Polley, Eric C.

PURPOSE This trial assessed the utility of applying tumor DNA sequencing to treatment selection for patients with advanced, refractory cancer and somatic mutations in one of four signaling pathways by comparing the efficacy of four study regimens that were either matched to the patient's aberrant pathway (experimental arm) or not matched to that pathway (control arm). MATERIALS AND METHODS Adult patients with an actionable mutation of interest were randomly assigned 2:1 to receive either (1) a study regimen identified to target the aberrant pathway found in their tumor (veliparib with temozolomide or adavosertib with carboplatin [DNA repair pathway], everolimus [PI3K pathway], or trametinib [RAS/RAF/MEK pathway]), or (2) one of the same four regimens, but chosen from among those not targeting that pathway. RESULTS Among 49 patients treated in the experimental arm, the objective response rate was 2% (95% CI, 0% to 10.9%). One of 20 patients (5%) in the experimental trametinib cohort had a partial response. There were no responses in the other cohorts. Although patients and physicians were blinded to the sequencing and random assignment results, a higher pretreatment dropout rate was observed in the control arm (22%) compared with the experimental arm (6%; P = .038), suggesting that some patients may have had prior tumor mutation profiling performed that led to a lack of participation in the control arm. CONCLUSION Further investigation, better annotation of predictive biomarkers, and the development of more effective agents are necessary to inform treatment decisions in an era of precision cancer medicine. Increasing prevalence of tumor mutation profiling and preference for targeted therapy make it difficult to use a randomized phase II design to evaluate targeted therapy efficacy in an advanced disease setting.

AbstractEmbolectomy is one of the emergency procedures performed to remove emboli. Assessing the composition of human blood clots is an important diagnostic factor and could provide guidance for an appropriate treatment strategy for interventional physicians. Immunostaining has been used to identity compositions of clots as a gold‐standard procedure, but it is time‐consuming and cannot be performed in situ. Here, we proposed that the optical attenuation coefficient of optical coherence tomography (OCT) can be a reliable indicator as a new imaging modality to differentiate clot compositions. Fifteen human blood clots with multiple red blood cell (RBC) compositions from 21% to 95% were prepared using healthy human whole blood. A homogeneous gelatin phantom experiment and numerical simulation based on the Lambert–Beer's law were examined to verify the validity of the attenuation coefficient estimation. The results displayed that optical attenuation coefficients were strongly correlated with RBC compositions. We reported that attenuation coefficients could be a promising biomarker to guide the choice of an appropriate interventional device in a clinical setting and assist in characterizing blood clots.

Abstract To evaluate the racial and ethnic differences in prevalence of germline pathogenic variants (PVs) and the effect of race and ethnicity on breast cancer (BC) risk among carriers, results of multigene testing of 77 900 women with BC (non-Hispanic White [NHW] = 57 003; Ashkenazi-Jewish = 4798; Black = 6722; Hispanic = 5194; and Asian = 4183) were analyzed, and the frequency of PVs in each gene were compared between BC patients (cases) and race- and ethnicity-matched gnomAD reference controls. Compared with NHWs, BRCA1 PVs were enriched in Ashkenazi-Jews and Hispanics, whereas CHEK2 PVs were statistically significantly lower in Blacks, Hispanics, and Asians (all 2-sided P < .05). In case-control studies, BARD1 PVs were associated with high risks (odds ratio > 4.00) of BC in Blacks, Hispanics, and Asians; ATM PVs were associated with increased risk of BC among all races and ethnicities except Asians, whereas CHEK2 and BRIP1 PVs were associated with increased risk of BC among NHWs and Hispanics only. These findings suggest a need for personalized management of BC risk in PV carriers based on race and ethnicity.

