Heritable susceptibility to breast cancer among African American women in the Detroit Research on Cancer Survivors Study

Abstract

Background:

African American women have high rates of breast cancer associated with hereditary features. However, no studies have reported the prevalence of inherited variation across all genes known to be breast cancer risk factors among African American breast cancer patients not selected for high risk characteristics.

Methods:

We evaluated 182 African American women diagnosed with invasive breast cancer in metropolitan Detroit via targeted capture and multiplex sequencing of thirteen well-established breast cancer risk genes and five suggested breast cancer risk genes.

Results:

We identified 24 pathogenic variants in 23 women (12.6%, 95% confidence interval (CI) 8.2%−18.4%) and five genes (BRCA2, BRCA1, ATM, RAD50, CDH1). BRCA1 and BRCA2 accounted for 58.3% of all pathogenic variants. An additional eight pathogenic variants were found in suggested breast cancer risk genes (MSH6, MUTYH, NF1, BRIP1).

Conclusion:

The prevalence of germline pathogenic variants is relatively high among African American breast cancer patients unselected for high risk characteristics across a broad spectrum of genes.

Impact:

This study helps to define the genomic landscape of breast cancer susceptibility in African American women who could benefit from enhanced surveillance and screening.

Introduction

African American women have higher rates of breast cancer associated with hereditary features such as the aggressive triple negative (TN) subtype and young age of onset (1–5) compared to non-Hispanic whites. The vast majority of studies evaluating inherited variants associated with breast cancer risk, however, are almost exclusively based on populations of non-Hispanic white women. Studies of familial breast cancers among African American women have focused largely on BRCA1 and BRCA2 and have been primarily conducted in breast cancer patients who meet National Comprehensive Cancer Network (NCCN) guidelines for genetic testing [diagnosed at age <50 years, having the triple negative subtype, or having a family history of a first degree relative with young onset breast cancer or a relative with ovarian cancer] (6). African American women meeting NCCN guidelines for genetic testing have been found to be equally or more likely to harbor pathogenic BRCA1/2 variants compared to white women (7–9), yet there is evidence for a vastly different spectrum of variation among African American women compared to white women, as represented by the identification of novel single base pair substitutions, an overrepresentation of rearrangements or copy number variations, and distinct African founder mutations (10).

Pathogenic variants in BRCA1 and BRCA2, however, account for only 25% of all hereditary breast cancers (11). Widespread implementation of massively-parallel “next-generation” sequencing has substantially increased our understanding of heritable breast cancer genetics beyond BRCA1/2 through the systematic exploration and identification of at least thirteen moderate- to high-risk breast cancer susceptibility genes [Moderate risk: 20–50% lifetime risk; High risk=50–85% lifetime risk] (12–18). Pathogenic variants have been identified in the following breast cancer susceptibility genes [High risk: BRCA1, BRCA2, TP53, PTEN, STK11; and Moderate risk: BARD1, CHEK2, RAD50, RAD51C, RAD51D, PALB2, CDH1, ATM], and there is evidence for several additional moderate breast cancer risk genes, although these are less conclusive [BRIP1, PMS2, NF1, MSH6, MUTYH] (11–20). Several studies have recently been published evaluating a subset of these genes in women of African ancestry, including a study of high-risk African American women and population-based studies of breast cancer patients in Nigeria, Uganda, and Cameroon (21–23). In the study of high-risk African Americans with breast cancer, 22% were found to have an unequivocally pathogenic variant in one of ten known breast cancer genes (21). The population-based studies of Sub-Saharan African women identified pathogenic variants in 14.7–15.8% of women across 16 known breast cancer genes, and in particular, demonstrated high proportions of pathogenic BRCA1/2 variants (7–11%) in these populations (22,23). Further, Zheng, et al were able to quantify gene-level risks in their study of 1,136 Nigerian women with invasive breast cancer, where BRCA1, BRCA2, PALB2, and TP53 contributed the highest cancer risks (22). However, to our knowledge, no studies of the prevalence of inherited variants across all genes currently known to be associated with breast cancer risk have been conducted in African Americans affected with breast cancer unselected for high risk characteristics in the United States.

