Efforts to Grow Genomic Research in Ancestrally Diverse and Admixed Populations

Recent initiatives by the research community to characterize the genomic and molecular landscapes of tumors in ancestrally diverse and admixed populations, including the publication by Ding and colleagues in this issue of Cancer Research, represent important efforts to improve our understanding of the entire spectrum of cancer genomic variation with potential clinical consequences. Ding and colleagues confirmed a similar prevalence of mutations in established breast cancer driver genes including PIK3CA, TP53, GATA3, MAP3K1, CDH1, CBFB, PTEN, and RUNX1 and recurrent amplifications in breast cancer drivers including MYC, FGFR1, CCND1, and ERBB2 in tumors from Hispanic/Latina women as compared with non-Hispanic White women. Importantly, they also identified Catalogue of Somatic Mutations in Cancer (COSMIC) signature 16 in a significant fraction of tumors from Hispanic/Latina women and a novel recurrent amplification on 17q11.2. This study highlights the potential for inclusion of participants from diverse populations to accelerate discoveries and advance equity in genomic medicine, as well as the need for even larger collaborative initiatives. See related article by Ding et al., p. 2600.

Predictors of nonadherence to breast cancer screening guidelines in a United States urban comprehensive cancer center

BACKGROUND

This study aimed to identify predictors of nonadherence to breast cancer screening guidelines in an urban screening clinic among high- and average-risk women in the United States.

METHODS

We reviewed records of 6090 women who received ≥2 screening mammograms over 2 years at the Karmanos Cancer Institute to examine how breast cancer risk and breast density were associated with guideline-concordant screening. Incongruent screening was defined as receiving supplemental imaging between screening mammograms for average-risk women, and as not receiving recommended supplemental imaging for high-risk women. We used t-tests and chi-square tests to examine bivariate associations with guideline-congruent screening, and probit regression to regress guideline-congruence unto breast cancer risk, breast density, and their interaction, controlling for age and race.

RESULTS

Incongruent screening was more likely among high- versus average-risk women (97.7% vs. 0.9%, p < 0.01). Among average-risk women, incongruent screening was more likely among those with dense versus nondense breasts (2.0% vs. 0.1%, p < 0.01). Among high-risk women, incongruent screening was more likely among those with nondense versus dense breasts (99.5% vs. 95.2%, p < 0.01). The significant main effects of density and high-risk on increased incongruent screening were qualified by a density by high-risk interaction, showing a weaker association between risk and incongruent screening among women with dense breasts (simple slope = 3.71, p < 0.01) versus nondense breasts (simple slope = 5.79, p < 0.01). Age and race were not associated with incongruent screening.

CONCLUSIONS

Lack of adherence to evidence-based screening guidelines has led to underutilization of supplementary imaging for high-risk women and potential overutilization for women with dense breasts without other risk factors.

Association between major discrimination and deficit accumulation in African American cancer survivors: The Detroit Research on Cancer Survivors Study

BACKGROUND

Discrimination can adversely affect health and accelerate aging, but little is known about these relationships in cancer survivors. This study examines associations of discrimination and aging among self-identified African American survivors.

METHODS

A population-based sample of 2232 survivors 20-79 years old at diagnosis were enrolled within 5 years of breast (n = 787), colorectal (n = 227), lung (n = 223), or prostate (n = 995) cancer between 2017 and 2022. Surveys were completed post-active therapy. A deficit accumulation index measured aging-related disease and function (score range, 0-1, where <0.20 is robust, 0.20 to <0.35 is pre-frail, and 0.35+ is frail; 0.06 is a large clinically meaningful difference). The discrimination scale assessed ever experiencing major discrimination and seven types of events (score, 0-7). Linear regression tested the association of discrimination and deficit accumulation, controlling for age, time from diagnosis, cancer type, stage and therapy, and sociodemographic variables.

RESULTS

Survivors were an average of 62 years old (SD, 9.6), 63.2% reported ever experiencing major discrimination, with an average of 2.4 (SD, 1.7) types of discrimination events. Only 24.4% had deficit accumulation scores considered robust (mean score, 0.30 [SD, 0.13]). Among those who reported ever experiencing major discrimination, survivors with four to seven types of discrimination events (vs. 0-1) had a large, clinically meaningful increase in adjusted deficits (0.062, p < .001) and this pattern was consistent across cancer types.

CONCLUSION

African American cancer survivors have high deficit accumulated index scores, and experiences of major discrimination were positively associated with these deficits. Future studies are needed to understand the intersectionality between aging, discrimination, and cancer survivorship among diverse populations.

Abstract P5-04-05: Predictors of guideline-incongruent breast cancer screening in an urban comprehensive cancer center

Background: Guideline-congruent breast cancer (BC) screening is imperative to systematically curb BC mortality. This study was conducted to identify predictors of BC screening behaviors congruent with guidelines from various nationally recognized organizations (e.g, American Cancer Society, National Comprehensive Cancer Network, American College of Radiology) among high- and average-risk women, and to elucidate the alternative screening behaviors of women who were incongruently screened. Methods: Medical records of 6,090 women who received at least two screening mammograms from January 2016 to March 2018 at the Karmanos Cancer Institute were reviewed to determine breast cancer risk status (classified by the Tyrer-Cuzick model) and breast density status to determine whether breast cancer screening was concordant with risk-driven screening guidelines. Breast density was determined by BI-RADS density scoring, with non-dense breasts defined by a score of A or B, and dense breasts as C or D. For women at average-risk of breast cancer, incongruent screening was defined as receiving supplemental imaging in the interval between screening mammograms. For high-risk women, incongruent screening was defined as not having a recommended supplemental image in the interval between screening mammograms. Further, we examined BC risk, breast density, age, and race as predictors for guideline-concordant screening. Results: The screening cohort included 73.3% Black and 26.7% White women of whom 86.5% were classified as average-risk, 7.7% intermediate risk and 5.8% high risk. Further analyses focused on women with average and high-risk of breast cancer. Among both average- and high-risk women, 390 (6.9%) were incongruently screened, however the rate of incongruent screening was much higher among high-risk vs. average risk women (97.7 vs. 0.9%, p&lt; 0.01). Among average-risk women, incongruent screening was more likely among women with dense vs. non-dense breasts (2.0% vs 0.1%, p&lt; .01). High-risk women were more likely to be incongruently screened if they had non-dense compared to dense breasts (99.5% vs 95.2%, p &lt; .01). Younger women more likely to be incongruently screened among average-risk women (55.11 [SD = 10.24] vs 62.20 [SD = 9.73]; t5267 = 4.87, p &lt; .01, d = 0.73), whereas older women were more likely to be incongruently screened among high-risk women, although this difference was not statistically significant (52.38 [SD = 7.27] vs 47.50 [SD = 8.57]; t351 = 1.87, p = .06, d = 0.67).There was no significant impact of race and incongruent screening for individual risk-level categories. With the exception of rendering the age effect non-significant, preliminary multivariable analyses did not significantly change the results. Further analyses will be conducted to assess the relationship between predictive factors and incongruent screening. Conclusions: An apparent lack of adherence to evidence-based screening guidelines for BC has led to underutilization of supplementary breast imaging for women at high-risk for BC. Further interventions are needed to promote increased supplemental imaging for this group of women.

