Topic: Data Analysis Insights

Aberrant Cell Fraction Estimation in NxClinical 5.0

NxClinical has very strong visualization tools which is important for cytogeneticists - a reviewer can easily view the allele patterns and estimate % aberrant cells. But NxClinical 5.0 makes this even easier by automatically performing this calculation on a per event basis. The software also uses a user-defined threshold to mark events as mosaic or not. The software looks at event-specific aberrant cell fraction using both the Log R value as well as BAF (where available). This approach uses platform-dependent scaling so that the correct calculation can be applied to samples from multiple platforms (e.g. ThermoFisher, Illumina, CNV from NGS).

Recent publications illustrate the wide applicability of BioDiscovery’s CNV from NGS algorithm

The BAM MSR algorithm uses a set of “normal” samples to create a pooled reference to be used against the samples under analysis. Here are a few recent publications showing the algorithm’s versatility in handling different types of NGS data from panels to low-pass whole genome.

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.