Considering the underrepresentation of African American women in genetic studies of breast cancer, the increased risk of second primaries and new primary cancers for women with hereditary cancers, and the clear clinical guidelines in terms of both treatment and follow-up for women with hereditary cancers, there is a critical need to identify and characterize disease-causing variants associated with breast cancer risk in the African American population. The main goal of this analysis was to establish the prevalence of pathogenic variants in genes associated with breast cancer risk in a sample of African American women with breast cancer in metropolitan Detroit unselected for age of onset, subtype, or family history. To do this, we performed targeted sequencing of germline DNA from African American women diagnosed with breast cancer in metropolitan Detroit.

Materials and Methods

Study population

We utilized DNA derived from saliva or peripheral blood lymphocytes from 192 African American women with breast cancer at the Karmanos Cancer Institute (KCI) in Detroit, MI enrolled in the Detroit Research on Cancer Survivors (ROCS) Study (24–26). Briefly, participants are eligible to join the cohort if they are African American, diagnosed with a first primary, invasive colorectal, lung, prostate, or female breast cancer on or after January 1, 2013, ages 20 to 79 at diagnosis, and for this study were diagnosed and/or treated at KCI in Detroit, MI. Women were contacted on average at 22.7 months post diagnosis (standard deviation=10.3 months, range=7–53 months). A total of 192 African American women with breast cancer in Detroit ROCS were sequenced, consisting of all women with breast cancer enrolled in Detroit ROCS at the time of sequencing who provided questionnaire data and consented to use of their biospecimens in future studies. Detroit ROCS provided written informed consent upon entry to the study and consented to future genetic studies using their blood or saliva. This study was conducted in accordance with the ethical principles outlined in the U.S. Common Rule and was approved by the Wayne State University Institutional Review Board.

Patient data collection

Clinical information for all Detroit ROCS participants was obtained from the Metropolitan Detroit Cancer Surveillance System registry, including histologic type, ER/PR/HER2 status, and stage of disease at diagnosis. Age at diagnosis and family history of cancer were obtained from baseline questionnaires.

Targeted sequencing of germline DNA

Samples were randomized into 96-sample pools based on triple negative status, family history, and age of onset. Custom libraries were prepared using 100ng of DNA using the Illumina TruSeq Custom Amplicon Kit (Illumina, San Diego, CA) using standard protocols. The custom sequencing panel was designed using Illumina Design Studio (Illumina, San Diego, CA) to capture the coding sequence of 43 genes with estimated 99% coverage. Our analyses focused on the eighteen genes selected on the basis of clinically defined contributions to familial breast cancer (well-established: ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, PALB2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53; BRIP1, MSH6, MUTYH, NF1, PMS2) (11,21,27,28). Sequencing was performed on the Illumina MiSeq platform with 500cycles using V2 reagents, multiplexed for 100X mean depth of coverage. DNA and library preparations were quality checked using the Agilent Tape station to check for uniformity in intensity and fragment size range, accordingly sample outliers were repeated or ultimately rejected. Library preparation and DNA sequencing was performed at the University of Michigan Advanced Genomics Core (UMAGC).

