Identifying a Recurrent BRCA1 Variant in the Qatari Population With Unique Genotype-Phenotype Correlations.

1
Introduction
Hereditary breast and ovarian cancer syndrome (HBOC) is a cancer predisposing syndrome caused by pathogenic variants in the BRCA1 and BRCA2 genes. It is associated with an increased risk for female breast and ovarian cancers and male breast and prostate cancers (Bujassoum et al. 2013). BRCA1 and BRCA2 pathogenic variants are associated with a lifetime risk of breast cancer that can reach up to 65% for BRCA1 versus 45% for BRCA2, ovarian, and prostate cancer (Lee et al. 2020).
HBOC is considered the most common cause of hereditary breast and ovarian cancers, with variable prevalence across different populations. It is well known that certain ethnic groups have a higher risk of carrying BRCA pathogenic variants than others due to founder variants (Ossa and Torres 2016). Founders are observed in minor isolated groups of individuals who have inbred, resulting in recurrent variants passing through several generations, leading to a founder effect in such populations (Ikolo et al. 2023).
The most well‐known example of founder effect in the BRCA genes is the three founder variants observed in the Ashkenazi Jews (AJ) ethnic groups/population. About 1 in 40 individuals of Ashkenazi Jewish ancestry harbor one of the three most three common founder variants: the c.68_69del p.Glu23fs and c.5266dup p.(Val1756fs), both in BRCA1 and c.5946del p.(Ser1982fs) in BRCA2 (Greenberg et al. 2023). Significant genotype–phenotype correlations were observed among these three founder variants (Greenberg et al. 2023). Women who carry the BRCA1 c.68_69del and BRCA1 c.5266dup variants have a lifetime risk of breast cancer ranging from 64% to 67%; on the other hand, carriers of the BRCA2 c.5946del variant have a lower lifetime risk for breast cancer, which can reach up to 43%. The lifetime risk of ovarian cancer associated with BRCA1 c.68_69del, BRCA1 c.5266dup, and BRCA2 c.5946del is 14%, 33%, and 20%, respectively (Greenberg et al. 2023).
In the Middle East and specifically in Qatar, no previous studies have identified any recurrent variants or possible founder variants in either BRCA1 or BRCA2 genes among the Qatari population. However, it has been observed that HBOC is the most common cancer syndrome identified in Qatar, especially among the native Qatari population, with unique BRCA1 variants suggesting the possibility of a founder effect (Bujassoum et al. 2013; Bujassoum et al. 2017; Al‐Bader et al. 2018).
The native Qatari population is characterized by distinct genomic characteristics and cultural aspects. One of the most unique aspects of this population is the high rate of consanguinity which accounts for approximately 67% among native Qatari families with marriages being mostly between first paternal cousins (Al‐Dewik et al. 2018). Similarly, the rate of consanguinity was also observed to be high within non‐native communities in Qatar leading to high prevalence of autosomal recessive disorders and founder effect (Al‐Dewik et al. 2018). The prevalence of genetic disorders is not restricted to autosomal recessive disorders; however, it has been observed that autosomal dominant disorders such as cancers are more frequent in Qatar especially in highly consanguineous families.
The aim of this retrospective study is to describe a common recurrent variant c.4787C>A p.(Ser1596Ter) in the BRCA1 gene that was observed commonly in the native Qatari population with unique genotype–phenotype correlations among high‐risk individuals who were assessed at the Cancer Genetic Clinic at the National Centre for Cancer Care and Research (NCCCR).

2
Materials and Methods
Medical records of Qatari affected patients and unaffected individuals who are positive for either pathogenic or likely pathogenic variants in the BRCA1 BRCA gene were reviewed between the period of July 2013 and March 2020. Data were collected through the cancer genetics registry at the Medical Oncology Department at the National Centre for Cancer Care and Research (the only governmental cancer hospital in Qatar). Only Qatari patients with personal and/or family history of breast cancer with BRCA1BRCA pathogenic variants were reviewed during the said period to identify possible recurrent BRCA1BRCA pathogenic variants. Non‐Qatari patients with BRCA1 BRCA pathogenic variants and patients with no pathogenic variants in the BRCA1 BRCA gene were excluded from this review.
Patients were offered genetic testing due to their personal history of young onset breast and/or ovarian cancer with or without family history, and those unaffected individuals with family history of breast, ovarian, and/or other cancers that fit the criteria of HBOC. In this cohort of patients, the BRCA pathogenic variants were identified either through next generation sequencing (NGS) of the BRCA1 and BRCA2 gene panel, using the Ion Torrent platform, or by Sanger sequencing of these genes at our in‐house CAP‐accredited laboratory at HMC. Additionally, a proportion of the above‐mentioned samples were tested at our collaborative external CAP‐accredited laboratories, where a comprehensive common cancer gene panel was sequenced by NGS, using the Illumina platform, and detected both small variants as well as copy number variants (CNV) (Table 1). All genetic testing results were reviewed thoroughly by the cancer genetics team to check for accuracy and identify recurrent BRCA pathogenic variants among the Qatari population.
Consanguinity among Qatari BRCA1 carriers is documented. Our BRCA positive patients/families are products of consanguineous marriages (1st and 2nd‐degree cousins).
Epidemiological information in addition to clinical information was collected including age, gender, ethnic background, personal history of cancer (if affected) including primary site, age at diagnosis, and histopathological features, family history of cancer, and presence of consanguinity.
Tumour characteristics such as phenotype, stage, and grade were collected from histopathology reports. Nuclear grade was assessed based on scoring of tubule formation, nuclear pleomorphism, and mitotic counts (1–3 for each factor). The grade is obtained by adding the three previous parameters and classifying the tumour as grade 1 (well differentiated or low‐grade), grade 2 (moderately differentiated or intermediate grade), and grade 3 (poorly differentiated or high‐grade). This grading system has prognostic implications.
According to the American Society of Clinical Oncology, when 1% or more of cells are stained by the corresponding immunoreactions, the hormone receptor status is labeled as positive. Based on IHC analysis, HER‐2/neu status was classified as 1+, 2+, or 3+ with further evaluation by fluorescent in situ hybridization for HER‐2/neu amplification or overexpression as needed according to ASCOP. Proliferation rate was considered high when 20% or more of the cells were stained by Ki‐67 antibody.
The study was conducted under the Declaration of Helsinki, and the protocol was approved by the Institutional Review Board (IRB) at Hamad Medical Corporation.
2.1
Statistical Analysis
We utilized frequencies and proportions to describe the data and employed categorical survival Kaplan–Meier curves to determine the probability of survival after 1 and 3 years. For the comparison of survival rates, we conducted log‐rank analysis and considered p‐values of 0.05 or less as statistically significant. To conduct the demographic, clinical, and survival characteristics analyses, we utilized the Stata Corp version of the statistical software (Stata Corp. 2015. Stata Statistical Software: Release 14, College Station, TX: Stata Corp. LP).

3
Results
Sixty‐three Qatari patients who carry the BRCA1 variant (affected and unaffected) were included in this review.
3.1
Demographics
The gender distribution is unequal; most of the patients are females, about 91.3%, while the 8.6% are males who belong to 8 large families. For affected patients, the median age of diagnosis is 42 years. For unaffected patients, the median age is 41 years. All affected and unaffected patients (100%) reported a positive family history of breast and/or ovarian cancers, and consanguinity is present in 100% of the reported families (Table 2).

3.2
Prevalence of
BRCA1
Gene Variants
Review of medical records of all Qatari patients with BRCA pathogenic variants revealed that BRCA1 is the most mutated gene in this cohort of patients, with 10 pathogenic variants identified (mentioned in Figure 1). A common recurrent pathogenic variant in BRCA1 c.4787C>A p.(Ser1596Ter) was significantly observed among the Qatari patients in both affected and unaffected individuals, accounting for 37% (N = 23) of all identified variants, followed by BRCA1 c.4065_4068del p.Asn1355fs, accounting for 24% (N = 15) (Figure 1). A Lollipop plot of the BRCA1 variants was created, as shown in Figure 2.

3.3
BRCA1
c.4787C>A and
BRCA1
c.4065_4068del Characteristics
The BRCA1 c.4787C>A p.(Ser1596Ter) is a nonsense variant predicted to result in protein truncation or nonsense‐mediated decay in a gene for which loss‐of‐function is a known mechanism of disease. This variant was observed in individuals with a personal or family history consistent with pathogenic/likely pathogenic variants in this BRCA1 gene (Trujillano et al. 2015). In a study among Saudi women, this variant was classified as “variant of unknown significance” found in only 1 case (Abulkhair et al. 2018).
This variant was not reported previously in the Middle East as a recurrent variant, suggesting it to be specifically enriched in the Qatari population.
Out of all Qatari carriers of the BRCA1 c.4787C>A variant, 48% are affected with breast and/or ovarian cancers or other types of tumours, and 52% were unaffected. A total of 23 individuals from 8 different families have been identified with the observed pathogenic variant. A total of 11 out of those 23 are affected with breast and/or ovarian cancers, while 12 patients are unaffected with a family history of cancers.
Majority of the affected patients with the BRCA1 c.4787C>A variant had breast cancer (73%), followed by 9% of patients who had both breast and ovarian cancers and 9% with ovarian cancer only (Figure 3a).

BRCA1 c.4065_4068del p.Asn1355fs is the second most common identified BRCA1 variant, which is a deletion of four nucleotides that causes a frameshift, changing Asparagine to a Lysine at codon 1355 and creating a premature stop codon at position 10 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense‐mediated mRNA decay. This variant was reported previously and is classified as pathogenic. It was observed and reported in 1 unaffected carrier in a study done among the Saudi population (Abulkhair et al. 2018).
In our cohort, 15 patients are found to be carriers of this pathogenic variant. A total of 5 patients are affected with breast and/or ovarian cancer and 10 are unaffected individuals. Most affected patients with BRCA1 c.4065_4068del had breast cancer only (60%); however, 20% of patients had breast and ovarian cancers, and the remaining 20% had ovarian cancer only (Figure 3b).

3.4
Clinical/Pathological Findings of Affected Patients
In terms of the clinical and pathological findings of affected patients, we focused on those who carry the most recurrent pathogenic variants in BRCA1 c.4787C>A and the second most common pathogenic variant in BRCA1 c.4065_4068del. We looked at the tumour type, age at diagnosis, tumour phenotype, stage and grade at first diagnosis, in addition to the molecular subtype of breast cancer, survival rate, presence of recurrence, and secondary primary tumour in affected carriers of the different identified BRCA pathogenic variants.
To compare breast and ovarian cancers in carriers of the most recurrent pathogenic variants in BRCA1 c.4787C>A with the second most common pathogenic variant in BRCA1 c.4065_4068del, the total number of patients carrying either variant was identified. A total of 11 patients were identified with the c.4787C>A variant, 8 patients with breast cancer, 1 patient with ovarian cancer, and 1 patient with both breast and ovarian cancers. A total of 5 patients were identified carrying the second most common variant c.4065_4068del, 3 patients had breast cancer, 1 patient had ovarian cancer, and 1 patient had both breast and ovarian cancer.
Among carriers of the c.4787C>A variant, the most common breast cancer phenotype is invasive ductal carcinoma (89%). Disease stage at diagnosis of breast cancer was stage I in 44% of patients, stage II in 34%, and stage III in 22% of cases. Most of breast cancer tumours were high‐grade tumours—grade 3—(67%). There were equal numbers of grade 1 and 2 tumours (11%).
Looking at the molecular subtypes of breast cancer, we found that 6 patients (67%) had triple negative disease (Estrogen receptor (ER) negative, progesterone receptor (PR) negative, HER2 new (HER2) negative). One patient had luminal B disease (ER, PR positive, HER2 negative Ki 67 ≥ 20%), and 1 patient had breast cancer with HER2 over‐expression (ER, PR negative, HER2 positive). A total of 73% of carriers of the most common pathogenic variant BRCA1 c.4787C>A p.(Ser1596Ter) were alive, and 27% passed away (Table 3).
Carriers of the second most common variant c.4065_4068del had IDC tumor phenotype in 3 patients compared to 8 patients in carriers of the most common variant c.4787C>A. The most common stage of breast cancer in the c.4787C>A pathogenic variant group was stage I (44%), while stage II was seen in 50% of carriers of the c.4065_4068del pathogenic variant. Six patients of c.4787C>A variant carriers were breast cancer grade 3 at diagnosis compared to 2 of the second most common variant carriers. According to our analysis of breast cancer molecular subtypes, 67% of carriers of the c.4787C>A variant had triple negative disease compared to 100% for the second group (Table 3).
All carriers of the c.4787C>A variant with ovarian cancer had high grade serous carcinoma (100%). One patient had squamous cell carcinoma of the larynx. For patients with ovarian cancer, the most common stages at diagnosis were stage III (50%) and stage IV (50%) similarly. All ovarian cancer tumours were grade 3 (100%). For the one patient who had squamous cell carcinoma of the larynx, she had stage II disease at diagnosis (100%).
Comparing ovarian cancer cases in the two groups, all cases in the most common variant c.4787 C>A had high‐grade serous tumours (100%) compared to only 50% in the c.4065_4068del group. Ovarian tumours in carriers of the most common variant were stages III and IV (50% each), while tumours in carriers of the second most common variant were stage I and III (50% each) (Table 4).

