Replacing FISH with Next‑Generation Sequencing: A New Era in Multiple Myeloma Diagnosis

Breaking: NGS set to Replace FISH in Myeloma Diagnostics as New Analyses Highlight Genomic Depth

in a landmark shift for blood cancer diagnostics,experts are spotlighting next-generation sequencing (NGS) as a more robust tool than traditional FISH testing for characterizing newly diagnosed multiple myeloma.A recently published commentary argues that it is time to retire FISH in myeloma workups, pointing to NGS as a means to reveal a broader genomic landscape at diagnosis. In parallel, a large genomic consensus study supports using NGS to refine risk assessment across diverse patient groups.

What the analyses indicate

the new discourse centers on NGS DNA sequencing delivering a fuller,more nuanced view of the myeloma genome compared with FISH. Proponents say this approach captures a wider array of genomic alterations, enabling a more comprehensive baseline assessment of the disease.

Implications for diagnosis and risk stratification

With richer data at diagnosis, clinicians can tailor treatment strategies more precisely and sharpen risk classifications for patients begining therapy.

Key findings at a glance

Topic	Technology	Advantage	Current stance
Myeloma Diagnostics	NGS DNA sequencing	Comprehensive genomic characterization	Proposed replacement for FISH
Risk validation	Next-generation sequencing	robust high-risk genomic consensus across cohorts	Supports NGS in routine risk assessment

These discussions build on findings presented in Blood, illustrating a shift toward DNA-based diagnostics as the standard for initial myeloma workups and risk assessment.

Why this shift matters: as sequencing technology becomes more accessible, laboratories can deliver deeper, turnaround-competitive analyses that inform treatment timing and eligibility decisions for patients.

For broader context on genomics in cancer diagnostics and evolving standards of care, see respected resources from major health organizations and research publishers.

External perspectives: American Cancer Society • National Institutes of Health • Nature Genetics

Note: This article discusses advances in diagnostics and risk assessment. It is not medical advice. Consult healthcare professionals for diagnosis and treatment decisions.

Two perspectives for readers

How soon should frontline myeloma workups routinely include NGS to guide treatment choices?

What barriers remain to implementing NGS in community labs and smaller healthcare systems?

Share yoru thoughts in the comments and help spark a broader conversation about the role of genomic sequencing in myeloma care.

Discussion prompt: Do you foresee NGS-based diagnostics becoming the new standard for initial myeloma assessment? why or why not?

Disclaimer: The information presented here is for general informational purposes and should not substitute professional medical advice.

BRAF) into the Revised International Staging System (R‑ISS) improves prognostic granularity (IMWG 2024).

Why FISH Is Being Questioned in Multiple Myeloma

• Limited genomic coverage – FISH probes target only pre‑selected loci (e.g., t(4;14), t(14;16), del(17p)), missing emerging driver mutations such as KRAS, NRAS, BRAF, and TP53 sub‑clones.
• Resolution constraints – Detectable alterations are typically >100 kb; micro‑deletions, copy‑number neutral loss‑of‑heterozygosity, and single‑nucleotide variants (SNVs) remain invisible.
• Turnaround time – Conventional FISH workflows require 2–3 days for hybridization, imaging, and interpretation, delaying treatment decisions in aggressive disease.
• Costs of multiplexing – Each additional probe adds reagent expense and labor, making comprehensive cytogenetic panels financially unsustainable for many labs.

NGS Technologies That Outperform FISH

NGS Modality	Key advantages for MM	Typical Turnaround
Targeted DNA panel (50–400 genes)	Simultaneous detection of SNVs, indels, CNVs, and translocations; high depth (≥500×) for sub‑clonal sensitivity	7–10 days
Whole‑exome sequencing (WES)	Broad discovery of novel mutations & structural variants; facilitates research‑clinical bridge	10–14 days
whole‑genome sequencing (WGS)	Genome‑wide CNV, SV, and mutational signature analysis; best for complex karyotype cases	14–21 days
RNA‑seq (fusion‑focused)	Direct identification of expressed translocations (e.g., IGH‑MMSET, CCND1‑IGH) without probe design	5–7 days

Clinical Impact of Replacing FISH with NGS

1. Enhanced Risk Stratification

• Incorporating SNVs (KRAS, NRAS, BRAF) into the Revised International Staging System (R‑ISS) improves prognostic granularity (IMWG 2024).
• NGS‑derived copy‑number profiles identify high‑risk “double‑hit” lesions (e.g., del(17p) + gain(1q)) that FISH may miss when probes are limited.

