Managing RT Schedules of Early-Stage Breast Cancer Patients with a Genetic-Dosimetric Validated Model for Late Fibrosis

PURPOSE/OBJECTIVE(S)

Define a multifactorial risk prediction model for RT-induced fibrosis and investigate the benefit of a personalized approach for breast cancer (BC) patients (pts) treated with whole breast RT.

MATERIALS/METHODS

In a previous study, we confirmed the predictive role of 30 SNPs from the literature and built an interaction aware Polygenic Risk Score (PRS, following the methods from Franco RO 2021) for Late Fibrosis (FG2+) on a cohort of 1500 pts from the REQUITE EU/USA prospective observational study. The PRS weights the radiosensitive (RS) and radioresistant (RR) genetic components and can be included in NTCP models. In a subgroup from the same cohort (390 pts), we have also confirmed an NTCP model based on biologically Equivalent Uniform Dose (BEUD) from PTV DVHs for pts treated at 40-50 Gy and no RT boost. Here, we combine PRS and BEUD into a sigmoid model allowing PRS to modulate BEUD50 (BEUD leading to 50% FG2+), i.e., we permitted a personalized BEUD50. We can also consider this as translating the PRS into a personalized equivalent BEUD, which is added/subtracted to the treatment BEUD. We evaluated model performances through ROC-AUC, calibration plot and Precision-Recall AUC.

RESULTS

A total of 381 pts had complete dosimetric/genetic data, prescribed dose 40-50 Gy, and no fibrotic alteration at RT start. We scored FG2+ in 87 pts (23%). PRS ranged from -13 (more RR pts) to 7 (more RS), and a unit in PRS corresponds to 5.3 Gy BEUD or 3 Gy in EQ EUD2 Gy. Table 1 summarizes model performances, with details for subgroups below/above the quartiles I/III of the BEUD distribution. The PRS-only model correctly describes the toxicity rates in the whole population (calibration slope/offset = 0/1). Still, it overestimates/underestimates the absolute risks in the low/high dose ranges. The integrated model improves AUC-ROC and AUC-PRC by 5% and 10% and guarantees a better calibration in pts receiving low/high BEUD to the PTV.

CONCLUSION

We developed a multifactorial model for FG2+ based on two previously validated models and reported the improvement against single-factor models. The BEUD+PRS model is suitable for assisting clinicians in managing early-stage BC pts. The number of fractions or the daily dose could be reduced for RS pts. The integrated model resulted in a possible quantitative tool for driving the planning decision process. Also, it showed a better performance in the high BEUD region, suggesting the potential value of its extension toward RT including boost or ultra hypofractionation. We are testing this extension in the whole REQUITE cohort.

Genome-wide association study of treatment-related toxicity two years following radiotherapy for breast cancer

BACKGROUND AND PURPOSE

Up to a quarter of breast cancer patients treated by surgery and radiotherapy experience clinically significant toxicity. If patients at high risk of adverse effects could be identified at diagnosis, their treatment could be tailored accordingly. This study was designed to identify common single nucleotide polymorphisms (SNPs) associated with toxicity two years following whole breast radiotherapy.

MATERIALS AND METHODS

A genome-wide association study (GWAS) was performed in 1,640 breast cancer patients with complete SNP, clinical, treatment and toxicity data, recruited across 18 European and US centres into the prospective REQUITE cohort study. Toxicity data (CTCAE v4.0) were collected at baseline, end of radiotherapy, and annual follow-up. A total of 7,097,340 SNPs were tested for association with the residuals of toxicity endpoints, adjusted for clinical, treatment co-variates and population substructure.

RESULTS

Quantile-quantile plots showed more associations with toxicity above the p < 5 × 10-5 level than expected by chance. Eight SNPs reached genome-wide significance. Nipple retraction grade ≥ 2 was associated with the rs188287402 variant (p = 2.80 × 10-8), breast oedema grade ≥ 2 with rs12657177 (p = 1.12 × 10-10), rs75912034 (p = 1.12 × 10-10), rs145328458 (p = 1.06 × 10-9) and rs61966612 (p = 1.23 × 10-9), induration grade ≥ 2 with rs77311050 (p = 2.54 × 10-8) and rs34063419 (p = 1.21 × 10-8), and arm lymphoedema grade ≥ 1 with rs643644 (p = 3.54 × 10-8). Heritability estimates across significant endpoints ranged from 25% to 39%. Our study did not replicate previously reported SNPs associated with breast radiation toxicity at the pre-specified significance level.

CONCLUSIONS

This GWAS for long-term breast radiation toxicity provides further evidence for significant association of common SNPs with distinct toxicity endpoints.

Development and optimisation of a machine-learning prediction model for acute desquamation following breast radiotherapy in the multi-centre REQUITE cohort

Purpose

Some patients with breast cancer treated by surgery and radiation therapy experience clinically significant toxicity, which may adversely affect cosmesis and quality of life. There is a paucity of validated clinical prediction models for radiation toxicity. We used machine learning (ML) algorithms to develop and optimise a clinical prediction model for acute breast desquamation after whole breast external beam radiation therapy in the prospective multicenter REQUITE cohort study.

Methods and Materials

Using demographic and treatment-related features (m = 122) from patients (n = 2058) at 26 centers, we trained 8 ML algorithms with 10-fold cross-validation in a 50:50 random-split data set with class stratification to predict acute breast desquamation. Based on performance in the validation data set, the logistic model tree, random forest, and naïve Bayes models were taken forward to cost-sensitive learning optimisation.

Results

One hundred and ninety-two patients experienced acute desquamation. Resampling and cost-sensitive learning optimisation facilitated an improvement in classification performance. Based on maximising sensitivity (true positives), the “hero” model was the cost-sensitive random forest algorithm with a false-negative: false-positive misclassification penalty of 90:1 containing m = 114 predictive features. Model sensitivity and specificity were 0.77 and 0.66, respectively, with an area under the curve of 0.77 in the validation cohort.

Conclusions

ML algorithms with resampling and cost-sensitive learning generated clinically valid prediction models for acute desquamation using patient demographic and treatment features. Further external validation and inclusion of genomic markers in ML prediction models are worthwhile, to identify patients at increased risk of toxicity who may benefit from supportive intervention or even a change in treatment plan.

Population Study of Ovarian Cancer Risk Prediction for Targeted Screening and Prevention

Unselected population-based personalised ovarian cancer (OC) risk assessment combining genetic/epidemiology/hormonal data has not previously been undertaken. We aimed to perform a feasibility study of OC risk stratification of general population women using a personalised OC risk tool followed by risk management. Volunteers were recruited through London primary care networks.

