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

Nurturing learning development through student feedback

Student evaluations of both teaching and student services are increasingly embedded into higher education. There is debate surrounding the reliability, effectiveness, and bias of such evaluations (Hefferman, 2022) and National Student Survey (NSS) results show that students typically respond poorly to questions relating to their learning community and their opportunities to give feedback on their experiences (student voice) (Office for Students, 2022). After receiving ethical approval to conduct research on evaluations, four students and a member of staff worked together to address how staff and students within the School of Mathematics and Statistics engage with student evaluations. Two surveys were conducted, the first aimed at staff (63 responses, 90% response rate) and the second at students (53 responses, 17% response rate). The results suggested that both staff and students agreed that evaluations are necessary and useful in building relationships. While staff implement the feedback they receive, students currently do not see it, and their learning may not benefit from being part of this process. When asked to describe the purpose of student evaluations, participating staff expressed that they provide students with opportunities to have direct input to courses, influence their learning environment, and feel part of the school. Students expressed that their feedback could improve a course’s content, quality and delivery, and provide a learning opportunity for lecturers. Students indicated a preference for informal mid-term feedback since they could see their feedback acted upon in real-time. In response, we propose the use of student evaluations as a feedback dialogue tool to encourage and enhance relationships between staff and students and help develop self-regulated learning. We will exemplify a feedback system that uses short, direct, and frequent surveys that students complete at the time of learning (Rowland, 2021), providing time to reflect on learning and creating a line of dialogic communication with the lecturer who can respond to the feedback to inform future learning. The system is applicable to any continuous student-staff learning-focused interaction

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

Disruption of the Non-Canonical WNT Pathway in Lung Squamous Cell Carcinoma

Disruptions of beta-catenin and the canonical Wnt pathway are well documented in cancer. However, little is known of the non-canonical branch of the Wnt pathway. In this study, we investigate the transcript level patterns of genes in the Wnt pathway in squamous cell lung cancer using reverse-transcriptase (RT)-PCR. It was found that over half of the samples examined exhibited dysregulated gene expression of multiple components of the non-canonical branch of the WNT pathway. In the cases where beta catenin (CTNNB1) was not over-expressed, we identified strong relationships of expression between wingless-type MMTV integration site family member 5A (WNT5A)/frizzled homolog 2 (FZD2), frizzled homolog 3 (FZD3)/dishevelled 2 (DVL2), and low density lipoprotein receptor-related protein 5 (LRP5)/secreted frizzled-related protein 4 (SFRP4). This is one of the first studies to demonstrate expression of genes in the non-canonical pathway in normal lung tissue and its disruption in lung squamous cell carcinoma. These findings suggest that the non-canonical pathway may have a more prominent role in lung cancer than previously reported

Reproducibility of optical coherence tomography airway imaging

Optical coherence tomography (OCT) is a promising imaging technique to evaluate small airway remodeling. However, the short-term insertion-reinsertion reproducibility of OCT for evaluating the same bronchial pathway has yet to be established. We evaluated 74 OCT data sets from 38 current or former smokers twice within a single imaging session. Although the overall insertion-reinsertion airway wall thickness (WT) measurement coefficient of variation (CV) was moderate at 12%, much of the variability between repeat imaging was attributed to the observer; CV for repeated measurements of the same airway (intra-observer CV) was 9%. Therefore, reproducibility may be improved by introduction of automated analysis approaches suggesting that OCT has potential to be an in-vivo method for evaluating airway remodeling in future longitudinal and intervention studies. (C) 2015 Optical Society of Americ

Comprehensive serial analysis of gene expression of the cervical transcriptome

<p>Abstract</p> <p>Background</p> <p>More than half of the approximately 500,000 women diagnosed with cervical cancer worldwide each year will die from this disease. Investigation of genes expressed in precancer lesions compared to those expressed in normal cervical epithelium will yield insight into the early stages of disease. As such, establishing a baseline from which to compare to, is critical in elucidating the abnormal biology of disease. In this study we examine the normal cervical tissue transcriptome and investigate the similarities and differences in relation to CIN III by Long-SAGE (L-SAGE).</p> <p>Results</p> <p>We have sequenced 691,390 tags from four L-SAGE libraries increasing the existing gene expression data on cervical tissue by 20 fold. One-hundred and eighteen unique tags were highly expressed in normal cervical tissue and 107 of them mapped to unique genes, most belong to the ribosomal, calcium-binding and keratinizing gene families. We assessed these genes for aberrant expression in CIN III and five genes showed altered expression. In addition, we have identified twelve unique HPV 16 SAGE tags in the CIN III libraries absent in the normal libraries.</p> <p>Conclusion</p> <p>Establishing a baseline of gene expression in normal cervical tissue is key for identifying changes in cancer. We demonstrate the utility of this baseline data by identifying genes with aberrant expression in CIN III when compared to normal tissue.</p

Transcriptome Profiles of Carcinoma-in-Situ and Invasive Non-Small Cell Lung Cancer as Revealed by SAGE

Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease.Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC.This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection