A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.

Characteristics and utilisation of the Mayo Clinic Biobank, a clinic-based prospective collection in the USA: cohort profile

PURPOSE

The Mayo Clinic Biobank was established to provide a large group of patients from which comparison groups (ie, controls) could be selected for case-control studies, to create a prospective cohort with sufficient power for common outcomes and to support electronic health record (EHR) studies.

PARTICIPANTS

A total of 56 862 participants enrolled (21% response rate) into the Mayo Clinic Biobank from Rochester, Minnesota (77%, n=43 836), Jacksonville, Florida (18%, n=10 368) and La Crosse, Wisconsin (5%, n=2658). Participants were all Mayo Clinic patients, 18 years of age or older and US residents.

FINDINGS TO DATE

Overall, 43% of participants were 65 years of age or older and female participants were more frequent (59%) than males at all sites. Most participants resided in the Upper Midwest regions of the USA (Minnesota, Iowa, Illinois or Wisconsin), Florida or Georgia. Self-reported race among Biobank participants was 90% white. Here we provide examples of the types of studies that have successfully utilised the resource, including (1) investigations of the population itself, (2) provision of controls for case-control studies, (3) genotype-driven research, (4) EHR-based research and (5) prospective recruitment to other studies. Over 270 projects have been approved to date to access Biobank data and/or samples; over 200 000 sample aliquots have been approved for distribution.

FUTURE PLANS

The data and samples in the Mayo Clinic Biobank can be used for various types of epidemiological and clinical studies, especially in the setting of case-control studies for which the Biobank samples serve as control samples. We are planning cohort studies with additional follow-up and acquisition of genetic information on a large scale.

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM -/- patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.

Two truncating variants in FANCC and breast cancer risk

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44-1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Abstract 4177: The joint effects of polygenic risk scores and pathogenic variants in cancer predisposition genes on breast cancer risk in the general population: results from the CARRIERS study

Background: Understanding the joint effect on breast cancer risk of rare pathogenic variants in cancer predisposition genes and polygenic risk scores (PRS) from common variants can enable a precision approach to breast cancer management. Previous work found that PRS were associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers recruited from cancer genetics clinics (Kuchenbaecker et al. JNCI 2017). The joint effects of pathogenic variants and PRS have not been studied in samples drawn from the general population. There is also no existing study evaluating the effect of PRS in mutation carriers in genes other than BRCA1/2. Here we evaluate the joint effects of PRS and pathogenic mutations in established cancer predisposition genes in a population-based case-control sample.

Method: We analyzed 53,199 European-ancestry individuals (20,730 controls and 21,272 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 dual bar-coded QIAseq. Mutation calling was conducted with Haplotype Caller and Vardict. We sequenced 18 breast cancer predisposition genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHECK2, FANCC, MLH1, MSH2, MSH6, NF1, PALB2, PTEN, RAD51C, RAD51D and TP53. The PRS was calculated based on 128 common variants using effect estimates from the largest published breast cancer GWAS. The PRS was standardized to a mean of 0 and standard deviation of 1. Logistic regression was performed to assess the combined effect of identified mutation and common variants (including main and interaction effects for carrier status and PRS).

Results: A total of 1,770 pathogenic mutations were observed. About 1% of the study sample had mutations in either BRCA1 (n=209) or BRCA2 gene (n=305), and 2.2% had mutations in other genes (n=1,176). The effect of PRS in BRCA1 carriers was OR= 0.97 (95%CI: 0.62, 1.52); however, this is not statistically significantly different from the PRS in non-carriers [OR=1.23 (95%CI: 1.20, 1.25)] or previous estimates in carriers [OR: 1.14, 95%CI: 1.11-1.17]. The effect of PRS in BRCA2 carriers was OR=1.87 (95%CI: 1.31, 2.78) which was statistically significantly different from that of the non-carriers. Among the mutation carriers in genes other than BRCA, the effect of PRS on breast cancer was OR=1.00 (95%CI: 0.88,1.15).

Conclusion: Consistent with previous studies, we did not find evidence that the effect of the PRS among BRCA1 carriers was statistically significantly different than non-carriers. We found some evidence that the PRS effect may be larger among BRCA2 carriers than non-carriers. Our results also suggest that PRS may not have a strong effect on breast cancer risk in mutation carriers of other predisposition genes; further work is needed for verification.

Citation Format: Chi Gao, Chunling Hu, Steven N. Hart, Rohan Gnanaolivu, Kun Y. Lee, Jenna Lilyquist, Nicholas J. Boddicker, Bruce Eckloff, Raed Samara, Josh Klebba, Paul Auer, Leslie Bernstein, Mia Gaudet, Hoda Anton-Culver, Amy Trentham-Dietz, Julie R. Palmer, Song Yao, Christopher Haiman, Janet E. Olson, Susan Domchek, Jeffrey Weitzel, David Goldgar, Katherine L. Nathanson, Eric C. Polley, Fergus J. Couch, Peter Kraft. The joint effects of polygenic risk scores and pathogenic variants in cancer predisposition genes on breast cancer risk in the general population: results from the CARRIERS study [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 4177.

Joint association of mammographic density adjusted for age and body mass index and polygenic risk score with breast cancer risk

BACKGROUND

Mammographic breast density, adjusted for age and body mass index, and a polygenic risk score (PRS), comprised of common genetic variation, are both strong risk factors for breast cancer and increase discrimination of risk models. Understanding their joint contribution will be important to more accurately predict risk.

METHODS

Using 3628 breast cancer cases and 5126 controls of European ancestry from eight case-control studies, we evaluated joint associations of a 77-single nucleotide polymorphism (SNP) PRS and quantitative mammographic density measures with breast cancer. Mammographic percent density and absolute dense area were evaluated using thresholding software and examined as residuals after adjusting for age, 1/BMI, and study. PRS and adjusted density phenotypes were modeled both continuously (per 1 standard deviation, SD) and categorically. We fit logistic regression models and tested the null hypothesis of multiplicative joint associations for PRS and adjusted density measures using likelihood ratio and global and tail-based goodness of fit tests within the subset of six cohort or population-based studies.

RESULTS

Adjusted percent density (odds ratio (OR) = 1.45 per SD, 95% CI 1.38-1.52), adjusted absolute dense area (OR = 1.34 per SD, 95% CI 1.28-1.41), and the 77-SNP PRS (OR = 1.52 per SD, 95% CI 1.45-1.59) were associated with breast cancer risk. There was no evidence of interaction of the PRS with adjusted percent density or dense area on risk of breast cancer by either the likelihood ratio (P > 0.21) or goodness of fit tests (P > 0.09), whether assessed continuously or categorically. The joint association (OR) was 2.60 in the highest categories of adjusted PD and PRS and 0.34 in the lowest categories, relative to women in the second density quartile and middle PRS quintile.

CONCLUSIONS

The combined associations of the 77-SNP PRS and adjusted density measures are generally well described by multiplicative models, and both risk factors provide independent information on breast cancer risk.

Acupuncture: Real-world patient-reported outcomes of treatment-related symptoms in breast cancer survivors

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Background: Acupuncture has been shown to reduce aromatase inhibitor-induced arthralgias, as well as possibly hot flashes and fatigue, but research has been limited. The purpose of this study was to evaluate real world perceived benefit of acupuncture for commonly experienced symptoms among breast cancer survivors. Methods: Breast cancer survivors who had used acupuncture for cancer- or treatment-related symptoms were identified using an ongoing prospective Mayo Clinic Breast Disease Registry (MCBDR) cohort. In addition, Mayo Clinic electronic health records (EHR) were queried to identify additional participants. All identified patients were mailed a survey with acupuncture-related questions. Respondents were also asked to recall their severity of arthralgia, myalgia, post-surgical pain, hot flashes, nausea/vomiting, fatigue, depression, anxiety, insomnia, lymphedema, headache, and neuropathy from 1 to 5 (1 = mild, 5 = severe) before and after acupuncture treatment. Results: Acupuncture use was reported among 413 participants in MCBDR (12% of all enrollees) and 73 patients were identified in the Mayo EHR. 241 eligible women returned surveys (median age at diagnosis 50 yrs). Mean symptom severity scores decreased from before to after acupuncture by at least 1 point for all queried symptoms (Table). Conclusions: Acupuncture is frequently used by patients for a variety of breast cancer-related symptoms. Those who do pursue acupuncture usually perceive few toxicities and substantial benefits. Cost may be a barrier to treatment for some. [Table: see text]