INCLUSION CRITERIA

women ≥18 years.

EXCLUSION CRITERIA

prior ovarian/tubal/peritoneal cancer, previous genetic testing for OC genes. Participants accessed an online/web-based decision aid along with optional telephone helpline use. Consenting individuals completed risk assessment and underwent genetic testing (BRCA1/BRCA2/RAD51C/RAD51D/BRIP1, OC susceptibility single-nucleotide polymorphisms). A validated OC risk prediction algorithm provided a personalised OC risk estimate using genetic/lifestyle/hormonal OC risk factors. Population genetic testing (PGT)/OC risk stratification uptake/acceptability, satisfaction, decision aid/telephone helpline use, psychological health and quality of life were assessed using validated/customised questionnaires over six months. Linear-mixed models/contrast tests analysed impact on study outcomes.

MAIN OUTCOMES

feasibility/acceptability, uptake, decision aid/telephone helpline use, satisfaction/regret, and impact on psychological health/quality of life. In total, 123 volunteers (mean age = 48.5 (SD = 15.4) years) used the decision aid, 105 (85%) consented. None fulfilled NHS genetic testing clinical criteria. OC risk stratification revealed 1/103 at ≥10% (high), 0/103 at ≥5%-<10% (intermediate), and 100/103 at <5% (low) lifetime OC risk. Decision aid satisfaction was 92.2%. The telephone helpline use rate was 13% and the questionnaire response rate at six months was 75%. Contrast tests indicated that overall depression (p = 0.30), anxiety (p = 0.10), quality-of-life (p = 0.99), and distress (p = 0.25) levels did not jointly change, while OC worry (p = 0.021) and general cancer risk perception (p = 0.015) decreased over six months. In total, 85.5-98.7% were satisfied with their decision. Findings suggest population-based personalised OC risk stratification is feasible and acceptable, has high satisfaction, reduces cancer worry/risk perception, and does not negatively impact psychological health/quality of life.

The genetic interplay between body mass index, breast size and breast cancer risk: a Mendelian randomization analysis

BACKGROUND

Evidence linking breast size to breast cancer risk has been inconsistent, and its interpretation is often hampered by confounding factors such as body mass index (BMI). Here, we used linkage disequilibrium score regression and two-sample Mendelian randomization (MR) to examine the genetic associations between BMI, breast size and breast cancer risk.

METHODS

Summary-level genotype data from 23andMe, Inc (breast size, n = 33 790), the Breast Cancer Association Consortium (breast cancer risk, n = 228 951) and the Genetic Investigation of ANthropometric Traits (BMI, n = 183 507) were used for our analyses. In assessing causal relationships, four complementary MR techniques [inverse variance weighted (IVW), weighted median, weighted mode and MR-Egger regression] were used to test the robustness of the results.

RESULTS

The genetic correlation (rg) estimated between BMI and breast size was high (rg = 0.50, P = 3.89x10-43). All MR methods provided consistent evidence that higher genetically predicted BMI was associated with larger breast size [odds ratio (ORIVW): 2.06 (1.80-2.35), P = 1.38x10-26] and lower overall breast cancer risk [ORIVW: 0.81 (0.74-0.89), P = 9.44x10-6]. No evidence of a relationship between genetically predicted breast size and breast cancer risk was found except when using the weighted median and weighted mode methods, and only with oestrogen receptor (ER)-negative risk. There was no evidence of reverse causality in any of the analyses conducted (P > 0.050).

CONCLUSION

Our findings indicate a potential positive causal association between BMI and breast size and a potential negative causal association between BMI and breast cancer risk. We found no clear evidence for a direct relationship between breast size and breast cancer risk.

Author Correction: Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma

The original version of this Article contained an error in the spelling of a member of the PRACTICAL Consortium, Manuela Gago-Dominguez, which was incorrectly given as Manuela Gago Dominguez. This has now been corrected in both the PDF and HTML versions of the Article. Furthermore, in the original HTML version of this Article, the order of authors within the author list was incorrect. The PRACTICAL consortium was incorrectly listed after Richard S. Houlston and should have been listed after Nora Pashayan. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.

Author Correction: Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility

The original version of this Article contained an error in the spelling of a member of the PRACTICAL Consortium, Manuela Gago-Dominguez, which was incorrectly given as Manuela Gago Dominguez. This has now been corrected in both the PDF and HTML versions of the Article.

Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma

Genome-wide association studies (GWAS) have transformed our understanding of susceptibility to multiple myeloma (MM), but much of the heritability remains unexplained. We report a new GWAS, a meta-analysis with previous GWAS and a replication series, totalling 9974 MM cases and 247,556 controls of European ancestry. Collectively, these data provide evidence for six new MM risk loci, bringing the total number to 23. Integration of information from gene expression, epigenetic profiling and in situ Hi-C data for the 23 risk loci implicate disruption of developmental transcriptional regulators as a basis of MM susceptibility, compatible with altered B-cell differentiation as a key mechanism. Dysregulation of autophagy/apoptosis and cell cycle signalling feature as recurrently perturbed pathways. Our findings provide further insight into the biological basis of MM.

Use of deep whole-genome sequencing data to identify structure risk variants in breast cancer susceptibility genes

Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analysed deep (> 30x) whole-genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease. To identify SV deletions in known or suspected breast cancer susceptibility genes, we used multiple SV calling tools including Genome STRiP, Delly, Manta, BreakDancer and Pindel. SV deletions were detected by at least three of these bioinformatics tools in five genes. Specifically, we identified heterozygous deletions covering a fraction of the coding regions of BRCA1 (with approximately 80kb in two patients), and TP53 genes (with ∼1.6 kb in two patients), and of intronic regions (∼1 kb) of the PALB2 (one patient), PTEN (three patients) and RAD51C genes (one patient). We confirmed the presence of these deletions using real-time quantitative PCR (qPCR). Our study identified novel SV deletions in breast cancer susceptibility genes and the identification of such SV deletions may improve clinical testing.

Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility

Several susceptibility loci for classical Hodgkin lymphoma have been reported. However, much of the heritable risk is unknown. Here, we perform a meta-analysis of two existing genome-wide association studies, a new genome-wide association study, and replication totalling 5,314 cases and 16,749 controls. We identify risk loci for all classical Hodgkin lymphoma at 6q22.33 (rs9482849, P = 1.52 × 10-8) and for nodular sclerosis Hodgkin lymphoma at 3q28 (rs4459895, P = 9.43 × 10-17), 6q23.3 (rs6928977, P = 4.62 × 10-11), 10p14 (rs3781093, P = 9.49 × 10-13), 13q34 (rs112998813, P = 4.58 × 10-8) and 16p13.13 (rs34972832, P = 2.12 × 10-8). Additionally, independent loci within the HLA region are observed for nodular sclerosis Hodgkin lymphoma (rs9269081, HLA-DPB1*03:01, Val86 in HLA-DRB1) and mixed cellularity Hodgkin lymphoma (rs1633096, rs13196329, Val86 in HLA-DRB1). The new and established risk loci localise to areas of active chromatin and show an over-representation of transcription factor binding for determinants of B-cell development and immune response.

