Using a combination of genomic sequencing technologies and bioinformatic tools, PerkinElmer Genomics is paving the way to replace traditional microarray analyses for constitutional genomics with NGS (next-generation sequencing). At a webinar today, Dr. Alka Chaubey, Head of Cytogenomics, PerkinElmer Genomics, presented development and validation of the new CNGnome™ Test and comparison to traditional CMA (chromosomal microarray analysis).
Non-uniform payments from payors/insurance is one of the reasons that PE Genomics sought to develop a new test that lowers costs while beating current CMA standards. Their approach utilized 5x WGS (low resolution WGS) and the NovaSeq™ 6000 sequencing platform. One of the biggest challenges they faced was the amount of data obtained and what to use for the analysis.
Dr. Chaubey listed the four tools they used for analysis and interpretation of CNV data from WGS and discussed how they compared. NxClinical was one of the software solutions evaluated and beat out the other tools especially in the ability to analyze challenging samples. Another huge benefit she mentioned is the rich visualization with integrated analysis of CNV, AOH, and sequence variants that is intrinsic to NxClinical. Some of the other benefits of NxClinical she finds valuable include
- A database system for managing CNV, AOH, and Sequence Variants
- Platform and technology independence
- Trio analysis
- Flexible decision tree system to pre-classify events following reporting guidelines
Dr. Chaubey presents some validation cases as well as real life cases and shows how NxClinical was used to interpret the results. Throughout the presentation, Dr. Chaubey emphasizes the importance of visualization in such assays and that NxClinical provides for this with numerous interactive tracks showing features such as probe-level plots and BAM read depth which provide visual and clear confirmation of the presence of CN and AOH events.
Dr. Chaubey's talk was about what the CNGnome test is, when it should be used, how it was developed and validated, and upcoming offerings in PE Genomics’ testing portfolio but in presenting her data, she shared a lot of great information with screenshots on how NxClinical is a key player in their workflow.
So whether you are looking for a testing service or analysis and interpretation software, Dr. Chaubey's talk will be enlightening. If you missed her presentation today, you can still catch the second session:
The CNGnome™ Test: Creating a new standard for detecting large copy number changes throughout the genome
August 16, 2018 from 12:00pm - 1:00pm (PST)