Clinical sequencing identifies potential actionable alterations in a high rate of urachal and primary bladder adenocarcinomas.

Objective: Administration of targeted therapies provides a promising treatment strategy for urachal adenocarcinoma (UrC) or primary bladder adenocarcinoma (PBAC); however, the selection of appropriate drugs remains difficult. Here, we aimed to establish a routine compatible methodological pipeline for the identification of the most important therapeutic targets and potentially effective drugs for UrC and PBAC.

Methods: Next-generation sequencing, using a 161 cancer driver gene panel, was performed on 41 UrC and 13 PBAC samples.

Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.

Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical laboratories, where sample volumes are limited, and low variant allele fractions may be present.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

Background: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S.

A scalable solution for tumor mutational burden from formalin-fixed, paraffin-embedded samples using the Oncomine Tumor Mutation Load Assay.

Background: Tumor mutational burden (TMB) is an increasingly important biomarker for immune checkpoint inhibitors. Recent publications have described strong association between high TMB and objective response to mono- and combination immunotherapies in several cancer types. Existing methods to estimate TMB require large amount of input DNA, which may not always be available.

De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance.

Background: Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach for the identification of chimeric transcripts of potential functional significance. We report here the development and use of an integrated computational pipeline for the de novo assembly and characterization of chimeric transcripts in 55 primary breast cancer and normal tissue samples.

Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation.

Background: Genomic rearrangements or structural variants (SVs) are one of the most common classes of mutations in cancer.

Methods: An integrated DNA sequencing and transcriptional profiling (RNA sequence and microarray gene expression data) analysis was performed on six ovarian cancer patient samples. Matched sets of control (whole blood) samples from these same patients were used to distinguish cancer SVs of germline origin from those arising somatically in the cancer cell lineage.

Study of characteristics of aperiodicity in Noh voices.

The feasibility of representing the excitation source characteristics in expressive voice signals by an aperiodic sequence of impulses in the time domain is examined in this paper. In particular, the aperiodic components of excitation of expressive voices, like the Noh voice, are examined in some detail. The aperiodic component is extracted from the speech signal using a modified zero-frequency filtering method, and it is represented using a sequence of impulses with amplitudes corresponding to the relative strength of excitation around each impulse.

Study of the effects of vocal tract constriction on glottal vibration.

Characteristics of glottal vibration are affected by the obstruction to the flow of air through the vocal tract system. The obstruction to the airflow is determined by the nature, location, and extent of constriction in the vocal tract during production of voiced sounds. The effects of constriction on glottal vibration are examined for six different categories of speech sounds having varying degree of constriction.

R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.

The rapid expansion in the quantity and quality of RNA-Seq data requires the development of sophisticated high-performance bioinformatics tools capable of rapidly transforming this data into meaningful information that is easily interpretable by biologists. Currently available analysis tools are often not easily installed by the general biologist and most of them lack inherent parallel processing capabilities widely recognized as an essential feature of next-generation bioinformatics tools. We present here a user-friendly and fully automated RNA-Seq analysis pipeline (R-SAP) with built-in multi-threading capability to analyze and quantitate high-throughput RNA-Seq datasets.

Characterization and potential functional significance of human-chimpanzee large INDEL variation.

Background: Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species.

RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN.

The problem of predicting non-long terminal repeats (LTR) like long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) from the DNA sequence is still an open problem in bioinformatics. To elevate the quality of annotations of LINES and SINEs an automated tool "RetroPred" was developed. The pipeline allowed rapid and thorough annotation of non-LTR retrotransposons.