Citation Format: Alexandra Wehbe, Madeleine Gonte, Suzanne O’Neill, Alit Amit-Yousif, Kristen Purrington, Mark Manning, Michael Simon. Predictors of guideline-incongruent breast cancer screening in an urban comprehensive cancer center [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-04-05.

Moderators of the effects of perceived racism and discrimination on cancer-related health behaviors among two samples of African Americans

BACKGROUND

Assumptions regarding within-race variation in the associations between measures of discrimination racism and health-related behaviors among African Americans have been largely unexplored.

METHODS

We conducted secondary analyses of two studies to examine support for a model which describes several theoretical moderators of the effects of discrimination and racism on health behaviors. The first study examined the effects of group-based behavioral information and racial identity on the association between perceived racism and requests for at home colorectal cancer screening tests among a sample of 205 geographically diverse African Americans who participated in an online experiment from 2019 to 2020.

RESULTS

Group-based behavioral information attenuated the association between perceived racism and requests for at-home screening kit. In the absence of group-based behavioral information, perceived racism was positively associated with screening kit requests for African Americans with weaker racial identity and negatively associated with requests for African Americans with stronger racial identity. The second study examined the influence of personal and group-based perceived discrimination, and behavior-relevant affective information related to a breast cancer risk notification, on 89 Michigan dwelling African American women's self-reported physician communication from 2015 to 2016. Results showed that perceived group-based discrimination was positively associated with physician communication in the absence of negative affective information, and perceived personal discrimination was negatively associated with physician communication as positive affective information increased.

CONCLUSIONS

Together, these results support our theoretical model highlighting variation in the effects of discrimination and racism on health behaviors among African Americans, and indicates group-relevant behavioral information, racial identity, behavior relevant affective information, and target of discrimination as moderators of the effect. Implications for conceptualizing the effects of racism and discrimination and for examining racially targeted interventions are discussed.

Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk

Differences by sex in lung cancer incidence and mortality have been reported which cannot be fully explained by sex differences in smoking behavior, implying existence of genetic and molecular basis for sex disparity in lung cancer development. However, the information about sex dimorphism in lung cancer risk is quite limited despite the great success in lung cancer association studies. By adopting a stringent two-stage analysis strategy, we performed a genome-wide gene-sex interaction analysis using genotypes from a lung cancer cohort including ~ 47 000 individuals with European ancestry. Three low-frequency variants (minor allele frequency < 0.05), rs17662871 [odds ratio (OR) = 0.71, P = 4.29×10-8); rs79942605 (OR = 2.17, P = 2.81×10-8) and rs208908 (OR = 0.70, P = 4.54×10-8) were identified with different risk effect of lung cancer between men and women. Further expression quantitative trait loci and functional annotation analysis suggested rs208908 affects lung cancer risk through differential regulation of Coxsackie virus and adenovirus receptor gene expression in lung tissues between men and women. Our study is one of the first studies to provide novel insights about the genetic and molecular basis for sex disparity in lung cancer development.

Uptake of genetic counseling and testing in a clinic based population of women with breast cancer

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Background: Carriers of pathogenic variants in cancer susceptibility genes have an elevated risk of developing breast, ovarian, and other cancers.We conducted a medical record review to determine the uptake of genetic counseling and testing in a clinic-based population of women with breast cancer. Methods: Medical records of 150 women with breast cancer seen at the Karmanos Cancer Institute between January-December 2018 were reviewed to determine the proportion eligible for genetic testing according to National Comprehensive Cancer Network guidelines. We also assessed genetics referral rates, appointment completion and results of genetic testing. Using chi-square and ANOVA tests, we analyzed the association of demographic and clinical factors with eligibility and referral to genetic counseling. Results: The average age of diagnosis was 57.1 years old, with 68.7% of women diagnosed with stage I-III disease, and 31.3% diagnosed with stage IV disease. There were 91 (60.7%) women who met NCCN criteria for genetic testing, of which 46.2% ultimately underwent genetic testing. Eligible women were more likely to be younger (52.6 vs. 64.0 years old), White (75.0% vs. 54.5%), and have Medicaid (75.0%) or private insurance (72.9%) vs. Medicare (44.8%). Women who met NCCN criteria were 3.5 times more likely to be referred for genetic counseling than those that did not meet eligibility criteria. Women were also more likely to be referred if they had early-stage disease compared to stage IV (67.8% vs. 48.3%), and Medicaid or private insurance compared to Medicare (71.4%, 72.0% and 40.0%, respectively). Of eligible women, 59.3% had a genetic counseling appointment scheduled, and of those, 78.0% attended their appointment. There were no apparent differences in appointment completion based on race with similar percentages of Black and White women completing their appointments (74.0% and 77.0% respectively). Women with stage IV disease were more likely to complete their appointments (83.0%) compared to women with stages I-III (74.0%) and fewer women with Medicare completed their genetic counseling appointment (56.0%) compared to women with Medicaid (83.0%) and women with private insurance (83.0%). Among women who attended their appointment, 95.9% underwent genetic testing. Of women who had genetic testing, 8.5% had a pathogenic variant and 30.4% had a variant of unknown significance. Conclusions: The results of this study indicate that lack of genetic counseling referrals contribute to a gap between the need for and completion of genetic testing. By understanding barriers to genetic counseling and testing, future clinical initiatives could effectively improve accessibility to genetic counseling services.

Physicians' perceptions of breast density notification laws and appropriate patient follow-up

Breast density notification laws have been adopted in the absence of consistent guidelines for post-notification follow-up. This can lead to inconsistent and potentially deficient management of women's health due to inconsistent physician practices. We examined physicians' knowledge and practices regarding follow-up for patients who receive density notifications. Physicians who referred patients to a Michigan hospital network for screening mammograms were recruited to participate in survey study; 105 (29.8%) responded. The survey assessed physicians' demographics, knowledge, and awareness of breast density and breast cancer risk and of density notification laws, and perceptions of appropriate follow-up behaviors for their patients who received density notifications. Most physicians (75%) knew about the notification law, and they were generally comfortable responding to breast density questions and deciding on follow-up. Most indicated that additional breast imaging (68.0%), followed by assessing breast cancer risk (24.7%) were appropriate follow-up responses. Physicians who performed breast cancer risk assessments, and who were more comfortable with breast density questions and follow-up decision making, were more likely to propose additional imaging. Male physicians were less likely to propose assessing breast cancer risk, and less likely to propose clinical and/or breast self-examinations. Divergence between practice and guidelines when it comes to supplemental breast cancer screening, coupled with density notification language that promotes additional screening in the absence of consistent evidence, remains concerning. Improved understanding of how density notification recipients and their physicians make decisions about supplemental screening is warranted to ensure that breast cancer risk is properly considered.

Family cancer patterns and variation by race and ethnicity among individuals with pathogenic variants in multi-gene cancer predisposition panels at a large urban comprehensive cancer center

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Background: The identification of pathogenic variants and variants of unknown significance (VUS) in multi-gene cancer predisposition testing raises new questions regarding cancer risk and management. We evaluated the personal and family cancer patterns and variation by race and ethnicity, among individuals positive for pathogenic variants in non-BRCA1/ 2 cancer predisposing genes. Methods: The Karmanos Cancer Institute (KCI) Cancer Genetics database was queried from May 13, 2013 through December 31, 2018. There were 3,544 unrelated individuals evaluated for hereditary cancer predisposition of whom 1,868 had 18-gene panel testing at 6 sites across Michigan. Data was collected on personal and family cancer history including ages at diagnosis utilizing a 3-generation pedigree, self-identified race and ethnicity and results of genetic testing. We describe the prevalence of pathogenic variants by proband cancer diagnosis, family history, race, and ethnicity. Results: The race/ethnic distribution of the tested cohort included 67.5% non-Hispanic White (NHW), 24.4% African American (AA), 2.1% Arab, 1.8% Ashkenazi Jewish (AJ), 1.0% Hispanic, and 3.4% other. The distribution of cancer diagnoses included 40.6% breast, 5.5% ovarian, 4.1% colon, 3.5% endometrial, 2.0% pancreas and 39.7% unaffected. Pathogenic variants were seen in 151 (8.1%) individuals and VUS in 309 (16.5%). The five most common pathogenic variants were CHEK2 (40), MUTYH (22), ATM (20), and PALB2 (18). The most common pathogenic variants by race and ethnicity were CHEK2 (NHW), RAD51C (AA), PALB2 (Arab), CHEK2, MSH6 (AJ), and none in Hispanics. Variants associated with the four most common cancer types were breast ( CHEK2 ), ovarian ( CHEK2, MUTYH, BRIP1), colon ( ATM), and endometrial ( MSH6, PALB2). Of 40 individuals with CHEK2 variants, 92.5% were NHW, and 34 (85%), 31 (78%), 10 (25%), 1 (2.5%) had family history of breast cancer, breast cancer before age 50, ovarian, and colon cancer, respectively. Of 20 with ATM variants, 95% were NHW, 13 had family history data and 10 (76.9%), 8 (61.5%), 2 (15.4%), 1 (7.7%) had family history of breast, breast cancer before age 50, ovarian, and colon cancer, respectively. Conclusions: Pathogenic variants seen using multigene panel testing differ by race, ethnicity and personal/family history of cancer. This data will inform genetic counseling strategies in regards to cancer risk and management. Data on additional genes updated through 2019 will be presented.

Abstract P6-08-15: Racial and ethnic variation in BRCA1 and BRCA2 genetic test results among individuals referred for genetic counseling at a large urban comprehensive cancer center

Background It is estimated that up to 10% of women diagnosed with breast cancer in the United States have a BRCA1 or BRCA2 inherited susceptibility, which accounts for approximately 125,000 women. There are racial and ethnic differences in the prevalence and types of pathogenic mutations and variants of uncertain significance (VUS) in BRCA1 and BRCA2. To better understand the prevalence of recurring pathogenic mutations and/or uncover novel mutations in specific racial and ethnic groups, we evaluated the mutational profile of individuals who had genetic counseling and testing at a large urban NCI designated Comprehensive Cancer Center. Methods Data was extracted from the Karmanos Cancer Institute (KCI) Cancer Genetic Counseling Service database over a 19 year period through 12/31/18. The cohort consisted of 5,929 individuals evaluated for high-risk of hereditary disease at 6 sites across Michigan including Detroit. We estimated the prevalence of BRCA1/2 pathogenic mutations and variants of uncertain significance (VUS) by race and ethnicity. Odds Ratios (OR) and 95% confidence intervals (CI) were calculated to compare the rate of pathogenic and VUS mutations in race and ethnic groups with non-Hispanic whites (NHW) indicated as the reference group. Results There were 3,114 (52.5%) unrelated individuals who underwent clinical BRCA1/2 testing. The racial/ethnic breakdown of the cohort included: 68.4% NHW, 21% African American (AA), 2.7% Ashkenazi Jewish (AJ), 2.2% Arab, 0.9% Hispanic (H), and 4.8% other. There were 290 individuals with pathogenic mutations (137 BRCA1 and 153 BRCA2) and 186 with VUS (61 BRCA1 and 125 BRCA2). For BRCA1, there were no differences by race and ethnicity in pathogenic mutations, however AA and Arab individuals were more likely to have VUS compared to NHW (OR & 95% CI, 2.63, 1.53-4.54 and 3.39, 1.01-11.41) respectively. For BRCA2, AJ individuals were more likely to have pathogenic mutations compared to NHW (OR & 95% CI, 2.51, 1.22-5.17) and both AA and AJ individuals were more likely to have VUS (OR & 95% CI, 1.55, 1.02-2.35 and 3.15, 95% CI 1.46-6.79) respectively. The table lists the most common pathogenic mutations seen in BRCA1 and BRCA2 by race and ethnicity. All mutations are unique and seen in more than one person unless indicated. Conclusions AA, Arab and AJ individuals were more likely to have VUS in BRCA1&BRCA2 than NHW suggesting the importance of variant reclassification in understanding cancer risk in racial and ethnic minority groups. Understanding the prevalence of BRCA1/2 mutations in specific racial and ethnic groups can potentially lead to customization of genetic testing and possible classification of new founder mutations.

