Ultra-low depth sequencing of plasma cell DNA for the detection of copy number aberrations in multiple myeloma

Plasma Cell Enrichment and New Genomic Approaches in Multiple Myeloma: A Scoping Review

BACKGROUND

Multiple myeloma (MM) is a genetically heterogeneous disease where specific genetic abnormalities have a significant impact on a patient's prognosis. Diagnostic and prognostic tools like fluorescence in situ hybridization (FISH), PCR, microarrays, and next-generation sequencing (NGS) have transformed MM management. However, the effectiveness of these techniques is often limited by the low concentration of plasma cells in bone marrow samples, which makes enrichment methods necessary. This review aims to clarify how these techniques enhance the detection of genetic abnormalities, reduce false-negative results, and facilitate more precise risk stratification for MM patients.

CONTENT

Following Preferred Reporting Items for Systematic reviews and Meta-Analyses Extension for Scoping Review (PRISMA-ScR) guidelines, the literature on plasma cell separation methods used in genetic studies of MM was systematically identified and mapped. Searches were conducted in the Medline and Embase databases using a structured strategy, supplemented by manual searches on Google Scholar. Of 399 publications evaluated, 69 met the inclusion criteria; 37% utilized FISH and 19% demonstrated an increasing use of NGS. Plasma cell enrichment significantly improved diagnostic accuracy, increasing the detection rates of genetic abnormalities from 61% in non-enriched samples to 95.5% in enriched samples. While FISH remains the gold standard, emerging technologies such as NGS offer superior sensitivity and the ability to identify critical genetic alterations to refine molecular subtypes.

SUMMARY

Clinically significant genetic alterations are detected more frequently with plasma cell enrichment techniques, contributing to improved prognosis and treatment strategies for MM patients.

Shallow whole-genome sequencing of bone marrow aspirates in myelodysplastic neoplasms: A retrospective comparison with cytogenetics

Copy number alterations (CNA) are powerful prognostic markers in myelodysplastic neoplasms (MDS) and are routinely analyzed by conventional cytogenetic analysis (CCA) on bone marrow (BM). Although CCA is still the gold standard, it requires extensive hands-on time and highly trained staff for the analysis, making it a laborious technique. To reduce turn-around-time per case, shallow whole genome sequencing (sWGS) technologies offer new perspectives for the diagnostic work-up of this disorder. We compared sWGS with CCA for the detection of CNAs in 33 retrospective BM samples of patients with MDS. Using sWGS, CNAs were detected in all cases and additionally allowed the analysis of three cases for which CCA failed. The prognostic stratification (IPSS-R score) of 27 out of 30 patients was the same with both techniques. In the remaining cases, discrepancies were caused by the presence of balanced translocations escaping sWGS detection in two cases, a subclonal aberration reported with CCA that could not be confirmed by FISH or sWGS, and the presence of an isodicentric chromosome idic(17)(p11) missed by CCA. Since sWGS can almost entirely be automated, our findings indicate that sWGS is valuable in a routine setting validating it as a cost-efficient tool.

Genome Instability in Multiple Myeloma: Facts and Factors

Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.

Ultra-low coverage whole genome sequencing of ccfDNA in multiple myeloma: A tool for laboratory routine?

Multiple myeloma (MM), is a heterogeneous disease in which chromosomal abnormalities are important for prognostic risk stratification. Cytogenetic profiling with FISH on plasma cells from bone marrow samples (BM-PCs) is the current gold standard, but variable infiltration of plasma cells or failed aspiration can hamper this process. Ultra-low coverage sequencing (ULCS) of circulating cell-free DNA (ccfDNA) may offer a minimally invasive alternative for the work-up of these cases. We compared ULCS, aCGH and FISH on selected BM-PCs in a routine setting with ULCS of ccfDNA for the detection of somatic copy number aberrations (CNAs) in MM.

METHODS

Purified CD138+ BM-PCs of 23 MM patients at initiation of their treatment were subjected to aCGH, FISH and ULCS. Paired samples of peripheral blood-ccfDNA obtained at diagnosis were analyzed by ULCS and compared to the results found in BM-PCs.

RESULTS

Using ULCS of ccfDNA, cytogenetic markers were identified in 18 out of 23 patients; five cases could not be analyzed due to low (≤3%) tumor fraction (TF). High similarity between CNA profiles of BM-PCs and ccfDNA was found. Moreover, 78% of the ccfDNA profiles resulted in the same risk classification as the routine FISH and/or BM-PCs ULCS and aCGH. Chromothripsis was detected in five patients; these had the highest TF values (range 7.1% to 42%) in our series and their profiles showed other high-risk anomalies.

CONCLUSION

This proof-of-principle study indicates that ULCS of ccfDNA can reveal CNAs in MM and should be explored further as a cost-efficient alternative, especially in cases where BM-PC purification fails.