Dr. Darine Villela and colleagues in Dr. Carla Rosenber's lab at the University of Sau Paulo, Brazil sought to find an integrated solution to combine two tests into one – one that was cost effective and easy to adopt in a clinical setting. They noted that there are several tools for CNV analysis from sequencing data, but the homemade tools are designed for a specific pipeline, are not user-friendly and require a high degree of bioinformatics expertise. They knew they needed a solution that would be easy to implement in a clinical lab and chose a commercial target enrichment kit and BioDiscovery’s Nexus Copy Number for analysis.
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.
We are excited to have been part of this historic event: this year is the 50th anniversary of the ESHG conference and the inaugural event was also held in Copenhagen, in 1967! An excellent lineup of speakers began with the opening plenary lectures where Drs. Read, Brunner, and Visel addressed respectively, the history, present day, and the future of genetics leading to lots of lively conversations.
Users are excited about the methods in Nexus Copy Number 9.0 for getting copy number from NGS BAM files. However, due to the size of the BAM files, sometimes users may find the analysis process to be slow. So, what can be done to improve the speed?
Recent genome sequencing studies in two different mammals have uncovered interesting differences in genomic content.
Cedar Sinai Medical Center in Los Angeles, CA has filed a patent for a method for prognosticating patient survival based on the ZEB1 gene. The application also describes methods for selecting therapies based on analysis of ZEB1 and several other genes.
Nexus Copy Number has helped many researchers to detect and interpret the profiles from cancer samples where contamination by normal cells is quite common.
This new method, BAM (Multiscale Reference), to be included in the upcoming Nexus Copy Number 8.1, can analyze NGS data from shallow (low pass) WGS (1x or below), targeted panels, and WES/WGS with normal depth of coverage (e.g. 30x).