Topic: Data Analysis Insights

OMIM data in NxClinical

OMIM (Online Mendelian Inheritance in Man) is a comprehensive database consisting of human genes and genetic phenotypes associated with Mendelian disorders. The database is used by genetic labs to assist in interpretation. It is maintained by Johns Hopkins University and is available freely via the online GUI for personal, educational, or research use but other uses, usage by certain types of organizations, as well as downloading or incorporating with products does carry licensing fees.

Does reanalysis improve diagnostic yield?

A recent paper on the project shared results from a reanalysis in 2017 of the initial 1133 children using new knowledge and findings that have accumulated since the initial analysis. The pace at which improvements in genomic data technologies, analysis, and knowledge are moving, the group hypothesized that it is likely that diagnostic yield would increase via the reanalysis. They sought to determine how much of an improvement can be made over time.

How does clustering work in Nexus Copy Number?

When studying genomic data, we are often looking for similarities and differences among a group of samples. We try to see if there are any patterns and whether the samples group together into subsets based on gain and loss profiles. One way to do this is with a clustering function. clustering.pngIn Nexus Copy Number, clustering is done by clicking on the "Cluster" button on the "Results" tab.

Customer publication: functional analysis of CNA in sporadic colorectal cancer showcases Nexus Copy Number's statistical analysis tools

Most are well-aware of Nexus Copy Number’s strengths in detection of copy number from different technologies and this often overshadows the many other powerful features of Nexus Copy Number. A recent customer publication illustrates nicely the power of these additional analysis tools. Here I’m going to walk through a recent customer publication highlighting the areas where the authors used these powerful research tools available within Nexus Copy Number.

Another successful AACR meeting with many presentations featuring Nexus Copy Number

Great to see so many customer posters featuring Nexus Copy Number at AACR 2017 and even some using the newly released version 9.0 for deriving CNVs from low-pass WGS and cancer panel data.

Nexus Copy Number – Casting a Wide Net

Nexus Copy Number has been used to work on a variety of organisms, including canines, monkeys, plants, humans, and more. View these highlighted publications.

Easy, integrated genomic data analysis with Nexus Copy Number 8.0

Our Nexus Copy Number software for years provided the ability to integrate sequence variants and gene expression results with copy number allowing identifications of genomic hotspots.

Using CoNIFER to Detect Copy Number Variations from Exome Sequencing Data

CoNIFER can be used to discover CNVs that might be missed by standard practices. Look at our considerations when evaluating the CoNIFER algorithm.

Estimating Copy Number From Log Ratios

Take a look at some common questions that customers have about using Nexus, and receive some advice on calculating the actual copy number of samples in Nexus.

From Raw Data to Copy Number Calls – Data processing workflow in Nexus Copy Number

Take a look at how Nexus Copy Number handles the different “Raw Data” and the three steps to analyzing the data.