Abstract 4288: Inherited mutations in BRCA1 and BRCA2 in an unselected multi-ethnic cohort of Asian breast cancer patients and healthy controls from Malaysia

Background: BRCA1 and BRCA2 are significant cancer predisposition genes which have hitherto primarily been tested in breast cancer patients selected on the basis of age of onset of breast cancer and family history of breast and ovarian cancer. Given that only 40% of breast cancer occur in post-menopausal women in many Asian countries including Malaysia, compared to close to 80% in many Caucasian countries, the proportion of risk attributable to genetic factors is likely to be correspondingly higher in Asians. We sought to determine the prevalence of germline mutations in BRCA1 and BRCA2 in an unselected cohort of Asian breast cancer patients and healthy controls.

Methods: Women diagnosed with invasive breast cancer recruited from University Malaya Medical Centre between October 2002 and April 2015, and Sime Darby Medical Centre between September 2012 and April 2015 [n=2,592]. Eligible control subjects were recruited from women attending an opportunistic mammography screening programme at University Malaya Medical Centre between January 2014 and April 2015, and Sime Darby Medical Centre between October 2011 and April 2015 [n=2,851]. Amplicon-based targeted sequencing of exonic and proximal splice site junction regions of 31 known and probable breast cancer susceptibility genes were performed on Fluidigm Access Array system, with sequencing conducted on the Illumina HiSeq2500 platform. Variant calling was performed as per GATK recommended best practices with UnifiedGenotyper using the default parameters except -minIndelFrac 0.05. Variants were annotated with ANNOVAR and variants with MAF &gt;1% as reported in population databases were filtered out. Nonsense, frameshift indels, and splice site variants were presumed to be deleterious.

Results: Overall, 111 distinct mutations (50 BRCA1 and 61 BRCA2) were identified in 143 carriers (70 BRCA1 and 73 BRCA2) among breast cancer patients, and 11 carriers (5 BRCA1 and 6 BRCA2) were identified among healthy controls. Germline carriers were more likely to be younger, have family history of breast and/or ovarian cancer, have higher grade tumours and for BRCA1 carriers, they were more likely to have breast cancers which are negative for estrogen receptor and ERBB2 receptor. Notably, 45% of breast cancer patients fulfilled the NCCN guidelines for recommendation for genetic counseling and genetic testing, and of these, 80% of carriers fulfill the NCCN guidelines. Taken together, our results show that ~5% of Asian breast cancer patients have pathogenic mutations in BRCA1 or BRCA2, and that germline testing can be cost-effectively delivered to Asian women by focusing primarily on women with early onset breast cancer in the presence of family history of breast and ovarian cancers.

Citation Format: Wei Xiong Wen, Kah Nyin Lai, Jamie Allen, Craig Luccarini, Shivaani Mariapun, Cheng Har Yip, Nur Aishah Mohd Taib, Alison Dunning, Douglas Easton, Soo Hwang Teo. Inherited mutations in BRCA1 and BRCA2 in an unselected multi-ethnic cohort of Asian breast cancer patients and healthy controls from Malaysia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4288. doi:10.1158/1538-7445.AM2017-4288

Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes

Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma. Gene expression quantitative trait locus (eQTL) analysis in 1,425 normal lung tissue samples highlights RNASET2, SECISBP2L and NRG1 as candidate genes. Other loci include genes such as a cholinergic nicotinic receptor, CHRNA2, and the telomere-related genes OFBC1 and RTEL1. Further exploration of the target genes will continue to provide new insights into the etiology of lung cancer.

Abstract S2-03: Does BRCA status affect outcome in young breast cancer patients? Results from the prospective study of outcomes in sporadic and hereditary breast cancer (POSH)

Background

Germline mutations in BRCA1/2 account for ∼3% of breast cancer cases but &gt;10% of young patients who present with triple negative (TN) breast cancer. Young age at diagnosis is also associated with an increased risk of recurrence and inferior survival compared to older patients. Numerous publications describe an increased incidence of adverse biological features in tumours from young breast cancer patients; however it is unclear whether these fully explain the poor outcome.

The effect of carrying a BRCA1/2 mutation on the prognosis of breast cancer remains controversial with retrospective studies reporting better, similar and worse outcomes for mutation carriers compared to patients with sporadic tumours. BRCA carriers could feasibly have enhanced or reduced sensitivity to certain chemotherapeutics; however retrospective studies are problematic due to missing data and biased ascertainment. POSH is multicentre prospective observational cohort study designed to investigate factors which affect prognosis in young breast cancer patients (Copson et al, JNCI, 2013). Here we report the pathology, treatment and outcome of patients with TN tumours as a preliminary analysis to determine the impact of a germline BRCA1 mutation on survival. The whole cohort analysis including BRCA1 and BRCA2 is in progress.

Methods

2956 patients aged ≤40 at breast cancer diagnosis were recruited from 127 UK oncology centres between 2000 and 2008. Patient characteristics, family history, risk factors, tumour pathology and treatment information, and blood DNA were collected at recruitment. Follow-up data were collected at 6 and 12 months, then annually. Summary statistics were used to describe patients by BRCA1 status. Kaplan-Meier estimates were used to describe univariate survival data.

Results

BRCA1 status is currently available for 542 patients with TN tumours. Pathogenic BRCA1 mutations were identified in 122 patients (BRCA1+); 420 had no BRCA1 mutation (BRCA1-). BRCA1+ were younger than BRCA1- (median age 34 vs 36 years, p&lt;0.001) and more likely to have a positive family history (p&lt;0.001). There were no significant differences between BRCA1+ vs BRCA1- for: median tumour size (20.8mm vs 23.0mm); tumour grade distribution (95.8% grade 3 vs 93.6%); nodal involvement (35.2% node positive vs 39.9%); or presence of metastases at diagnosis (0.0% vs 1.0%).

