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.
A recent study from Arthur Beaudet’s lab at Baylor College of Medicine published in the American Journal of Human Genetics (AJHG) looks at the ability to detect fetal aneuploidies and copy number variants (CNVs) at 1Mb resolution from single circulating trophoblast (SCT) cells in maternal blood.
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.
The 2019 Tumor Profiling: Methods and Protocols book is out and we are particularly excited about the Whole-Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis chapter! Read more.
NxClinical provides a novel, integrated approach to clinical genome analysis and interpretation.
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.
At the American Society of Clinical Oncology (ASCO) meeting last month, Dr. Nathan Pennell, Director of the Lung Cancer Medical Oncology Program at the Cleveland Clinic, and his colleagues presented cost analysis in a model with different types of genetics testing in metastatic non-small cell lung cancer (mNSCLC). The team showed that upfront NGS leads to significant cost savings vs. sequential single-gene testing modalities.