Long-term neurotoxicity in women with breast cancer

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Background: Taxanes (paclitaxel and docetaxel) are commonly administered as part of chemotherapy for breast cancer, but long-term data on chemotherapy-induced peripheral neuropathy (CIPN) are limited in this population. We aimed to assess CIPN approximately three years after an initial exposure to paclitaxel or docetaxel. Methods: In a cross-sectional observation study, which surveyed consented enrollees annually after receipt of care at Mayo Clinic for a new breast cancer diagnosis over age 18, we collected patient-reported EORTC CIPN20 data by mailed questionnaire at baseline and three years after a breast cancer diagnosis. We then confirmed patient-reported chemotherapy data by chart abstraction and only included those who had received a standard course of docetaxel-based or paclitaxel-based chemotherapy, but had not had other neurotoxic treatment for cancer. CIPN20 overall and sensory scale raw scores were converted to a 0-100 linear scale with lower scores indicating more severe symptoms. Results: 84 women who received a taxane for breast cancer completed the survey. 82 were treated in the adjuvant or neo-adjuvant setting, while 2 received a taxane for metastatic breast cancer. 67 women received paclitaxel, while 17 received docetaxel. The median age at diagnosis was 51.5 years (range 31-86). 37 had estrogen receptor (ER) and/or progesterone receptor (PR) positive and human epidermal growth factor receptor-2 (Her2) negative, 31 Her2 positive, and 16 triple negative breast cancer. The median CIPN20 score was 92.98 (range 33.33-100). The median sensory CIPN score was 92.59 (range 25.94-100). 81% of women had an overall CIPN20 score of less than 100, and 68% had a sensory score of less than 100. Conclusions: The majority of women who received a taxane based chemotherapy regimen for breast cancer reported at least mild neuropathic symptoms three years out from treatment. Additional research is needed to help tailor chemotherapy decisions to toxicity risks and to reduce the likelihood of long-term CIPN, which can impair quality of life.

Managing the Unimaginable: Biobank Participant Views on Reconsent for Whole Genome Sequencing of Stored Biospecimens

Background: DNA biobanks frequently obtain broad permissions from sample donors, who agree to allow their biospecimens to be used for a variety of future purposes. A limitation of this approach is that it may not be possible to discuss or anticipate all potential uses of biospecimens at the time patient consent is obtained. We surveyed biobank participants to clarify their views regarding the need to be informed about research involving whole genome sequencing (WGS). Methods: We invited 1200 participants in the Mayo Clinic Biobank to complete a survey inquiring about their support for WGS; their interest in being recontacted before WGS of their biospecimens; whether they would consent to WGS if asked; and the acceptability of proceeding with WGS if sample donors could not be reached. Results: Six hundred eighty-seven biobank participants returned completed surveys (57% response). More than 96% of biobank participants were supportive of WGS and would give permission for WGS of their sample, if asked. Nonetheless, 61% of biobank participants felt they should be recontacted before WGS was done. Participants were divided regarding the permissibility of conducting WGS if efforts to recontact sample donors were unsuccessful. Discussion: Our findings highlight a potential discrepancy between the broad permissions granted by biobank participants at the time they donated biospecimens and their views about the application of WGS to their samples. Biobank participants appear to value the ability to confirm their commitment to genetic research when the studies in question involve WGS, a technological capacity they may not have anticipated at the time they donated their biospecimens. Efforts to reevaluate biobank participants' views about the acceptability of new technologies may help to ensure alignment of participants' current beliefs and research applications that would have been difficult to anticipate at the time biospecimens were collected.