Abstract Purpose: To compare the clinical characteristics and overall survival (OS) of germline mutation carriers in homologous recombination repair (HRR) genes and noncarriers with pancreatic ductal adenocarcinoma (PDAC). Experimental Design: Germline DNA from 3,078 patients with PDAC enrolled in a prospective registry at Mayo Clinic between 2000 and 2017 was analyzed for mutations in 37 cancer predisposition genes. Characteristics and OS of patients with mutations in eight genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, PALB2, RAD51C, and RAD51D) involved in HRR were compared with patients testing negative for mutations in all 37 genes. Results: The 175 HRR mutation carriers and 2,730 noncarriers in the study had a median duration of follow-up of 9.9 years. HRR mutation carriers were younger (median age at diagnosis: 63 vs. 66 years, P < 0.001) and more likely to have metastatic disease at diagnosis (46% vs. 36%, P = 0.004). In a multivariable model adjusting for sex, age at diagnosis, and tumor staging, patients with germline HRR mutations had a significantly longer OS compared with noncarriers [HR, 0.83; 95% confidence interval (CI), 0.70–0.97; P = 0.02]. Further gene-level analysis demonstrated that germline ATM mutation carriers had longer OS compared with patients without germline mutations in any of the 37 genes (HR, 0.72; 95% CI, 0.55–0.94; P = 0.01). Conclusions: This study demonstrates that germline mutation carrier status in PDAC is associated with longer OS compared with noncarriers. Further research into tumor biology and response to platinum-based chemotherapy in germline mutation carriers with PDAC are needed to better understand the association with longer OS.

Abstract We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.

Abstract Background: Pathogenic variants detected in multi-gene cancer predisposition panels are increasingly used to counsel women regarding their risk for breast cancer. However, the clinical implications of moderate penetrance genes (e.g. CHEK2, ATM) remain unclear. Breast MRI is indicated for women with a lifetime risk of breast cancer of >20%, and polygenic risk scores (PRS) based on common variants discovered in recent genome-wide association studies (GWAS) may identify women with pathogenic variants in CHEK2 and ATM who are above or below this level of risk. PRS may also stratify carriers with substantially elevated lifetime risks of breast cancer. Previous work found that PRS modified breast cancer risk in carriers of pathogenic variant in BRCA1 or BRCA2, but the joint effects of pathogenic variants and PRS have not been studied in samples drawn from the general population. There is also no published study evaluating the effect of PRS among women with pathogenic variants in genes other than BRCA1/2 and CHEK2. Here, we evaluated the joint effects of PRS and pathogenic variants in ten established breast cancer predisposition genes in a population-based case-control sample. Method: We analyzed 43,144 non-Hispanic European-ancestry individuals (20,988 controls and 22,120 cases) drawn from 7 cohorts and 2 population-based case-control studies in the CAnceR RIsk Estimates Related to Susceptibility” (CARRIERS) consortium. Targeted sequencing was performed using a dual bar-coded QIAseq panel of breast cancer predisposition genes. Variant calling was conducted with Haplotype Caller and Vardict. The PRS was calculated based on 106 common variants using effect estimates from the largest published breast cancer GWAS. Genetic status was evaluated for 10 breast cancer predisposition genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, NF1, PALB2 and TP53. Lasso Penalized regression was performed to assess the combined effect on overall breast cancer of pathogenic variants and common variants (including main and interaction effects between age, family history, carrier status and PRS). The fraction of women at >2-fold increased risk (which is associated with approximately 20% lifetime risk of breast cancer) was calculated for pathogenic variant carriers and non-carriers of different family history and age groups (<40, 40-50, 50-60, 60-70, >70yrs old). Results: Among non-carriers, one standard deviation change in the PRS was associated with a 1.63x change in odds of breast cancer. The best-fitting risk model did not include any PRS-by-carrier interaction terms, implying the relative risk gradient associated with PRS among women with pathogenic variants is similar to that among non-carriers. For carriers of pathogenic variants in moderate penetrance genes with no family history of breast cancer, the PRS can identify 60.6% of ATM pathogenic variant carriers and 30% of CHEK2 pathogenic variant carriers that have less than 2-fold risk of breast cancer; when carriers have a family history of breast cancer, the PRS can identify 30% of ATM pathogenic variant carriers and 11.8% of CHEK2 pathogenic variant carriers with less than 2-fold risk of breast cancer. Conclusion: In our large, population-based case-control study, the effect of the PRS among pathogenic variant carriers was not significantly different than among non-carriers. However, the PRS may be particularly important for estimating breast cancer risk among carriers of pathogenic variants in moderate penetrance genes such as CHEK2 and ATM, enabling a more precise approach for MRI screening strategy and breast cancer risk management. Citation Format: Chi Gao, Eric C. Polley, Chunling Hu, Steven N. Hart, Rohan Gnanaolivu, Kun Y. Lee, Jie Na, Nicholas J. Boddicker, Raed Samara, Paul Auer, Leslie Bernstein, Mia Gaudet, Amy Trentham-Dietz, Song Yao, Christopher Haiman, Janet E. Olson, Susan Neuhausen, Jeffrey N. Weitzel, David E. Goldgar, Susan Domchek, Katherine L. Nathanson, Fergus J. Couch, Peter Kraft, on behalf of the CARRIERS consortium. Polygenic risk scores provide clinically meaningful risk stratification among women carrying moderate penetrance pathogenic variants in breast cancer predisposition genes: Results from the CARRIERS study [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 PD3-02.

