Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms

Genome remodelling in a basal-like breast cancer metastasis and xenograft

Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour

Methodological trends in disability and higher education research: Historical analysis of the Journal of Postsecondary Education and Disability.

In order to assess the status of the research base that informs “what works†for students with disabilities in higher education, it is necessary to conduct an examination of the methodologies used in the literature. The authors of the current study analyzed the methodological trends across the thirty-year lifespan of the Journal of Postsecondary Education and Disability, spanning the years 1983 to 2012. Every article published by JPED was coded using an electronic tool comprised of four domains and corresponding subdomains. The authors concluded that data-based studies constitute more than half of all studies published in the Journal, with the majority of articles being descriptive and quantitative in nature. Only six studies used a control or comparison condition. Additional findings and implications are discussed

Thirty-five years of transition topics: A review of CDTEI issues from 1978 to 2012.

A systematic review was conducted of 581 articles published in 76 issues of Career Development and Transition for Exceptional Individuals from the journal’s initial issue in 1978 to the final issue of its 35th year in 2012. Articles were coded based on inclusion of original or secondary data and if not, what type of information the article contained. In the case of articles that presented data, statistics were collected related to sample demographics and the location of the study. In addition, the topic of each article was coded. The most common topical areas were program descriptions and professional development. Trends throughout the analysis are discussed to forecast topical areas needing study as the journal goes forward

Literature on postsecondary disability services: A call for research guidelines.

Support services for students with disabilities is now a distinct field of practice in higher education, with a significant increase in the number of students receiving services, programs to serve them, and professionals who oversee the programs. The field has professional and program standards, a code of ethics, and a disability service specific professional organization. Correspondingly, an extensive corpus of professional literature has emerged. However, though the research base has great breadth, it lacks significant depth, has poor sample and setting descriptions, and lacks methodological rigor. The result is that there is insufficient evidence spelling out what practices work with which students and in which settings. Guidelines intended to steer future research could have significant impact upon scholars conducting research and, subsequently, higher education. The present article describes the current state of the research base and proposes future directions to guide research