Molecular characteristics and prognostic insights into BRCA-associated breast cancer in Kazakhstan.

Introduction
Breast cancer (BC) remains one of the most significant medical and social challenges of modern healthcare, consistently ranking among the leading causes of cancer incidence and mortality in women worldwide. According to the Global Cancer Observatory (GLOBOCAN, 2022), over 2.3 million new cases of BC are diagnosed annually, accounting for 11.6% of all malignancies, with 665,684 deaths attributed to the disease worldwide. By incidence, it is second only to lung cancer (12.4%) and ahead of colorectal cancer (9.6%), while in terms of mortality, it ranks fourth globally (6.9%), following lung (18.7%), colorectal (9.3%), and liver cancer (7.8%)1.
In Kazakhstan, the burden of breast cancer remains persistently high, with over 5,500 new cases and more than 1,000 related deaths registered in 2023. In the same year, BC accounted for 14.9% of all malignant neoplasms, compared with 14.7% in 2022, indicating a stable yet unfavorable epidemiological trend. In mortality structure, BC ranks third (8.1%), following lung (15.8%) and gastric cancer (11.9%), which exceed the global average mortality rate for this malignancy2. These data underscore the urgent need to investigate the biological and molecular characteristics of BC within the Kazakhstani population, accounting for regional, ethnogenetic, and molecular diversity.
Hereditary predisposition, particularly BRCA1/2 mutations, is a significant determinant of breast cancer biology. Although 25–30% of cases have a hereditary component, only 5–10% involve germline mutations, with BRCA1/2 conferring over a fourfold increase in lifetime risk and raising cumulative risk to nearly 80%3,4. Beyond genetic susceptibility, BRCA1/2-associated tumors show marked genomic instability, structural DNA alterations, and global hypomethylation, distinguishing them from sporadic forms5. BRCA1 tumors are typically triple-negative, poorly differentiated, and highly proliferative, whereas BRCA2 tumors more often display luminal characteristics and endocrine responsiveness, though some may behave aggressively6–9. These molecular and phenotypic distinctions underscore the need for region-specific studies, as the frequency and expression of BRCA mutations vary considerably among populations.
Despite extensive international research, data on the prevalence and clinicopathological characteristics of BRCA1/2 mutations in Central Asia, including Kazakhstan, remain scarce. A systematic review comprising 70 studies and 17,872 cases reported that BRCA1/2 mutation frequencies varied widely - from 1.8% to 36.9% - depending on geography, inclusion criteria, and molecular subtype10. For instance, in Japan, BRCA1/2 mutations were identified in 20.0% of triple-negative BC cases, increasing to 41.4% among those with a positive family history11. In Turkey, BRCA1 and BRCA2 mutations were detected in 7.8% and 5.4% of patients, respectively, with significantly earlier onset of disease among mutation carriers (39.7 and 41.1 vs. 43.2 years; p < 0.001), particularly in the triple-negative subgroup12. However, no systematic studies have been conducted in Kazakhstan to evaluate the relationship between BRCA status, age at onset, tumor stage, molecular and morphological patterns, hormonal profiles, metastatic patterns, and survival outcomes.
International evidence suggests that BRCA1 mutations are generally associated with more aggressive disease, early metastatic spread, and poorer survival outcomes13,14. Conversely, BRCA2 mutations are more frequent in hormone receptor–positive subtypes, yet may also contribute to unfavorable prognoses under certain conditions15. Moreover, BRCA-deficient tumors demonstrate heightened sensitivity to DNA-damaging agents, including PARP inhibitors and platinum-based chemotherapy, but may exhibit resistance to endocrine therapy in some HR⁺ cases16. These biological distinctions emphasize the importance of studying BRCA-associated breast cancer within diverse populations, as genetic background and environmental factors may substantially influence mutation prevalence and clinical manifestations.
Consistent with these biological observations, findings from the large multicenter ESME cohort (2008–2016, n = 20,624) revealed that the prognostic impact of BRCA1/2 mutations varies by molecular subtype. In the triple-negative subgroup, BRCA mutations were associated with improved survival outcomes (OS: HR = 0.76; PFS: HR = 0.69), whereas among HR+/HER2- patients, decreased progression-free survival (HR = 1.23; p = 0.024) and a trend toward reduced overall survival were observed17. These results further highlight the heterogeneity of BRCA-associated breast cancers and underscore the need for molecularly guided, personalized therapeutic approaches.
Comprehensive characterization of BRCA-associated breast cancer in Kazakhstan is essential to address existing knowledge gaps. Defining the prevalence and spectrum of BRCA1/2 mutations will enable the identification of high-risk women and improve precision screening and management. Analysis of clinicopathological and molecular features will refine prognostic markers and inform therapeutic strategies, including PARP inhibitors, platinum agents, and targeted combinations. This first large-scale study aims to elucidate the genetic and clinical landscape of BRCA-associated BC in Kazakhstan, advancing personalized oncology and contributing regional data to global research on hereditary breast cancer.

