BRAF Mutations in Myeloid Neoplasms: Prevalence, Co-Mutation Landscape, and Clinical Outcomes—A Comprehensive Review

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors systematically reviewed data from 12 published studies regarding the distribution, genomic profile, and clinical significance of BRAF mutations across myeloid neoplasms. Collectively, BRAF alterations were identified in <1 % of cases, with notable enrichment in chronic myelomonocytic leukemia (CMML; ~7 %). Both V600E and non-V600E variants were detected, often accompanied by co-occurring mutations in ASXL1, TET2, DNMT3A, SRSF2, K/N-RAS, and TP53. The authors conclude that BRAF mutations are rare, heterogeneous, and usually represent secondary events acquired during clonal evolution. While the compiled data provide a useful reference, they are insufficient to establish definitive genotype-phenotype correlations or to clarify the prognostic weight of BRAF mutations in any specific myeloid entity the authors covered.

 Major concerns

 1. The 12 studies span 2004–2024 and employed assays ranging from PCR to comprehensive targeted NGS. PCR-based approaches, in particular, may miss non-hot-spot or indel variants, introducing uncertainty about both the true incidence and the full mutational spectrum of BRAF in myeloid malignancies.

 2. Recurrent co-mutations—most notably in ASXL1, TET2, DNMT3A, SRSF2, KRAS/NRAS, and TP53—are themselves associated with adverse outcomes. This molecular complexity obscures any independent effect that BRAF mutations might exert on disease biology or prognosis.

 3. Tables 2–4 contain limited, fragmented information; their specific contribution to the narrative is unclear and could be streamlined or expanded to enhance interpretability.

Author Response

Comments 1: The 12 studies span 2004–2024 and employed assays ranging from PCR to comprehensive targeted NGS. PCR-based approaches, in particular, may miss non-hot-spot or indel variants, introducing uncertainty about both the true incidence and the full mutational spectrum of BRAF in myeloid malignancies.

Response 1: We thank the reviewer for highlighting this important methodological consideration. We agree that the wide temporal span of included studies and the evolution from PCR-based hotspot assays to comprehensive next-generation sequencing platforms introduce uncertainty regarding both the true incidence and the full mutational spectrum of BRAF alterations in myeloid neoplasms. We have explicitly reinforced this limitation in the Discussion, acknowledging the potential under-detection of non–hot-spot and indel variants in earlier PCR-based studies and its impact on prevalence estimates and variant distribution. Section 3 discussion (line 284-287).

Comments 2: Recurrent co-mutations—most notably in ASXL1, TET2, DNMT3A, SRSF2, KRAS/NRAS, and TP53—are themselves associated with adverse outcomes. This molecular complexity obscures any independent effect that BRAF mutations might exert on disease biology or prognosis.

Response 2: We fully agree with the reviewer. As discussed in the Results and Discussion, BRAF mutations in myeloid neoplasms almost invariably occur within a complex genomic background enriched for recurrent adverse co-mutations, including ASXL1, TET2, DNMT3A, SRSF2, RAS-pathway genes, and TP53. This molecular complexity substantially confounds attribution of disease biology or prognosis to BRAF mutations alone. We have further clarified this point in the Discussion to emphasize that current data do not permit assessment of an independent prognostic role for BRAF alterations. Section 3 discussion (line 249-259). Importantly, myeloid neoplasms (e.g., AML, MDS, MDS/MPN) are inherently heterogeneous disorders characterized by variable mutational landscapes, branching clonal evolution, and shifting clonal dominance over time and/or under treatment pressure. In this setting, it is often difficult (and sometimes not possible) to ascribe a given clinical phenotype or outcome to a single lesion—particularly when BRAF may represent a secondary/subclonal event acquired during clonal evolution. At the same time, we acknowledge that some cases describe BRAF as the sole detectable abnormality (within the limits of the assays used), raising the possibility that BRAF could act as a more central driver in select patients. Because the included studies span different testing eras and platforms (PCR vs broader NGS), improvements in sequencing breadth and sensitivity may increasingly clarify whether there exists a subset with more “isolated” BRAF lesions or more interpretable clonal architecture. Accordingly, we have strengthened the Discussion to emphasize that current evidence is insufficient to confirm an independent prognostic impact of BRAF mutations across myeloid neoplasms, and that larger, clinically annotated cohorts with harmonized genomic profiling (including variant allele frequencies and serial sampling) are needed.  Section 3 discussion (line 256-259).   Comments 3:  Tables 2–4 contain limited, fragmented information; their specific contribution to the narrative is unclear and could be streamlined or expanded to enhance interpretability..   Response 3: We revised the tables to improve clarity and reduce fragmentation. Table 2 now focuses exclusively on disease distribution and enrichment of BRAF mutations, while former Tables 3 and 4 were merged into a single clinicogenetic table summarizing molecular features, clinical characteristics, and outcomes. The Results section was revised accordingly to align with the streamlined table structure and eliminate redundancy.

Reviewer 2 Report

Comments and Suggestions for Authors

The subject of this review article is the prevalence of BRAF mutation in myeloid neoplasms: acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPN) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN).

Bearing in mind that the frequency of this mutation in myeloid malignancies is very low, around 1%, the topic of this article is very interesting and bravely chosen. However, the authors analyzed a very extensive literature: PubMed, Google Scholar, and Scopus from database inception to 2025.

The association of the BREF mutation with recurrent molecular aberrations, as well as the cytogenetic findings of patients with myeloid malignancies and BREF mutation, was very systematically explained.

Also, Table 5 provides an overview of the therapy used in these patients, depending on the myeloid neoplasm.

The limitations of this research were stated very objectively, from the fact that most of the research was retrospective, based on a small number of cases, that the technique of detecting this mutation was uneven, ie, in earlier research PCR was applied, and in more recent NGS, as well as that the applied therapy was very heterogeneous.

The conclusion explained the given research very well and emphasized the need for prospective research on a larger sample.

 

 

Author Response

Comments: The subject of this review article is the prevalence of BRAF mutation in myeloid neoplasms: acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPN) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). Bearing in mind that the frequency of this mutation in myeloid malignancies is very low, around 1%, the topic of this article is very interesting and bravely chosen. However, the authors analyzed a very extensive literature: PubMed, Google Scholar, and Scopus from database inception to 2025. The association of the BREF mutation with recurrent molecular aberrations, as well as the cytogenetic findings of patients with myeloid malignancies and BREF mutation, was very systematically explained. Also, Table 5 provides an overview of the therapy used in these patients, depending on the myeloid neoplasm. The limitations of this research were stated very objectively, from the fact that most of the research was retrospective, based on a small number of cases, that the technique of detecting this mutation was uneven, ie, in earlier research PCR was applied, and in more recent NGS, as well as that the applied therapy was very heterogeneous. The conclusion explained the given research very well and emphasized the need for prospective research on a larger sample.

Response : We sincerely thank the reviewer for their thoughtful and encouraging evaluation of our manuscript. We are grateful for their positive assessment of the conclusions and their emphasis on the need for future prospective studies. We also revised manuscript as suggested by other reviewers.

Reviewer 3 Report

Comments and Suggestions for Authors

The aim of the submitted manuscript is to provide a comprehensive review focused on the prevalence and the role of BRAF mutations in  myeloid neoplasms. In this respect the authors interrogated PubMed, Google Scholar, and Scopus databases searching for publications related to this topic and identified 12 studies of various types (prospective/retrospective cohort study, cross-sectional analysis, and case report). 
The Introduction specifies clearly the objectives of the study. The Results are well structured including the distribution of BRAF mutations across several categories of myeloid neoplasms, the spectrum of BRAF variants, and the associated clinical features, cytogenetic anomalies, profile of co-mutations, outcomes, survival data, and therapeutic approaches. Biological and clinical implications of BRAF mutation occurrence in myeloid neoplasms are discussed in the light of available data from the literature, the limitations of the actual analysis being also formulated.
As it seems that BRAF mutations have a higher incidence in myeloid neoplasms with a prominent monocytic component (e.g. acute monocytic leukemia, chronic myelomonocytic leukemia) please provide an explanation for this association.