The most common pathogenic mutations by race and ethnicityRace/EthnicityBRCA1 (n)BRCA2 (n)% of Total MutationsNHWp.Glu1756Pro (14)p.Ile605Asn (7)p.Cys61Glu (5)p.Arg645Glu (2)p.Ser1253Arg (4)p.Ala938Pro (2)BRCA1: 28/102=27.5%p.Lys894Thr (3)p.Glu2198Asn (2)BRCA2: 17/103=16.5%p.Asp825Glu (2)2)p.Gln1886Ter (2)p.Asn312Ile (2)AA5296del4 (2)p.Gly1013Glu (2)IVS16+6T&gt;C (2)p.Lys2496Ter (2)BRCA1: 6/23=26.1%p.Thr276Ala (2)p.Lys936Asn (2)BRCA2: 8/32=25%p.Lys1872Asn (2)AJp.Glu23Val (1)p.Ser1982Arg (5)BRCA1: 1/1=100%BRCA2: 5/9=55.6%Arabp.Gln12X(1)p.Ile1859Lys (2)BRCA1: 1/5=20%BRCA2: 2/3 = 66.7%Hispanicp.Arg71Gly (1)p.Glu1308Ter (1)BRCA1: 1/1=100%BRCA2: 1/1=100%

Citation Format: Michael Steven Simon, Nadline Abdallah, Hadeel Assad, Rachel Reagle, Nancie Petrucelli, Kristen Purrington. Racial and ethnic variation in BRCA1 and BRCA2 genetic test results among individuals referred for genetic counseling at a large urban comprehensive cancer center [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-15.

Abstract P4-09-05: Somatic genomic profiles of breast tumors differ by BRCA1 and BRCA2 variants of unknown significance status

Background: Among women with invasive breast cancer, the clinical significance of BRCA1 and BRCA2 variants of unknown significance (VUS) remain uncertain. A closer analysis of the somatic mutational profiles of women with invasive breast cancer and BRCA1 or 2 VUS could provide a better understanding of the pathogenesis of the disease and potentially allow for the development of targeted treatment regimens. We hypothesized that breast cancers with BRCA1/2 VUS will have different somatic genomic profiling patterns and tumor mutational burden (TMB) compared with BRCA1/2 wildtype (WT). Methods: We compared the tumor molecular profiling patterns for breast cancer with somatic BRCA1/2 VUS to BRCA1/2 WT using a multiplatform profiling service (Caris Life Sciences) consisting of next generation sequencing (NGS), protein expression (immunohistochemistry [IHC]) and gene amplification (fluorescence or chromogenic in situ hybridization [FISH or CISH]). We also determined the differences in TMB between VUS and WT. We defined ER/PR/Her2 status based on IHC and/or CISH results. DNA or mutation results with &gt;1% frequency were analyzed using Chi Square test; p&lt;0.05 was considered statistically significant. Results: Among 4,172 breast cancer specimens available in the Caris database acquired from more 800 participating institutions between 2013 and 2018, 125 (3%) and 341 (5.5%) had VUS in BRCA1 and BRCA2 respectively. Women with BRCA1 VUS were more likely to have tumors that are hormone receptor (HR) negative, Her2/neu positive (6.1%) compared to triple negative, triple positive or HR positive, Her2 negative (3.6%, 3.6% and 2.3% respectively) (p-value=0.0096) however BRCA2 VUS were more evenly distributed among tumor subtypes. Tumors with either BRCA1 or BRCA2 VUS were more likely to have a high TMB compared to WT (mean TMB 10.3 mut/Mb vs. 7.5 mut/Mb, p=7.2 × 10−7). Compared to WT tumors, tumors with BRCA1 or BRCA2 VUS were more likely to have pathogenic mutations in RB1 (6.4% vs 3.9%) and TP53 (62.5% vs 56%) and less likely to have GATA3 mutations (5.9% vs 8.8%) and PIK3CA amplifications (0.3% vs 35.3 %%). Furthermore, BRCA1/2 VUS cancers were 3 times more likely to have FGFR2 amplification (P=0.0065). There was no difference in AR or PD-L1 expression between VUS and WT, however breast cancer associated with BRCA1/2 VUS had a significantly less WT1 amplification compared to WT (0.3% vs 72.9%, p value &lt;0.001). Conclusion: Our results suggest that breast cancer associated with BRCA 1 or 2 VUS may be phenotypically and genetically different than WT. Our findings suggest the potential for different responses to immune and targeted therapies, which should be investigated in future prospective studies.

Citation Format: Hadeel Assad, Isabel Hart, Kristen Purrington, Joanne Xiu, Paula R Pohlmann, Sandra Swain, Gregory Vidal, Michael Simon. Somatic genomic profiles of breast tumors differ by BRCA1 and BRCA2 variants of unknown significance status [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-09-05.

Abstract P6-08-22: Racial and ethnic variation in multi-gene panel genetic test results among individuals referred for genetic counseling at a large urban comprehensive cancer center

Background There are racial and ethnic differences in the prevalence and types of pathogenic mutations and variants of uncertain significance (VUS) in BRCA1 and BRCA2. Since the landmark May 13, 2013 Supreme Court Ruling invalidating the patent for BRCA1 and BRCA2 genetic testing, numerous gene panels have been utilized to identify individuals at high risk for hereditary disease due to mutations in other cancer predisposing genes. To better understand the prevalence of recurring pathogenic mutations and/or uncover novel mutations in specific racial and ethnic groups, we evaluated the mutational profile of individuals who had genetic counseling and testing at a large urban NCI designated Comprehensive Cancer Center. Methods Data was extracted from the Karmanos Cancer Institute (KCI) Cancer Genetic Counseling Service data base from May 13, 2013 through December, 31, 2018. The cohort consisted of 3,544 unrelated individuals evaluated for high-risk of hereditary disease and 1,868 who had panel testing at 6 sites across Michigan including Detroit. We estimated the prevalence of pathogenic mutations and VUS from multigene panels by race and ethnicity. Odds Ratios (OR) and 95% confidence intervals (CI) were calculated to compare the rate of pathogenic mutations and VUS in race and ethnic groups with non-Hispanic whites (NHW) indicated as the reference group. Results There were 1,868 (52.7%) individuals who had panel testing which included 67.4% NHW, 24.1% African American (AA), 2.2% Arab, 1.9% Ashkenazi Jewish (AJ), 1.0% Hispanic (H), and 3.4% other. There were 174 individuals with pathogenic mutations and 312 with VUS. Compared to NHW, AA individuals were less likely to have pathogenic mutations on multi-panel testing (OR, 95% CI, 0.20, 0.10-0.37) and more likely to have VUS (OR, 95% CI, 1.41, 1.07-1.85). There were no differences in pathogenic mutations or VUS for other race or ethnic groups. Within a common 18 gene panel (excluding BRCA1 and BRCA2), the five most common genes with a pathogenic mutation were ATM (23), CHEK2 (21), PALB2 (13) and MSH6 (11). The three most common genes and number of pathogenic mutations identified by race and ethnicity were NHW (ATM -21, CHEK2-21&MSH6 -8), AA (MSH6-1, RAD51C-1&TP53-1), and Arab (PALB2-2, RAD50-1 and BARD1-1). For AJ individuals there were 2 pathogenic mutations identified in the MSH6 gene. There were no pathogenic mutations seen in Hispanics. Conclusions Understanding the prevalence of mutations in multi-gene panels in specific racial and ethnic groups can lead to better identification of individuals at risk for hereditary cancer who can benefit from enhanced surveillance and risk reducing management.