Materials and methods

Patients
Between December 2023 and June 2024, 186 patients aged 21 to 90 years were referred to OLYMP, Kazakhstan’s largest molecular diagnostic laboratory, for germline whole-genome sequencing. This was a single-center ambispective observational cohort study. The cohort did not represent an unselected consecutive series; only patients diagnosed and treated at the Astana Multidisciplinary Medical Center who met the National Comprehensive Cancer Network (NCCN) Genetic/Familial High-Risk Assessment: Breast and Ovarian Guidelines (version 2022)18 were eligible. Eligibility criteria included age at diagnosis, tumor subtype (including triple-negative breast cancer), sex, personal and/or family history of breast, ovarian, pancreatic, or aggressive prostate cancer, and the presence of known pathogenic variants in relatives.
Given the high cost and limited availability of germline whole genome sequencing in Kazakhstan, the study intentionally included both early-stage and metastatic breast cancer patients who met high-risk criteria. Early-stage cases were included to allow comparative assessment of clinical behavior and disease aggressiveness associated with BRCA1/2 pathogenic variants, while metastatic cases were included at the time of progression to evaluate outcomes and therapy response. Patients with early-stage and metastatic breast cancer were analyzed separately due to differences in clinical course, treatment strategies, and outcome measures.
The study cohort also included patients whose primary breast cancer diagnosis had been established more than five years before the onset of metastatic disease and who had been under longitudinal follow-up during remission. Pathogenic variants in BRCA1 or BRCA2 were identified in 58 patients. Demographic data, family cancer history, treatment types, and tumor histopathology were collected through retrospective chart review and patient interviews, while clinical outcomes and treatment data from the time of metastatic progression were collected prospectively. All patients included in the study were managed in strict accordance with the standardized national breast cancer treatment protocols of the Republic of Kazakhstan, with therapeutic interventions determined according to disease stage and individual clinical characteristics, ensuring comprehensive adherence to national guidelines19.
Patients were classified according to disease setting as having early breast cancer (non-metastatic disease at diagnosis) or metastatic breast cancer (presence of distant metastases) (Fig. 1). A patient selection flowchart is provided to illustrate eligibility criteria, cohort composition, and subgroup stratification. Patients will continue to be followed longitudinally to capture subsequent disease progression and outcomes.

Potential ethical concerns
The study was reviewed and approved by the Ethics Committee before initiation. Approval was granted by the Local Ethics Committee of Kazakhstan’s Astana Multidisciplinary Medical Center (Protocol No: IRB-A14, dated 15/06/2023). All procedures were conducted in accordance with relevant guidelines and regulatory standards. Written informed consent was obtained from all participants after they were fully informed about the study’s purpose, procedures, and their right to withdraw at any time. Confidentiality and anonymity were ensured throughout the study, in full compliance with bioethical principles and international research guidelines.

Immunohistochemical profile: Estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki-67
The expression levels of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki-67 were determined from pathology reports. Negativity for ER and PR was defined as immunohistochemical (IHC) staining in less than 1% of tumor cells. HER2 status was evaluated by IHC using a three-point scale: +1 indicated negativity, + 3 indicated positivity, and 2 + required confirmation of gene amplification by fluorescence in situ hybridization (FISH). Ki-67 status was assessed by IHC and reported as the percentage of positive tumor cell nuclei. Triple-negative breast cancer (TNBC) was characterized by the absence of ER and PR expression and a negative HER2 status.

Detection of mutations in the BRCA1/2 genes by next generation sequencing (NGS)
Identification of BRCA1/2 gene alterations was performed exclusively using NGS. NGS is a high-throughput, highly sensitive, and specific molecular technique. It enables comprehensive detection of sequence variants across the entire coding region of the gene. For NGS, genomic DNA was extracted from peripheral venous blood samples using standardized, commercially available reagent kits. Extraction followed the manufacturer’s recommendations. The amplified libraries were evaluated qualitatively and quantitatively. Library preparation used the “Quasar-BRCA1/2” reagent kit (TestGen, Russia; TU 21.20.23–038.23-97638376-2020) and followed validated laboratory protocols. Sequencing was performed on the Illumina MiSeq platform (Illumina, USA). The mean sequencing depth exceeded 50×. This ensured reliable identification of heterozygous and homozygous variants with high analytical accuracy. Variant annotation and interpretation followed the ACMG guidelines for sequence variant classification20.

Statistical analysis
Survival endpoints were defined as follows: overall survival (OS) - the time from breast cancer diagnosis to death or last follow-up; disease-free survival (DFS) - the interval from complete remission or completion of primary treatment to the first documented recurrence; and progression-free survival (PFS) - the time from the initiation of systemic therapy to disease progression or death, whichever occurred first. Patients alive at the end of observation were censored at their last contact. Survival distributions were estimated using the Kaplan–Meier method. Intergroup differences were assessed with the log-rank test.
Comparative analyses of clinical and tumor characteristics used the Pearson χ² test. Fisher’s exact test was applied when expected cell frequencies were < 5. Continuous variables were analyzed with the non-parametric Mann-Whitney U test. All statistical analyses were performed using SPSS Statistics version 28.0 (IBM) and SAS software version 9.3 (SAS Institute). Statistical significance was a two-sided p-value < 0.05.