Author Response

Comments 1: The aim of the submitted manuscript is to provide a comprehensive review focused on the prevalence and the role of BRAF mutations in  myeloid neoplasms. In this respect the authors interrogated PubMed, Google Scholar, and Scopus databases searching for publications related to this topic and identified 12 studies of various types (prospective/retrospective cohort study, cross-sectional analysis, and case report).  The Introduction specifies clearly the objectives of the study. The Results are well structured including the distribution of BRAF mutations across several categories of myeloid neoplasms, the spectrum of BRAF variants, and the associated clinical features, cytogenetic anomalies, profile of co-mutations, outcomes, survival data, and therapeutic approaches. Biological and clinical implications of BRAF mutation occurrence in myeloid neoplasms are discussed in the light of available data from the literature, the limitations of the actual analysis being also formulated. As it seems that BRAF mutations have a higher incidence in myeloid neoplasms with a prominent monocytic component (e.g. acute monocytic leukemia, chronic myelomonocytic leukemia) please provide an explanation for this association.

Response 1: We thank the reviewer for this insightful observation. We have expanded the Discussion to address the apparent enrichment of BRAF mutations in myeloid neoplasms with prominent monocytic differentiation, including chronic myelomonocytic leukemia and acute monocytic leukemia. We propose that lineage-specific reliance on MAPK signaling during monocytic differentiation and activation, together with parallels observed in histiocytic disorders where MAPK pathway mutations are central to disease biology, may partially explain this association. We emphasize that this represents a biologically plausible hypothesis rather than a proven mechanism and warrants further functional investigation. Section 3 discussion (line 264-274).

Reviewer 4 Report

Comments and Suggestions for Authors

The authors report comprehensive review of BRAF prevalence and impact on myeloid neoplasms.

1. The authors should clearly describe the BRAF signal shown in the figure and include a corresponding description in the main text.
2. The authors should clarify the association between BRAF mutations and co-occurring genetic alterations, such as ASXL1 and TET2.
3. Publicly available databases should be used to provide additional information on the frequency and genetic context of BRAF mutations.

Author Response

Comments 1:  The authors should clearly describe the BRAF signal shown in the figure and include a corresponding description in the main text.

Response 1: We have revised the Results section to explicitly describe the BRAF signal illustrated in Figure 1, clarifying the relative enrichment of BRAF mutations in CMML-specific cohorts compared with other myeloid neoplasms and emphasizing that this reflects relative distribution rather than high absolute prevalence.

 

 

Comments 2:  The authors should clarify the association between BRAF mutations and co-occurring genetic alterations, such as ASXL1 and TET2.

Response 2: We thank the reviewer for this comment. We have clarified throughout the Results and Discussion that the association between BRAF mutations and recurrent alterations such as ASXL1 and TET2 reflects frequent co-occurrence within a complex genomic landscape rather than a defined biological dependency. We emphasize that current data support BRAF as a secondary event in clonal evolution rather than a primary initiating mutation.

 

 

Comments 3: Publicly available databases should be used to provide additional information on the frequency and genetic context of BRAF mutations.

Response 3: We appreciate the reviewer’s suggestion regarding the use of publicly available databases. Given the scope of this work as a review, we focused on synthesizing data from published studies, many of which already incorporate large institutional cohorts and analyses derived from publicly available or registry-based sequencing efforts. Owing to the rarity of BRAF mutations in myeloid neoplasms and the heterogeneity and limited clinical annotation of public databases, we did not perform additional independent database mining. We have clarified this point in the Discussion and highlight the value of future dedicated database-driven analyses to further refine prevalence estimates and genetic context. Section 3 discussion (line 289-292).

Reviewer 5 Report

Comments and Suggestions for Authors

This study aims to review the clinical landscape of BRAF-mutated myeloid neoplasms, which is an important topic.

I have the following comments:

Title: This study focuses on the clinical prevalence of BRAF mutations rather than normal BRAF in myeloid neoplasms. Therefore, the title needs to be revised accordingly.

