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Short summary of the research and contribution to the field

This preprint evaluates a tumor-only, high-depth whole genome sequencing workflow (WGS TO) for acute myeloid leukemia (AML), designed to detect clinically relevant small variants, structural variants (SVs), copy number alterations (CNAs), and loss of heterozygosity in a single assay. The authors describe a workflow using commercially available extraction methods, Illumina PCR-free library preparation, NovaSeq 6000 sequencing, and DRAGEN Somatic tumor-only analysis, targeting approximately 220× coverage with a reported turnaround time of approximately 5 days from DNA extraction to reporting.

The study reports strong analytical performance across variant classes: 97.6% sensitivity for small variants, 89.7% for SVs, and 92.9% for CNAs across 68 AML clinical samples, using multiple orthogonal reference methods including targeted NGS, WGS, optical genome mapping, FISH, and karyotyping. The authors also estimate limits of detection at 140× coverage: 5% VAF for small variants, 7.3% VAF for SVs, and CNA detection thresholds based on copy-number fold change and tumor purity.

This work moves the field forward by supporting the feasibility of a rapid, high-depth WGS approach as a potentially comprehensive alternative or complement to the fragmented AML testing landscape, where cytogenetics, FISH, targeted panels, and structural-variant methods are often performed separately. If validated further, this approach could simplify AML genomic profiling and improve detection of clinically relevant alterations across multiple variant classes.

Positive feedback / strengths

1. Clinically important problem. AML classification, prognosis, and treatment selection depend heavily on molecular and cytogenetic findings. A single WGS assay capable of detecting SNVs, indels, SVs, CNAs, and LOH could reduce fragmentation across multiple testing platforms.

2. Comprehensive variant-class coverage. The study evaluates small variants, FLT3-ITDs, SVs, CNAs, and CNLOH, which is appropriate for AML because clinically relevant alterations span several variant types.

3. Use of multiple orthogonal comparator methods. The authors compare WGS TO against reference sets from targeted sequencing, 60× WGS, FISH, karyotype, and optical genome mapping. This is a strength because each modality captures different classes and resolutions of AML alterations.

4. Practical turnaround-time goal. The reported ~5-day turnaround time is clinically meaningful for AML, where diagnostic and treatment decisions can be time-sensitive. The workflow breakdown—wet lab under 1 day, sequencing around 2 days, and bioinformatics around 13 hours—is helpful for clinical laboratories assessing feasibility.

5. Analytical LoD modeling is useful. The use of titration, downsampling, and PROBIT modeling to estimate detection thresholds provides a structured analytical validation framework.

6. Transparent discussion of discordant findings. The authors discuss missed variants and note that some lacked read support or had inconsistent support across orthogonal methods, which is important for interpreting sensitivity against imperfect reference standards.

Major issues

1. Tumor-only WGS interpretation needs more careful discussion

The assay is explicitly described as a tumor-only WGS workflow. This is practical and faster, but tumor-only analysis can make it harder to distinguish somatic variants from germline variants, clonal hematopoiesis, sequencing artifacts, or rare inherited variants.

Suggested improvement: The authors should discuss the limitations of tumor-only interpretation more explicitly, especially for AML where blood or marrow samples may contain malignant cells, preleukemic clones, clonal hematopoiesis, and germline predisposition variants. It would be helpful to describe:

• whether matched normal testing is recommended in specific cases

• how possible germline variants are filtered or flagged

• how CHIP/preleukemic variants are handled

• whether clinically important germline predisposition genes are excluded, reported, or referred for confirmatory germline testing

• how tumor-only filtering affects sensitivity and specificity

This is especially relevant because at least one small variant was detected but filtered as a possible germline variant.

2. Discordant SV and CNA results require deeper orthogonal resolution

The study reports lower sensitivity for SVs and CNAs compared with small variants, especially when benchmarked against karyotype and FISH. The authors appropriately note that some missed SVs and CNAs had inconsistent support across other methods, but additional adjudication would strengthen the conclusions.

Suggested improvement: The authors should include a dedicated discordance table for all missed or WGS-only SV/CNA calls showing:

• variant type and genomic coordinates

• orthogonal method reporting the event

• WGS TO read-depth / split-read / discordant-pair support

• OGM/FISH/karyotype support if available

• whether the event was clinically relevant

• whether the discrepancy likely reflects WGS limitation, comparator limitation, tumor heterogeneity, sample differences, or reporting threshold differences

Because the manuscript notes that additional testing is warranted to resolve conflicting calls, this should be elevated as a key limitation rather than a secondary point.

3. The reference standard is heterogeneous and may not be equally appropriate for all variant classes

The comparator set comes from multiple modalities, including targeted sequencing, 60× WGS, FISH, karyotype, and OGM. This is realistic, but it also complicates sensitivity estimates because each method has different resolution, false-positive risk, sensitivity, specimen requirements, and reporting conventions.

Suggested improvement: The authors should more clearly define the “truth set” construction process. Specifically:

• Were variants considered true positives if detected by one method only?

• Were conflicting reference calls adjudicated?

• Were methods performed on the same specimen or different aliquots/timepoints?

• Were variant coordinates harmonized across platforms?

• Were lower-resolution cytogenetic calls converted into genome coordinates?

• Were WGS-only additional calls orthogonally confirmed?

This would make the reported sensitivity values easier to interpret.

4. Precision testing for low-VAF variants should be expanded

The study reports 100% repeatability/reproducibility for clinical samples and Kasumi-1, but Seraseq showed 92.3% median concordance due to two ASXL1 variants near the LoD that were inconsistently detected across replicates. This is expected near detection limits, but it is highly relevant for AML subclonal detection.