Results

Patient characteristics and BRCA status
Among 186 patients with breast cancer, 58 carried pathogenic or likely pathogenic germline BRCA1/2 variants (41 BRCA1, 17 BRCA2), while 128 patients had no clinically significant alterations. The median age was 51 years (range: 46–62) in BRCA-negative patients, 44 years40–46 in BRCA1-positive patients, and 48 years (43–54) in BRCA2-positive patients. Overall, 22% of patients were BRCA1 carriers and 9% were BRCA2 carriers.

Disease stage and pathological characteristics
Stage distribution differed significantly between BRCA subgroups (p < 0.001). In the BRCA-negative group, most patients presented with stage II or III disease (n = 60 and 44, respectively). In contrast, stage III and IV disease predominated in BRCA1-positive patients (n = 17 and 10, respectively), whereas BRCA2-positive patients had no stage I cases and primarily stage III or IV disease. Tumor size and lymphovascular invasion did not differ significantly among groups, while axillary lymph node involvement was observed in 61% of BRCA-negative, 46% of BRCA1-positive, and 71% of BRCA2-positive patients (Table 1).

Metastatic patterns
Distant metastases varied significantly across subgroups (p = 0.001). Among BRCA-negative patients, 69 (54%) had no metastases, compared with 32% in the BRCA1-positive group and 6% in the BRCA2-positive group. Lung metastases were more frequent in BRCA1-positive patients, while multiple organ involvement was most common in BRCA2-positive patients. Concurrent breast and ovarian cancers were observed predominantly in BRCA1-positive cases (Table 1).

Family history
A family history of breast cancer was identified in 77 BRCA-negative, 6 BRCA1-positive, and 3 BRCA2-positive patients. A family history of ovarian cancer was observed in 51, 1, and 6 patients, respectively. Multiple affected relatives were documented exclusively among BRCA-positive patients (n = 34 BRCA1, n = 8 BRCA2) and were absent in the BRCA-negative cohort (Table 1).

Tumor grade, histological subtype, proliferation, and receptor status
Tumor grade differed significantly between BRCA subgroups (p = 0.002): moderately differentiated tumors (G2) predominated in BRCA-negative patients (45%), whereas poorly differentiated tumors (G3) were more frequent in BRCA1 (61%) and BRCA2 (53%) carriers. Histological subtype distribution did not differ by BRCA status (p = 0.926). Invasive ductal carcinoma predominated in all groups (BRCA-negative: 108/128, 84%; BRCA1-positive: 35/41, 86%; BRCA2-positive: 14/17, 82%), followed by invasive lobular carcinoma (13/128, 10%; 5/41, 12%; 2/17, 12%, respectively). Mixed histology was rare (7/128, 6%; 1/41, 2%; 1/17, 6%). The median Ki-67 index was 40% (IQR 20–55), higher in BRCA1 carriers than in non-carriers (63% vs. 16%, p = 0.001). BRCA1-associated tumors showed higher proliferative activity than BRCA2-associated tumors, with median Ki-67 values of 75% and 55%, respectively. Among BRCA-negative patients, 80% were ER-positive, 79% PR-positive, and 22% HER2-positive. In the BRCA2 subgroup, 65% of tumors were ER/PR-positive, and HER2 positivity was detected in 18% of cases (n = 3). In contrast, only 12% of BRCA1 carriers expressed ER/PR, and none expressed HER2. Consequently, triple-negative tumors were more frequent in BRCA1 than in BRCA2 (88% vs. 29%) and BRCA-negative groups (88% vs. 12%; p = 0.001) (Table 2).

BRCA1/2 variant spectrum
A total of 22 pathogenic or likely pathogenic variants were identified in the BRCA1 and BRCA2 genes, with 11 variants detected in each gene. In BRCA1 (transcript NM_007294.4), the majority were loss-of-function alterations, including frameshift, nonsense, and splice-site variants, predominantly located in exons 10, 12, 21, and 23. The most frequent variant was c.5381_5382insC (p.Glu1794Aspfs36) in exon 21 (n = 12). Other recurrent variants included c.981_982del (p.Cys328), c.3214del (p.Leu1072), and c.5470_5477del (p.Ile1824Aspfs3), while the splice-site variant c.5277 + 1G > A was observed in three cases. In BRCA2 (transcript NM_000059.4), most alterations were predicted to result in protein truncation or aberrant splicing, distributed mainly across exons 11, 16, and 24. Loss of exon 16 was detected in six patients, and recurrent frameshift variants included c.2600_2601insA (p.Thr868Tyrfs13) and c.9241_9242insA (p.Val3081Aspfs*30). Several splice-site variants occurred in single cases, and one missense variant, c.631G > A (p.Val211Ile), was classified as likely pathogenic. Notably, three patients carried two pathogenic BRCA2 variants each (Patient 1: c.631G > A and c.7008–2 A > T; Patient 2: c.2557 C > T and c.517-1G > A; Patient 3: c.3860del and c.2600_2601insA). In all three cases, the variants were germline, and it is likely that both variants in each patient are located on the same allele, as both variants in each pair are classified as pathogenic according to ACMG. Compound heterozygosity affecting both BRCA2 alleles would be incompatible with embryonic viability (Table 3).