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.

Developing a Process for Returning Medically Actionable Genomic Variants to Latino Patients in a Federally Qualified Health Center

AIM

To develop a process for returning medically actionable genomic variants to Latino patients receiving care in a Federally Qualified Health Center.

METHODS

Prior to recruitment, researchers met with primary care providers to (1) orient clinicians to the project, (2) establish a process for returning actionable and nonactionable results to participants and providers through the electronic health record, and (3) develop a process for offering clinical decision support for follow-up education and care. A Community Advisory Board was engaged to provide input on recruitment strategies and materials for conveying results to participants. Participants in the Sangre Por Salud (Blood for Health) Biobank with hyperlipidemia or colon polyps represented the pool of potentially eligible participants.

RESULTS

A total of 1,621 individuals were invited to participate and 710 agreed to an in- person consenting visit (194 no-showed and 16 declined). Over 12-months, 500 participants were enrolled. Participants were primarily Spanish-speaking (81.6%), female (74.2%), and enrolled because of hyperlipidemia (95.4%). All but 2 participants opted to receive primary (i.e., related to enrollment phenotypes) as well as secondary actionable results.

CONCLUSION

Efforts to bring precision medicine to community-based health centers serving minority patients may require multilevel engagement activities to include individuals, providers, health systems, and the community.

CDKN2A Germline Rare Coding Variants and Risk of Pancreatic Cancer in Minority Populations

Background: Pathogenic germline mutations in the CDKN2A tumor suppressor gene are rare and associated with highly penetrant familial melanoma and pancreatic cancer in non-Hispanic whites (NHW). To date, the prevalence and impact of CDKN2A rare coding variants (RCV) in racial minority groups remain poorly characterized. We examined the role of CDKN2A RCVs on the risk of pancreatic cancer among minority subjects.Methods: We sequenced CDKN2A in 220 African American (AA) pancreatic cancer cases, 900 noncancer AA controls, and 183 Nigerian controls. RCV frequencies were determined for each group and compared with that of 1,537 NHW patients with pancreatic cancer. Odds ratios (OR) and 95% confidence intervals (CI) were calculated for both a case-case comparison of RCV frequencies in AAs versus NHWs, and case-control comparison between AA cases versus noncancer AA controls plus Nigerian controls. Smaller sets of Hispanic and Native American cases and controls also were sequenced.Results: One novel missense RCV and one novel frameshift RCV were found among AA patients: 400G>A and 258_278del. RCV carrier status was associated with increased risk of pancreatic cancer among AA cases (11/220; OR, 3.3; 95% CI, 1.5-7.1; P = 0.004) compared with AA and Nigerian controls (17/1,083). Further, AA cases had higher frequency of RCVs: 5.0% (OR, 13.4; 95% CI, 4.9-36.7; P < 0.001) compared with NHW cases (0.4%).Conclusions: CDKN2A RCVs are more common in AA than in NHW patients with pancreatic cancer and associated with moderately increased pancreatic cancer risk among AAs.Impact: RCVs in CDKN2A are frequent in AAs and are associated with risk for pancreatic cancer. Cancer Epidemiol Biomarkers Prev; 27(11); 1364-70. ©2018 AACR.

Association of mitochondrial DNA copy number with self-rated health status

Purpose

In aging adults, mitochondrial dysfunction may be an important contributor. We evaluated the association between mitochondrial DNA (mtDNA) copy number, which is a biomarker for mitochondrial function, and self-rated health status.

Patients and methods

We conducted a cross-sectional study of patients enrolled within the Mayo Clinic Biobank. We utilized the questionnaire and sequence data from 944 patients. We examined the association between mtDNA copy number and self-rated health status with 3 collapsed categories for the latter variable (excellent/very good, good, and fair/poor). For analysis, we used proportional odds models after log-transforming mtDNA copy number, and we adjusted for age and sex.

