The clinical workflow, retinoblastoma and split alignment

    Retinoblastoma is an “oma” named for its surface effect, its “presentation”:  it’s a cancer that attacks the eye. Worse, because 80% of retinoblastoma diagnoses occur before the age of 3, it’s a cancer that attacks the eyes—almost exclusively—of little children. Retinoblastoma is a “good cancer”: 90% of all RB cases survive into adulthood. … Continue reading “The clinical workflow, retinoblastoma and split alignment”

Webinar on Detection of Structural Variants in Targeted Sequencing

Live Webinar on Detection of Structural Variants in Targeted Sequencing Structural Variants (SVs) have long been implicated in many human diseases such as cancer, making their detection important in clinical genomics. Strand NGS 2.5 includes a new workflow step for detecting these variants based on split reads that span the breakpoints corresponding to the variants. … Continue reading “Webinar on Detection of Structural Variants in Targeted Sequencing”

Benford’s Law and NGS Gene Counts

This may be a piece of trivia more than anything else, but anyway, let’s begin with the surprising part. Take any RNASeq sample and assign to each gene a count corresponding to the number of reads aligning to that gene (what we call Quantification in Avadis NGS). For the purposes of this post, ignore all … Continue reading “Benford’s Law and NGS Gene Counts”

Webinar: Find Significant SNPs in your Samples

In this month’s webinar, we will show you how to use the Find Significant SNPs analysis workflow in Avadis NGS 1.3. SNP verification and prioritization is one of the most time consuming tasks in variant analysis. The workflows and algorithms built-into Avadis NGS 1.3 make end-to-end SNP analysis easy, intuitive, and accurate. These workflows support … Continue reading “Webinar: Find Significant SNPs in your Samples”

Mutations Causing CHIME Disease

Here is publication from Sanford-Burnham Medical Research Institute that uses Avadis NGS: The goal in this paper is to find the underlying genomic cause of CHIME syndrome, a disease so rare that there are only 8 reported cases in the world. CHIME is an abbreviation derived from the main symptoms: Colobomas (hole in the … Continue reading “Mutations Causing CHIME Disease”

RNA-Seq Analysis of Functional Compartments in the Rat Placentation Site

We just read a recent publication by Shankar et al that uses Avadis NGS to analyze RNA-Seq data. They study cells involved in rat placenta formation. The placenta is an organ that connects the foetus to the wall of the uterus, thus allowing for nutrients/oxygen to flow from mother to foetus, and waste to flow … Continue reading “RNA-Seq Analysis of Functional Compartments in the Rat Placentation Site”

Webinar Series: Benchtop Sequencing Data Analysis

We are hosting an online seminar series on the alignment and analysis of genomics data from “benchtop” sequencers, i.e. MiSeq and Ion Torrent. Our webinar panelists will give a tour of various bioinformatics functions in Avadis NGS that will enable researchers and clinicians to derive biological insights from their benchtop sequencing data. Webinar attendees are … Continue reading “Webinar Series: Benchtop Sequencing Data Analysis”

Release Announcement – Version 1.3

We are really happy to announce that version 1.3 of Avadis NGS is now available. Special thanks to everyone who participated in the Beta program and helped us by providing valuable feedback! What’s New Avadis NGS 1.3 includes several new features and enhancements, which are documented in the release notes. Below is a quick summary … Continue reading “Release Announcement – Version 1.3”