Treatment patterns
Treatment differed significantly according to BRCA status and tumor subtype (p = 0.001). CDK4/6 inhibitors were administered exclusively in the metastatic HR + setting: BRCA-negative (n = 34), BRCA2-positive (n = 10), and BRCA1-positive (n = 1). PARP inhibitors were administered exclusively to patients with germline BRCA mutations, including BRCA1-positive (n = 15) and BRCA2-positive (n = 2) cases. Among these patients, PARP inhibitors were used in both early-stage (n = 6) and metastatic (n = 9) disease settings. Neoadjuvant chemotherapy was administered mainly to triple-negative patients, including 15 early-stage BRCA-negative and 2 metastatic BRCA-negative patients. Chemoimmunotherapy was administered to patients with triple-negative breast cancer in both early and metastatic disease settings. In the early-stage breast cancer group, chemoimmunotherapy was provided to 12 BRCA-negative, 4 BRCA1-positive, and 1 BRCA2-positive patients. In the metastatic setting, chemoimmunotherapy was administered to 5 BRCA-negative, 14 BRCA1-positive, and 2 BRCA2-positive patients. HER2-targeted therapy plus chemotherapy was mostly delivered to HER2-positive BRCA-negative patients (n = 28) and a few BRCA2-positive metastatic patients (n = 2). Adjuvant chemotherapy without neoadjuvant treatment was given to 22 BRCA-negative patients. (Table 4) (Supplementary Table 1). The median follow-up time for the entire cohort was 24 months (range 24–72).

Survival outcomes
Among 103 metastatic breast cancer patients, median progression-free survival (PFS) for the metastatic cohort differed significantly by BRCA status (log-rank test, p = 0.001): BRCA-negative (n = 59) 34 months (95% CI, 29–38), BRCA1-positive (n = 28) 12 months (95% CI, 10–14), and BRCA2-positive (n = 16) 8 months (95% CI, 6–10) (Fig. 2). Overall survival (OS) differed significantly: no deaths occurred in BRCA-negative metastatic patients; mortality was observed in 3/28 (10%) BRCA1-positive and 7/16 (44%) BRCA2-positive patients (log-rank test, p = 0.001). In pairwise log-rank analyses among metastatic patients, no statistically significant difference in PFS was observed between BRCA1 and BRCA2 carriers (p = 0.158), while OS differed significantly, with poorer survival in the BRCA2 subgroup (p = 0.001). Overall, carriers of germline BRCA1/2 mutations demonstrated an unfavorable survival profile compared with expectations for unselected metastatic populations; however, these findings should be considered hypothesis-generating and require confirmation in larger, well-powered cohorts (Fig. 2).

In triple-negative metastatic patients (n = 33), median PFS was 35 months (95% CI, 25–45) for BRCA-negative (n = 9) and 14 months (95% CI, 11–17) for BRCA1-positive patients (n = 24) (Fig. 3). In HR + metastatic patients treated with CDK4/6 inhibitors (n = 43), median PFS was 40 months (95% CI, 36–44) in BRCA-negative (n = 33) and 9 months (95% CI, 6–11) in BRCA2-positive patients (n = 10) (Fig. 3).