Results

We found the median age at enrollment was 61 years (25th–75th percentile: 51–71), and 64% reported excellent or very good health, 31% reported good health, and 6% reported fair/poor health. Overall, the median mtDNA copy number was 88.9 (25th–75th percentile: 77.6–101.1). Higher mtDNA copy number was found for subjects reporting better self-rated health status after adjusting for age, sex, and comorbidity burden (OR =2.3 [95% CI: 1.2–4.5] for having better self-rated health for a one-unit increase in log-transformed mtDNA copy number).

Conclusion

We found that a higher mtDNA copy number is associated with better self-rated health status after adjustment for age, sex, and comorbidity burden. The current study implies that mtDNA copy number may serve as a biomarker for self-reported health. Further studies, potentially including cohort studies, may be required.

Acceptability of Electronic Visits for Return of Research Results in the Mayo Clinic Biobank

Objective

To understand patient characteristics related to acceptability of returning individual research results via various modalities, focusing on electronic visits (e-visits).

Patients and Methods

Twelve hundred participants from the Mayo Clinic Biobank were selected using a stratified random sampling approach based on sex, age, and education level. Mailed surveys ascertained return of results preferences for 2 disease vignettes (cystic fibrosis and hereditary breast cancer) and a pharmacogenomics vignette. The study was conducted from October 1, 2013, through March 31, 2014.

Results

In all, 685 patients (57%) responded, and 60% reported liking e-visits, although the option of receiving results in an office visit was liked most frequently. Multivariable logistic models showed that the odds of liking the use of e-visits for returning results for cystic fibrosis and hereditary breast cancer were higher among those with higher education and better genetic knowledge and among those not living in proximity to the Mayo Clinic (Rochester, Minnesota). Level of genetic knowledge was not considerably associated with accepting e-visits, whereas education level remained important. For all vignettes, those who are divorced were less likely to accept e-visits.

Conclusion

Researchers are faced with a difficult challenge of returning results with a method that is both acceptable to recipients and logistically feasible. This study implies that the use of e-visits may be a viable option for return of results to stratify the chasm between in-person genetic counseling and online portal receipt of results.

A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer

The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P < 5.82 × 10-6, including 14 genes at loci not yet reported for breast cancer. We silenced 13 genes and showed an effect for 11 on cell proliferation and/or colony-forming efficiency. Our study provides new insights into breast cancer genetics and biology.

Association between an individual housing-based socioeconomic index and inconsistent self-reporting of health conditions: a prospective cohort study in the Mayo Clinic Biobank

OBJECTIVE

Using surveys to collect self-reported information on health and disease is commonly used in clinical practice and epidemiological research. However, the inconsistency of self-reported information collected longitudinally in repeated surveys is not well investigated. We aimed to investigate whether a socioeconomic status based on current housing characteristics, HOUsing-based SocioEconomic Status (HOUSES) index linking current address information to real estate property data, is associated with inconsistent self-reporting.

STUDY SETTING AND PARTICIPANTS

We performed a prospective cohort study using the Mayo Clinic Biobank (MCB) participants who resided in Olmsted County, Minnesota, USA, at the time of enrolment between 2009 and 2013, and were invited for a 4-year follow-up survey (n=11 717).

PRIMARY AND SECONDARY OUTCOME MEASURES

Using repeated survey data collected at the baseline and 4 years later, the primary outcome was the inconsistency in survey results when reporting prevalent diseases, defined by reporting to have 'ever' been diagnosed with a given disease in the baseline survey but reported 'never' in the follow-up survey. Secondary outcome was the response rate for the 4-year follow-up survey.

RESULTS

Among the MCB participants invited for the 4-year follow-up survey, 8508/11 717 (73%) responded to the survey. Forty-three per cent had at least one inconsistent self-reported disease. Lower HOUSES was associated with higher inconsistency rates, and the association remained significant after pertinent characteristics such as age and perceived general health (OR=1.46; 95% CI 1.17 to 1.84 for the lowest compared with the highest HOUSES decile). HOUSES was also associated with lower response rate for the follow-up survey (56% vs 77% for the lowest vs the highest HOUSES decile).

