Meta-analysis of the association between emphysematous change on thoracic computerized tomography scan and recurrent pneumothorax

OBJECTIVES

At least a third of patients go on to suffer a recurrence following a first spontaneous pneumothorax. Surgical intervention reduces the risk of recurrence and has been advocated as a primary treatment for pneumothorax. But surgery exposes patients to the risks of anaesthesia and in some cases can cause chronic pain. Risk stratification of patients to identify those most at risk of recurrence would help direct the most appropriate patients to early intervention. Many studies have addressed the role of thoracic computerized tomography (CT) in identifying those individuals at increased risk of recurrence, but a consensus is lacking.

AIM

Our objective was to clarify whether CT provides valuable prognostic information for recurrent pneumothorax.

DESIGN

Meta-analysis.

METHODS

We conducted an exhaustive search of the literature for thoracic CT imaging and pneumothorax, and then performed a meta-analysis using a random effects model to estimate the common odds ratio and standard error.

RESULTS

Here, we show by meta-analysis of data from 2475 individuals that emphysematous change on CT scan is associated with a significant increased odds ratio for recurrent pneumothorax ipsilateral to the radiological abnormality (odds ratio 2.49, 95% confidence interval 1.51-4.13).

CONCLUSIONS

The association holds true for primary spontaneous pneumothorax when considering emphysematous changes including blebs and bullae. Features, such as bullae at the azygoesophageal recess or increased Goddard score similarly predicted recurrent secondary pneumothorax, as shown by subgroup analysis. Our meta-analysis suggests that CT scanning has value in risk stratifying patients considering surgery for pneumothorax.

Abstract P1-09-04: Association between a breast cancer polygenic risk score and contralateral breast cancer risk

Background

Breast cancer patients are at significant risk of a second contralateral, breast cancer (CBC). Identification of women at high or low CBC risk could improve patient management decisions. Previous research has shown that breast cancer-associated single nucleotide polymorphisms (SNPs) summarized in a polygenic risk score (PRS) predict the risk of a first breast cancer with an odds ratio (OR) per 1 SD of 1.55 (95% confidence interval (95%CI)=1.52-1.58) (77-SNP PRS). The aim of this study was to evaluate the association between a recently developed PRS and CBC risk.

Methods

We identified 19 studies from the Breast Cancer Association Consortium (BCAC) with follow-up information on participating patients and at least 10 patients diagnosed with CBC. This included 38,228 females of European ancestry diagnosed with first invasive breast cancer since 1990. Genotyping was done using the iCOGS array or OncoArray, with genotypes for SNPs not on the arrays estimated by imputation. We used a 313-SNP PRS, optimized for prediction of overall (first) breast cancer in the BCAC dataset. Metachronous CBC risk by PRS was quantified using univariable and multivariable Cox regression analyses stratified by country and adjusted for multiple patient, tumor, and treatment characteristics. We assessed PRS interaction with age, family history, adjuvant systemic therapy, and ER-status.

Results

Median time to develop a CBC (N=1,046) after a first breast cancer was 5.8 years (range 0.3-21.9). Higher PRS was associated with increased CBC risk: hazard ratio (HR) per 1 SD=1.31 (95%CI=1.23-1.39). Patients in the highest and lowest 5% of the PRS had 1.95 fold and 0.67 fold risks of CBC, respectively, compared with patients in the middle quintile. Adjustments for age, year of diagnosis, family history, tumor size, nodal status, ER-status, or treatment (chemotherapy, endocrine therapy, radiotherapy) did not substantially alter these results. We found an interaction with age at first breast cancer diagnosis (Pinteraction=.002); the PRS was associated with an increased CBC risk for patients aged ≥40 years (HR=1.37, 95%CI=1.28-1.47), but not for patients <40 years (HR=1.06, 95%CI=0.93-1.21).

Conclusion

The PRS is predictive for the development of CBC in patients ≥40 years at first breast cancer diagnosis. For this group, the PRS could be incorporated in CBC risk prediction models to help define high and low risk patients, and hence optimize screening and treatment strategies.

Citation Format: Kramer I, Hooning MJ, Breast Cancer Association Consortium (BCAC), Mavaddat N, Canisius S, Keeman R, van den Broek AJ, Steyerberg E, Hauptmann M, Pharoah PD, Easton DF, Hall P, Schmidt MK. Association between a breast cancer polygenic risk score and contralateral breast cancer risk [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-09-04.