Discussion

Mutational and clinical profile of BRCA-associated breast cancer
Analysis of the mutational profile of breast cancer indicates that abnormalities in DNA repair genes, particularly BRCA1 and BRCA2 mutations, are critical in the development of aggressive tumor phenotypes and are linked to reduced survival21. This research represents the first systematic analysis of BRCA-associated breast cancer in Kazakhstan, assessing molecular, morphological, and clinical characteristics, as well as survival differences by BRCA status and treatment modality. The findings underscore the importance of investigating BRCA-associated breast cancer within the local population to improve prognosis and guide personalized therapeutic strategies.
Among the Kazakhstani cohort, patients with BRCA1 and BRCA2 mutations exhibited a significantly lower median age at breast cancer onset compared to those with wild-type BRCA, with median ages of 44 years (IQR: 41–48) and 48 years (IQR: 43–54), respectively, versus 51 years (IQR: 46–62) (p = 0.001). Additionally, 22% of patients harbored pathogenic variants in BRCA1, and 9% harbored pathogenic variants in BRCA2 (Table 1). This finding indicates that BRCA-associated breast cancers develop at a younger age, consistent with multicenter studies from Greece and Japan, highlighting the need for early detection and monitoring in the Kazakhstani population22,23. Prospective studies demonstrate that BRCA1/2 mutation carriers develop breast cancer at a younger age. One cohort reported a median age of 38 years (IQR 30–46) among carriers24. While another found the highest risk in BRCA1 carriers under 35 years, decreasing with age25. Similarly, BRCA1/2 mutations were detected in 15.1% of Moroccan women diagnosed at ≤ 40 years26. Together, these findings confirm that BRCA-associated breast cancers predominantly arise at a young age, underscoring the importance of early genetic testing, personalized surveillance, and targeted prevention.
Significant differences in disease stage were observed across BRCA subgroups (p < 0.001). Stages II–III predominated in BRCA-negative cases, whereas stages III–IV were more common in BRCA1-positive tumors; stage I was absent among BRCA2 carriers, who mainly presented with stages III–IV (Table 1). These patterns suggest the aggressive nature of BRCA1-associated disease and highlight the need for earlier detection in the Kazakhstani population. Similar findings were reported in a Korean cohort, where the frequency of BRCA1/2 mutations was lower in stage I than in stage 0 and higher in stage II27. Most tumors were under 2 cm, with no significant differences in size or lymphovascular invasion among BRCA subgroups (p = 0.147). Axillary lymph node involvement was more frequent in BRCA-negative (61%) and BRCA2-positive (71%) patients than in BRCA1-positive cases (46%), suggesting distinct invasion patterns (Table 1). The overall high rate of lymphovascular invasion supports the aggressive profile of BRCA-related cancers in the Kazakhstani population, consistent with van Barele et al. (2022), who reported increased nodal involvement and reduced 10-year survival with larger tumors28.
The identification of recurrent BRCA1/2 pathogenic variants in our cohort is notable from a population genetics perspective. Notably, the BRCA1 c.5266dupC (5382insC) variant, the most frequently observed alteration, is a known founder mutation in several Eastern European populations, including Poland29, suggesting possible shared ancestral origins or regional mutation patterns. However, our study was not designed to formally assess founder effects. These variants are therefore reported as recurrent pathogenic alterations rather than confirmed founder mutations. Future large-scale studies incorporating haplotype analysis and representative population controls will be necessary to clarify founder contributions in Kazakhstan (Table 3).
Metastatic patterns differed across BRCA subgroups. Absence of metastases was observed in 54% of BRCA-negative, 32% of BRCA1, and 6% of BRCA2 carriers (p = 0.001). BRCA1 tumors more often spread to the lungs and distant lymph nodes, whereas BRCA2 tumors showed multiple bone and multi-organ metastases (Table 1). Similar trends have been reported previously, with predominant lung and nodal metastases in BRCA1 and bone involvement in BRCA2 and BRCA-negative cases (p = 0.010)30. Multiple primary cancers, mainly breast–ovarian combinations, were frequent among BRCA1 carriers31. Moreover, a meta-analysis found higher mean OncotypeDX scores in BRCA-mutated versus sporadic cases (25 vs. 18.4; p < 0.001), indicating a more aggressive molecular phenotype32. These findings emphasize the need for early risk stratification and population-specific research in Kazakhstan.
The pathological profile showed notable differences between subgroups. Moderately differentiated tumors (G2, 45%) were more common in the BRCA-negative group, while poorly differentiated tumors (G3, 61% and 53%; p = 0.002) were more frequent in the BRCA-positive group (Table 2). A retrospective study by Krammer et al. (2017) reported similar findings, with most BRCA1-associated tumors classified as G3 and having a higher histological grade than BRCA2 (p < 0.001)33. The median Ki-67 proliferation index was 40% (IQR: 20–55) and was significantly higher in BRCA1-positive patients compared to BRCA-negative patients (63% vs. 16%, p = 0.001), indicating increased cellular proliferation and more aggressive tumor behavior. Furthermore, BRCA1-associated tumors exhibited higher proliferative activity than BRCA2-associated tumors, with median Ki-67 values of 75% and 55%, respectively (Table 2), supporting the association of BRCA1 mutations with a more aggressive tumor phenotype34.
In the Kazakhstani population, BRCA1-associated tumors were predominantly triple-negative (88%), compared with 29% of BRCA2 and 12% of BRCA-negative cases (p = 0.001) (Table 2), reflecting disrupted hormonal signaling and endocrine resistance. Owing to defects in homologous recombination, these tumors remain sensitive to platinum-based agents and PARP inhibitors35. In our cohort, 88% of BRCA1-positive patients had triple-negative tumors, compared to 29% of BRCA2 carriers and 12% of BRCA-negative patients (p = 0.001) (Table 2).
Similar findings were reported in a Japanese cohort, where 75.8% of BRCA1-associated tumors were triple-negative36. BRCA2-associated tumors showed hormone receptor positivity (ER/PR, 65%; p = 0.001), moderate differentiation, and a low Ki-67 index, consistent with luminal phenotypes and favorable clinical behavior. Guzmán-Arocho et al. (2022) reported comparable results, with 32.9% luminal A-like and 55.3% luminal B-like BRCA2-positive tumors37. In our sample, 65% of BRCA2-positive patients were ER- and PR-positive (p = 0.001) (Table 2). Despite these features, BRCA2 carriers in our cohort exhibited a trend toward shorter progression-free and overall survival, underscoring the need for tailored therapeutic approaches in the Kazakhstani population; however, this observation should be interpreted with caution and requires confirmation in larger, well-powered cohorts.
In Poland, systematic BRCA1/2 screening has been implemented over the past two decades, with a focus on three founder mutations (5382insC, C61G, and 4153delA). This program, conducted at the Pomeranian Medical University in collaboration with the Women’s College Research Institute, University of Toronto, has enrolled thousands of carriers and provided robust prospective data on hereditary breast and ovarian cancer29. The experience demonstrates how population-specific genetic programs can facilitate early detection and preventive strategies, offering a model that may inform the development of similar initiatives in other countries, including multiethnic populations like Kazakhstan.
Our analysis revealed distinct molecular and clinical features of BRCA-associated breast cancer, marked by earlier onset, poor differentiation, triple-negative phenotype, high proliferative activity, and frequent visceral metastases, indicating a more aggressive course than sporadic cases. These findings emphasize the role of DNA repair defects in reduced survival and highlight the need for early molecular testing and personalized treatment in Kazakhstan.

