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Whole-Genome Sequencing Provides Rapid and Accurate Genomic Profiling in Patients with AML or MDS

Clinical utility of whole-genome sequencing demonstrated for the genomic evaluation of patients with acute myeloid leukaemia or myelodysplastic syndromes
11 Mar 2021
Haematologic malignancies;  Personalised medicine

The researchers from the Washington University School of Medicine in St. Louis, MO, US reported on 11 March 2021 issue of The New England Journal of Medicine findings from the genomic profiling performed in 263 patients with acute myeloid leukaemia (AML) or myelodysplastic syndromes (MDS). The study results show that whole-genome sequencing is equivalent to or better than conventional cytogenetic analysis, both in analytical performance and clinical applicability. Whole-genome sequencing provided a greater diagnostic yield and more efficient risk stratification on the basis of standard risk categories according to Dr. David H. Spencer and colleagues.

Conventional cytogenetic analysis is currently an essential component of the diagnostic work-up for patients with AML or MDS. The authors wrote in background that advances in sequencing have improved the ability to identify genetic mutations, but the detection of chromosomal rearrangements is primarily performed through conventional cytogenetic analysis, e.g. karyotyping, which is effective, but has several limitations, including the need to obtain viable cells, low sensitivity, and limited resolution. Fluorescence in situ hybridisation (FISH) and targeted sequencing assays that use DNA, RNA, or both are also used, but these methods are informative only in the regions selected for analysis and may provide incomplete information regarding identified chromosomal rearrangements.

Variety of clinically relevant mutations suggest that whole-genome sequencing could be used instead standard testing. However, its accuracy, feasibility, and clinical utility have not been demonstrated. In this study, the researchers applied whole-genome sequencing for genomic profiling of patients with AML or MDS in real time to evaluate its feasibility, accuracy, and clinical utility.

The study team detected mutations for risk stratification by using European Leukemia Network guidelines. They analyzed the performance of whole-genome sequencing by comparing the results with findings from cytogenetic analysis and targeted sequencing. From 263 patients with myeloid cancers, 235 had undergone successful cytogenetic analysis.

Whole-genome sequencing detected all 40 recurrent translocations and 91 copy-number alterations that had been identified by cytogenetic analysis. In addition, it identified new clinically relevant genomic events in 40 of 235 patients (17.0%).

Prospective sequencing of samples obtained from 117 consecutive patients was performed in a median of 5 days and provided new genetic information in 29 patients (24.8%), which changed the risk category for 19 patients (16.2%).

Standard AML risk groups, as defined by sequencing results instead of cytogenetic analysis, correlated with clinical outcomes. Whole-genome sequencing was also used to stratify patients who had inconclusive results by cytogenetic analysis into risk groups in which clinical outcomes were measurably different.

The authors concluded that whole-genome sequencing detected 100% of the clinically significant abnormalities that had been identified by cytogenetic analysis and clinical FISH assays. In addition, sequencing provided new genetic information in almost 25% of patients, more than half of whom would have been assigned to a different genetic risk category with results from conventional testing. 

Prospective real-time sequencing of samples yielded complete genomic information in a clinically relevant timeframe. Although larger studies are needed to firmly establish the clinical performance of whole-genome sequencing, this proof-of-concept study showed that this method has the potential to add prognostic value by expanding risk stratification to more patients, especially for those with inconclusive results on cytogenetic analysis and where whole-genome sequencing could have an immediate effect on treatment decisions.

The study was funded by the Siteman Cancer Research Fund and others.

Reference

Duncavage EJ, Schroeder MC, O’Laughlin M, et al. Genome Sequencing as an Alternative to Cytogenetic Analysis in Myeloid Cancers. N Engl J Med 2021;384:924-935. DOI: 10.1056/NEJMoa2024534.

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