3.5
Survival and Recurrence in
BRCA1
Carriers With Breast, Ovarian and SCC Cancer
At follow‐up, 8 patients diagnosed with cancer were alive in the c.4787C>A variant carriers group compared to 4 patients in the second common variant carriers. None of the carriers of the BRCA pathogenic variant c.4787C>A had breast cancer recurrence while 1 of the carriers of the c.4065_4068del variant had a breast cancer recurrence (Table 3).
Carriers of the recurrent variant c.4787C>A who were diagnosed with cancer (Breast, ovarian/SCC) had a survival of 125 months compared to 91 months in carriers of the c.4065_4068del BRCA1 pathogenic variant (Figure 4a,b).

3.6
Unaffected Carriers of
BRCA1
c.4787C>A and c.4065_4068del Variants' Characteristics
The 12 unaffected carriers of the BRCA1 c.4787C>A—(age ranging from 20 to 65 years) were identified through extensive family history of breast and/or ovarian cancers. A total of 7 (58%) were identified with the BRCA1 c.4787C>A variant through NGS of the BRCA1/2 gene panel due to family history of cancers, while 5 individuals (41%) were identified through predictive genetic testing of known familial variants.
All the unaffected individuals (100%) reported a family history of breast and/or ovarian cancers. A total of 12 (92%) have a family history of at least two generations with breast and/or ovarian cancers and at least one first‐degree relative affected with breast and/or ovarian cancers.
A total of 8 (62%) individuals for BRCA1 c.4065_4068del have a family history of breast cancer only, while 3 (23%) have a family history of breast and ovarian cancers. A total of 2 (15%) individuals had a family history of breast, ovarian, and colon cancers.

