Validation of the Nextseq 500 and Development of a High-Throughput NGS Pipeline for Identifying Clinically-Relevant Gene Variants in Multiple Myeloma Specimens

As molecular profiling technologies have evolved, our understanding of multiple myeloma heterogeneity and the relative effectiveness of treatment options have increased dramatically. Most recently, next generation sequencing (NGS) studies have provided a new degree of molecular resolution into this disease, however it remains a challenge to translate these methodologies and insights from research tools to widely-available clinical assays which can be performed as part of routine patient care.

MyPRS® is a clinically and scientifically validated high-throughput gene-expression (Affymetrix) based assay available in all 50 US states. The CLIA and CAP-accredited laboratory workflow is able to isolate sufficient RNA from small amounts of fresh bone marrow aspirate, up to 72 hours post collection[1]. In order to expand the content of the MyPRS assay to include DNA-sequencing based variant, copy number and mutation detection, we have validated highly-scalable methods for isolating RNA and DNA separately and in parallel from individual patient specimens of varying quality and quantity.

Yet another challenge of translational NGS profiling is performing complex laboratory procedures, developed primarily for research use only, with the requisite reproducibility and accuracy required for submission to regulatory agencies and ultimately for clinical use. Coupled with the protocols we developed for isolation of both DNA and RNA from small amounts of patient bone marrow aspirate, we performed an investigation of the Illumina NextSeq 500 and "on-site" BaseSpace data processing server. With the multiplexing and parallel processing capability of this platform we estimate being able to sequence, align and variant-call up to 150 myeloma-relevant genes at 1000x coverage per run.

Results from our MM cell-line-, normal human- and NIST reference-DNA whole-exome-profiling studies show extremely high levels of technical reproducibility and agreement with results generated from 3^rd party laboratories. In addition, we describe associations between the (RNA-expression based) prognostic, molecular subtyping and virtual karyotyping currently included in the MyPRS assay, with results from DNA-based exome profiling, performed on matched specimens. We believe findings underscore the need for comprehensive DNA and RNA based molecular profiling in order to make the most informed patient management decisions.

1. van Laar R, Flinchum R, Brown N, Ramsey J, Riccitelli S, Heuck C, Barlogie B, Shaughnessy Jr J: Translating a gene expression signature for multiple myeloma prognosis into a robust high-throughput assay for clinical use. BMC Medical Genomics 2014, 7 (1):25.