Median follow-up was 7.3 years. Overall survival of patients with stage 1-3 disease treated with anthracycline +/- taxane neoadjuvant chemotherapy (n=538; 151 deaths) was better for BRCA1+ vs BRCA1- (79.1% vs 73.6% at 5-yrs; HR[95%CI]=0.84[0.57,1.25],p=0.388). Distant disease-free survival (DDFS) was also higher for BRCA1+ (5-yr DDFS 76.1% vs 71.5%; HR[CI]=0.92[0.63,1.35], p=0.682). Moreover, survival after first distant relapse was better for BRCA1+ patients (41.9% vs 36.8% at 1-yr; HR[CI]=0.78[0.51,1.18], p=0.233).

Conclusions

Our prospective data show better survival in young BRCA1+ patients with early TN breast cancer treated with anthracycline/-taxane chemotherapy than BRCA1- patients. However, the difference between the groups was not significant in this partial sample. Results for the whole cohort will be available by the time of the meeting.

Citation Format: Eccles DM, Copson ER, Maishman T, Tapper W, Cutress R, Gerty S, Stanton L, Altman DG, Durcan L, Simmonds P, Decker B, Allen J, Luccarini C, Easton D, Dunning A, POSH Steering Group and Collaborators. Does BRCA status affect outcome in young breast cancer patients? Results from the prospective study of outcomes in sporadic and hereditary breast cancer (POSH) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-03.

Quantitative apparent diffusion coefficient (ADC) values as an imaging biomarker for fibrosis in pediatric Crohn's disease: preliminary experience

PURPOSE

To compare histopathology with ADC values in strictured bowel segments in pediatric patients with known Crohn's disease and surgical bowel resection.

METHODS

Magnetic resonance enterography (MRE) images of 14 subjects with Crohn's disease who had surgical bowel resection for strictures were retrospectively reviewed. Five of 14 subjects had DWI (b=0, 500, 1000) sequences included in the MRE study. ADC measurements were made by placing ROI's in the strictured bowel wall and compared to full-thickness histologic analysis of resected specimens. ADC values were also compared to control ADC measurements (in normal and inflamed-nonstenotic bowel segments) as well as the mean ADC values of Crohn's patients published in the literature.

RESULTS

All five subjects had transmural fibrosis. The mean ADC value with b = 500 was 0.92 ± 0.10 × 10(-3) mm(2)/s and with b = 1000 was 0.8 ± 0.05 × 10(-3) mm(2)/s. There was a significant difference in ADC values between strictures and inflamed-nonstenotic segments (p=0.0143) and between normal and diseased bowel segments (p=0.009-0.0143).

CONCLUSIONS

Quantitative ADC measures of transmural fibrosis are lower compared to the reported values of inflammation in Crohn's disease. To our knowledge, this is the first pediatric pilot study to investigate the correlation of quantitative DWI with histology of surgical specimens in pediatric patients with Crohn's disease. Our results are comparable to a recently published study in adult Crohn's patients showing a significant correlation between a decrease in ADC values and fibrosis.

CD4 deficit and tuberculosis risk persist with delayed antiretroviral therapy: 5-year data from CIPRA HT-001

SETTING

Port-au-Prince, Haiti.

OBJECTIVE

To determine long-term effects of early vs. delayed initiation of antiretroviral therapy (ART) on immune recovery and tuberculosis (TB) risk in human immunodeficiency virus (HIV) infected individuals.

DESIGN

Open-label randomized controlled trial of immediate ART in HIV-infected adults with CD4 counts between 200 and 350 cells/mm(3) vs. deferring ART until the CD4 count was <200 cells/mm(3). The primary comparisons were CD4 counts over time and risk for incident TB, with 5 years of follow-up.

RESULTS

A total of 816 participants were enrolled, with 408 in each treatment arm. The early treatment group started ART within 2 weeks, while the deferred treatment group started ART a median of 1.3 years after enrollment. After 5 years, the mean CD4 count in the early treatment group was significantly higher than in the deferred treatment group (496 cells/mm(3), 95% confidence interval [CI] 477-515 vs. 373 cells/mm(3), 95%CI 357-389; P < 0.0001). TB risk was higher in the deferred treatment group (unadjusted HR 2.41, 95%CI 1.56-3.74; P < 0.0001) and strongly correlated with lower CD4 counts in time-dependent multivariate analysis.

CONCLUSION

Delays in ART initiation for HIV-infected adults with CD4 counts of 200-350 cells/mm(3) can result in long-term immune dysfunction and persistent increased risk for TB.

Abstract 2783: Common functional mechanisms underlying pleiotropy at the 19p13.1 breast and ovarian cancer cusceptibility locus

Genome-wide association studies (GWAS) have identified several susceptibility regions that confer risk of two or more cancers. A region at 19p13 is associated with both breast and ovarian cancer risk in the general population as well as in BRCA1/BRCA2 mutation carriers. Using the iCOGs custom genotyping array, we analyzed 438 SNPs in this region in 7,435 ER-negative breast cancer cases and 42,599 controls from BCAC, and 15,347 ovarian cancer cases and 30,845 controls from OCAC and 15,252 BRCA1 mutation carriers. We identified two significant peaks of association. Peak 1, consisting of 13 highly correlated SNPs (r2&gt;0.95), spans a 19.4kb region harboring the BABAM1, ANKLE1 and ABHD8 genes. Peak 1 SNPs are associated with serous ovarian cancer (top hit rs4808075, P = 9.2×10-20), ER-negative breast cancer (rs61494113, P = 1.1×10-13) and breast cancer in BRCA1 mutation carriers (rs61494113, P = 7.7×10-16). Peak 2 spans over 100kb and contains 7 SNPs associated with breast cancer in BRCA1 mutation carriers only (rs4464206, P = 8.9×10-8). Multiple assays were used to establish the putative functional roles of risk SNPs and candidate susceptibility genes in this region. Expression quantitative trait locus (eQTL) analyses identified significant genotype-gene expression correlations between genotype at the Peak 1 SNP rs480816 and ABHD8 expression in ovarian tumors (P = 3.0×10-5) and normal breast tissues (P = 2.8×10-3). The Peak 2 SNP, rs7246243, was significantly associated with BABAM1 expression (P = 5×10-3) in normal breast tissue only. Overexpression of BABAM1 in normal ovarian and breast cells did not modulate neoplastic phenotypes, whereas overexpression of ABHD8 induced a significant reduction in migration in both cell types in vitro. Differentially expressed genes in ABHD8 models, identified by RNAseq, were associated with cellular movement (P&lt;1.82×10-44). Chromosome conformation capture (3C) identified an interaction between the ABHD8 promoter and a region containing 4 risk SNPs (rs4808075, rs10419397, rs56069439 and rs4808076) in breast and ovarian normal and cancer cells but only rs56069439 coincides with epigenetic enhancer marks in breast and ovarian cells. CRISPR/Cas9 genome editing was used to delete a 57bp region containing rs56069439 and expression of BABAM1, ANKLE1 and ABHD8 were measured. Taken together, these data suggest a common functional mechanism underlying risk of breast and ovarian cancer at this locus, mediated by rs56069439 variants differentially regulating expression of ABHD8, a gene involved in cell motility.