Abstract Germline mutations in several cancer predisposition genes included in hereditary multigene testing panels have been associated with increased breast cancer risk. However, estimates of breast cancer risks for each gene have in large part been derived from studies of high-risk populations enriched for family history of breast and ovarian cancer, young age of breast cancer diagnosis, or founder mutations. The breast cancer risks associated with mutations in many of these genes in the general population remain to be clearly defined. As clinical hereditary cancer genetic testing is already provided to many women at increased risk and may soon be offered to all breast cancer patients, population-based risk estimates associated with predisposition gene mutations will be needed for appropriate clinical management of mutation carriers. The “CAnceR RIsk Estimates Related to Susceptibility” (CARRIERS) consortium of 17 cohort-based case-control, population-based case-control, and family studies focused on estimation of population-based breast cancer risks and penetrance analysis for mutations in known and candidate breast cancer predisposition genes. Germline DNA from 39486 breast cancer cases and 35868 matched controls was subjected to dual bar-coded QIAseq multiplex amplification of 1733 target regions in 37 predisposition genes. Products from sets of 768 samples were pooled and sequenced in each lane of a HiSeq 4000 system. Mutations were called by GATK Haplotype Caller and Verdict. High quality sequence data was obtained for 99.3% of target regions. Here we report on results from 34741 population-based breast cancer cases and 32728 matched unaffected controls. The mean age of breast cancer diagnosis for cases was 61.2 years and mean age for controls was 61.1 years. Overall, 20.9% of cases and 14.3% of controls had a family history of breast cancer. Furthermore, 74.3% of cases and 75.8% of controls were non-Hispanic white, whereas 13.3% of cases and 15.3% of controls were African American. Among cases with tumor information available, 81.7% were ER-positive and 7.7% were triple negative breast cancers (TNBC). We assessed mutation frequencies in 24 genes including 12 established breast cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, NF1, PALB2, PTEN, RAD51C, RAD51D, andTP53). The overall mutation frequency was 6.2% in cases and 2.7% in controls. Case-control association analysis after adjusting for study, age, family history of breast cancer, and race/ethnicity showed that BRCA1(OR=7.45; 95%CI:5.24-10.95) and BRCA2(OR=5.31; 95%CI:4.15-6.88) were associated with high risks of breast cancer in the general population. However, PALB2mutations were only associated with moderate risks (OR=3.63; 95%CI:2.57-5.26). ATMmutations conferred attenuated risks (OR=1.83; 95%CI:1.47-2.28) relative to studies of high-risk families or young onset breast cancers. NBNmutations were not associated with increased breast cancer risk. Mutations in BARD1, RAD51C, RAD51Dand XRCC2were specifically significantly associated with moderate risks of ER-negative breast cancer and TNBC, whereas mutations in ATM, CDH1and CHEK2were specifically significantly associated with ER-positive disease. On the basis of these findings age-related absolute breast cancer risks for commonly mutated genes were estimated. Overall, results from the CARRIERS study establish that mutations in predisposition genes are associated with lower risks of breast cancer in the general population than in enriched populations including high-risk families and young onset, bilateral, or multiple primary cases. We anticipate that the results from this study will inform cancer screening and other risk management strategies for women in the general population with mutations in predisposition genes. Citation Format: Fergus J Couch, Chunling Hu, Steven N Hart, Rohan Gnanaolivu, Kun Y Lee, Jie Na, Chi Gao, Nicholas J Boddicker, Bruce Eckloff, Raed Samara, Josh Klebba, Christine B Ambrosone, Hoda Anton-Culver, Paul Auer, Leslie Bernstein, Mia M Gaudet, Christopher Haiman, Esther M John, Susan Neuhausen, Janet E Olson, Tuya Pal, Julie R Palmer, Dale P Sandler, Jack A Taylor, Amy Trentham-Dietz, Celine M Vachon, Clarice Weinberg, Song Yao, Jeffrey N Weitzel, David E Goldgar, Susan M Domchek, Katherine L Nathanson, Peter Kraft, Eric C Polley. Population-based breast cancer risk estimates for predisposition gene mutations: Results from the CARRIERS study [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 PD3-01.