References: This manuscript contains numerous references that are not presented in the appropriate order.

Please provide an overview diagram of the BRAF/RAS/MAPK signaling pathway, along with other major signaling pathways in leukemia cells, in Figure 1 or Figure 2. Clinicians and researchers would benefit from a clear view of intracellular signaling pathways to better understand the significance of BRAF mutations or dysregulated BRAF, whether secondary to treatment or due to de novo intracellular adaptations in response to targeted monotherapies with limited durability.

Finally, the tables could be combined to avoid redundancy.

Author Response

This study aims to review the clinical landscape of BRAF-mutated myeloid neoplasms, which is an important topic.

I have the following comments:

Title: This study focuses on the clinical prevalence of BRAF mutations rather than normal BRAF in myeloid neoplasms. Therefore, the title needs to be revised accordingly.

Answer

We thank the reviewer for this helpful suggestion. The title has been revised to BRAF Mutations in Myeloid Neoplasms: Prevalence, Co-mutation Landscape, and Clinical Outcomes—A Comprehensive Review

 

References: This manuscript contains numerous references that are not presented in the appropriate order.

Answer

We thank the reviewer for highlighting this issue. All in-text citations have been carefully reviewed and renumbered to ensure that references follow the correct numerical order according to their first appearance in the manuscript. The reference list has been updated accordingly

 

Please provide an overview diagram of the BRAF/RAS/MAPK signaling pathway, along with other major signaling pathways in leukemia cells, in Figure 1 or Figure 2. Clinicians and researchers would benefit from a clear view of intracellular signaling pathways to better understand the significance of BRAF mutations or dysregulated BRAF, whether secondary to treatment or due to de novo intracellular adaptations in response to targeted monotherapies with limited durability.

Answer

We thank the reviewer for this helpful suggestion. An overview schematic of the RAS–RAF–MEK–ERK (MAPK) signaling pathway and its interaction with other major signaling pathways relevant to leukemogenesis has now been added as Figure 1 in the Introduction section. This figure provides a conceptual overview of intracellular signaling mechanisms to better contextualize the biological significance of BRAF mutations in myeloid neoplasms.

Finally, the tables could be combined to avoid redundancy.

Answer

We thank the reviewer for this suggestion. To reduce redundancy and improve clarity, Table 4 has been moved to the Supplementary Materials, and Table 2 has been revised and reorganized to provide clearer classification of disease subgroups (AML, MDS, CMML, and MPN) with explicit case numbers for each category.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors have addressed several concerns resulting in a somewhat improved manuscript. However, significant limitations persist. Based on the available data and the current scope of the review, limited firm conclusions can be drawn beyond establishing a rough—and notably low—incidence of BRAF mutations across heterogeneous myeloid neoplasms.

Specifically, the review lacks supporting data for the claim that "mutation clearance appears prognostically relevant." Similarly, no evidence is provided for the assertion that "targeted approaches provide limited durability" (e.g., which specific agents for which disease subtypes? What are the response rates?). Consequently, my original concern remains valid: "Current data are insufficient to establish definitive genotype-phenotype correlations or to clarify the prognostic weight of BRAF mutations in any specific myeloid entity this review article covered."

The methodology for determining BRAF mutation distribution across myeloid malignancies in figure 1 is unclear. Are these incidence rates pooled from multiple studies? While the CMML data appears to derive from Zhang et al. (2014), the sources for other entities are not specified. For instance, Abusaab et al. (2024) reported an incidence of 0.8% (22/2,538) in MDS/CMML—data that appear inconsistent with 7% for CMML shown in this figure. Without clear methodological transparency, Figure 1 risks being misleading.

The tables continue to present fragmented, limited information, requiring readers to synthesize data across multiple tables to grasp the complete picture.

Author Response

Comments: 

The authors have addressed several concerns resulting in a somewhat improved manuscript. However, significant limitations persist. Based on the available data and the current scope of the review, limited firm conclusions can be drawn beyond establishing a rough—and notably low—incidence of BRAF mutations across heterogeneous myeloid neoplasms.

