Combining State Space Models and Statistical Decision Theory forPrecision Profiling of Thalassemia
Pillar developed a Bayesian caller inside PiVAT® that pairs a state space model for copy number estimation with statistical decision theory to identify alpha thalassemia subtypes from the inheritReveal™ Thalassemia research-use panel. Thirteen normal controls and 44 alpha thalassemia samples were expanded to 220 sample/normal pairs by four-fold evaluation and sequenced on the Illumina MiSeq at roughly 2,800 read pairs per amplicon. The new caller reached 88% annotation accuracy with 96% sensitivity and 93% specificity, rising to 93.7% accuracy once its own quality metric filtered poor samples, against 67% for the previous PiVAT® caller.
Validation of a Rapid Targeted Next Generation Sequencing Oncology Panel
Memorial Sloan Kettering built MSK-REACT (Rapid Evaluation of Actionable Cancer Targets) on Pillar’s oncoReveal® Nexus 21 Gene kit, an amplicon NGS assay covering hotspot regions of 19 genes across solid and hematologic malignancies. Validation used 196 clinical samples — FFPE, bone marrow, blood, cytology, and cell-free DNA — plus five commercial controls, benchmarked against MSK-IMPACT® and MSK-ACCESS®. Of 914 clinical variants, 912 were concordant (99.8%), precision and reproducibility were both 100%, and actionable results are delivered in 3–7 business days.
Evaluation of the Pillar Biosciences oncoRevealTM Solid Tumor v2 (oRSTv2) Application on the Beckman Coulter Biomek NGeniuS System
Pillar built and evaluated an automated application for its 48-gene oncoReveal® Solid Tumor v2 (oRSTv2) research-use panel on the Beckman Coulter Biomek NGeniuS library preparation system, taking DNA through to indexed libraries with minimal intervention. Twenty NA12878 replicates and 22 moderately formalin-compromised DNA samples at 19.35 ng input were processed across three runs of 24, 16, and 8 libraries, sequenced on Illumina NextSeq 550 and MiSeq with PiVAT® analysis. Every expected variant was called at its expected allele frequency — 478 of 478 across the study — with no cross-contamination in no-template controls.
Clinical Verification of an FDA-Approved NGS Solid Tumor IVD Assay
Evaluation of the QIAxcel Connect system for NGS library prep QC analysis: experience from a clinical diagnostic laboratory
Carolinas Pathology Group and Atrium Health evaluated the QIAGEN QIAxcel Connect system for library quantification and quality control across three NGS workflows: Archer’s FUSIONPlex Pan Solid Tumor v2, Pillar’s oncoReveal® Solid Tumor v2, and Pillar’s oncoReveal® Essential MPN panel. Libraries from 160 FFPE scrolls, 134 FFPE slides, and 126 blood or bone marrow specimens were normalized on QIAxcel concentrations, pooled per panel, and sequenced on the Illumina NextSeq 550 Dx. Pillar panels showed the tightest peak-size reproducibility, and the approach removed the need to quantify every individual library.
Analytical Validation of oncoReveal CDx as a FDA approved, Pan-Cancer Solid Tumor IVD Assay
oncoReveal® CDx is the first FDA-approved distributed, kit-based NGS assay for both companion diagnostic use and pan-cancer tumor profiling, covering more than 3,600 SNV and indel targets across 22 genes from FFPE DNA on the Illumina MiSeqDx. Validation spanned 10 tumor types and addressed DNA input range, minimum tumor content, necrosis tolerance, limit of detection by probit analysis, accuracy against two externally validated NGS comparators, and a three-site reproducibility study. The assay achieved 100% positive and 99.996% negative percent agreement at 30 ng input, with valid results down to 3.3% tumor content.
Automation of oncoReveal Solid Tumor 22 Gene Panel and the Illumina TruSight Oncology 500 DNA/RNA
Beckman Coulter Life Sciences automated both Pillar’s oncoReveal® Solid Tumor 22 Gene Panel and Illumina’s TruSight Oncology 500 DNA/RNA kit on the Biomek NGeniuS library preparation system to reduce manual pipetting and hands-on time. Three test runs per assay used engineered controls including Horizon Discovery fcDNA and SeraSeq® reference standards, sequenced on Illumina MiSeq and NextSeq 500 and analyzed with PiVAT® and DRAGEN. The Pillar panel reached sequencing by the end of day one at batch sizes from 4 to 24 samples, while the 523-gene TSO500 workflow ran into day three.
JAK2 Exon 12-15, CALR and MPL Essential MPN NGS Panel
Labcorp’s Center for Molecular Biology and Pathology validated Pillar’s oncoReveal® Essential MPN Panel — a single-tube SLIMamp® assay covering JAK2 exons 12–15, CALR, and MPL — as a high-throughput clinical test for BCR/ABL-negative myeloproliferative neoplasms including polycythemia vera, essential thrombocythemia, and primary myelofibrosis. Across 126 blood, bone marrow, and cell pellet specimens every reportable mutation was confirmed by a secondary method, giving 100% concordance, with 100% repeatability and reproducibility over 30 specimens. The panel is now offered clinically, and average laboratory turnaround shortened by four days versus cascading reflex orders.