Abstract Background: Invasive lobular carcinoma (ILC) of the breast accounts for approximately 10-15% of all histologic subtypes of breast cancer. However, apart from germline mutations in CDH1, the contributions of mutations in other cancer predisposition genes to ILC are largely unknown. Methods: The study population included 3,893 women with ILC of the breast who underwent germline multigene panel testing of cancer predisposition genes at Ambry Genetics from March 2012 to December 2016. The prevalence of predisposition gene mutations in women with ILC was assessed relative to 38,004 women with invasive ductal carcinoma (IDC) who underwent germline multigene panel testing at Ambry Genetics during the same timeframe. Associations between mutations in each gene and risk of ILC were evaluated using reference controls. Results: Of the 3,893 women with ILC included in this study, 70.7% were non-Hispanic white, 65.1% had a family history of breast cancer, and 96.4% had estrogen receptor (ER) positive breast cancer. The overall frequency of germline mutations in cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHEK2, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, PALB2, PTEN, RAD51C, RAD51D and TP53) was 7.8% for women with ILC and 10.7% for women with IDC. Mutations in CDH1 were significantly more frequent (Odds Ratio (OR)=12.1, p<0.001), whereas mutations in BRCA1 (OR=0.1; p<0.001) and PALB2 (OR=0.4; p<0.001)were less frequent in women with ILC, compared to women with IDC. When restricting the analysis to ER positive cases only, significant differences in frequencies of ATM (OR=0.6, p=0.03), BRCA1 (OR=0.3, p<0.001), CDH1 (OR=7.7, p<0.001) and PALB2 (OR=0.3, p<0.001) were observed in ILC compared to IDC. By comparison with gnomAD reference controls, ATM, BRCA2, CDH1, CHEK2, PALB2 and PTEN mutations were significantly associated with an increased risk of lLC and IDC (OR>2), NBN mutations were associated with ILC (OR=3.4; p<0.001) but not IDC, and BRCA1 mutations were not associated with increased risk of ILC. Among 274 women with ILC over the age of 50 without history of any other cancer or a family history of breast or ovarian cancer, 14 (5.1%) were found to carry a mutation in one of the genes evaluated. Conclusions: In a large cohort of patients with ILC, the frequencies of germline mutations in cancer predisposition genes were similar between ILC and IDC except for ATM, BRCA1, CDH1 and PALB2. Six genes, in addition to CDH1, were found to be germline predisposition genes for ILC. A substantial proportion of patients older than 50 with ILC without a family history of breast or ovarian cancer or a personal history of other cancers were found to be mutation carriers. These findings improve our understanding of germline genetic drivers of ILC and suggest that multigene genetic testing should be considered for all ILC patients. Citation Format: Siddhartha Yadav, Holly LaDuca, Eric C. Polley, Chunling Hu, Steven N. Hart, Jie Na, Rohan Gnanaolivu, Brandon Smith, David E Goldgar, Tina Pesaran, Jill S. Dolinsky, Fergus J. Couch. Germline mutations in cancer predisposition genes in patients with invasive lobular carcinoma of the breast [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 P6-08-04.

