High-throughput sequencing of mGluR signaling pathway genes reveals enrichment of rare variants in autism.

Identification of common molecular pathways affected by genetic variation in autism is important for understanding disease pathogenesis and devising effective therapies. Here, we test the hypothesis that rare genetic variation in the metabotropic glutamate-receptor (mGluR) signaling pathway contributes to autism susceptibility. Single-nucleotide variants in genes encoding components of the mGluR signaling pathway were identified by high-throughput multiplex sequencing of pooled samples from 290 non-syndromic autism cases and 300 ethnically matched controls on two independent next-generation platforms.

Standardization of HER2 immunohistochemistry in breast cancer by automated quantitative analysis.

Context: There is critical need for standardization of HER2 immunohistochemistry testing in the clinical laboratory setting. Recently, the American Society of Clinical Oncology and the College of American Pathologists have submitted guidelines recommending that laboratories achieve 95% concordance between assays and observers for HER2 testing.

Objective: As a potential aid to pathologists for achieving these new guidelines, we have conducted an examination using automated quantitative analysis (AQUA analysis) to provide a standardized HER2 immunohistochemistry expression score across instruments (sites), operators, and staining runs.

Development of an unsupervised pixel-based clustering algorithm for compartmentalization of immunohistochemical expression using Automated QUantitative Analysis.

Inherent to most tissue image analysis routines are user-defined steps whereby specific pixel intensity thresholds must be set manually to differentiate background from signal-specific pixels within multiple images. To reduce operator time, remove operator-to-operator variability, and to obtain objective and optimal pixel separation for each image, we have developed an unsupervised pixel-based clustering algorithm allowing for the objective and unsupervised differentiation of signal from background, and differentiation of compartment-specific pixels on an image-by-image basis. We used the Automated QUantitative Analysis (AQUA) platform, a well-established automated fluorescence-based immunohistochemistry image analysis platform used for quantification of protein expression in specific cellular compartments to demonstrate utility of this methodology.

Gene expression profiling reveals putative HOXA10 downstream targets in the periimplantation mouse uterus.

HOXA10 encodes a transcription factor required for endometrial receptivity and embryo implantation. The objective of this study was to identify and to characterize those molecular markers regulated by HOXA10 expression. The authors have identified putative HOXA10 target genes identified by microarray analysis employing a murine model of transient HOXA10 expression during the anticipated implantation window.

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.

Background: Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes.

Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1.

Within the hairpin ribozyme, structural elements required for formation of the active tertiary structure are localized in two independently folding domains, each consisting of an internal loop flanked by helical elements. Here, we present results of a systematic examination of the relationship between the structure of the helical elements and the ability of the RNA to form the catalytically active tertiary structure. Deletions and mutational analyses indicate that helix 1 (H1) in domain A can be entirely eliminated, while segments of helices 2, 3, and 4 can also be deleted.