Molecular heterogeneity and prognostic significance of BRCA mutations in different subtypes of breast cancer
In the overall survival analysis, statistically significant differences were observed between BRCA2-positive patients and both BRCA1-positive and BRCA-negative groups, with BRCA2 carriers demonstrating inferior outcomes. In contrast, no statistically significant difference in overall survival was detected between BRCA1-positive and BRCA-negative patients (log-rank p = 0.40). Notably, a numerically more favorable survival trend was observed in the BRCA1-positive subgroup compared with BRCA2-positive patients. Given the limited sample size and the number of observed events, these findings should be considered hypothesis-generating. Further studies in larger, independent cohorts with sufficient statistical power are required to clarify potential differences in overall survival between BRCA1-positive and BRCA-negative patients and to confirm the observed survival gradient across BRCA subgroups.
The prognostic value of germline BRCA mutations in breast cancer remains controversial. Among metastatic patients, BRCA1 carriers exhibited a median progression-free survival (PFS) of 12 months, while BRCA2 carriers had a shorter PFS of 8 months, compared with 34 months in BRCA-negative patients. Overall survival (OS) was markedly reduced in BRCA2-positive patients, whereas no deaths were observed in BRCA-negative metastatic patients (p = 0.001) (Fig. 2). These findings contrast with the prospective POSH study (Copson et al., 2018), which reported no survival difference between BRCA-positive and BRCA-negative patients (HR = 0.96; 95% CI: 0.76–1.22; p = 0.76)38. While Schmidt et al. (2017) observed worse early survival in BRCA1 and later in BRCA2 carriers39, our data indicate earlier progression and poorer outcomes in BRCA2-associated tumors, likely reflecting population-specific factors, tumor biology, and access to modern therapy.
These findings are partly consistent with Liu et al. (2021), who analyzed 30 studies including 35,972 patients (mean age 45.6 years) and reported reduced OS in BRCA1 carriers (HR = 1.20; 95% CI: 1.08–1.33; p < 0.001), lower PFS (HR = 1.35; 95% CI: 1.10–1.67; p = 0.0049), and decreased breast cancer–specific survival in BRCA2 carriers (HR = 1.46; 95% CI: 1.26–1.70; p < 0.0001). In triple-negative breast cancer, BRCA1 mutations further worsened PFS (HR = 1.65; 95% CI: 1.08–2.54; p = 0.0216)21. Similarly, Feszak et al. (2025) showed that the prognostic effect of BRCA mutations varies by tumor subtype, with BRCA1/2 carriers with DCIS demonstrating favorable outcomes over 110 months. Consistent with these observations, in our cohort of triple-negative metastatic breast cancer patients, BRCA1-positive individuals exhibited shorter PFS compared with BRCA-negative patients. Although limited by small sample size, these findings support the notion that BRCA1-associated triple-negative tumors display more aggressive clinical behavior (Fig. 3). Together, these data highlight the biological heterogeneity of BRCA-associated tumors and suggest that poorer PFS and OS in BRCA2 carriers may reflect more aggressive invasive disease or therapy response differences40.
This study, among the first in Kazakhstan, evaluated the impact of BRCA status on survival in metastatic breast cancer, accounting for hormonal profiles. BRCA-associated tumors, particularly BRCA2-mutated, exhibited more aggressive behavior, possibly reflecting population-specific and biological factors. Among metastatic HR⁺ breast cancer patients, our results showed significant variation by BRCA status: BRCA-negative patients had the longest PFS (median: 40 months; p = 0.001), whereas BRCA2 carriers progressed earlier (median: 9 months), likely due to impaired DNA repair and reduced endocrine sensitivity, despite receiving CDK4/6 inhibitors (Fig. 4). Similarly, a meta-analysis of 22 studies (n = 34,960) found poorer relapse-free (HR = 1.64; 95% CI: 1.00–2.69; p = 0.05) and overall survival (HR = 1.52; 95% CI: 1.20–1.92; p = 0.0006) in HR-positive patients with BRCA mutations. These data align with Azim et al. (2025), who linked RB1 loss of heterozygosity in BRCA2-positive tumors to endocrine and CDK4/6 inhibitor resistance41.
In recent studies, both BRCA mutation type and tumor hormonal status have been shown to influence breast cancer outcomes. Lambertini et al. (2021) (n = 1236) reported that BRCA1 carriers more often developed HR-negative tumors and second malignancies, while BRCA2 mutations were associated with poorer relapse-free survival (adjusted HR = 0.76; 95% CI: 0.60–0.96)42. Similarly, our data revealed worse prognosis among HR⁺ BRCA2 carriers (p = 0.001). Vocka et al. (2019) found that HR⁺ patients with BRCA mutations had higher recurrence (38.3% vs. 16.6%; p < 0.001) and mortality (21.7% vs. 6.3%; p < 0.001), confirming the aggressive behavior of hormone-dependent subtypes43.
Consistent with these findings, a real-world observational analysis from the French ESME metastatic breast cancer platform evaluated the prognostic impact of germline BRCA1/2 mutations specifically in HR+/HER2- metastatic breast cancer. Among 13,776 patients, 170 were germline BRCA1/2 mutations (gBRCAm) carriers, 676 had BRCA wild-type tumors, and 12,930 were untested. Multivariable time-dependent analyses demonstrated inferior overall survival in gBRCAm carriers compared with BRCA wild-type patients (adjusted HR 1.26; 95% CI: 1.03–1.55). In the subgroup receiving frontline endocrine therapy, gBRCAm status was associated with significantly worse overall survival (adjusted HR 1.54; 95% CI: 1.03–2.32) and first-line progression-free survival (adjusted HR 1.58; 95% CI: 1.17–2.12). These data corroborate the detrimental prognostic impact of BRCA mutations in HR+ metastatic disease and underscore the need for genotype-guided therapeutic strategies44.
In our cohort, metastases were more frequent in BRCA1/2 carriers (p = 0.001): BRCA1 was associated with lung and genital tract involvement, whereas BRCA2 was associated with multi-organ spread. The ESME study (Mailliez et al., 2023) similarly reported increased visceral metastases and a more aggressive course in BRCA-positive patients, with shorter OS but no independent prognostic effect. Notably, TNBC patients with BRCA mutations had better OS and PFS1, while HR⁺/HER2⁻ carriers had worse outcomes17, highlighting the prognostic relevance of molecular subtype and metastatic pattern.
Our study in a Kazakhstani cohort demonstrates that population-specific and molecular factors influence the prognostic impact of BRCA mutations in HR⁺ breast cancer. The reduced PFS and OS observed in BRCA2 carriers may reflect genetic heterogeneity and differences in treatment. These findings highlight the need for routine BRCA testing in HR⁺ metastatic breast cancer and support personalized therapeutic strategies integrating endocrine therapy, CDK4/6, and PARP inhibitors.

Impact of BRCA1 and BRCA2 mutations on clinical outcomes and therapeutic effectiveness
The study revealed distinct clinical and therapeutic differences between BRCA1 and BRCA2 mutation carriers, reflecting the biological heterogeneity of BRCA-associated breast cancer. Nowadays, BRCA-positive patients are preferentially treated with PARP inhibitors, reflecting enhanced sensitivity of BRCA-deficient tumors to DNA-damaging agents45. Among our cohort, PARP inhibitors were administered in both early-stage (n = 6) and metastatic (n = 9) settings. Neoadjuvant chemotherapy was mainly given to triple-negative patients (15 early-stage and 2 metastatic BRCA-negative); however, due to the small cohort size, survival outcomes could not be reliably assessed (Supplementary Table 1). Given the small number of HER2-positive cases among BRCA-positive patients, particularly the absence of BRCA1/HER2-positive tumors, treatment-specific prognostic conclusions, including response to neoadjuvant chemotherapy and anti-HER2 therapy, could not be sufficiently evaluated and require validation in larger cohorts. Phase III trials demonstrated the superiority of PARP inhibitors over standard chemotherapy in BRCA-mutated, HER2-negative metastatic breast cancer. Olaparib improved median progression-free survival (7.0 vs. 4.2 months; HR = 0.58; p < 0.001) and response rate (59.9% vs. 28.8%), while talazoparib showed similar benefits (8.6 vs. 5.6 months; HR = 0.54; p < 0.001; responses 62.6% vs. 27.2%), with both agents offering better tolerability46.
In the triple-negative subgroup, progression-free survival significantly differed by BRCA status (Log-rank test, p = 0.001) (Fig. 3): BRCA-negative patients (n = 9) had a median PFS > 30 months, whereas BRCA1 (n = 24) carriers showed accelerated progression within 10–15 months. These findings are consistent with those of Copson et al. (2018) and support the enhanced short-term responsiveness of BRCA-mutated TNBC to DNA-damaging and platinum-based therapies38.