CONCLUSION

This study demonstrates the importance of using the HOUSES index that reflects current SES when using self-reporting through repeated surveys, as the HOUSES index at baseline survey was inversely associated with inconsistent self-report and the response rate for the follow-up survey.

The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity

Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10-115 . There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.

E-cadherin breast tumor expression, risk factors and survival: Pooled analysis of 5,933 cases from 12 studies in the Breast Cancer Association Consortium

E-cadherin (CDH1) is a putative tumor suppressor gene implicated in breast carcinogenesis. Yet, whether risk factors or survival differ by E-cadherin tumor expression is unclear. We evaluated E-cadherin tumor immunohistochemistry expression using tissue microarrays of 5,933 female invasive breast cancers from 12 studies from the Breast Cancer Consortium. H-scores were calculated and case-case odds ratios (OR) and 95% confidence intervals (CIs) were estimated using logistic regression. Survival analyses were performed using Cox regression models. All analyses were stratified by estrogen receptor (ER) status and histologic subtype. E-cadherin low cases (N = 1191, 20%) were more frequently of lobular histology, low grade, >2 cm, and HER2-negative. Loss of E-cadherin expression (score < 100) was associated with menopausal hormone use among ER-positive tumors (ever compared to never users, OR = 1.24, 95% CI = 0.97-1.59), which was stronger when we evaluated complete loss of E-cadherin (i.e. H-score = 0), OR = 1.57, 95% CI = 1.06-2.33. Breast cancer specific mortality was unrelated to E-cadherin expression in multivariable models. E-cadherin low expression is associated with lobular histology, tumor characteristics and menopausal hormone use, with no evidence of an association with breast cancer specific survival. These data support loss of E-cadherin expression as an important marker of tumor subtypes.

Publisher Correction: Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation

This corrects the article DOI: 10.1038/ncomms5999.

Abstract OT3-02-01: Development of cell-free nucleic acid-based tests for early detection of breast cancer: The STRIVE study

Background:

Mammography (digital 2D or digital 3D/tomosynthesis) is the cornerstone of current screening strategies for breast cancer, but new approaches are needed to further reduce the proportion of cancers diagnosed at advanced stages and more effectively identify those women in need of additional testing and biopsies. Circulating cell-free nucleic acids (cfNAs) shed from tumors, isolated from peripheral blood, and analyzed with ultra-deep and broad sequencing of cancer-associated genes, have great potential for early cancer detection. The ultimate goal is to develop blood cfNA cancer screening tests for use in conjunction with established risk factors and/or radiographic features for improved cancer detection. Development of these tests requires large, well-annotated cohorts of asymptomatic participants with adequate volumes of prediagnostic blood. The STRIVE Study cohort was recently established to train and validate cfNA-based tests for early detection of breast cancer.

Eligibility criteria and trial design: The STRIVE Study is a new prospective, multi-ethnic mammography cohort that will recruit 120,000 subjects from 15+ US breast cancer screening centers (including Mayo Clinic and Sutter Health sites). Eligibility criteria require only that a participant has a scheduled routine screening mammogram at a participating center and has not received a biopsy prior to the research blood draw. Participants are recruited within 28 days of screening mammography (digital or tomosynthesis), consent electronically, provide blood samples, and complete an on-line risk factor questionnaire. Participants will be followed for all cancer diagnoses, cancer recurrences, and death for at least 5 years. Pertinent medical record information, imaging findings (including breast density), and follow-up data will be transferred electronically to a central database throughout the study period. Additional blood samples will be collected from participants with abnormal mammogram results, or who are diagnosed with cancer, to document and better understand the evolution of cfNA signals. Recruitment began in February 2017.

Primary Aims: To train and validate a cfNA blood-based test to identify breast cancer overall in a cohort of women undergoing screening mammography.

Statistical Methods: The study will be divided into a training phase (1/3 of participants) and an independent clinical validation phase (remaining 2/3 of participants). In the training phase, statistical machine learning techniques will be used to develop algorithms incorporating cfNA signals, clinical characteristics, or radiological features. In the validation phase, the prespecified locked algorithm developed from the training phase will be clinically validated in an independent group of women.