Citation Format: Kate Lawrenson, Siddhartha Kar, Karoline Kuckenbaeker, Stacey Edwards, Qiyuan Li, Jonathan Tyrer, Jonathan Beesley, Kyriaki Michailidou, Susan Ramus, Alison Dunning, Fergus Couch, Alvaro Monteiro, Jacques Simard, Matthew Freedman, Douglas Easton, Georgia Chenevix-Trench, Paul Pharoah, Antonis Antoniou, Simon Gayther, OCAC, BCAC and CIMBA. Common functional mechanisms underlying pleiotropy at the 19p13.1 breast and ovarian cancer cusceptibility locus. [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 2783. doi:10.1158/1538-7445.AM2015-2783

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.

Radiogenomics: the search for genetic predictors of radiotherapy response

'Radiogenomics' is the study of genetic variation associated with response to radiotherapy. Radiogenomics aims to uncover the genes and biologic pathways responsible for radiotherapy toxicity that could be targeted with radioprotective agents and; identify genetic markers that can be used in risk prediction models in the clinic. The long-term goal of the field is to develop single nucleotide polymorphism-based risk models that can be used to stratify patients to more precisely tailored radiotherapy protocols. The field has evolved over the last two decades in parallel with advances in genomics, moving from narrowly focused candidate gene studies to large, collaborative genome-wide association studies. Several confirmed genetic variants have been identified and the field is making progress toward clinical translation.

2q36.3 is associated with prognosis for oestrogen receptor-negative breast cancer patients treated with chemotherapy

Large population-based registry studies have shown that breast cancer prognosis is inherited. Here we analyse single-nucleotide polymorphisms (SNPs) of genes implicated in human immunology and inflammation as candidates for prognostic markers of breast cancer survival involving 1,804 oestrogen receptor (ER)-negative patients treated with chemotherapy (279 events) from 14 European studies in a prior large-scale genotyping experiment, which is part of the Collaborative Oncological Gene-environment Study (COGS) initiative. We carry out replication using Asian COGS samples (n=522, 53 events) and the Prospective Study of Outcomes in Sporadic versus Hereditary breast cancer (POSH) study (n=315, 108 events). Rs4458204_A near CCL20 (2q36.3) is found to be associated with breast cancer-specific death at a genome-wide significant level (n=2,641, 440 events, combined allelic hazard ratio (HR)=1.81 (1.49-2.19); P for trend=1.90 × 10(-9)). Such survival-associated variants can represent ideal targets for tailored therapeutics, and may also enhance our current prognostic prediction capabilities.

The REQUITE project: Validating predictive models and biomarkers of radiotherapy toxicity to reduce side effects

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Background: Recently the first replicated genetic associations for adverse reactions to radiotherapy (RT) have been reported. These will help to build predictive statistical models for optimising RT delivery or interventions to alleviate the side effects. It is now timely to start a project that aims to validate known predictors of adverse reactions and develop the statistical models to become clinically useful. REQUITE is a European Union funded FP7 project that aims to do this. Methods: REQUITE’s objectives: (1.) Perform a multi-centre, cohort study collecting: blood samples, epidemiology and treatment data, longitudinal side-effect and QOL data (before and after treatment, yrs 1 and 2). (2.) Produce a centralised biobank of DNA from 5,300 patients and a centralised data management system. (3.) Validate published biomarkers of radiosensitivity. (4.) Validate clinical predictors of RT toxicity in breast, prostate, and lung cancer and incorporate biomarker data. (5.) Design interventional trials to reduce long-term side effects. (6.) Provide a resource for dissemination and exploitation to the RT community. Results: REQUITE is funded for 60 mos and organised into 7 work packages. Overall management and scientific oversight is run by Manchester. The central activity of the project is a multi-centre, observational study. Enrolment will proceed for 2 yrs in 9 clinical centres, with 2 yrs follow-up. The primary endpoints are change in breast appearance; rectal bleeding (prostate); pneumonitis (lung). Blood samples will be collected before radiotherapy. Tracking, biobanking, DNA preparation and validation of biomarkers (genetic markers and apoptosis assays) as predictive factors will be carried out in WP3-4. Some clinical factors have suggested predictive value for RT side-effects, but there is no consensus. Validation of published models in existing cohorts will be performed, leading to replicated models that can be validated using the REQUITE cohorts. Conclusions: The predictive models will be used to design clinical interventional trials and produce protocols that seek to lower RT side-effects in those individuals at high risk of developing them without affecting tumour control. Dissemination will follow.

CT perfusion for detection of delayed cerebral ischemia in aneurysmal subarachnoid hemorrhage: a systematic review and meta-analysis

BACKGROUND AND PURPOSE

Delayed cerebral ischemia is a significant cause of morbidity and mortality after aneurysmal SAH, leading to poor outcomes. The purpose of this study was to evaluate the usefulness of CTP in determining delayed cerebral ischemia in patients with aneurysmal SAH.

MATERIALS AND METHODS

We conducted a systematic review evaluating studies that assessed CTP in patients with aneurysmal SAH for determining delayed cerebral ischemia. Studies using any of the following definitions of delayed cerebral ischemia were included in the systematic review: 1) new onset of clinical deterioration, 2) cerebral infarction identified on follow-up CT or MR imaging, and 3) functional disability. A random-effects meta-analysis was performed assessing the strength of association between a positive CTP result and delayed cerebral ischemia.

RESULTS

The systematic review identified 218 studies that met our screening criteria, of which 6 cohort studies met the inclusion criteria. These studies encompassed a total of 345 patients, with 155 (45%) of 345 patients classified as having delayed cerebral ischemia and 190 (55%) of 345 patients as not having delayed cerebral ischemia. Admission disease severity was comparable across all groups. Four cohort studies reported CTP test characteristics amenable to the meta-analysis. The weighted averages and ranges of the pooled sensitivity and specificity of CTP in the determination of delayed cerebral ischemia were 0.84 (0.7-0.95) and 0.77 (0.66-0.82), respectively. The pooled odds ratio of 23.14 (95% CI, 5.87-91.19) indicates that patients with aneurysmal SAH with positive CTP test results were approximately 23 times more likely to experience delayed cerebral ischemia compared with patients with negative CTP test results.

CONCLUSIONS

Perfusion deficits on CTP are a significant finding in determining delayed cerebral ischemia in aneurysmal SAH. This may be helpful in identifying patients with delayed cerebral ischemia before development of infarction and neurologic deficits.