Abstract GS3-06: Dynamics of breast cancer relapse reveal molecularly defined late recurring ER-positive subgroups: Results from the METABRIC study

Background: Recent studies have demonstrated that women with early stage ER-positive (ER+) and HER2-negative (HER2-) breast cancer have a persistent risk of recurrence and cancer related death up to 20 years post diagnosis, highlighting the chronic nature of ER+ breast cancer and critical need to identify tumor characteristics that are more predictive of risk of recurrence than standard clinical covariates. However, progress in delineating the dynamics of breast cancer relapse and biomarkers of late recurrence has been hindered by the lack of large cohorts with long-term clinical follow-up and molecular information.

Methods: We report the results of a cohort of 3,240 breast cancer patients from the United Kingdom and Canada with 20 years of follow-up (median 9.75 years), including 1,980 with accompanying molecular data from the primary breast tumor. Information for each patient on loco-regional recurrence (LR), distant recurrence (DR), and site(s) of metastases was collected. We developed a non-homogenous Markov chain model that accounted for different clinical endpoints and timescales, as well as competing risks of mortality and the distinct baseline hazards that characterize different molecular subgroups. This approach enabled robust analysis of the spatio-temporal dynamics of breast cancer recurrence across the clinical subgroups, PAM50 subgroups and the integrative clusters, while also enabling individual risk of relapse predictions.

Results: We employed our multistate model to compute the probability of experiencing a LR or DR, as well as the baseline transition probabilities from surgery, LR or DR at various time intervals for average individuals in each of the clinical/molecular subgroups. These analyses reveal four late-recurring ER+ (predominantly HER2-) subgroups, together accounting for 26% of all ER+ tumors, with high (median 42-55%) risk of recurrence up to 20 years post-diagnosis. Each of these four subgroups maps to one of the Integrative Clusters, defined based on genomic copy number alterations and gene expression, and is enriched for a characteristic copy number amplification events: 11q13 (CCND1, RSF1), 8p12 (FGFR1, ZNF703), 17q23 (RPS6KB1) and 8q24 (MYC). These four molecular subgroups are superior in predicting late DR than standard clinical variables.

Conclusions: A detailed understanding of the rates and routes of metastasis and their variability across the distinct molecular subtypes is essential for devising personalized approaches to breast cancer care. We describe a molecularly characterized breast cancer cohort with long-term clinical follow-up and a statistical modeling framework, enabling delineation of the dynamics of breast cancer recurrence at unprecedented resolution. These analyses reveal four late recurring ER+ subgroups and accompanying biomarkers that collectively define the quarter of ER+ cases at highest risk of recurrence. Our findings highlight opportunities for improved patient stratification and biomarker-driven clinical trials directed at the subset of breast cancer patients with persistent risk of recurrence.

Citation Format: Curtis C, Rueda OM, Sammut S-J, Chin S-F, Caswell-Jin JL, Seoane JA, Callari M, Batra R, Pereira B, Bruna A, Ali HR, Provenzano E, Liu B, Parisien M, Gillett C, McKinney S, Green A, Murphy L, Purushotham A, Ellis I, Pharoah P, Rueda C, Aparicio S, Caldas C. Dynamics of breast cancer relapse reveal molecularly defined late recurring ER-positive subgroups: Results from the METABRIC study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS3-06.

Weibull regression with Bayesian variable selection to identify prognostic tumour markers of breast cancer survival

As data-rich medical datasets are becoming routinely collected, there is a growing demand for regression methodology that facilitates variable selection over a large number of predictors. Bayesian variable selection algorithms offer an attractive solution, whereby a sparsity inducing prior allows inclusion of sets of predictors simultaneously, leading to adjusted effect estimates and inference of which covariates are most important. We present a new implementation of Bayesian variable selection, based on a Reversible Jump MCMC algorithm, for survival analysis under the Weibull regression model. A realistic simulation study is presented comparing against an alternative LASSO-based variable selection strategy in datasets of up to 20,000 covariates. Across half the scenarios, our new method achieved identical sensitivity and specificity to the LASSO strategy, and a marginal improvement otherwise. Runtimes were comparable for both approaches, taking approximately a day for 20,000 covariates. Subsequently, we present a real data application in which 119 protein-based markers are explored for association with breast cancer survival in a case cohort of 2287 patients with oestrogen receptor-positive disease. Evidence was found for three independent prognostic tumour markers of survival, one of which is novel. Our new approach demonstrated the best specificity.