Abstract Purpose: To determine the sensitivity of germline hereditary cancer genetic testing recommendations for detection of pathogenic mutations in breast cancer predisposition genes in an unselected cohort of breast cancer patients. Patients and Methods: The study population included patients enrolled in a prospective breast cancer registry after being seen at Mayo Clinic for newly diagnosed breast cancer between 2004 and 2016. All patients were subjected to germline mutation testing for 12 known breast cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, NF1, PALB2, PTEN, RAD51C, RAD51D and TP53). Results from testing of all breast cancer patients according to American Society of Breast Surgeons (ASBrS) genetic testing recommendations and patients meeting National Comprehensive Cancer Network (NCCN) criteria for BRCA1/2 testing, based on age at diagnosis and personal and family history of cancer, were compared. Results: Among the 4516 patients in the cohort, the median age at diagnosis of breast cancer was 57 years, 80.5% had estrogen receptor positive tumors, and 43% had a family history of breast cancer. All patients in the cohort met ASBrS criteria for hereditary cancergenetic testing, 2050 (45.4%) met NCCN criteria, 1892 (41.9%) did not meet NCCN criteria, and 574 (12.7%) patients could not be fully evaluated for NCCN testing criteria due to missing data. The frequencies of pathogenic variants in the cohort are shown in Table 1. Patients meeting NCCN criteria were more likely to carry a pathogenic variant compared to those who did not (9.8% vs. 3.8%, p<0.001, Table 1). However, 72 (26.5%) out of the 272 patients with mutations in 12 breast cancer predisposition genes and 15 (12.4%) out of 121 with mutations in BRCA1/2 were overlooked when NCCN selection criteria alone were applied. When testing was expanded to include all patients with breast cancer diagnosed at age ≤65 and/or meeting NCCN testing criteria, only 20 (7.4%) out of 272 mutation carriers in 12 breast cancer genes and 2 (1.6%) out of 121 BRCA1/2 mutation carriers were overlooked. However, this increased the number tested to detect one mutation carrier on average from 17 to 25 for BRCA1/2 and from 9 to 12 for the 12 breast cancer predisposition genes. In total, this age cutoff led to an increase in the number of patients tested by 28% while the number of patients in the cohort that need not undergo germline genetic testing was 20%. Conclusions: Although NCCN criteria for BRCA1/2 germline genetic testing detect the majority of predisposition gene mutation carriers, a significant number of carriers are missed in an unselected cohort of breast cancer patients using these criteria. Expanding the current NCCN criteria to include all women with breast cancer diagnosed ≤ 65 years of age, will substantially improve the sensitivity of mutation testing, without the need for evaluation of all breast cancer patients. Table 1: Comparison of frequency of germline mutations between patients who met and did not meet NCCN guidelines for germline genetic testing#Total, Meets ASBrS guidelines N=3942Meets NCCN guidelines, N=2050Did not meet NCCN guidelines, N=1892P-value€ NCCN vs non-NCCNPercent mutation carriers missed by NCCN criteria* BRCA1/2121 (3.1%)106 (5.2%)15 (0.8%)<0.00112.4%6 High risk genes$150 (3.8%)120 (5.8%)30 (1.6%)<0.00120.0%12 Breast cancer genes:272 (6.9%)200 (9.8%)72 (3.8%)<0.00126.5%ATM45 (1.1%)32 (1.56%)13 (0.69%)28.9%BARD16 (0.2%)5 (0.24%)1 (0.05%)16.7%BRCA158 (1.5%)53 (2.59%)5 (0.26%)8.6%BRCA263 (1.6%)53 (2.59%)10 (0.53%)15.9%CDH16 (0.2%)3 (0.15%)3 (0.16%)50.0%CHEK267 (1.7%)41 (2.00%)26 (1.36%)38.8%NF10 (0.0%)0 (0.00%)0 (0.00%)0.0%PALB216 (0.4%)7 (0.34%)9 (0.48%)56.3%PTEN1 (0.0%)1 (0.05%)0 (0.00%)0.0%RAD51C6 (0.2%)6 (0.29%)0 (0.00%)0.0%RAD51D4 (0.1%)2 (0.10%)2 (0.11%)50.0%TP537 (0.2%)3 (0.15%)4 (0.21%)57.1%#: Patients who did not meet NCCN criteria excluded from analysis$: BRCA1, BRCA2, CDH1, PALB2, PTEN and TP53;€: Fisher exact test comparing frequency of germline mutations between those who met NCCN guidelines and those who did not;*: Denominators for percentages are the total mutation carriers in respective categories. Citation Format: Siddhartha Yadav, Chunling Hu, Steven N. Hart, Nicholas Boddicker, Eric C. Polley, Jie Na, Rohan Gnanaolivu, Kun Y. Lee, Janet E. Olson, Kathryn J. Ruddy, Fergus J. Couch. Comparison of recommendations for germline genetic testing in an unselected cohort of patients with breast cancer [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 P6-08-01.