Comprehensive detection of recurring genomic abnormalities: a targeted sequencing approach for multiple myeloma

Venkata D Yellapantula ,Even H Rustad,Minal Patel,Yanming Zhang,Theresia Akhlaghi,Dory Londono,Max F Levine ,Sham Mailankody,Juan Arango Ossa ,Francesco Maura,Juan S Medina-Martínez ,A Ciardiello ,Ester Wasserman,Niccolò Bolli ,Heather Landau,Ahmet Doğan ,Elli Papaemmanuil,Robert Cimera,Malin Hultcrantz,Ola Landgren

doi:10.1038/s41408-019-0264-y

Abstract

Recent genomic research efforts in multiple myeloma have revealed clinically relevant molecular subgroups beyond conventional cytogenetic classifications. Implementing these advances in clinical trial design and in routine patient care requires a new generation of molecular diagnostic tools. Here, we present a custom capture next-generation sequencing (NGS) panel designed to identify rearrangements involving the IGH locus, arm level, and focal copy number aberrations, as well as frequently mutated genes in multiple myeloma in a single assay. We sequenced 154 patients with plasma cell disorders and performed a head-to-head comparison with the results from conventional clinical assays, i.e., fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarray. Our custom capture NGS panel had high sensitivity (>99%) and specificity (>99%) for detection of IGH translocations and relevant chromosomal gains and losses in multiple myeloma. In addition, the assay was able to capture novel genomic markers associated with poor outcome such as bi-allelic events involving TP53. In summary, we show that a multiple myeloma designed custom capture NGS panel can detect IGH translocations and CNAs with very high concordance in relation to FISH and SNP microarrays and importantly captures the most relevant and recurrent somatic mutations in multiple myeloma rendering this approach highly suitable for clinical application in the modern era.

Highlights

Multiple myeloma is a heterogeneous disease in terms of genomic alterations, clinical presentation, and survival outcomes
We included 120 genes that were selected on the basis of (a) genes frequently mutated in multiple myeloma from earlier reports5–7,21–26, (b) genes that are involved in important signaling pathways in multiple myeloma, e.g. the MAPK and NFKB pathways (Supplementary Table)6, (c) treatment targets and candidate genes for drug resistance in multiple myeloma (e.g., CRBN, IKZF1, and IKZF3)27, and (d) candidate genes and singlenucleotide polymorphism (SNP) associated with an increased susceptibility of developing multiple myeloma28
We found an extremely high concordance between our custom capture next-generation sequencing (NGS) assay and conventional multiple myeloma targeted fluorescence in situ hybridization (FISH)/SNP microarrays for detection of IGH translocations and copy number alterations (CNAs)

Summary

Introduction

Multiple myeloma is a heterogeneous disease in terms of genomic alterations, clinical presentation, and survival outcomes. In the standard of care setting, conventional chromosome analysis, multiple myeloma targeted fluorescence in situ hybridization (FISH) panels, and singlenucleotide polymorphism (SNP) microarrays are used to detect chromosome translocations and gains and losses in multiple myeloma. FISH is accurate to define distinct recurrent aberrations, it is limited to the targets of the selected probes not allowing a comprehensive cytogenetic characterization. SNP microarrays have been used to summarize copy number changes in multiple myeloma. This approach still relies on FISH for the detection of IGH translocations and usually requires about 15–20% or more aberrant plasma cell infiltration of the bone marrow which in turn limits the availability to do parallel comprehensive genomic analysis including V(D)J profiling for minimal residual disease characterization/tracking. Neither FISH nor SNP microarray approaches are able to capture somatic point mutations

Methods

Results

Conclusion