Contact information for people with a specific interest in the trial: Additional details regarding the STRIVE Study are available on the ClinicalTrials.gov website (NCT03085888). For site-specific questions, please call 844-366-9738 for the Mayo Clinic and 1-855-578-7483 for Sutter Health.

Citation Format: Liu MC, Cummings S, Vachon CM, Kerlikowske K, Couch FJ, Morris EA, Olson JE, Polley EC, Conners AL, Ellis RL, Patel B, Maimone IV S, Zhang N, Hamilton S, Clarke CA, Allen BA, Maddala T, Hartman A-R. Development of cell-free nucleic acid-based tests for early detection of breast cancer: The STRIVE study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT3-02-01.

Abstract WP213: Discovery of a Serum Protein Panel to Stratify Stroke and Stroke-Mimic Patients

Introduction: A rapid diagnostic tool that appropriately triages stroke and non-stroke patients would decrease patients’ time to treatment and therefore lower the risk of morbidity. Single blood protein biomarkers for stroke have not shown clinical utility. Our objective in this biomarker discovery study is to examine a wide array of proteins to identify a panel that stratifies stroke patients from stroke-mimicking patients.

Hypothesis: Serum from ischemic stroke patients contains proteins identified by the SOMAscan biomarker discovery assay that can stratify stroke from non-stroke patients.

Methods: Patients presenting to the emergency department with stroke-like symptoms had peripheral blood drawn upon arrival according to Stroke Alert protocols. Once informed consent was obtained, serum was analyzed with the SOMAscan assay to quantify the expression of 1305 proteins. These data were analyzed using the semi-supervised machine learning algorithm, random forest analysis (RFA), to determine a combination of proteins which best predicted the final patient discharge diagnosis.

Results: Twenty-two stroke patients, 9 transient ischemic attack (TIA) patients, and 23 patients with other stroke-mimicking symptoms participated in the study. Normal age- and sex-matched serum controls were obtained commercially. RFA identified four panels encompassing a total of nine proteins to stratify patients between the stroke, TIA, other stroke mimic, and control groups. Applying these panels to the same training set of patient data, one panel of two proteins distinguished stroke from stroke-mimics with a sensitivity of 50% and specificity of 100%. A second panel of three proteins identified stroke from non-stroke patients with a sensitivity of 78% and specificity of 95%. A provisional patent application describing these panels is underway.

Conclusion: Ischemic stroke patients and stroke-mimic patients exhibit a differential expression of serum proteins at the time of clinical presentation. The simultaneous analysis of two or three proteins in a biomarker panel exhibits high specificity and may be clinically useful as a stroke “rule in” tool for emergency personnel. This would facilitate triage and avoid inappropriate treatment of non-stroke patients.

Body mass index and breast cancer survival: a Mendelian randomization analysis

Background

There is increasing evidence that elevated body mass index (BMI) is associated with reduced survival for women with breast cancer. However, the underlying reasons remain unclear. We conducted a Mendelian randomization analysis to investigate a possible causal role of BMI in survival from breast cancer.

Methods

We used individual-level data from six large breast cancer case-cohorts including a total of 36 210 individuals (2475 events) of European ancestry. We created a BMI genetic risk score (GRS) based on genotypes at 94 known BMI-associated genetic variants. Association between the BMI genetic score and breast cancer survival was analysed by Cox regression for each study separately. Study-specific hazard ratios were pooled using fixed-effect meta-analysis.

Results

BMI genetic score was found to be associated with reduced breast cancer-specific survival for estrogen receptor (ER)-positive cases [hazard ratio (HR) = 1.11, per one-unit increment of GRS, 95% confidence interval (CI) 1.01-1.22, P = 0.03). We observed no association for ER-negative cases (HR = 1.00, per one-unit increment of GRS, 95% CI 0.89-1.13, P = 0.95).

Conclusions

Our findings suggest a causal effect of increased BMI on reduced breast cancer survival for ER-positive breast cancer. There is no evidence of a causal effect of higher BMI on survival for ER-negative breast cancer cases.

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.