Low Pass Genome Sequencing (LP-GS) for detection of CNVs as a replacement to constitutional microarray analysis. The team evaluated a number of different tools and found NxClinical to have superiority in CNV detection and classification.
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).
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 (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.
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.
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.
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.
CoNIFER can be used to discover CNVs that might be missed by standard practices. Look at our considerations when evaluating the CoNIFER algorithm.