Bioinformatics and variant filtering

Raw and aligned data (using BWA-MEM (29)) were checked with FastQC (30) and MultiQC (31). Samples that failed MultiQC quality control criteria were excluded (n=10 failed per base sequence quality or per tile sequence quality metrics). The Broad Institute GATK best practices workflow was followed (32), using HaplotypeCaller multi-sample calling. Ts/Tv ratios was checked as a standard quality control measure. Variants were annotated using SnpEff to identify variants predicted to disrupt the primary structure of the protein. Variants were annotated using ANNOVAR (33), which includes the databases SIFT, Polyphen HDIV & HVAR, LRT, MutationTaster, MutationAssessor, FATHMM, RadialSVM, and LR to evaluate predicted pathogenicity for missense variants. Frequency of variants in African populations in the 1000 Genomes, ExAC, or NHLBI ESP6500SI databases were annotated. Variants were filtered to retain only coding or canonical (+/−2) splice site variants that met the following criteria: (1) missense, nonsense, start gain, stop loss, or indel, (2) <1% minor allele frequency in African populations in the 1000 Genomes, ExAC, or NHLBI ESP6500SI databases, (3) <1% frequency in the sequenced patient cohort, and (4) not located in a simple repeat region as defined by the Simple Repeat track coordinates from the UCSC Genome Browser (https://genome.ucsc.edu/).

Variant classification

We followed the American College of Medical Genetics and Genomics guidelines for interpreting sequence variants (34), adapted based on the availability of information for this cohort (Tables S1–2). Individual criteria met for each variant are shown in Table S3. Benign variants were filtered in the previous step given that frequency >5% in public databases is a stand-alone criterion to classify a variant as benign. Functional data were obtained from the Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk). Any variant that did not meet the set criteria in Tables S1 and S2 for establishing pathogenicity was considered a variant of uncertain significance. We cross-referenced our variant classifications with those in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/). Variants classified as pathogenic in ClinVar with no discrepancies were also considered pathogenic. Variants classified as either “pathogenic” or “likely pathogenic” were considered pathogenic in the current analysis.

Statistical analyses

Proportions of pathogenic variant carriers and exact 95% confidence intervals (CI) were estimated using the binominal distribution using the “DescTools” package in R (https://cran.r-project.org/). Fisher’s exact tests were used to examine whether variant proportions vary across age groups or among patients meeting different numbers of eligibility criteria. Figures showing variant types and frequency by gene were generated using Mutplot (https://bioinformaticstools.shinyapps.io/lollipop/) (35). All definitions of family history include first- and second-degree relatives. A cancer family history suggestive of a hereditary breast cancer syndrome was defined as having (1) a first or second degree relative with breast cancer diagnosed under the age of 50 years, (2) a first or second degree relative with ovarian cancer diagnosed at any age, or (3) three or more first or second degree relatives with breast, prostate, colorectal, or kidney cancer diagnosed at any age. Associations between pathogenic variant status and high-risk characteristics were estimated using logistic regression.

Results

A total of 192 women were eligible for this analysis, of which 182 had sufficient sequencing coverage and quality for analysis. The sequencing panel yielded 225-fold mean coverage for these 182 samples, with individual gene coverage ranging from 133- to 318-fold (Table S4). The demographic and clinical data for our patient population are shown in Table 1. The majority of patients (65.7%) were fifty years or older at diagnosis, thus not considered early-onset. About 80% patients had early onset breast cancer (Stage I or II) and either intermediate or high grade tumors. Slightly more than half of women had hormone receptor positive (ER+ or PR+), HER2- breast cancer and ~20% had triple negative breast cancer. About three in ten participants had a family history of breast cancer.

Table 1.

Demographic and clinical characteristics of study participants

	Detroit ROCS n=171
Age (years)	n	(%)
<50	62	34.3%
50–59	43	23.8%
60–69	59	32.6%
70+	17	9.4%
Stage
I	71	39.2%
II	72	39.8%
III	31	17.1%
IV	7	3.9%
Grade
1	19	10.5%
2	70	38.7%
3	82	45.3%
Unknown	10	5.5%
Family history of breast cancer
Yes	52	28.6%
No	130	71.4%
Subtype
ER−/PR−/HER2+	14	7.7%
ER+ or PR+, HER2−	102	56.4%
ER+ or PR+, HER2+	24	13.3%
Triple negative	34	18.8%
Unknown	7	3.9%