Citation Format: Michael Steven Simon, Nadine Abdallah, Hadeel Assad, Malini Surapaneni, Rachel Reagle, Nancie Petrucelli, Kristen Purrington. Racial and ethnic variation in multi-gene panel genetic test results among individuals referred for genetic counseling at a large urban comprehensive cancer center [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-22.

Between-Race Differences in Processes Predicting Physician Communication for African American and European American Recipients of Breast Density Notifications

BACKGROUND

Breast density notification laws mandate reporting of dense breast to applicable women. The same psychological and systemic barriers that yield between-race differences in mammography use will probably yield between-race differences in women's psychological and behavioral responses to breast density notifications.

PURPOSE

We used the theory of planned behavior as a framework to examine between-race differences in the likelihood of following-up with physicians after receiving breast density notifications and to examine differences in African American and Caucasian American women's behavioral decision-making processes.

METHODS

A subset of 212 African American and Caucasian American women who participated in an initial and follow-up survey examining responses to breast density notifications were examined for this study. Participants reported background and demographic measures, psychological responses to receiving notifications, and planned behavior measures related to following up with physicians approximately 2 weeks after receiving their mammogram reports. Participants self-reported their behaviors 3 months later.

RESULTS

There were no between-race differences in self-reported physician communication; however, there were differences in processes that predicted behavior. For Caucasian American women, behavioral intentions, education, and income predicted behaviors. Instead of intentions, group-based medical suspicion, confusion, breast cancer worry, and breast density anxiety predicted behaviors for African American women.

CONCLUSIONS

Behavioral decision-making processes for Caucasian American women were in line with well-validated theoretical predictions. For African American women, race-related medical suspicion, prior breast density awareness, and emotional responses to breast density notifications predicted behavior. The results highlight the need to focus on racially distinct psychological targets when designing interventions to support guideline concordant behavioral decisions among women who receive breast density notifications.

Abstract 4175: Spectrum of heritable mutations in 43 known and candidate breast cancer susceptibility genes in African American women with breast cancer

Mutations in twenty genes have been associated with heritable breast cancer (BCA), yet the prevalence and clinical implications of most of these genes have not been well described in African American women (AAW). AAW who harbor inherited mutations in BCA susceptibility (BCS) genes are less likely to be identified and thus less likely to receive standard of surgical and preventive care for heritable BCA. A better understanding of heritable mutations in AAW with BCA would ultimately help to define guidelines for clinical management of high risk AAW. We performed targeted sequencing for 288 AAW diagnosed with invasive BCA unselected for family history, age, or BCA subtype. Participants were enrolled in the Detroit Research on Cancer Survivors (ROCS) cohort study or the Karmanos Cancer Institute Biobank. A custom sequencing panel captured the coding sequence of 43 genes (Known: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53; Candidate: MLH1, MSH2, PMS1, SEC23B, BLM, ATR, BAP1, BBC3, CDKN1A, FAM175A, FANCA, FANCC, FANCI, FANCL, FANCM, GEN1, RAD51B, RBBP8, RECQL, RINT1, TP53BP1, XRCC1, XRCC3). Samples were sequenced using the Illumina MiSeq platform multiplexed for 100X mean depth of coverage. Intronic or synonymous exonic variants and those with &lt;40 reads, or alternative allele frequency &gt;3% in African populations in the 1000 Genomes, ExAC, or NHLBI ESP6500SI databases were filtered. Only variants in known BCS genes could be considered definitively pathogenic (DP), defined as missense variants categorized as pathogenic in ClinVar and all frameshift, nonsense, and splice site variants. All other variants were defined as variants of uncertain significance (VUS). We identified 54 women harboring DP mutations in 15 known BCS genes. Mutations in BRCA1/2 accounted for 32% of all DP mutations. Notably, nearly 17% of DP mutations were in MSH6, a gene only recently described as associated with increased risk of BCA in the general population. Among women with these DP mutations, nearly 25% had no high-risk characteristics. Ten VUS in known BCS genes were identified, where 4 were reported in ClinVar (BARD1, RAD5C, BRCA2, PMS2) and 6 were novel (PMS2, BRCA1, MUTYH, MSH6, NBN, MRE11). Among the candidate BCS genes, 63 VUS were identified: 51 frameshift variants, 5 nonsense variants, 3 splice site variants, and 4 missense mutations predicted to be pathogenic by ≥8/9 algorithms. Nearly 60% of participants had neither a DP mutation or VUS. These data suggest that AAW with BCA have a unique mutation spectrum and may benefit from BCS gene sequencing regardless of family history, age, or subtype. Additional sequencing in AAW will lay the foundation for identification of germline factors associated with BCA risk and prognosis specifically in AAW and offer opportunities for personalized risk assessment.

Citation Format: Kristen Purrington, Gregory Dyson, Douglas Craig, Julie Boerner, Julie Madden, Jennifer Beebe-Dimmer, Ann G. Schwartz, Michael Simon. Spectrum of heritable mutations in 43 known and candidate breast cancer susceptibility genes in African American women with breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4175.

Profiling the Mutational Landscape in Known Driver Genes and Novel Genes in African American Non-Small Cell Lung Cancer Patients

PURPOSE

Identifying novel driver genes and mutations in African American non-small cell lung cancer (NSCLC) cases can inform targeted therapy and improve outcomes for this traditionally underrepresented population.

EXPERIMENTAL DESIGN

Tumor DNA, RNA, and germline DNA were collected from African American NSCLC patients who participated in research conducted at the Karmanos Cancer Institute (KCI) in Detroit, Michigan. Known mutations were ascertained through the Sequenom LungCarta panel of 214 mutations in 26 genes, RET/ROS1 fusions, amplification of FGFR1, and expression of ALK. Paired tumor and normal DNA was whole-exome sequenced for a subset of cases without known driver mutations.

RESULTS

Of the 193 tumors tested, 77 known driver mutations were identified in 66 patients (34.2%). Sixty-seven of the 127 patients without a known driver mutation were sequenced. In 54 of these patients, 50 nonsynonymous mutations were predicted to have damaging effects among the 26 panel genes, 47 of which are not found in The Cancer Genome Atlas NSCLC white or African American samples. Analyzing the whole-exome sequence data using MutSig2CV identified a total of 88 genes significantly mutated at FDR q < 0.1. Only 5 of these genes were previously reported as oncogenic.