Intraplaque high-intensity signal on 3D time-of-flight MR angiography is strongly associated with symptomatic carotid artery stenosis

BACKGROUND AND PURPOSE

Intraplaque hemorrhage in carotid artery atherosclerotic plaque has been shown to be a marker of risk, associated with prior and future ischemic events, and has been associated with regions of intraplaque high-intensity signal on 3D-TOF MRA. We assessed the association of intraplaque high-intensity signal determined on 3D-TOF MRA with the incidence of prior ipsilateral stroke or TIA.

MATERIALS AND METHODS

We assessed intraplaque hemorrhage by evaluating for intraplaque high-intensity signal adapting a recently validated technique on 3D-TOF source images in participants with high-grade (≥ 70%) extracranial carotid stenosis. Logistic regression analyses were used to assess the strength of association between the presence of intraplaque high-intensity signal on routine MRA sequences and prior stroke or TIA.

RESULTS

Intraplaque high-intensity signal was present in 22 (41.5%) of 53 carotid arteries studied in 51 patients. Ipsilateral ischemic events occurred in 15 (68.1%) of 22 in the intraplaque high-intensity signal-positive group (10 strokes, 5 TIAs) and in 4 (12.9%) of 31 in the intraplaque high-intensity signal-negative group (3 strokes, 1 TIA). Ischemic events occurred within the 6-month period preceding imaging in 18 (94.7%) of 19 cases. The univariate odds ratio of the association of intraplaque high-intensity signal with any prior ischemic event was 14.5 (95% CI, 3.6-57.6), and the multivariate age- and sex-adjusted odds ratio was 14.2 (95% CI, 3.3-60.5). The association remained present across 1.5 T and 3T magnet field strengths.

CONCLUSIONS

Intraplaque high-intensity signal determined from MRA sequences already in place to measure luminal stenosis is strongly associated with prior ipsilateral ischemic events. Prospective validation of these findings to predict outcome in carotid artery stenosis could provide a valuable and widely accessible stroke risk stratification tool.

Abstract 3182: A GWAS-based cross-disease approach suggests genes predisposing to risk of endometriosis and endometrial cancer

While endometriosis is a known risk factor for endometrioid and clear-cell ovarian cancer subtypes, a convincing link between endometriosis and endometrial cancer has been difficult to establish epidemiologically. Such a link has been speculated as both are hormonally regulated diseases of abnormal endometrium growth and they share a number of risk factors (e.g. early menarche, low parity) and pathological features (e.g. progesterone resistance). To investigate the genetic relationship between endometriosis and endometrial cancer, we recently applied a cross-disease analysis approach utilizing genome-wide association study (GWAS) data1,2. Genetic prediction analyses revealed significant (P=7.8 × 10-10) shared genetic architecture underlying endometriosis and endometrial cancer, indicating the existence of genetic loci that influence the risk of both diseases. We then performed a cross-disease meta-analysis which revealed 102 SNPs at 65 independent genetic loci with good support (P-values &lt; 10-5) for association with risk of both diseases. To date, we have validation for two of these loci in an independent sample of 4,400 endometrial cancer cases and 28,000 controls. A gene at one locus, the protein tyrosine phosphatase receptor type D gene (PTPRD: best SNP P-value =8.8 × 10-8, Odds Ratio=1.08±0.03) has been suggested as a tumour suppressor in neuroblastoma, and as a type II diabetes candidate. The second locus is in the region of the transcription factor A-P 2 beta-like 1 (TFAP2D) and beta (TFAP2B) genes (best SNP P-value 8.2 × 10-7, Odds Ratio 1.07±0.03), the latter of which has been recently associated with metabolic syndrome, BMI and overweight. These genes are entirely plausible candidates for involvement in endometrial cancer aetiology given the increased risk of endometrial cancer with increasing BMI. Imputation to the April 2012 release of the 1000 Genomes project data has revealed additional SNPs in both regions with equal or better evidence of statistical support, and we are currently performing bioinformatic analyses to search for potentially functional SNPs in both regions for genotyping in additional endometrial cancer samples. In summary, our results from prediction analysis indicate that genetic loci contribute to both endometriosis and endometrial cancer susceptibility, and case-control association analyses suggest two plausible candidate genes for further study. These findings support the value of cross-disease meta-analyses for finding new genes contributing to cancer susceptibility.

Citation Format: Jodie N. Painter, Stuart Macgregor, Ian Tomlinson, Dale R. Nyholt, Krina Zondervan, Deborah Thompson, Alison Dunning, Douglas Easton, Grant W. Montgomery, Amanda B. Spurdle. A GWAS-based cross-disease approach suggests genes predisposing to risk of endometriosis and endometrial cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3182. doi:10.1158/1538-7445.AM2013-3182

Polymorphisms in inflammation pathway genes and endometrial cancer risk

BACKGROUND

Experimental and epidemiologic evidence have suggested that chronic inflammation may play a critical role in endometrial carcinogenesis.

METHODS

To investigate this hypothesis, a two-stage study was carried out to evaluate single-nucleotide polymorphisms (SNP) in inflammatory pathway genes in association with endometrial cancer risk. In stage I, 64 candidate pathway genes were identified and 4,542 directly genotyped or imputed SNPs were analyzed among 832 endometrial cancer cases and 2,049 controls, using data from the Shanghai Endometrial Cancer Genetics Study. Linkage disequilibrium of stage I SNPs significantly associated with endometrial cancer (P < 0.05) indicated that the majority of associations could be linked to one of 24 distinct loci. One SNP from each of the 24 loci was then selected for follow-up genotyping. Of these, 21 SNPs were successfully designed and genotyped in stage II, which consisted of 10 additional studies including 6,604 endometrial cancer cases and 8,511 controls.

RESULTS

Five of the 21 SNPs had significant allelic odds ratios (ORs) and 95% confidence intervals (CI) as follows: FABP1, 0.92 (0.85-0.99); CXCL3, 1.16 (1.05-1.29); IL6, 1.08 (1.00-1.17); MSR1, 0.90 (0.82-0.98); and MMP9, 0.91 (0.87-0.97). Two of these polymorphisms were independently significant in the replication sample (rs352038 in CXCL3 and rs3918249 in MMP9). The association for the MMP9 polymorphism remained significant after Bonferroni correction and showed a significant association with endometrial cancer in both Asian- and European-ancestry samples.

CONCLUSIONS

These findings lend support to the hypothesis that genetic polymorphisms in genes involved in the inflammatory pathway may contribute to genetic susceptibility to endometrial cancer. Impact statement: This study adds to the growing evidence that inflammation plays an important role in endometrial carcinogenesis.