Within well-established breast cancer susceptibility genes, we identified twenty-four pathogenic variants in 23 out of the 182 women sequenced (12.6%, 95% confidence interval (CI) 8.2%−18.4%) (Tables 2, S3). These variants were identified in five genes (Figure 1): BRCA2 (n=8), BRCA1 (n=6), ATM (n=6), RAD50 (n=3), and CDH1 (n=1). The overall frequency of pathogenic BRCA1/2 variants in this cohort was 7.7%. BRCA2 had the highest frequency of pathogenic variants (33.3% of pathogenic variants), which were mostly frameshift deletions (Figure 2a), followed by ATM (25.0% of pathogenic variants) which also showed frameshift deletion/insertion or missense variants (Figure 2b). BRCA1 accounted for 25.0% of all pathogenic variants, which were either frameshift deletion, missense or nonsense variants (Figure 2c). The remaining genes had lower frequencies of pathogenic variants (RAD50 13.0%, CDH1 8.7%). Time from diagnosis to enrollment did not differ between those with and without pathogenic mutations (Pathogenic variant carrier: mean=20.3 months, No pathogenic variant: mean=23.0 months, t-test p-value=0.10). Among genes with suggestive, although less definitive, evidence as breast cancer susceptibility genes, we identified an additional six women (3.5%) with pathogenic variants in four genes: NF1 (n=2), MSH6 (n=2), BRIP1 (n=1), MUTYH (n=1) (Tables S3,5). We identified 109 variants of uncertain significance (VUS) in well-established breast cancer risk genes and an additional 34 VUS in probable breast cancer genes (Table S6). One patient carried two pathogenic variants (Table 2). Patient 92333 had a frameshift deletion of BRCA2 (p.L1227fs) and a missense variant in ATM (p. R2443L). She was diagnosed at age 60 with a stage II, grade 3, hormone receptor positive/HER2- breast cancer. She reported no family history of breast cancer, however she had one first degree relative with prostate cancer.

Table 2.

Spectrum of 24 pathogenic variants among 23 African American women diagnosed with breast cancer in metropolitan Detroit

							Family history
Patient	Gene	Variant	Age at dx.*	Subtype**	Stage	Grade	BrCa†	BrCa† (age<50)	OvCa‡
92161	ATM	NM_000051(ATM):c.4709dupT(p.Val1570fs)	65	HR+, HER2−	I	2	No	No	No
92167	ATM	NM_000051(ATM):c.2543delA(p.Glu848fs)	66	HR+, HER2−	II	2	No	No	No
92269	ATM	NM_000051(ATM):c.2543delA(p.Glu848fs)	59	HR+, HER2−	II	3	Yes	No	No
92291	ATM	NM_000051(ATM):c.9132delT(p.Asn3044fs)	46	Triple Negative	II	2	No	No	No
92333	ATM	NM_000051(ATM):c.7328G>T(p.Arg2443Leu)	60	HR+, HER2+	II	3	No	No	No
92380	ATM	NM_000051(ATM):c.9132delT(p.Asn3044fs)	68	HR−,HER2+	III	3	Yes	Yes	No
92131	BRCA1	NM_007294(BRCA1):c.754C>T(p.Arg252Cys)	66	HR+, HER2−	III	3	No	No	No
92147	BRCA1	NM_007294(BRCA1):c.1961delA(p.Lys654fs)	51	HR+, HER2−	I	1	No	No	No
92154	BRCA1	NM_007294(BRCA1):c.439T>A(p.Leu147Met)	58	HR+, HER2−	I	2	No	No	No
92195	BRCA1	NM_007294(BRCA1):c.2489_2492del(p.Lys830fs)	43	Triple Negative	I	3	No	No	No
92268	BRCA1	NM_007294(BRCA1):c.5033delA(p.Asn1678fs)	62	HR+, HER2+	IV	3	Yes	No	No
92351	BRCA1	NM_007294(BRCA1):c.3607C>T(p.Arg1203stop)	43	Triple Negative	II	3	Yes	Yes	No
92149	BRCA2	NM_000059(BRCA2):c.1806delA(p.Gly602fs)	55	HR+, HER2−	I	3	No	No	No
92239	BRCA2	NM_000059(BRCA2):c.1055delA(p.Tyr352fs)	61	HR+, HER2+	III	3	No	No	No
92262	BRCA2	NM_000059(BRCA2):c.1806delA(p.Gly602fs)	51	HR+, HER2−	II	2	Yes	Yes	Yes
92286	BRCA2	NM_000059(BRCA2):c.2830delA(p.Lys944fs)	42	HR+, HER2−	I	3	No	No	No
92333	BRCA2	NM_000059(BRCA2):c.3680_3681del(p.Leu1227fs)	60	HR+, HER2+	II	3	No	No	No
92350	BRCA2	NM_000059(BRCA2):c.5200dupG(p.Ser1733fs)	60	HR+, HER2−	I	3	No	No	No
92352	BRCA2	NM_000059(BRCA2):c.5461delA(p.Lys1821fs)	58	HR+, HER2−	II	2	No	No	No
92355	BRCA2	NM_000059(BRCA2):c.2830delA(p.Lys944fs)	36	HR−,HER2+	II	3	Yes	Yes	No
92301	CDH1	NM_001317184(CDH1):c.1796dupT(p.Val599fs)	43	HR+, HER2−	II	2	Yes	No	No
92205	RAD50	NM_005732(RAD50):c.2348delA(p.Glu783fs)	35	HR+, HER2+	I	3	Yes	Yes	No
92211	RAD50	NM_005732(RAD50):c.2157delA(p.Leu719fs)	78	HR+, HER2−	I	2	Yes	No	No
92344	RAD50	NM_005732(RAD50):c.1114C>T(p.Gln372stop)	64	HR+, HER2−	IV	3	No	No	No

^*Age at dx.=age at diagnosis

^**Hormone receptor (HR) status: HR+ = ER+ or PR+; HER− = ER− and PR−

^†BrCa=Breast cancer

^‡OvCa=Ovarian cancer

Figure 1.

Five genes with pathogenic variants identified in 23 African American women with breast cancer. A total of 24 pathogenic variants were identified.

Figure 2.

Locations of pathogenic variants resulting in 16 unique amino acid changes, truncated protesting, or frameshifts (6 in BRCA2, 6 in BRCA1, 4 in ATM) are shown. These 16 pathogenic variants were seen a total of 20 times in our cohort (8 in BRCA2, 6 in BRCA1, 6 in ATM). A schematic of each gene is represented by grey rectangles, where functional domains are indicated by colored rectangles. Each unique pathogenic variants is shown as a circle, where amino acid position is indicated by vertical lines.

We next evaluated the distributions of high-risk characteristics-- defined as age of onset less than 50 years, having triple negative breast cancer, or a cancer family history suggestive of a hereditary breast cancer syndrome-- by pathogenic variant status (Table 3). We did not observe significant differences in triple negative status, age of onset, or family history by pathogenic variant status. Women with pathogenic variants were 60% more likely to have a family history of breast cancer than women without pathogenic variants, although this was not statistically significant. These distributions did not change substantially when we included the eight pathogenic variants identified in suggestive breast cancer susceptibility genes (Table S7). Given that there is known heterogeneity in the patient and/or tumor characteristics associated with specific genes (e.g. high rates of the TN subtype in BRCA1-associated tumors (36)), we also examined the distribution of high-risk characteristics by individual gene. Among women with pathogenic variants, the three women with TN tumors had pathogenic variants in ATM (n=1) and BRCA1 (n=2). Women with young onset breast cancer as a family history of breast cancer had mutations in each of the five genes.

Table 3.

