Genotyping and Minimal Residual Disease (MRD) Assessment in cfDNA By the Euroclonality-NGS DNA Capture (EC-NDC) Panel in Mantle Cell Lymphoma (MCL)

Background Modern concepts for the treatment of mantle cell lymphomas (MCL) increasingly integrate clinical and biological variables for risk-adapted treatment strategies. Novel next-generation sequencing (NGS) technologies are highly suited for tumor genotyping as well as disease monitoring by minimal residual disease (MRD) assessment, identifying patients (pts) with a high risk of relapse. Here, we investigated whether the EuroClonality (EC)-NGS DNA Capture (EC-NDC) assay is a) applicable for genotyping of MCL in peripheral blood (PB) and plasma cell-free (cf)DNA and b) suitable for MRD assessment in plasma as compared to the amplicon-based EuroClonality Immunoglobulin-based (IG‑)NGS assay.

Patients and methods A total of 109 PB samples (55 baseline and 54 interim staging) from a cohort of MCL treated within the TRIANGLE trial by the European MCL network (NCT02858258) were selected according to a PB infiltration ≥10% at diagnosis. From prospectively collected PB samples in national reference labs, DNA from the cellular blood compartment (PBC) and plasma cfDNA was extracted. For targeted capture, the EC-NDC assay (Univ8® Genomics, UK) was used to simultaneously detect immunoglobulin and T cell receptor (IG/TR) rearrangements, structural variants (SV) and single nucleotide variants (SNVs) in 72 genes (Stewart, Blood Adv, 2021). For diagnostic PBC and cfDNA samples, IG clonotypes were called with ≥6 unique reads and ≥5% of annotated IG reads, SV were called with ≥4 unique reads and SNV were called with ≥6 unique reads at ≥4% variant allele frequency (VAF). For amplicon-based MRD analysis the EuroClonality IG-NGS (IG-NGS) assay was used with IG clonotypes called with ≥5% of annotated IG reads and at ≥1 log higher abundance to the polyclonal background.

MRD was analyzed by IG-NGS in PBC using 8 µg PBC DNA to reach a sensitivity of 10^-6. For MRD analysis in cfDNA, we aimed to use ≥5000 genome equivalents (GE) for both IG‑NGS and EC‑NDC. Data were analyzed by ARResT/Interrogate (Bystry, Bioinformatics, 2017) with an adapted pipeline for targeted capture in cfDNA. MRD status was defined as positive by detecting a lymphoma-specific IG clonotype and/or SV at ≥1 read, or alternatively by retrieval of ≥1 disease-specific mutation at ≥3 reads.

Results Total cfDNA amounts at baseline were high (mean 92.6 ng/mL plasma) and even increasing at interim staging (mean 123.8 ng/mL) while decreasing by 10‑fold in 38 samples at end of treatment (EoT)(mean 11.45 ng/mL).

At baseline, a tumor-specific IGH-VJ clonotype was detected by IG-NGS in all 55 PBC and cfDNA samples. Genotyping by EC-NDC showed fully concordant results in 55 PBC and cfDNA samples with respect to IG clonotypes, SV and SNV, except for 3 PBC samples with low usable reads covering IGH-VJ regions. The presence of a t(11;14)(q13;q32) translocation was confirmed in 54/55 pts in PBC and cfDNA, while one patient with unknown t(11;14) translocation status by FISH was negative by EC-NDC. EC-NDC identified 106 putative somatic SNVs (VAF 2.7-75%, median 30%) in PBC and cfDNA, and among those were genes described as drivers in MCL (ATM (25/55), TP53 (11/55), KMT2D (9/55), SAMHD1 (5/55), CCND1 (5/55) and 18 other genes (Fig. 1). Six pts with detectable t(11;14) and IG rearrangement did not show additional SNVs. On average, 6 MRD markers/pt were identified (range: 3‑10).

At interim staging, MRD was analyzed in 54 PBC and 44 cfDNA samples. Twenty-five (47%) pts were MRD+ in PBC by IG-NGS. Twenty (46%) pts were MRD+ in cfDNA by EC-NDC (8 cases with ≥2 markers, 4 with 2 markers, and 8 with 1 marker). From 10/44 (23%) cfDNA samples MRD+ by IG-NGS, 9 were also MRD+ by ED-NDC. From 44 pts with parallel analysis of PBC and cfDNA, 14 (32%) were MRD+ and 18 (41%) were MRD-, while 12 (27%) showed discordant results.

Conclusion To the best of our knowledge, this is the first analysis comparing targeted capture and amplicon assays for application in PBC and cfDNA in MCL. The capture-based EC-NDC assay allows a comprehensive liquid biopsy-based genotyping of MCL. In addition, both IG-NGS and EC-NDC assays are suitable for MRD assessment in cfDNA with evidence of more sensitive MRD detection EC-NDC due to multiple MRD targets detected and traced by this assay. Clinical data are still needed to explore the potential prognostic impact of MRD assessment in plasma vs PBC. Updated MRD analysis at EoT and correlation with clinical data will be presented at the meeting.