Suggested improvement: The authors should expand discussion of repeatability near LoD and provide more low-VAF replicate data across variant types. A table showing detection probability by VAF bin—especially 2–5%, 5–10%, and >10%—would be very helpful for clinical interpretation.

5. The claimed ~5-day turnaround time needs operational context

The workflow’s fast turnaround time is one of the strongest clinical features. However, the study should clarify whether the 5-day TAT reflects a routine clinical workflow or an optimized validation workflow.

Suggested improvement: Please clarify:

• whether 5 days is from sample receipt, DNA extraction, or library start

• whether batching is required to reach this TAT

• number of samples per run

• whether weekend/holiday processing was included

• whether variant interpretation/reporting is included or only VCF generation

• staffing and computational requirements

• whether SV/CNA manual review adds additional time

This would help laboratories assess implementation feasibility.

6. Clinical reporting scope should be defined more clearly

The authors state that the assay can identify variants indicative of AML treatment options, but the manuscript would benefit from a more explicit description of clinical reporting.

Suggested improvement: The manuscript should clarify whether the final report includes:

• WHO/ICC classification-relevant alterations

• ELN risk stratification variants

• therapy-associated mutations

• MRD-relevant or subclonal variants

• SV/CNA findings

• germline-suspected findings

• variants below LoD or low-confidence findings

A mock report structure or reportable-variant framework would improve clinical interpretability.

7. WGS-only additional variants need follow-up validation

The manuscript reports that WGS TO identified 339 additional small variants, 32 additional SVs, and 122 additional CNAs >5 Mb not detected by orthogonal methods, and the authors state that additional validation is warranted. This is potentially very important, but without orthogonal confirmation or clinical annotation, the meaning of these additional findings is uncertain.

Suggested improvement: The authors should stratify these WGS-only findings by:

• likely pathogenic/clinically relevant vs uncertain

• variant type and size

• VAF/tumor fraction

• recurrence in AML genes or cytogenetic regions

• manual review status

• orthogonal confirmation status

• potential clinical impact

This would clarify whether WGS TO is identifying meaningful additional biology or lower-confidence findings.

8. Funding and conflicts of interest should be discussed in relation to validation design

The study includes substantial Illumina involvement, Illumina funding, and multiple Illumina-employed authors. This does not reduce the value of the work, but it increases the importance of transparent benchmarking and independent validation.

Suggested improvement: The manuscript already provides disclosures and funding information. It would further strengthen the paper to include a statement on independent data review, whether analysis was blinded to comparator results, and whether any validation steps were performed independently of the platform developer.

Minor issues

1. Fix inconsistent sensitivity values for SVs. The abstract reports 89.5% SV sensitivity, while Table 2 reports 89.7% and earlier text includes 83.9% in one place. Please harmonize all SV sensitivity values across the abstract, results, tables, and discussion.

2. Clarify WGS TO versus WGS 60× terminology. Because both are WGS-based methods, the paper should consistently distinguish high-depth WGS TO from the 60× WGS comparator.

3. Define “clinically important AML genes.” The manuscript states that small variants were filtered using a list of 156 clinically important AML genes. Please provide the full list prominently and explain how it was selected.

4. Clarify CNA size thresholds. The manuscript excludes CNAs below 500 kb from comparator analysis and focuses on CNA calls larger than 5 Mb for some prioritization. Please explain the clinical rationale for these thresholds.

5. Add confidence intervals for all major performance metrics. Sensitivity, precision, and LoD estimates should include confidence intervals where possible.

6. Clarify how FLT3-ITD detection was validated. The 100% detection of seven FLT3-ITDs is clinically important. Please provide ITD size range, VAF range, read support, and comparator method.

7. Improve figure/table readability. Figure 2 and Table 3 are useful, but a simplified summary table separating SNV/indel, FLT3-ITD, SV, CNA, and CNLOH performance would improve readability. The chart on page 13 clearly shows TP/FN distributions across variant classes and comparator methods, and this visual could be paired with a concise interpretation paragraph.

8. Clarify whether RNA fusions are out of scope. AML testing may include fusion detection by RNA-based methods. Since WGS can identify many SVs but not expression-level fusion evidence, the authors should clarify whether RNA testing remains necessary.

9. Discuss sample quality requirements. Please include minimum DNA input, DNA quality thresholds, acceptable specimen types, blast percentage/tumor purity requirements, and failure rates.

10. Clarify clinical deployment status. The manuscript should clearly state whether WGS TO is research-use only, analytically validated for a specific clinical laboratory context, or intended for broader clinical implementation.

Overall assessment

This is a valuable and timely analytical validation study of a high-depth tumor-only WGS workflow for AML. The study is strong because it addresses multiple clinically relevant variant classes, uses a rapid workflow, compares performance across multiple orthogonal technologies, and provides LoD estimates for small variants, SVs, CNAs, and CNLOH. The reported 5-day turnaround time and broad variant coverage make the approach potentially important for modern AML diagnostic profiling.

The major areas needing improvement are clearer handling of tumor-only interpretation, deeper resolution of discordant SV/CNA results, more transparent truth-set construction, expanded low-VAF precision analysis, and more operational detail around turnaround time and clinical reporting. With these additions, the manuscript would provide a stronger and more clinically actionable framework for laboratories evaluating high-depth WGS as a comprehensive AML testing modality.

Competing interests

The author declares that they have no competing interests.

Use of Artificial Intelligence (AI)

The author declares that they used generative AI to come up with new ideas for their review.