High-risk characteristics of patients by pathogenic variant status and gene

	Pathogenic variant in:
	ATM	BRCA1	BRCA2	CDH1	RAD50	Any pathogenic variant	No pathogenic variant	p-value*
TN	1 (17%)	2 (33%)	0 (0%)	0 (0%)	0 (0%)	3 (12%)	31 (20%)
Not TN	5 (83%)	4 (67%)	8 (100%)	1 (100%)	3 (100%)	21 (88%)	127 (80%)	0.58
Age <50	1 (17%)	2 (33%)	2 (25%)	1 (100%)	1 (33%)	7 (29%)	55 (34%)
Age 50+	5 (83%)	4 (67%)	6 (75%)	0 (0%)	2 (67%)	17 (71%)	98 (64%)	0.65
FH breast cancer	2 (33%)	2 (33%)	2 (25%)	1 (100%)	1 (33%)	9 (37%)	43 (27%)	0.33
No FH breast cancer	4 (67%)	4 (67%)	6 (75%)	0 (0%)	2 (67%)	15 (63%)	115 (73%)
Suggestive FH	1 (17%)	1 (17%)	2 (25%)	0 (0%)	1 (33%)	5 (21%)	29 (18%)
No suggestive FH	5 (83%)	5 (83%)	6 (75%)	1 (100%)	2 (67%)	19 (79%)	129 (82%)	0.78

^*Fisher’s exact test comparing any pathogenic variant carriers to non-carriers

Discussion

We undertook a hospital-based study of heritable pathogenic variation in eighteen known and probable breast cancer susceptibility genes among African American women with breast cancer who were unselected for age of onset, subtype, or family history. Of the 182 women who were analyzed, 23 women (12%) had pathogenic variants in 5 genes (24 total pathogenic variants in BRCA2, BRCA1, ATM, RAD50, CDH1). BRCA2 had the highest proportion of variants, accounting for 33% of all pathogenic variants, followed by ATM and BRCA1 (25% of all pathogenic variants each). The total frequency of pathogenic BRCA1/2 variants in our unselected African American cohort was 7.7%, which is lower than hospital-based studies of women with breast cancer in Nigeria (11.1%) (22), Uganda (9.7%), and Cameroon (12.9%) (23). Interestingly, we also found a relatively high pathogenic variation rate (3.3%) of ATM compared to the hospital-based African studies (0.4–1.5%) (22,23), as well as to the study of African American breast cancer patients with high risk characteristics (1.7%) (21). Only two of the six ATM pathogenic variant carriers in our study met high risk criteria and would have been included in a study using inclusion criteria similar to Churpek et al. (21). Differences in pathogenic variation frequencies also may reflect population admixture of European and African ancestry in African Americans (37).

Five genes in our sequencing panel (well established: RAD50; probable: MSH6, MUTYH, NF1, PMS2) were unique to our study compared to recent next-generation sequencing-based studies of breast cancer among women of African ancestry. We identified eight pathogenic variants in MSH6, MUTYH, NF1, and RAD50 for a prevalence of 4.4% in the overall cohort. We identified two women with germline pathogenic MSH6 variants, one with triple negative breast cancer diagnosed at age 61 with a family history of ovarian cancer and one with hormone receptor positive, HER2 negative breast cancer diagnosed at age 45. Neither woman reported a family history of breast cancer. We included MSH6 in this study based on mounting evidence for breast cancer associated with Lynch syndrome genes. A recent report demonstrated that MSH6 pathogenic variants carriers are at 2-fold increased risk of breast cancer compared to the general population (38). Women with breast cancer have also been shown to harbor pathogenic variants in MSH2, PMS2, and MLH1 (38–41). Lifetime breast cancer risk for MLH1 and MSH2 pathogenic variant carriers has been estimated at 18.6–22% (40,41). Further work on the association between pathogenic variation in mismatch repair genes and breast cancer risk, particularly in minority populations, is needed.