Decreased breast cancer risk in systemic lupus erythematosus: the search for a genetic basis continues

PURPOSE

Recent work has demonstrated an important decrease in breast cancers for women with systemic lupus erythematosus (SLE). The reason behind this phenomenon is unknown. Our purpose was to explore whether the single nucleotide polymorphisms (SNPs) predisposing to SLE might be protective against breast cancer (in women in the general population).

METHODS

We focused on loci relevant to 10 SNPs associated with SLE (with a p value of <10(-9)). We determined whether we could establish a decreased frequency of these SNPs in breast cancer cases versus controls, within the general population. To do this we used a large breast cancer genome-wide association study (GWAS) dataset, involving 3,659 breast cancer cases and 4,897 controls. These subjects were all primarily of European ancestry.

RESULTS

The population-based GWAS breast cancer data we examined suggested little evidence for important associations between breast cancer and SLE-related SNPs. Within the general population GWAS data, a cytosine(C) nucleotide substitution at rs9888739 (on chromosome 16p11.2) showed a very weak inverse association with breast cancer. The odds ratio (OR) for the rs9888739-C allele was 0.907551 (p value 0.049899) in the GWAS breast cancer sample, compared to controls. There was a slightly stronger, positive, association with breast cancer for rs6445975-G (Guanine) on chromosome 3p14.3, with a breast cancer OR of 1.0911 (p value 0.0097).

CONCLUSIONS

Within this large breast cancer dataset, we did not demonstrate important associations with 10 lupus-associated SNPs. If decreased breast cancer risk in SLE is influenced by genetic profiles, this may be due to complex interactions and/or epigenetic factors.

Genome-wide association study identifies a possible susceptibility locus for endometrial cancer

BACKGROUND

Genome-wide association studies (GWAS) have identified more than 100 genetic loci for various cancers. However, only one is for endometrial cancer.

METHODS

We conducted a three-stage GWAS including 8,492 endometrial cancer cases and 16,596 controls. After analyzing 585,963 single-nucleotide polymorphisms (SNP) in 832 cases and 2,682 controls (stage I) from the Shanghai Endometrial Cancer Genetics Study, we selected the top 106 SNPs for in silico replication among 1,265 cases and 5,190 controls from the Australian/British Endometrial Cancer GWAS (stage II). Nine SNPs showed results consistent in direction with stage I with P < 0.1. These nine SNPs were investigated among 459 cases and 558 controls (stage IIIa) and six SNPs showed a direction of association consistent with stages I and II. These six SNPs, plus two additional SNPs selected on the basis of linkage disequilibrium and P values in stage II, were investigated among 5,936 cases and 8,166 controls from an additional 11 studies (stage IIIb).

RESULTS

SNP rs1202524, near the CAPN9 gene on chromosome 1q42.2, showed a consistent association with endometrial cancer risk across all three stages, with ORs of 1.09 [95% confidence interval (CI), 1.03-1.16] for the A/G genotype and 1.17 (95% CI, 1.05-1.30) for the G/G genotype (P = 1.6 × 10(-4) in combined analyses of all samples). The association was stronger when limited to the endometrioid subtype, with ORs (95% CI) of 1.11 (1.04-1.18) and 1.21 (1.08-1.35), respectively (P = 2.4 × 10(-5)).

CONCLUSIONS

Chromosome 1q42.2 may host an endometrial cancer susceptibility locus.

IMPACT

This study identified a potential genetic locus for endometrial cancer risk.

Diagnostic accuracy of 4D-CT for parathyroid adenomas and hyperplasia

BACKGROUND AND PURPOSE

4D-CT is a novel method of multiphase CT imaging. When used to localize parathyroid adenomas and hyperplasia, this technique may allow for more robust diagnostic accuracy than traditional sonography and nuclear scintigraphy techniques. The purpose of our study is to assess the accuracy of 4D-CT for localizing pathologically proved parathyroid adenomas and hyperplasia found during surgery.

MATERIALS AND METHODS

A total of 35 pathologically proved cases of parathyroid adenoma and hyperplasia were retrospectively reviewed between January 2009 and March 2011. Inclusion criteria were availability of final surgical pathology and performance of preoperative 4D-CT. No cases were excluded. Sensitivity, specificity, and accuracy of 4D-CT were ascertained including both the side and quadrant of the pathologically proved lesion.

RESULTS

Of the 35 pathologically proved cases collected over the study period, 32 (sensitivity = 91%) patients were found positive for parathyroid disease using 4D-CT, including 3 cases of multigland disease. For lateralization of single-gland disease, 4D-CT demonstrated an accuracy of 93%. 4D-CT revealed a suboptimal 44% sensitivity, but 100% specificity, for multigland disease.

CONCLUSIONS

4D-CT demonstrated a high diagnostic accuracy for single and multigland disease in our cohort. Importantly, 4D-CT accurately lateralized single-gland adenomas in >90% of cases, allowing the surgeon to employ a directed operative approach. 4D-CT also showed a very high specificity for the detection of multigland disease.

Prognostic factors of cancer recurrence and progression in non-muscle-invasive urothelial carcinoma: A multicenter study of over 4,300 patients

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Background: The outcomes of patients with non-muscle-invasive urothelial carcinoma of the bladder (NMIUCB) remain poorly understood. The aim of our study was to identify prognostic factors of cancer recurrence and progression in patients with primary UCB.

Methods: We performed a combined analysis on individual data from 4,325 patients with primary NMIUCB.

Results: Within a median follow-up of 64 months, 1,960 patients (45.4%) experienced disease recurrence, 498 (11.5%) experienced progression to muscle-invasive stage, 1,155 (26.7%) died of any cause, and 310 (7.2%) died of their cancer. In multivariable Cox regression analysis, advanced age, higher grade, larger tumor size, higher number of tumors, number of prior recurrences, and type of intravesical therapy were independent predictors of disease recurrence and progression. While treatment intravesical chemotherapy was only associated with decreased/delayed cancer recurrence, intravesical BCG therapy was associated with decreased/delayed cancer recurrence and progression. The predictive accuracies of the models for recurrence and progression were 63.5% and 71.3%, respectively.

Conclusions: Even in a heterogenous patient population, BCG therapy appears to decrease frequency and delay time to cancer recurrence and progression in patients with NMIUCB. Predictive tools based on combination of multiple clinical variables which capture the biological and clinical potential of nonmuscle-invasive disease could help with patient counseling and individualized risk assessment for adjuvant intravesical therapy and clinical trial design.

[Table: see text]

No significant financial relationships to disclose.

