Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma

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David G. Coffey^1,2, Francesco Maura¹, Edgar E. Gonzalez-Kozlova³, J. Javier Diaz-Mejia⁴, Ping Luo⁴, Yong Zhang⁵, Yuexin Xu², Edus H. Warren², Travis Dawson³, Brian Lee³, Hui Xie³, Eric Smith⁶, Amanda Ciardiello⁷, Hearn J. Cho³, Adeeb Rahman³, Seunghee Kim-Schulze³, Benjamin Diamond¹, Alexander Lesokhin^7†, Dickran Kazandjian^1†, Trevor Pugh^4†, Damian J. Green^2†, Sacha Gnjatic^3†, Ola Landgren^1†

¹Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL; ²Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA; ³Icahn School of Medicine at Mount Sinai, New York, NY; ⁴Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada; ⁵Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD; ⁶Dana-Farber Cancer Institute, Boston, MA; ⁷Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; ^†These authors contributed equally

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Supplemental code

This repository contains R code for analyzing single-cell RNA sequencing (scRNAseq) combined with V(D)J sequencing, CyTOF mass cytometry, and T cell receptor $\beta$ sequencing.

• scRNAseq Methods.R This file demonstrates how gene expression matrix files output from the cell ranger v4.0.0 (10X Genomics) pipeline were processed into cell count matrices for differential cellular abundance analysis. Also shown is code for differential gene expression per cell type and methods for identifying exhausted T cells.

• scRNAseq VDJ Methods.R This file demonstrates how all_contig_annotations.csv V(D)J files generated by cell ranger v4.0.0 (10X Genomics) pipeline were filtered to exclude doublets, unpaired, and multi-chain T and B cell receptors.

• CyTOF Methods.R This file demonstrates how output from the Astrolabe Mass Cytometry Platform (Astrolabe Diagnostics, Inc.) was input into R using the orloj package, filtered, and analyzed for differential cellular abundance.

• TCRB Methods.R This file demonstrates how tab delimited files output from the ImmunoSeq platform (Adaptive Biotechnology) were input into R using the LymphoSeq package, repertoire statistics were calculated, and differential abundance analysis was performed.