Specifically, the review lacks supporting data for the claim that "mutation clearance appears prognostically relevant." Similarly, no evidence is provided for the assertion that "targeted approaches provide limited durability" (e.g., which specific agents for which disease subtypes? What are the response rates?). Consequently, my original concern remains valid: "Current data are insufficient to establish definitive genotype-phenotype correlations or to clarify the prognostic weight of BRAF mutations in any specific myeloid entity this review article covered."

The methodology for determining BRAF mutation distribution across myeloid malignancies in figure 1 is unclear. Are these incidence rates pooled from multiple studies? While the CMML data appears to derive from Zhang et al. (2014), the sources for other entities are not specified. For instance, Abusaab et al. (2024) reported an incidence of 0.8% (22/2,538) in MDS/CMML—data that appear inconsistent with 7% for CMML shown in this figure. Without clear methodological transparency, Figure 1 risks being misleading.

The tables continue to present fragmented, limited information, requiring readers to synthesize data across multiple tables to grasp the complete picture. 

Reply: 

1) Regarding BRAF mutation interpretation and clinical implications

We thank the reviewer for their careful reading of the manuscript and their insightful comments. We fully agree that myeloid neoplasms represent a biologically heterogeneous group of diseases with complex and diverse mutational landscapes. Accordingly, any individual genetic alteration—including BRAF—should be interpreted as one component of a broader clonal architecture rather than as a unifying driver mutation. This principle underpins the framework of our review, which intentionally focuses on summarizing the distribution, molecular context, and reported clinical associations of BRAF mutations across heterogeneous myeloid entities, rather than proposing definitive genotype–phenotype relationships.

Based on the reviewer’s comments, we would like to further clarify that our discussion reflects findings reported across multiple independent studies, and we have highlighted these comparative observations in Table 4, which summarizes outcomes and key clinicopathologic correlates reported in the available literature. Notably, several published reports have suggested an association between BRAF mutations and worse outcomes in selected myeloid neoplasm contexts; however, the direction and magnitude of these associations vary across studies, consistent with the underlying biological and clinical heterogeneity.

Regarding the statement that “mutation clearance appears prognostically relevant,” this observation is derived from published retrospective data, most notably Abuasab et al., which evaluated BRAF-mutated myeloid neoplasms longitudinally and reported improved survival among patients who achieved molecular clearance compared with those with persistent BRAF mutations. Importantly, that study also highlighted clonal dynamics—including loss of BRAF at relapse in some patients—reinforcing the concept that BRAF is often a secondary and evolutionarily unstable event rather than a dominant founder lesion. Our manuscript presents these findings as associative signals, not as definitive prognostic claims.

Similarly, our statement regarding the limited durability of targeted approaches reflects the collective experience reported in the literature, in which BRAF and/or MEK inhibitors have produced transient hematologic or morphologic responses in selected cases, without consistent or durable molecular remission. Given the rarity of these cases and the absence of prospective trials, our intent was to synthesize currently available evidence rather than to quantify response rates or establish treatment standards.

Finally, because of substantial heterogeneity across disease entities, cohort selection, sequencing methods, and outcome definitions—and the rarity of BRAF-mutated cases—we could not perform a formal systematic review or meta-analysis. To avoid overinterpretation and improve precision, we will revised the the manuscript to remove strong language implying certainty (e.g., replacing terms such as “established” with more appropriate qualifiers such as “reported”

 

2) Regarding Figure 1

With respect to Figure 1, the figure is designed to illustrate relative enrichment patterns across disease categories, rather than to provide pooled or meta-analytic incidence estimates. However, we agree that the figure is not a crucial component of the review’s core message, and therefore it can be removed if the reviewer and editor feel it does not add sufficient value or may introduce ambiguity in interpretation.

 

3) Regarding the Table

Regarding the table, our goal is to provide a structured and accessible synthesis of published cohorts and case-based literature describing BRAF-mutated myeloid neoplasms, including the molecular context, co-mutation patterns, treatment exposures, and reported outcome signals. In response to the reviewer’s suggestion, we will add clarifying details directly within the table, using footnotes and/or brief annotations under the table to specify key methodological and interpretive points (e.g., cohort composition, sequencing platform/coverage, definitions of molecular clearance, follow-up duration, and how outcomes were reported).