Endometrial cancer and genetic variation in PTEN, PIK3CA, AKT1, MLH1, and MSH2 within a population-based case-control study

OBJECTIVE

We assessed whether common genetic variation in PTEN, PIK3CA, AKT1, MLH1, and MSH2-genes that reportedly are frequently altered in endometrial cancer-was associated with risk of endometrial cancer.

METHODS

Using data from a population-based case-control study in Poland (PECS) of 417 cases and 407 matched controls, we genotyped 76 tagging single nucleotide polymorphisms (tagSNPs; located in or within 10 kb upstream or 5 kb downstream of the gene of interest, minor allele frequency >=5% among various ethnic groups, and not already represented by another tagSNP at a LD of r(2) >=0.80) on an Illumina Custom Infinium iSelect assay that included over 29,000 SNPs in 1316 genes. For individual SNPs, we used unconditional logistic regression models, adjusted for age and site, to generate odds ratios (ORs) and 95% confidence intervals (CIs). To replicate the one statistically significant association in PECS, we independently genotyped that tagSNP among 1141 endometrial cancer cases and 2275 controls from the SEARCH study in the UK. We assessed haplotypes via extended haplotype blocks and the sequential haplotype scan method.

RESULTS

The rs2677764 tagSNP in PIK3CA was statistically significantly associated with endometrial cancer in PECS (OR=1.42, 95% CI, 1.03-1.95; P=0.03) but not SEARCH (OR=0.98, 95% CI=0.82-1.17). Of the 25 haplotypes observed in at least 5% of cases and controls in PECS, only 1, in PIK3CA, was statistically significantly associated with endometrial cancer (OR=1.39, 95% CI, 1.00-1.93). All haplotype global p-values were null.

CONCLUSION

Common genetic variation in PTEN, PIK3CA, AKT1, MLH1, or MSH2 was not statistically significantly associated with endometrial cancer.

Abstract 2850: Endometrial cancer and genetic variation in PTEN, PIK3CA, AKT1, MLH1, and MSH2: results and replication in two case-control studies

PTEN, PI3KCA, AKT, MLH1, and MSH2 likely influence endometrial carcinogenesis. PTEN regulates the crucial PI3K signaling pathway, which influences AKT, a serine-threonine kinase that affects apoptosis and cell proliferation; inadequate progesterone-stimulated apoptosis plus excess estrogen-driven proliferation are crucial for endometrial carcinoma. MLH1 and MSH2 influence DNA mismatch repair and microsatellite instability, which are often defective in endometrial cancers. We investigated common genetic variation in these genes among 417 cases and 407 matched controls from the population-based Poland Endometrial Case-control Study (PECS). We genotyped 76 tagging single nucleotide polymorphisms (tagSNPs) that were located in or within 10kb upstream or 5kb downstream of these genes, had a MAF&gt;=5% in various ethnic groups, and were not already represented by another tagSNP at a linkage disequilibrium of r2&gt;=0.80. Genotyping was performed on an Illumina Custom Infinium iSelect assay that includes 29,289 SNPs in 1316 genes. For individual SNPs, we used unconditional logistic regression, adjusted for age and site, to generate odds ratios (ORs) and 95% confidence intervals (CIs) for heterozygous genotypes, minor homozygous genotypes, and trends for number of minor alleles under log-additive inheritance. Only 1 tagSNP, rs2677764 in PIK3CA, was statistically significantly associated with endometrial cancer. Compared with a referent group of CC, the ORs (95% CIs) were 1.47 (1.03-2.10) for CT and 1.56 (0.43-5.60) for TT. The OR for the trend was 1.42 (95% CI, 1.03-1.95; P=0.03). We chose extended blocks as the main haplotype analysis, used an E-M algorithm to simultaneously reconstruct haplotypes and estimate ORs, and used a sequential-scan method to identify statistically significant haplotypes. All global p-values for the 25 haplotypes observed in at least 5% of cases and controls were null. One haplotype in PIK3CA was significantly associated with endometrial cancer (OR=1.39. 95% CI, 1.00-1.93). We also used adaptive rank truncated product (ARTP) methods to detect gene associations, but none were statistically significant. To further assess the validity of the association with rs2677764, we genotyped that SNP in a 2nd study, the SEARCH study in the UK, with 1141 endometrial cancer cases and 2275 controls. For rs2677764, the ORs (95% CIs) were 0.93 (0.77-1.13) for CT, 1.27 (0.68-2.39) for TT, and 0.98 (0.82-1.17) for the trend test. In a fixed-effect meta-analysis combining PECS and SEARCH, rs2677764 was not associated with endometrial cancer: OR=1.15 (95% CI, 0.80-1.66; P=0.45 for trend test). The absence of replication in SEARCH of an association with rs2677764 in PIK3CA in PECS and the null results from haplotype and ARTP analyses indicate that these common genetic variations in PTEN, PI3KCA, AKT, MLH1, and MSH2 do not substantially affect endometrial cancer risk.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2850.

HSD17B1 genetic variants and hormone receptor-defined breast cancer

HSD17B1 is an important candidate gene in breast cancer via its role in converting estrone to estradiol. A nonsynonymous G-to-A transition (rs605059) and an intronic C-to-A (rs676387) single-nucleotide polymorphism, which captured most common variation in HSD17B1, were evaluated in several breast cancer studies with inconclusive results. We followed up these findings in the Polish Breast Cancer Study (1,995 cases; 2,296 controls) and the British Studies of Epidemiology and Risk Factors in Cancer Heredity study (4,470 cases; 4,560 controls). Meta-analyses of published data and our own were also conducted among Caucasian women. Consistent with previous reports, we found little to no association with overall risk for heterozygotes and minor allele homozygotes compared with major allele homozygotes for rs605059 [summary odds ratios (95% confidence intervals), 0.93 (0.87-0.99) for GA and 0.96 (0.85-1.08), based on 11,762 cases and 14,329 controls from 10 studies] and for rs676387 [summary odds ratios (95% confidence intervals), 1.04 (0.97-1.12) and 1.12 (0.99-1.27), based on analyses of 11,074 cases and 13,605 controls from 8 studies]. Data from the Polish [n=586 estrogen receptor-negative (ER-) cases] and British (n=407) studies did not support the previous findings that ER- tumors were inversely associated with rs676387 AA genotype and positively associated with rs605059 GG genotype, based on subanalyses in 5 prospective cohorts with 354 ER- cases. In conclusion, it is unlikely that common genetic variation in HSD17B1 is associated with a moderate modulation in breast cancer risk overall; however, we cannot exclude the possibility of a very weak effect. Associations between HSD17B1 genotypes and risk for ER- breast cancer were inconsistent across studies and should be studied further.