CONCLUSIONS

These findings suggest that broader mutation profiling including both known and novel driver genes in African Americans with NSCLC will identify additional mutations that may be useful in treatment decision-making.

Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes

Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (SNPs) were selected by stepwise regression or lasso penalized regression. The best performing PRSs were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from UK Biobank (3,215 incident breast cancers). For the best PRSs (313 SNPs), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%CI: 1.57-1.65) with area under receiver-operator curve (AUC) = 0.630 (95%CI: 0.628-0.651). The lifetime risk of overall breast cancer in the top centile of the PRSs was 32.6%. Compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing ER-positive and ER-negative disease, respectively. Goodness-of-fit tests indicated that this PRS was well calibrated and predicts disease risk accurately in the tails of the distribution. This PRS is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs.

Between-Race Differences in Supplemental Breast Cancer Screening Before and After Breast Density Notification Law

Guidelines recommend supplemental breast cancer screening for women at increased breast cancer risk; however, the passage of breast density notification laws may lead to supplemental screening that is incongruent with women's risk. We examined supplemental screening (ie, MRI, ultrasound, or tomosynthesis within 6 months of screening mammogram) among a sample of 2,764 African American (AA) and 691 European American (EA) women with negative or benign screening mammograms for whom we had data from both before and after implementation of breast density notification laws in the state of Michigan. Results indicated a 5-fold increase (from 0.14% to 0.7% of women) in supplemental screening among screen-negative women after passage of the law, driven in large part by an increase in supplemental screening among AA women. Breast density was more predictive of supplemental screening and had a marginally greater explanatory role in between-race differences in supplemental screening after passage of the law. Subgroup analyses (n = 250) indicated that whereas 5-year breast cancer risk was positively associated with supplemental screening before the law and negatively associated after the law for EA women, 5-year risk was not associated with supplemental screening either before or after passage of the law for AA women. Our findings suggest that whereas passage of the breast density notification laws may have motivated supplemental screening among AA women in particular, it lessened the consideration of breast cancer risk in supplemental screening decision making.

Explaining between-race differences in African-American and European-American women's responses to breast density notification

BACKGROUND

Prior research shows between-race differences in women's knowledge and emotions related to having dense breasts, thus suggesting that between-race differences in behavioral decision-making following receipt of breast density (BD) notifications are likely. Guided by the theory of planned behavior, this study examined differences in emotion-related responses (i.e., anxiety, worry, confusion) and behavioral cognition (e.g., intentions, behavioral attitudes) following receipt of BD notifications among African American (AA) and European American (EA) women. This study also examined whether race-related perceptions (i.e., discrimination, group-based medical mistrust), relevant knowledge and socioeconomic status (SES) explained the between race differences.

METHOD

Michigan women (N = 457) who presented for routine screening mammogram and had dense breasts, no prior breast cancer diagnoses, and had screen-negative mammograms were recruited from July, 2015 to March 2016. MANOVA was used to examine between race differences in psychological responses (i.e., emotional responses and behavioral cognition), and a multi-group structural regression model was used to examine whether race-related constructs, knowledge and SES mediated the effect of race on emotional responses and behavioral cognition. Prior awareness of BD was accounted for in all analyses.

RESULTS

AA women generally reported more negative psychological responses to receiving BD notifications regardless of prior BD awareness. AA women had more favorable perceptions related to talking to their physicians about the BD notifications. Generally, race-related perceptions, SES, and related knowledge partially accounted for the effect of race on psychological response. Race-related perceptions and SES partially accounted for the differences in behavioral intentions. Between-race differences in emotional responses to BD notifications did not explain differences in women's intentions to discuss BD notifications with their physicians.

CONCLUSIONS

Future examinations are warranted to examine whether there are between-race differences in actual post-BD notification behaviors and whether similar race-related variables account for differences.

The effect of genetic variants on the relationship between statins and breast cancer in postmenopausal women in the Women's Health Initiative observational study

PURPOSE

Statins have been postulated to have chemopreventive activity against breast cancer. We evaluated whether germline genetic polymorphisms modified the relationship between statins and breast cancer risk using data from the Women's Health Initiative. We evaluated these interactions using both candidate gene and agnostic genome-wide approaches.

METHODS

To identify candidate gene-statin interactions, we tested interactions between 22 SNPS in nine candidate genes implicated in the effect of statins on lipid metabolism in 1687 cases and 1687 controls. We then evaluated statin use interaction with the remaining 30,380 SNPs available in this sample from the CGEMS GWAS study.

RESULTS

After adjusting for multiple comparisons, no SNP interactions with statin usage and risk of breast cancer were statistically significant in either the candidate genes or genome-wide approaches.

CONCLUSIONS

We found no evidence of SNP interactions with statin usage for breast cancer risk in a population of 3374 individuals. These results suggest that genome-wide common genetic variants do not moderate the association between statin usage and breast cancer in the population of women in the Women's Health Initiative.

Influences of race and breast density on related cognitive and emotion outcomes before mandated breast density notification

RATIONALE

Many states have adopted laws mandating breast density (BD) notification for applicable women; however, very little is known about what women knew or felt about BD and related breast cancer (BC) risk before implementation of BD notification laws.

OBJECTIVE

We examined between-race differences in the extent to which having dense breasts was associated with women's related BD cognition and emotion, and with health care providers' communication about BD.

METHODS

We received surveys between May and October of 2015 assessing health care provider (HCP) communication about BD, BD-related knowledge, BD-related anxiety and BC worry from 182 African American (AA) and 113 European American (EA) women in the state of Michigan for whom we had radiologists' assessments of BD.

RESULTS

Whereas having dense breasts was not associated with any BD-related cognition or emotion, there were robust effects of race as follows: EA women were more likely to have been told about BD by a HCP, more likely to know their BD status, had greater knowledge of BD and of BC risk, and had greater perceptions of BC risk and worry; AA women had greater BD-related anxieties. EA women's greater knowledge of their own BD status was directly related to the increased likelihood of HCP communication about BD. However, HCP communication about BD attenuated anxiety for AA women only.

CONCLUSION

We present the only data of which we are aware that examines between-race differences in the associations between actual BD, HCP communication and BD related cognition and emotion before the implementation of BD notification laws. Our findings suggest that the BD notification laws could yield positive benefits for disparities in BD-related knowledge and anxiety when the notifications are followed by discussions with health care providers.

Between-race differences in the effects of breast density information and information about new imaging technology on breast-health decision-making

OBJECTIVES

Some US states have mandated that women be informed when they have dense breasts; however, little is known about how general knowledge about breast density (BD) affects related health decision-making. We examined the effects of BD information and imaging technology information on 138 African-American (AA) and European-American (EA) women's intentions to discuss breast cancer screening with their physicians.

