Tag: 2025

Performance Comparison of the Illumina MiSeq i100 with Established Instruments for Amplicon-Based Somatic and Liquid Biopsy Sequencing Panels

Pillar benchmarked seven oncoReveal® amplicon NGS panels — BRCA1/BRCA2 Somatic with CNV, Multi-Cancer v4 with CNV, Myeloid, Essential MPN, Nexus 21 Gene, Rapid AML, and Essential LBx — on Illumina’s new MiSeq i100 against the legacy MiSeq and NextSeq 550. Fifty-nine paired samples, including SeraCare and Horizon Discovery reference standards, cancer cell line DNA, and biobanked clinical specimens, were run from identical libraries across six sequencing runs. Every expected true-positive variant was detected on the i100 with no false positives, confirming that the portfolio transfers cleanly to the new platform.

Detecting Contamination in Cell-free DNA Sequencing Libraries using Germline Markers

Pillar developed a panel-agnostic Bayesian method to detect sample-to-sample contamination within cell-free DNA (cfDNA) sequencing batches, where variant allele fractions below 0.5% make false positive calls especially costly. The algorithm genotypes germline single nucleotide polymorphisms (SNPs) across a batch, flags sites with discordant allele fractions, and computes the posterior probability that observed read counts reflect contamination rather than stochastic noise. Across in silico mixes, contrived cell line mixes, and CNV-positive tumor samples it detected contamination down to 1% using 30 homozygous SNPs while holding 99–100% specificity.