4
Discussion
In the state of Qatar, hereditary breast and ovarian cancer syndrome (HBOC) is the most prevalent cancer syndrome, accounting for ~62% of all identified hereditary cancer syndromes, with BRCA1 pathogenic variants being the most common (Al‐Bader et al. 2018). In this retrospective study, we observed a recurrent pathogenic variant c.4787C>A in the BRCA1 gene, which is highly enriched in the Qatari population and especially among consanguineous families with extensive family histories of breast and/or ovarian cancers. This pathogenic variant has not been reported previously in the Middle East as pathogenic and was only reported in one study (Abulkhair et al. 2018) as a variant of unknown significance. This suggests that c.4787 C>A is a selectively recurrent variant in the native Qatari population. Identifying the recurrent pathogenic variant c.4787C>A in the Qatari population might partially explain the younger onset diagnosis of breast cancer in the Qatari population compared to other ethnic groups in Qatar. In terms of the second most common variant identified in the Qatari population (c.4065_4068del), it has been previously reported in the Middle East (Rawashdeh et al. 2024) but only describes its prevalence rather than the associated phenotype.
The most common clinical manifestations observed in affected patients with BRCA1 c.4787C>A are early onset breast cancer, specifically invasive ductal carcinoma (IDC), triple negative breast cancer (stage I, grade III), in addition to high grade serous ovarian cancers, which go in line with the most common types of breast and ovarian cancers associated with BRCA1 variants. However, it has been noticed that the BRCA1 c.4787C>A is associated with a higher incidence of breast cancer than ovarian cancer, unlike the c.4065_4068del variant.
Carriers of the c.4787C>A pathogenic variant who were diagnosed with cancer (breast, ovarian, and SCC) had survival of 125 months compared to 91 months in carriers of the second common BRCA1 pathogenic variant. This difference might be attributed to less triple‐negative breast cancer, lack of breast cancer recurrence in this group, and the finding of 1 case with squamous cell carcinoma with good outcome.
In terms of family history, the BRCA1 c.4787C>A is associated with a strong family history of breast cancer and less with ovarian cancer. All affected and unaffected patients with the recurrent variant have a family history of at least two generations affected and at least one first‐degree relative with breast cancer, suggesting that this variant is highly penetrant and associated with a higher risk of young‐onset breast cancer rather than ovarian or other cancers.
For those unaffected carriers of c.4787C>A, given that they were identified early based on their family history and eligibility as per NCCN guidelines, those individuals were tested either by NGS panel or predictive genetic testing and had the opportunity to pursue risk‐reducing strategies. This included surveillance or prophylactic surgeries reducing their risk of developing breast and/or ovarian cancers. All the unaffected carriers are still asymptomatic with the median age group of 41 years.
The identification of the c.4787C>A pathogenic variant in the Qatari high‐risk patients did not only help to explain the young onset diagnosis of breast cancer in Qatar, but has significant clinical implications on diagnosis, treatment, and prevention moving forward for patients and their families. Targeting the c.4787C>A variant in the future diagnostic and premarital screening programs will aid in identifying high‐risk individuals, thus offering them risk‐reducing strategies, personalized treatment, and reproductive options to reduce the mortality and morbidity associated with hereditary breast and ovarian cancers in the Qatari population.

5
Conclusion
In this retrospective study, we have identified two common recurrent pathogenic variants in the BRCA1 gene among the Qatari population (BRCA1 c.4787C>A and BRCA1 c.4065_4068del p.Asn1355fs) that are highly recurrent among highly consanguineous Qatari families. These variants were associated with high penetrance and young‐age onset of breast cancer.
We suggest that BRCA1 c.4787C>A to be considered in the differential diagnosis of Qatari patients with personal and/or family history of breast and ovarian cancers who belong to highly consanguineous families and to be offered as first‐tier testing. Early identification of this variant can facilitate timely and appropriate treatment and/or preventive measures. In addition, identifying asymptomatic carriers may enable preventative measures to reduce the risk of cancers in these high‐risk individuals, thereby reducing the burden of cancer in Qatar. Moreover, awareness of this variant can provide individuals with the opportunity to benefit from genetic counselling in the premarital and periconceptional period.
We believe that the incorporation of targeted testing for the identified recurrent variant as an option in the Qatari National Premarital Screening program can enable early identification of carriers, allowing for the provision of risk‐reduction strategies and minimizing the risk of homozygosity in their offspring by offering reproductive options such as preimplantation genetic diagnosis (PGD).

Author Contributions
All authors contributed significantly to this work including study design, data collection, data analysis and interpretation, and manuscript draft and revision.

Ethics Statement
Ethical approval was obtained from Hamad Medical Corporation MRC IRB, protocol reference number MRC‐01‐20‐1086.

Consent
The authors have nothing to report.

Conflicts of Interest
The authors declare no conflicts of interest.