BRCA-positive patients in our cohort received targeted therapies reflecting tumor biology, including PARP inhibitors in early-stage (n = 6) and metastatic (n = 9) settings, as well as chemoimmunotherapy for triple-negative disease. Neoadjuvant chemoimmunotherapy was given to 15 early-stage and 2 metastatic BRCA-negative patients, and to BRCA1/2 carriers in both settings; however, survival outcomes could not be reliably assessed due to the small cohort size (Supplementary Table 1). Although the small cohort size precluded reliable assessment of survival outcomes, these treatment patterns align with previous evidence demonstrating the benefit of combining immunotherapy with chemotherapy. For instance, Schmid et al. (2020) reported that adding pembrolizumab to neoadjuvant chemotherapy in early TNBC improved pathological complete response (64.8% vs. 51.2%; p < 0.001) and reduced the risk of progression or death (HR = 0.63; 95% CI: 0.43–0.93), highlighting the potential synergistic interaction between immunotherapy and DNA repair-targeted strategies47. PARP inhibitors demonstrate strong antitumor potential in this group and warrant further study to define their optimal integration into treatment48.
Patients with BRCA-negative status receiving CDK4/6 inhibitors had a markedly longer progression-free interval during the first 40 months compared with BRCA-mutated patients with metastatic breast cancer. This observation aligns with findings from a meta-analysis including 618 gBRCAm patients with HR+/HER2 − metastatic breast cancer, in which gBRCAm status was consistently associated with inferior outcomes on CDK4/6 inhibitors. Specifically, gBRCAm carriers experienced significantly shorter PFS (HR 1.68; 95% CI 1.37–2.05) and OS (HR 1.73; 95% CI 1.12–2.67) compared with gBRCAwt patients. Collectively, these data suggest a clinically meaningful reduction in CDK4/6 inhibitor efficacy in gBRCAm tumors, possibly related to dysregulated DNA damage response pathways and altered cell-cycle control49.
Our findings demonstrate that BRCA1/2 mutations shape tumor biology and treatment response, emphasizing the need for genotype-guided therapy. In the Kazakhstani population, which is multiethnic, BRCA2-positive patients exhibited a more aggressive disease course, likely reflecting molecular and population-specific differences. Due to the high cost of genetic testing and limited resources, the study included all eligible patients rather than a homogeneous cohort, providing a realistic representation of clinical practice. Consistent with global evidence, these results support routine BRCA testing for HR + and TNBC subtypes and the implementation of personalized regimens integrating PARP inhibitors, selective CDK4/6 blockade, and immunotherapy. As the first comprehensive analysis of BRCA-associated breast cancer in Kazakhstan, this study highlights disparities in access to genetic testing and targeted therapies, particularly in rural regions. Strengthening national programs for genetic counseling and expanding access to precision treatments are essential to improving survival outcomes and ensuring equitable cancer care.

Conclusion
In conclusion, our findings emphasize the clinical and prognostic importance of germline BRCA testing in breast cancer management. BRCA1-positive tumors were characterized by earlier onset, high-grade histology, elevated proliferative activity, and a predominance of triple-negative subtypes, underscoring the need for tailored therapeutic strategies. BRCA2-associated cancers, although frequently hormone receptor–positive, presented with advanced disease and inferior survival, indicating the potential benefit of early systemic interventions and inclusion in trials evaluating novel targeted therapies. The observed patterns confirm the biological heterogeneity of BRCA-driven breast cancer and align with international data, suggesting the absence of major region-specific modifier genes. These results highlight the value of integrating molecular diagnostics into clinical practice to identify high-risk patients for genotype-guided interventions, including PARP inhibitors, and support the implementation of nationwide genetic screening and counseling programs. Overall, personalized treatment strategies that account for genetic background, tumor characteristics, and healthcare system factors are crucial for improving outcomes and advancing precision oncology in Kazakhstan.

Limitations
The ambispective design and the relatively small, single-center cohort may limit the generalizability of the findings. Also, the study was not designed to assess founder effects, and the absence of haplotype analysis or population-based reference data limits interpretation of recurrent variants in the Kazakhstani population. Data on subsequent lines of therapy, including novel targeted agents and participation in clinical trials, were incomplete. Additionally, the lack of comprehensive genomic profiling beyond BRCA1/2 mutations limits our ability to fully characterize co-occurring mutations that may influence prognosis and therapy response. The restricted availability and high cost of BRCA testing further constrained broader genetic screening, and both metastatic and non-metastatic patients were analyzed together due to time limitations. Finally, follow-up duration varied across patients, potentially affecting long-term survival estimates.

Future directions
Future research should focus on multicenter prospective studies to validate these findings and assess long-term outcomes. Expanding genomic profiling beyond BRCA1/2 to include other homologous recombination repair genes may improve risk stratification and treatment selection. Clinical trials evaluating the efficacy and safety of PARP inhibitors, CDK4/6 inhibitors, and immunotherapy in young BRCA1/2 carriers are urgently needed in Kazakhstan. Integration of regional genetic data with treatment response and survival outcomes will enable the development of personalized, evidence-based protocols tailored to the Central Asian population.

Supplementary Information
Below is the link to the electronic supplementary material.