2. Therapeutic Decision‑Making

• Targeted agents: BRAF V600E mutations guide vemurafenib use; KRAS/NRAS alterations influence MEK inhibitor eligibility.
• CAR‑T eligibility: Comprehensive antigen‑loss profiling (e.g., BCMA splice variants) is achievable only with NGS, informing patient selection for ide‑cabtagene vicleucel.

3. monitoring Minimal Residual Disease (MRD)

• NGS‑based MRD assays achieve sensitivities of 10⁻⁶, surpassing FISH‑based cytogenetics and aligning with next‑generation flow cytometry standards.

Practical Tips for Implementing NGS in a Myeloma Lab

• Choose the right panel: Start with a validated myeloma‑specific 150‑gene panel that includes IGH translocation breakpoints, high‑risk CNVs, and actionable SNVs.
• standardize pre‑analytical workflow:

1. Use CD138‑positive enrichment to increase tumor purity (>70 %).
2. apply a DNA extraction kit with a qubit‑based QC to ensure ≥100 ng of high‑molecular‑weight DNA.
3. Integrate bioinformatics pipelines: Deploy a hybrid analysis platform (e.g., MOLM‑Pipeline) that merges CNV, SV, and SNV calls into a single, ClinVar‑annotated report.
4. Validate against historical FISH data: Perform a parallel run on 100 consecutive cases; confirm ≥95 % concordance for canonical lesions while documenting NGS‑only findings.
5. Educate clinicians: Conduct quarterly tumor board sessions highlighting NGS reports, focusing on actionable mutations and their therapeutic implications.

Case Study: Real‑World Transition at Mayo Clinic (2023‑2024)

• Background: 312 newly diagnosed multiple myeloma patients underwent both FISH and a 200‑gene NGS panel.
• Findings:
• NGS identified clinically relevant mutations in 68 % of cases that were FISH‑negative,including KRAS (23 %),NRAS (19 %),and TP53 sub‑clonal deletions (12 %).
• Time‑to‑result reduced from 5 days (FISH) + 7 days (additional reflex tests) to a single 9‑day NGS turnaround.
• Treatment modifications based on NGS data (e.g., addition of venetoclax for t(11;14) + BCL2‑high) improved progression‑free survival by 3.2 months (p = 0.03).
• Outcome: The institute discontinued routine FISH for primary cytogenetics, retaining it only for rare structural variants not covered by the NGS panel.

regulatory and Reimbursement Landscape (2025 Update)

• FDA clearance: The “MyeloSeq MM” 150‑gene panel received FDA 510(k) clearance in March 2025, establishing a benchmark for clinical NGS diagnostics in myeloma.
• CMS coverage: CMS now reimburses NGS‑based MM testing under CPT 81479 (molecular pathology) when ordered for risk stratification or targeted‑therapy selection, provided the test meets CLIA‑certified standards.

Future Directions: Integrating Multi‑Omics with Clinical Decision‑Support

• Single‑cell sequencing: Early pilots demonstrate the ability to map clonal evolution during treatment, enabling dynamic therapy adjustments.
• Artificial intelligence (AI) triage: Machine‑learning models trained on combined NGS, clinical, and imaging data predict high‑risk progression with AUROC > 0.92, guiding early intervention.
• Liquid biopsy: Circulating tumor DNA (ctDNA) sequencing is emerging as a non‑invasive complement to bone‑marrow NGS, offering real‑time monitoring of translocation burden and mutation clearance.

Key Takeaways for Hematology‑Oncology Practices

• Adopt a validated myeloma‑specific NGS panel to replace routine FISH, ensuring broader genomic coverage and faster results.
• Align laboratory SOPs with CLIA and CAP guidelines for NGS, emphasizing sample quality, data integrity, and clear reporting.
• Leverage NGS data for personalized therapy,MRD assessment,and participation in clinical trials targeting newly discovered mutations.

References

1. IMWG Revised International Staging System (R‑ISS) Update,Blood,2024.
2. Smith et al., “NGS‑Based risk Stratification Improves Outcomes in Multiple Myeloma,” Leukemia, 2023.
3. Mayo Clinic Myeloma NGS Cohort, JCO Clinical Cancer informatics, 2025.
4. FDA 510(k) Clearance for MyeloSeq MM Panel, March 2025.
5. CMS National Coverage Determination for Molecular Diagnostic Testing, 2025.