Leslie Cope

Linearity and comparison of DNA quantification across genes and extraction kits.

Comparison of cf-MMSP and cMethDNA in detecting plasma from Stage IV breast cancer.

Background:The use of liquid biopsy to analyze cell-free DNA (cfDNA) provides a noninvasive approach for breast cancer detection, but its low abundance necessitates highly sensitive assays. Methods:We developed cell-free multiplex methylation–specific PCR (cf-MMSP) through optimized cfDNA extraction and primer design. We compared the extraction efficiency of three commercial kits using normal plasma spiked with 12.5 to 50 copies of fully methylated genomic DNA and 50 copies of STD_HOXB4 plasmid. A nine-gene methylation panel (AKR1B1, COL6A2, HIST1H3C, HOXB4, RASGRF2, RASSF1A, TM6SF1, TMEFF2, and ZNF671) was amplified from bisulfite-converted DNA using a nested PCR that pairs a methylation-independent external forward primer with a reverse methylation (RM)–specific primer in the first multiplex reaction. Results:The QIAamp MinElute Virus Spin Kit yielded superior cfDNA recovery of the STD_HOXB4 control (P < 0.0001 vs. both MAGicBead cfDNA Isolation Kit and QIAamp MinElute ccfDNA Mini Kit). The new primer combination significantly lowered cycle threshold values for genes (median, 17.9 vs. 19.8; P = 0.0001) and STD_HOXB4 (median, 16.8 vs. 18.8; P < 0.0001), translating to a fourfold improvement in analytical detection sensitivity. In an evaluation of 21 stage IV breast cancer plasma samples and 20 benign controls, cf-MMSP distinguished cases from controls with 81% sensitivity [95% confidence interval (CI), 58.1%–94.6%], 85% specificity (95% CI, 62.1%–96.8%), and area under the receiver operating characteristic curve = 0.89 (P < 0.0001). Conclusions:Optimization of DNA extraction and primer design in cf-MMSP improved low-input analytical sensitivity while maintaining performance comparable with cMethDNA in stage IV breast cancer. Impact:cf-MMSP improves low-input methylated cfDNA detection and warrants further validation in earlier-stage breast cancer.

Sequences of primers and probes used for amplification of gene panel

The limit of detection for 9 target genes

Multiple linear regression analysis for Ct of 9 genes with MAGicBead isolation

Motivation: The Functional Expansion of Specific T cell (FEST)-based assays combine short-term peptide stimulation with TCR sequencing to identify clonotypes that expand in response to specific antigens. These approaches have proven invaluable for detecting neoantigen-specific T cell responses, guiding vaccine development, and assessing checkpoint blockade efficacy. However, variability introduced by biological and technical replicates poses challenges for reproducibility and interpretation, and existing computational tools do not address replicate-level analysis in these assays. Results: We developed replicateFest, a computational framework implemented as an R package and Shiny web application, to analyze FEST-based TCR-seq data with and without replicates. replicateFest applies Fisher’s exact test for non-replicate datasets and negative binomial modeling for replicate experiments, returning adjusted p-values and odds ratios to identify clonotypes significantly expanded in antigen-stimulated conditions. The framework distinguishes FEST-expanded clonotypes (relative to a no-antigen control) and FEST-positive clonotypes (expanded compared to all other conditions). Validation using synthetic datasets confirmed accurate detection of antigen-specific clonotypes. Application to published HIV-1 epitope stimulation data reproduced original findings and demonstrated replicateFest’s utility for reproducibility assessment and quality control. Availability and Implementation: replicateFest is freely available under the Apache-2.0 license as an R package at https://github.com/OncologyQS/replicateFest and as an interactive Shiny application at http://www.stat-apps.onc.jhmi.edu/FEST/ .

Background:The use of liquid biopsy to analyze cell-free DNA (cfDNA) provides a noninvasive approach for breast cancer detection, but its low abundance necessitates highly sensitive assays. Methods:We developed cell-free Multiplex Methylation-specific PCR (cf-MMSP) through optimized cfDNA extraction and primer design. We compared extraction efficiency of three commercial kits using normal plasma spiked with 12.5 – 50 copies of fully methylated genomic DNA and 50 copies of STD_HOXB4 plasmid. A nine-gene methylation panel (AKR1B1, COL6A2, HIST1H3C, HOXB4, RASGRF2, RASSF1A, TM6SF1, TMEFF2, ZNF671) was amplified from bisulfite-converted DNA using a nested PCR that pairs a methylation-independent external forward primer (Ext_F) with a reverse methylation-specific primer (RM) in the first multiplex reaction. Results:The QIAamp MinElute Virus Spin Kit yielded superior cfDNA recovery of the STD_HOXB4 control (P < 0.0001 versus both MAGicBead cfDNA Isolation Kit and QIAamp MinElute ccfDNA Mini Kit). The new primer combination significantly lowered Ct values for genes (median 17.9 vs 19.8, P = 0.0001) and STD_HOXB4 (median 16.8 vs 18.8, P < 0.0001), translating to a four-fold improvement in analytical detection sensitivity. In an evaluation of 21 stage IV breast cancer plasma and 20 benign controls, cf-MMSP distinguished cases from controls with 81% sensitivity (95% CI, 58.1–94.6%), 85% specificity (95% CI, 62.1–96.8%) and AUC = 0.89 (P < 0.0001). Conclusions:Optimization of DNA extraction and primer design in cf-MMSP improved low-input analytical sensitivity while maintaining performance comparable to cMethDNA in stage IV breast cancer. Impact:cf-MMSP improves low-input methylated cfDNA detection and warrants further validation in earlier-stage breast cancer.

Analyses of stromal differential expression and related pathways

Differential expression and pathway analyses of STIC molecular subtypes