We also identified two women with pathogenic variants in NF1, three women with pathogenic variants in RAD50, and one woman with a pathogenic variant in MUTYH. NF1 was relatively recently established as a breast cancer susceptibility gene (42,43). Breast cancers in women with NF1 pathogenic variants are typically diagnosed at younger ages, with the highest incidence in women under 40 years of age, and are associated with relatively poor breast cancer survival (43). One of the NF1 pathogenic variant carriers in our study were diagnosed under the age of 50. NCCN guidelines now recommend enhanced breast cancer screening for women with germline pathogenic NF1 variants (42). MUTYH, a gene typically associated with colorectal polyposis and colorectal cancer risk, is also associated with moderate breast cancer risk (44–51). The MUTYH pathogenic variant carrier identified in our study had no high-risk characteristics. RAD50 is also considered an intermediate risk breast cancer gene, although the breast cancer phenotypes associated with m pathogenic variants in this gene are still unclear (52–55). One of the women with a RAD50 frameshift variant in our study was diagnosed at the age of 35 with triple positive breast cancer and also had a family history of young onset breast cancer.

We did not find an association between age at diagnosis, subtype, and cancer family history and pathogenic variant carrier status, although we were underpowered to detect significant associations between pathogenic variant status in individual genes and patient characteristics. Specifically, we did not find an association between BRCA1 and triple negative subtype, although we did note that triple negative breast cancer was more frequent in BRCA1 compared to BRCA2 pathogenic variant carriers (33% vs 0%, respectively). This is in contrast to previous findings where ~70% of breast tumors arising in BRCA1 pathogenic variant carriers are triple negative (36,56,57). In 2018, a large international clinic-based triple negative breast cancer consortium further demonstrated that pathogenic variants in BARD1, BRCA1, BRCA2, PALB2 and RAD51D were strongly associated with high risk of triple negative breast cancer (58). Pathogenic variants in BRCA1 were also associated with a 3-fold increased risk of triple negative breast cancer compared to other subtypes in the hospital-based cohort of Nigerian women (22). We also found that 21% of our patients with pathogenic variants had a family history suggestive of a hereditary breast cancer syndrome, and 29% of these women had early onset breast cancer (<50 years). Adedokun et al (16) have previously reported that patients with pathogenic variants in BRCA1/2, did not have a family history of breast cancer. The authors importantly emphasized that the absence of a family history does not preclude the presence of pathogenic BRCA1/2 variants and family history provided by the patient population is limited in most published reports.

One of the major strengths of our study is examines a population of African American women in metropolitan Detroit previously unstudied for a wide spectrum of breast cancer risk genes, compared to currently published studies, not selected for age of onset, subtype, or family history of breast cancer within the catchment area of the Karmanos Cancer Institute in metropolitan Detroit. We also included a broader gene panel than has been reported in any single study of Africans Americans to date. Patient information was collected for the Detroit ROCS study participants using a standardized questionnaire. At the same time, we were limited in analyses of family history because these data were not collected using a standardized questionnaire in the KCI Biobank and Detroit ROCS family history data were based on self-report without confirmation or multiple source report. Our study was also underpowered to detect associations between patient characteristics and pathogenic variant status in individual genes, which is important due to the known phenotypic heterogeneity of hereditary breast cancers. We were also unable to evaluate loss of heterozygosity in tumors for women with novel pathogenic variants, which is important for establishing causality, particularly for missense variants. This limits our ability to make causal inferences about these variants, and future tumor-based studies will be important in definitively determining their pathogenicity. We also relied on self-reported race to classify women as African American given that we were unable to estimate ancestry using data from our targeted sequencing panel. This is important given that, as we describe above, pathogenic variation frequencies could be influenced by reflect population admixture.

This study adds substantially to the current literature describing the spectrum of pathogenic variants among an unselected cohort of African American women with breast cancer, thus helping to define the genomic landscape of breast cancer susceptibility in African American women with hereditary breast cancers. This will help identify high risk individuals who would benefit from enhanced screening, surveillance, and personalize treatment in the future.