métacognition lors des devoirs à domicile

À travers ce mémoire professionnel, nous nous sommes intéressées au fait que certains élèves rencontrent des difficultés lorsqu’ils se retrouvent seuls face à leurs devoirs. Nous nous sommes particulièrement intéressées aux élèves les plus en difficulté, qui ont déjà de la peine à suivre en classe et se retrouvent fréquemment avec un agenda rempli de devoirs de toutes sortes. Ainsi, sans aide externe, ils ne savent pas comment travailler et risquent de tomber dans le « faire » pour compléter plutôt que d’apprendre. Nous avons donc eu pour ambition de créer un outil permettant d’instrumenter l’activité de l’élève pour le soutenir dans son travail. Pour ce faire, nous sommes parties de la grille d’Anderson & Krathwohl, qui énumère six habiletés différentes touchant aux apprentissages. Ce travail s’est porté sur l’habileté « comprendre », qui selon nous, est une habileté essentielle à mobiliser dans de nombreux devoirs. Ensuite, dans le but d’outiller l’élève d’un aidemémoire, nous avons fait tout un travail en amont portant sur l’analyse de l’activité de l’élève d’un point de vue cognitif et métacognitif. Notre attention s’est portée d’une part sur la compréhension de l’élève (cognition), mais également sur sa stratégie de travail lorsqu’il planifie et régule son travail (métacognition). Pour parvenir à nos fins, nous avons mené plusieurs instructions aux sosies : une technique d’entretien qui a pour but d’accéder à l’activité de l’acteur, dans ce cas-ci l’élève. Notre recherche repose sur l’analyse de devoirs et de stratégies d’élèves démontrant certaines difficultés scolaires dans l’écologie d’une classe de 5ème HarmoS (H) et de 6ème HarmoS (H). Au sein de ces deux classes, nous avions la volonté d’apporter un dispositif externe qui permettrait aux élèves, particulièrement ceux en difficulté, de cibler l’attente des devoirs pour mieux les comprendre. Un travail ambitieux qui, par manque de temps, n’a pas pu être mené à terme. Nous avons toutefois été en mesure d’analyser l’activité des élèves et d’y apporter nos interprétations, une étape fondamentale avant d’intégrer un outil médiateur

SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

BACKGROUND: The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. RESULTS: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. CONCLUSION: In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at

Bright galaxies at Hubble's redshift detection frontier: Preliminary results and design from the redshift z~9-10 BoRG pure-parallel HST survey

We present the first results and design from the redshift z~9-10 Brightest of the Reionizing Galaxies {\it Hubble Space Telescope} survey BoRG[z9-10], aimed at searching for intrinsically luminous unlensed galaxies during the first 700 Myr after the Big Bang. BoRG[z9-10] is the continuation of a multi-year pure-parallel near-IR and optical imaging campaign with the Wide Field Camera 3. The ongoing survey uses five filters, optimized for detecting the most distant objects and offering continuous wavelength coverage from {\lambda}=0.35{\mu}m to {\lambda}=1.7{\mu}m. We analyze the initial ~130 arcmin$^2$ of area over 28 independent lines of sight (~25% of the total planned) to search for z>7 galaxies using a combination of Lyman break and photometric redshift selections. From an effective comoving volume of (5-25) $times 10^5$ Mpc$^3$ for magnitudes brighter than $m_{AB}=26.5-24.0$ in the $H_{160}$-band respectively, we find five galaxy candidates at z~8.3-10 detected at high confidence (S/N>8), including a source at z~8.4 with mAB=24.5 (S/N~22), which, if confirmed, would be the brightest galaxy identified at such early times (z>8). In addition, BoRG[z9-10] data yield four galaxies with $7.3 \lesssim z \lesssim 8$. These new Lyman break galaxies with m$\lesssim26.5$ are ideal targets for follow-up observations from ground and space based observatories to help investigate the complex interplay between dark matter growth, galaxy assembly, and reionization.Comment: Accepted for publication on ApJ. 21 pages, 11 figures, 4 table

Characterizing faint galaxies in the reionization epoch: LBT confirms two L<0.2L* sources at z=6.4 behind the CLASH/Frontier Fields cluster MACS0717.5+3745

We report the LBT/MODS1 spectroscopic confirmation of two images of faint Lyman alpha emitters at $z=6.4$ behind the Frontier Fields galaxy cluster MACSJ0717.5+3745. A wide range of lens models suggests that the two images are highly magnified, with a strong lower limit of mu>5. These are the faintest z>6 candidates spectroscopically confirmed to date. These may be also multiple images of the same z=6.4 source as supported by their similar intrinsic properties, but the lens models are inconclusive regarding this interpretation. To be cautious, we derive the physical properties of each image individually. Thanks to the high magnification, the observed near-infrared (restframe ultraviolet) part of the spectral energy distributions and Ly-alpha lines are well detected with S/N(m_1500)>~10 and S/N(Ly-alpha)~10-15. Adopting mu>5, the absolute magnitudes, M_1500, and Ly-alpha fluxes, are fainter than -18.7 and 2.8x10^(-18)erg/s/cm2, respectively. We find a very steep ultraviolet spectral slope beta=-3.0+/-0.5 (F_lambda=lambda^(beta)), implying that these are very young, dust-free and low metallicity objects, made of standard stellar populations or even extremely metal poor stars (age<~30Myr, E(B-V)=0 and metallicity 0.0-0.2 Z/Zsolar). The objects are compact (< 1 kpc^(2)), and with a stellar mass M* < 10^(8) M_solar. The very steep beta, the presence of the Ly-alpha line and the intrinsic FWHM (<300 km/s) of these newborn objects do not exclude a possible leakage of ionizing radiation. We discuss the possibility that such faint galaxies may resemble those responsible for cosmic reionization.Comment: Accepted by ApJL; 6 pages, 4 figures, 1 table, emulateapj forma

CLASH: The enhanced lensing efficiency of the highly elongated merging cluster MACS J0416.1-2403

We perform a strong-lensing analysis of the merging galaxy cluster MACS J0416.1-2403 (M0416; z=0.42) in recent CLASH/HST observations. We identify 70 new multiple images and candidates of 23 background sources in the range 0.7<z_{phot}<6.14 including two probable high-redshift dropouts, revealing a highly elongated lens with axis ratio ~5:1, and a major axis of ~100\arcsec (z_{s}~2). Compared to other well-studied clusters, M0416 shows an enhanced lensing efficiency. Although the critical area is not particularly large (~0.6 \square\arcmin; z_{s}~2), the number of multiple images, per critical area, is anomalously high. We calculate that the observed elongation boosts the number of multiple images, \emph{per critical area}, by a factor of ~2.5\times, due to the increased ratio of the caustic area relative to the critical area. Additionally, we find that the observed separation between the two main mass components enlarges the critical area by a factor of ~2. These geometrical effects can account for the high number (density) of multiple images observed. We find in numerical simulations, that only ~4% of the clusters (with M_{vir}>6 x 10^{14} h^{-1}M_{\odot}) exhibit as elongated critical curves as M0416.Comment: 7 pages, 4 figures, 1 table. V2: accepted to ApJ Letters; minor changes and updates; in Fig.3 labeling error corrected. Mass models available online: ftp://wise-ftp.tau.ac.il/pub/adiz/M0416