We will also explicitly note that, given the limitations inherent to rare-mutation datasets (small numbers, referral bias, differing sequencing platforms, and variable follow-up), the table is intended as a descriptive summary and consolidated reference, rather than a source for uniform prognostic weighting or treatment recommendations. These additions will help ensure the table is interpreted consistently with the aims of the review and that cross-study differences are transparently presented.

 

Reviewer 4 Report

Comments and Suggestions for Authors

none

Author Response

We would like to thank the reviewers and the Editor for their time and consideration. As no reviewer comments were provided, no revisions were required.

Reviewer 5 Report

Comments and Suggestions for Authors

Thanks for the revision.

Please revise the typing errors: impaired not “impated” and relevant not “releveant”  in Class 3 of figure 1A.

Please add Class 3 mutations in figure 1A legends. Also, please add the contents of 1B in figure 1 legends.

Author Response

We thank the reviewer for the comments. An adjustment has been done to figure 1 as requested. 

Round 3

Reviewer 1 Report

Comments and Suggestions for Authors

Although the authors have made efforts to improve the manuscript, my main concerns remain inadequately addressed, "based on the available data and the current scope of the review, limited firm conclusions can be drawn beyond establishing a rough—and notably low—incidence of BRAF mutations across heterogeneous myeloid neoplasms". 

Besides, there are several points need to be noticed:

1. The patient outcomes presented in Table 4 cannot be convincingly attributed to BRAF mutations. Based on the co-mutation profiles shown in Figure 3, most co-occurring mutated genes are classified as ELN adverse-risk genes, suggesting that the reported outcomes likely reflect the adverse-risk molecular background rather than the BRAF mutation itself.
2. The figure legend in Fig 1 states that "prevalence values represent approximate ranges summarized from multiple published cohorts." However, if specific values are derived from representative studies, the precision should be maintained. For example, if the CMML incidence of 7.0% originates from Reference ID2, it should be cited as 7.1% (the actual reported value), with the data source explicitly indicated. Similar corrections and source annotations are needed for all prevalence numbers in this figure, not just (e.g., Abuasab 2024, Fei 2024, 120 Papaemmanuil 2016, Zhang 2014, Santos 2014).
3. The information presented across five tables remains fragmented and difficult to interpret due to inconsistent nomenclature and lack of clear definitions. Just a few examples:

Table 2 - "Classification" column: In ID 9 and ID 12, do the numbers represent BRAF-mutated patients?  In ID 2, what do "CMML:2" and "CMML:3" signify? If these denote CMML-2 and CMML-3 subtypes, how are MPN and MDS cases classified in the same study? Classification of MPN and MDS are more important and clinically more meaningful than classification of CMML 1-3.

Terms such as "t-MDS" appear under "underlying disease" in some entries (e.g., ID 3) but under "classification" in others (e.g., ID 1), creating confusion regarding the distinction between these categories.

For the entry "t-MDS: 89; t-AML: 51" in ID 3, do these figures represent the total patient cohorts or only BRAF-mutated cases? Furthermore, the classification is listed as "AML-M5"—does this imply that all 51 t-AML cases were both AML-M5 subtype and BRAF-mutated?

These inconsistencies across different study IDs make the data difficult to interpret and substantially limit the manuscript's clarity and scientific rigor. Similar ambiguities are present in other tables.

Author Response

Although the authors have made efforts to improve the manuscript, my main concerns remain inadequately addressed, "based on the available data and the current scope of the review, limited firm conclusions can be drawn beyond establishing a rough—and notably low—incidence of BRAF mutations across heterogeneous myeloid neoplasms". 

Answer

We thank the reviewer for their continued careful evaluation of our manuscript and for the constructive comments provided. We appreciate the opportunity to further clarify several points.