METHODS

Women were randomly assigned to receive BD information and/or imaging technology information via 2 by 2 factorial design, and completed planned behavior measures (e.g., attitudes, intentions) related to BC screening.

RESULTS

Attitudes mediated the effects of BD information, and the mediation was stronger for AA women compared to EA women. Effects were more robust for BD information compared to imaging technology information. Results of moderator analyses revealed suppressor effects of injunctive norms that were moderated by imaging technology information.

CONCLUSION

Information about BD favorably influences women's intentions to engage in relevant breast health behaviors. Stronger attitude mediated-effects for AA women suggest greater scrutiny of BD information.

PRACTICE IMPLICATIONS

Since BD information may influence women's intentions to discuss BC screening, strategies to effectively present BD information to AA women should be investigated given the likelihood of their increased scrutiny of BD information.

Abstract 1924: Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes

Distinct subtypes of triple negative (TN) breast cancer have currently been identified by tumor expression profiling and are thought to be influenced by the tumor microenvironment. However, little is known about the relationship between distinguishing histopathologic features of TN tumors, which reflect aspects of both tumor behavior and tumor microenvironment, and molecular TN subtypes. We analyzed whole genome expression profiles of 593 TN tumors from the Triple Negative Breast Cancer Consortium (TNBCC) using the Illumina Whole Genome DASL array. Histopathologic review of mitotic index, grade, trabecular pattern, growth pattern, involution, presence of ductal carcinoma in situ, and degree of lymphoid infiltrate, necrosis, fibrosis, and lobulitis was completed for 310 of these tumors. Clusters were identified both agnostically and using genes associated with these histopathologic features, and subtypes were evaluated for enriched pathways and associations with histopathologic features. Agnostic clustering identified four stable clusters which represented a basal-like (BL) signature, a luminal signature with overexpression of androgen receptor and targets, an immune signature, and a stromal (STR) signature. Overall, the TN tumors tended to have little or no necrosis (91%), high grade (88%), a high mitotic index (80%), fibrosis (77%), an epicentric growth pattern (62%), incomplete lobular involution (55%), trabecular structures (37%), lymphocytic infiltration (25%), adjacent ductal carcinoma in situ (24%), and variable amounts of lobulitis. Using a combined total of 2,776 unique probes individually associated with the ten histopathologic features measured, we identified six distinct TN subtypes, with an additional BL and STR signature compared to the four agnostic subtypes. Our findings suggest that histopathologic features that reflect heterogeneity in tumor cell structure and behavior as well as the tumor microenvironment, particularly the presence of lymphocytic infiltrate, are critical for TN subtype identification. Further work is needed to validate these signatures and to better understand the immunologic pathways associated with each subtype.

Citation Format: Kristen Purrington, Daniel Visscher, Drakoulis Yannoukakos, Jane Carpenter, Heli Nevanlinna, Arto Mannerma, Xianshu Wang, Graham Giles, Wei Zheng, Angela Cox, Hiltrud Brauch, Ute Hamann, Diana Eccles, Celine M. Vachon, Fergus J. Couch. Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1924. doi:10.1158/1538-7445.AM2015-1924

Novel Associations between Common Breast Cancer Susceptibility Variants and Risk-Predicting Mammographic Density Measures

Mammographic density measures adjusted for age and body mass index (BMI) are heritable predictors of breast cancer risk, but few mammographic density-associated genetic variants have been identified. Using data for 10,727 women from two international consortia, we estimated associations between 77 common breast cancer susceptibility variants and absolute dense area, percent dense area and absolute nondense area adjusted for study, age, and BMI using mixed linear modeling. We found strong support for established associations between rs10995190 (in the region of ZNF365), rs2046210 (ESR1), and rs3817198 (LSP1) and adjusted absolute and percent dense areas (all P < 10(-5)). Of 41 recently discovered breast cancer susceptibility variants, associations were found between rs1432679 (EBF1), rs17817449 (MIR1972-2: FTO), rs12710696 (2p24.1), and rs3757318 (ESR1) and adjusted absolute and percent dense areas, respectively. There were associations between rs6001930 (MKL1) and both adjusted absolute dense and nondense areas, and between rs17356907 (NTN4) and adjusted absolute nondense area. Trends in all but two associations were consistent with those for breast cancer risk. Results suggested that 18% of breast cancer susceptibility variants were associated with at least one mammographic density measure. Genetic variants at multiple loci were associated with both breast cancer risk and the mammographic density measures. Further understanding of the underlying mechanisms at these loci could help identify etiologic pathways implicated in how mammographic density predicts breast cancer risk.

Inherited variants in the inner centromere protein (INCENP) gene of the chromosomal passenger complex contribute to the susceptibility of ER-negative breast cancer

The chromosomal passenger complex (CPC) plays a pivotal role in the regulation of cell division. Therefore, inherited CPC variability could influence tumor development. The present candidate gene approach investigates the relationship between single nucleotide polymorphisms (SNPs) in genes encoding key CPC components and breast cancer risk. Fifteen SNPs in four CPC genes (INCENP, AURKB, BIRC5 and CDCA8) were genotyped in 88 911 European women from 39 case-control studies of the Breast Cancer Association Consortium. Possible associations were investigated in fixed-effects meta-analyses. The synonymous SNP rs1675126 in exon 7 of INCENP was associated with overall breast cancer risk [per A allele odds ratio (OR) 0.95, 95% confidence interval (CI) 0.92-0.98, P = 0.007] and particularly with estrogen receptor (ER)-negative breast tumors (per A allele OR 0.89, 95% CI 0.83-0.95, P = 0.0005). SNPs not directly genotyped were imputed based on 1000 Genomes. The SNPs rs1047739 in the 3' untranslated region and rs144045115 downstream of INCENP showed the strongest association signals for overall (per T allele OR 1.03, 95% CI 1.00-1.06, P = 0.0009) and ER-negative breast cancer risk (per A allele OR 1.06, 95% CI 1.02-1.10, P = 0.0002). Two genotyped SNPs in BIRC5 were associated with familial breast cancer risk (top SNP rs2071214: per G allele OR 1.12, 95% CI 1.04-1.21, P = 0.002). The data suggest that INCENP in the CPC pathway contributes to ER-negative breast cancer susceptibility in the European population. In spite of a modest contribution of CPC-inherited variants to the total burden of sporadic and familial breast cancer, their potential as novel targets for breast cancer treatment should be further investigated.

Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk

Previous studies have suggested that polymorphisms in CASP8 on chromosome 2 are associated with breast cancer risk. To clarify the role of CASP8 in breast cancer susceptibility, we carried out dense genotyping of this region in the Breast Cancer Association Consortium (BCAC). Single-nucleotide polymorphisms (SNPs) spanning a 1 Mb region around CASP8 were genotyped in 46 450 breast cancer cases and 42 600 controls of European origin from 41 studies participating in the BCAC as part of a custom genotyping array experiment (iCOGS). Missing genotypes and SNPs were imputed and, after quality exclusions, 501 typed and 1232 imputed SNPs were included in logistic regression models adjusting for study and ancestry principal components. The SNPs retained in the final model were investigated further in data from nine genome-wide association studies (GWAS) comprising in total 10 052 case and 12 575 control subjects. The most significant association signal observed in European subjects was for the imputed intronic SNP rs1830298 in ALS2CR12 (telomeric to CASP8), with per allele odds ratio and 95% confidence interval [OR (95% confidence interval, CI)] for the minor allele of 1.05 (1.03-1.07), P = 1 × 10(-5). Three additional independent signals from intronic SNPs were identified, in CASP8 (rs36043647), ALS2CR11 (rs59278883) and CFLAR (rs7558475). The association with rs1830298 was replicated in the imputed results from the combined GWAS (P = 3 × 10(-6)), yielding a combined OR (95% CI) of 1.06 (1.04-1.08), P = 1 × 10(-9). Analyses of gene expression associations in peripheral blood and normal breast tissue indicate that CASP8 might be the target gene, suggesting a mechanism involving apoptosis.

Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium

Candidate variant association studies have been largely unsuccessful in identifying common breast cancer susceptibility variants, although most studies have been underpowered to detect associations of a realistic magnitude. We assessed 41 common non-synonymous single-nucleotide polymorphisms (nsSNPs) for which evidence of association with breast cancer risk had been previously reported. Case-control data were combined from 38 studies of white European women (46 450 cases and 42 600 controls) and analyzed using unconditional logistic regression. Strong evidence of association was observed for three nsSNPs: ATXN7-K264R at 3p21 [rs1053338, per allele OR = 1.07, 95% confidence interval (CI) = 1.04-1.10, P = 2.9 × 10(-6)], AKAP9-M463I at 7q21 (rs6964587, OR = 1.05, 95% CI = 1.03-1.07, P = 1.7 × 10(-6)) and NEK10-L513S at 3p24 (rs10510592, OR = 1.10, 95% CI = 1.07-1.12, P = 5.1 × 10(-17)). The first two associations reached genome-wide statistical significance in a combined analysis of available data, including independent data from nine genome-wide association studies (GWASs): for ATXN7-K264R, OR = 1.07 (95% CI = 1.05-1.10, P = 1.0 × 10(-8)); for AKAP9-M463I, OR = 1.05 (95% CI = 1.04-1.07, P = 2.0 × 10(-10)). Further analysis of other common variants in these two regions suggested that intronic SNPs nearby are more strongly associated with disease risk. We have thus identified a novel susceptibility locus at 3p21, and confirmed previous suggestive evidence that rs6964587 at 7q21 is associated with risk. The third locus, rs10510592, is located in an established breast cancer susceptibility region; the association was substantially attenuated after adjustment for the known GWAS hit. Thus, each of the associated nsSNPs is likely to be a marker for another, non-coding, variant causally related to breast cancer risk. Further fine-mapping and functional studies are required to identify the underlying risk-modifying variants and the genes through which they act.

A large-scale assessment of two-way SNP interactions in breast cancer susceptibility using 46,450 cases and 42,461 controls from the breast cancer association consortium

Part of the substantial unexplained familial aggregation of breast cancer may be due to interactions between common variants, but few studies have had adequate statistical power to detect interactions of realistic magnitude. We aimed to assess all two-way interactions in breast cancer susceptibility between 70,917 single nucleotide polymorphisms (SNPs) selected primarily based on prior evidence of a marginal effect. Thirty-eight international studies contributed data for 46,450 breast cancer cases and 42,461 controls of European origin as part of a multi-consortium project (COGS). First, SNPs were preselected based on evidence (P < 0.01) of a per-allele main effect, and all two-way combinations of those were evaluated by a per-allele (1 d.f.) test for interaction using logistic regression. Second, all 2.5 billion possible two-SNP combinations were evaluated using Boolean operation-based screening and testing, and SNP pairs with the strongest evidence of interaction (P < 10(-4)) were selected for more careful assessment by logistic regression. Under the first approach, 3277 SNPs were preselected, but an evaluation of all possible two-SNP combinations (1 d.f.) identified no interactions at P < 10(-8). Results from the second analytic approach were consistent with those from the first (P > 10(-10)). In summary, we observed little evidence of two-way SNP interactions in breast cancer susceptibility, despite the large number of SNPs with potential marginal effects considered and the very large sample size. This finding may have important implications for risk prediction, simplifying the modelling required. Further comprehensive, large-scale genome-wide interaction studies may identify novel interacting loci if the inherent logistic and computational challenges can be overcome.

FGF receptor genes and breast cancer susceptibility: results from the Breast Cancer Association Consortium

BACKGROUND

Breast cancer is one of the most common malignancies in women. Genome-wide association studies have identified FGFR2 as a breast cancer susceptibility gene. Common variation in other fibroblast growth factor (FGF) receptors might also modify risk. We tested this hypothesis by studying genotyped single-nucleotide polymorphisms (SNPs) and imputed SNPs in FGFR1, FGFR3, FGFR4 and FGFRL1 in the Breast Cancer Association Consortium.

METHODS

Data were combined from 49 studies, including 53 835 cases and 50 156 controls, of which 89 050 (46 450 cases and 42 600 controls) were of European ancestry, 12 893 (6269 cases and 6624 controls) of Asian and 2048 (1116 cases and 932 controls) of African ancestry. Associations with risk of breast cancer, overall and by disease sub-type, were assessed using unconditional logistic regression.

RESULTS

Little evidence of association with breast cancer risk was observed for SNPs in the FGF receptor genes. The strongest evidence in European women was for rs743682 in FGFR3; the estimated per-allele odds ratio was 1.05 (95% confidence interval=1.02-1.09, P=0.0020), which is substantially lower than that observed for SNPs in FGFR2.

CONCLUSION

Our results suggest that common variants in the other FGF receptors are not associated with risk of breast cancer to the degree observed for FGFR2.

Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions

Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10(-07)), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m(2) (OR = 1.26, 95% CI 1.15-1.38) but not in women with a BMI of 30 kg/m(2) or higher (OR = 0.89, 95% CI 0.72-1.11, P for interaction = 3.2 × 10(-05)). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci.

Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1

The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ERα to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease.