95 MDAF: Modeling Noise in NGS Data with Per-Base Resolution for Statistically Informed, Position-Dependent Variant Calling
Archer® Analysis expresses LOD as the minimum allele fraction at which a variant can be distinguished from underlying noise at a statistical power of 0.95, referred to as 95 MDAF. This enables precise detection of sensitivity at each base position.
Six popular commercially-available FFPE extraction panels are tested for performance in conjunction with Anchored Multiplex PCR (AMP™) chemistry.
Detection of Internal Tandem Duplications in FLT3 with Anchored Multiplex PCR and next-generation sequencing (NGS)
FLT3 encodes a receptor tyrosine kinase that is involved in p53 activation and has roles in cell growth arrest and apoptosis. Internal tandem duplications (ITDs) in the juxtamembrane domain result in constitutive activation of FLT3, causing aberrant cell growth leading to tumorigenesis. FLT3-ITDs are associated with poor prognosis of acute myeloid leukemia (AML) and are detected in about 25% of AML cases. As FLT3-ITD expressed kinases are sensitive to tyrosine kinase inhibitors, they are of considerable interest for the development of novel AML treatments.
Sample barcoding, also called sample indexing, is a common approach to labeling samples for multiplex sequencing and analysis. All nucleic acids in a sample are labeled with the same sequence tag, and the resulting library is pooled with other libraries and sequenced in parallel in a single run. Then, during analysis, the sample-specific indexes enable the software to separate the multiplexed sequence data in sample-specific data sets.
We conducted an analytical and methodological validation of the LiquidPlex™ assay for solid tumors. This next generation sequencing (NGS) assay is designed to identify variants within circulating tumor DNA (ctDNA) following extraction from the plasma fraction of blood. While the genomic targets covered by the assay are broad, the scope of this validation includes 58 genomic positions across 25 genes.
Hematologic malignancies, including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN) are oligoclonal disorders caused by germline or acquired genetic abnormalities in hematopoietic cells. Testing based on targeted next-generation sequencing (NGS) of the genes associated with these disorders can help identify somatic mutations.