Abstract 5710: Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens

Xiaotong Li, Lao H. Saal, Christian Brueffer, Yilun Chen, Johanna Asklin, Saman Alvi, Srinivas Venkatram, Jeremy A. Ross
April, 2023
DOI

Abstract

Venetoclax (Ven) is a selective B-cell lymphoma 2 inhibitor being studied in t(11;14)+ relapsed/refractory multiple myeloma (MM). Detection of t(11;14) in MM requires bone marrow (BM) aspiration and evaluation of CD138+ plasma cells by fluorescence in situ hybridization (FISH). Innovative techniques may provide less invasive detection of t(11;14) in liquid biopsies. Here we present results of the SAGAsign® integrated approach combining low-coverage whole-genome sequencing (WGS) to characterize t(11;14) breakpoints together with personalized digital polymerase chain reaction (dPCR) assays to efficiently detect and monitor the genomic rearrangements in circulating tumor DNA (ctDNA). Baseline BM aspirates were collected from 270 patients (pts) from Ven clinical trials (NCT02755597, NCT01794520, NCT03314181, NCT02899052). Previously generated WGS to an average coverage ~22X was used. Paired samples of peripheral blood mononuclear cell (PBMC) DNA and plasma circulating cell-free DNA (cfDNA) were analyzed by dPCR at timepoints after Ven-based treatment. Of the 90 t(11;14)+ pts by FISH, 160 t(11;14) breakpoints were identified by WGS in 74 pts. At the time of data cutoff, dPCR assays were designed and evaluated in 8 t(11;14)+ pts; 7/8 (88%) and 6/8 (75%) pts had detectable t(11;14) in cfDNA or PBMCs, respectively. Higher levels of t(11;14) mutant allele frequency (MAF) were observed in cfDNA compared with PBMCs. After Ven-based treatment, t(11;14) MAF in cfDNA became undetectable in pts with a complete response. In conclusion, this approach has the capability to reconstruct t(11;14) breakpoints from WGS data that is highly concordant with FISH; translocations appear more readily detectable in cfDNA than PBMC samples from pts with MM SAGAsign assays detected and monitored t(11;14) in liquid biopsies thus highlighting its potential utility for identifying pts with t(11;14) for targeted therapies

Type
Conference paper
Publication
Cancer Research, 2023. 83:7_Supplement
Cancer Multiple Myeloma Bioinformatics Whole Genome Sequencing Structural Variants Liquid Biopsy Digital PCR ctDNA
Christian Brueffer
Christian Brueffer
Bioinformatician and Data Scientist

Freelance Bioinformatician and Data Scientist with interests including disease biology and diagnostics, particularly in cancer, and open source bioinformatics.