We agree with the reviewer that, given the rarity of BRAF mutations and the biological heterogeneity of myeloid neoplasms, the currently available data allow only limited firm conclusions beyond confirming the low overall incidence of BRAF mutations across these diseases. Our intent in this review was not to establish definitive genotype–phenotype associations, but rather to summarize the currently available literature describing the occurrence, molecular context, and reported clinical observations associated with BRAF mutations in myeloid malignancies.

We believe the manuscript already reflects this cautious interpretation and presents the available evidence in a descriptive manner without claiming definitive biological or prognostic conclusions. The discussion consistently emphasizes the limited number of reported cases, heterogeneous study designs, and the need for larger genomic studies to clarify the clinical significance of BRAF mutations in specific disease entities.

 

Besides, there are several points need to be noticed:

1. The patient outcomes presented in Table 4 cannot be convincingly attributed to BRAF mutations. Based on the co-mutation profiles shown in Figure 3, most co-occurring mutated genes are classified as ELN adverse-risk genes, suggesting that the reported outcomes likely reflect the adverse-risk molecular background rather than the BRAF mutation itself.

Answer

We appreciate the reviewer’s observation regarding the potential influence of co-mutation profiles on the clinical outcomes summarized in Table 4. As correctly noted, many co-occurring mutations identified in these patients involve genes classified within ELN adverse-risk molecular categories, suggesting that the observed outcomes may reflect the broader adverse-risk molecular background rather than the isolated presence of a BRAF mutation.

To avoid potential overinterpretation, Table 4 has been moved to the Supplementary Materials, and the corresponding text has been revised to clarify that the outcomes summarized in this table represent findings reported in the original studies and should not be interpreted as being directly attributable to BRAF mutations alone. We now explicitly emphasize that the co-mutational context likely plays a major role in determining clinical phenotype and prognosis in these cases. These clarifications have been incorporated in the results section (Section 2.3, page 11, lines 175-178) and further discussed in the Discussion section (page 14, lines 252-255).

 

1. The figure legend in Fig 1 states that "prevalence values represent approximate ranges summarized from multiple published cohorts." However, if specific values are derived from representative studies, the precision should be maintained. For example, if the CMML incidence of 7.0% originates from Reference ID2, it should be cited as 7.1% (the actual reported value), with the data source explicitly indicated. Similar corrections and source annotations are needed for all prevalence numbers in this figure, not just (e.g., Abuasab 2024, Fei 2024, 120 Papaemmanuil 2016, Zhang 2014, Santos 2014).

 

Answer

We thank the reviewer for this helpful suggestion. We agree that maintaining numerical precision and clearly indicating data sources improves the accuracy and transparency of the figure.

Accordingly, Figure 1 and its legend have been revised and renamed to ensure that prevalence values correspond to the exact values reported in the original studies, and that the corresponding references are explicitly indicated in the figure legend.

 

 

 

1. The information presented across five tables remains fragmented and difficult to interpret due to inconsistent nomenclature and lack of clear definitions. Just a few examples:

Table 2 - "Classification" column: In ID 9 and ID 12, do the numbers represent BRAF-mutated patients?  In ID 2, what do "CMML:2" and "CMML:3" signify? If these denote CMML-2 and CMML-3 subtypes, how are MPN and MDS cases classified in the same study? Classification of MPN and MDS are more important and clinically more meaningful than classification of CMML 1-3.

Terms such as "t-MDS" appear under "underlying disease" in some entries (e.g., ID 3) but under "classification" in others (e.g., ID 1), creating confusion regarding the distinction between these categories.

For the entry "t-MDS: 89; t-AML: 51" in ID 3, do these figures represent the total patient cohorts or only BRAF-mutated cases? Furthermore, the classification is listed as "AML-M5"—does this imply that all 51 t-AML cases were both AML-M5 subtype and BRAF-mutated?

These inconsistencies across different study IDs make the data difficult to interpret and substantially limit the manuscript's clarity and scientific rigor. Similar ambiguities are present in other tables.

answer

We thank the reviewer for highlighting the issue of fragmented presentation across tables. To improve clarity and consistency, the tables have been reorganized. Table 2 has been revised to clearly distinguish underlying disease categories and subtype classifications across studies

 

 

Author Response File: Author Response.docx