Hypertension and mortality in the Golestan Cohort Study: A prospective study of 50 000 adults in Iran

High blood pressure has been the second most important determinant of disease burden in Iran since the 1990s. Despite well-recognized evidence on the association of high blood pressure and mortality in other countries, this relationship has not been fully investigated in the demographic setting of Iran. The current study is the first large-scale longitudinal study of this association in Iran. Briefly, 50 045 subjects between 40 and 75 years of age have been recruited and followed. Blood pressure measurements were carried out at baseline. Causes of death were reported and verified by verbal autopsy throughout the follow-up period. The outcomes of interest were all-cause deaths and deaths due to ischemic heart disease (IHD) or stroke. Cox proportional hazards regression models were used to estimate hazard ratios (HRs). A total of 46 674 subjects free from cardiovascular disease at baseline were analyzed. Absolute mortality rates increased along with increasing systolic or diastolic blood pressure above 120 and 80 mm Hg, respectively. Adjusted HRs (95% confidence intervals) for each 20 mm Hg increase in systolic blood pressure in all age groups were 1.18 (1.13-1.23) for all-cause mortality, 1.21 (1.13-1.31) for deaths due to IHD and 1.50 (1.39-1.63) for deaths due to stroke. Unadjusted and adjusted HRs were higher in younger subjects and decreased with increasing age of the participants. High blood pressure is a serious threat to the health of Iranians. The entire health-care system of Iran should be involved in a comprehensive action plan for controlling blood pressure.

An evaluation of the prognostic model PREDICT using the POSH cohort of women aged ⩽40 years at breast cancer diagnosis

BACKGROUND

Breast cancer is the most common cancer in younger women (aged ⩽40 years) in the United Kingdom. PREDICT (http://www.predict.nhs.uk) is an online prognostic tool developed to help determine the best available treatment and outcome for early breast cancer. This study was conducted to establish how well PREDICT performs in estimating survival in a large cohort of younger women recruited to the UK POSH study.

METHODS

The POSH cohort includes data from 3000 women aged ⩽40 years at breast cancer diagnosis. Study end points were overall and breast cancer-specific survival at 5, 8, and 10 years. Evaluation of PREDICT included model discrimination and comparison of the number of predicted versus observed events.

RESULTS

PREDICT provided accurate long-term (8- and 10-year) survival estimates for younger women. Five-year estimates were less accurate, with the tool overestimating survival by 25% overall, and by 56% for patients with oestrogen receptor (ER)-positive tumours. PREDICT underestimated survival at 5 years among patients with ER-negative tumours.

CONCLUSIONS

PREDICT is a useful tool for providing reliable long-term (10-year) survival estimates for younger patients. However, for more accurate short-term estimates, the model requires further calibration using more data from young onset cases. Short-term prediction may be most relevant for the increasing number of women considering risk-reducing bilateral mastectomy.

The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape

Human mRNA DeXD/H-box helicases are ubiquitous molecular motors that are required for the majority of cellular processes that involve RNA metabolism. One of the most abundant is eIF4A, which is required during the initiation phase of protein synthesis to unwind regions of highly structured mRNA that would otherwise impede the scanning ribosome. Dysregulation of protein synthesis is associated with tumorigenesis, but little is known about the detailed relationships between RNA helicase function and the malignant phenotype in solid malignancies. Therefore, immunohistochemical analysis was performed on over 3000 breast tumors to investigate the relationship among expression of eIF4A1, the helicase-modulating proteins eIF4B, eIF4E and PDCD4, and clinical outcome. We found eIF4A1, eIF4B and eIF4E to be independent predictors of poor outcome in ER-negative disease, while in contrast, the eIF4A1 inhibitor PDCD4 was related to improved outcome in ER-positive breast cancer. Consistent with these data, modulation of eIF4A1, eIF4B and PCDC4 expression in cultured MCF7 cells all restricted breast cancer cell growth and cycling. The eIF4A1-dependent translatome of MCF7 cells was defined by polysome profiling, and was shown to be highly enriched for several classes of oncogenic genes, including G-protein constituents, cyclins and protein kinases, and for mRNAs with G/C-rich 5'UTRs with potential to form G-quadruplexes and with 3'UTRs containing microRNA target sites. Overall, our data show that dysregulation of mRNA unwinding contributes to the malignant phenotype in breast cancer via preferential translation of a class of genes involved in pro-oncogenic signaling at numerous levels. Furthermore, immunohistochemical tests are promising biomarkers for tumors sensitive to anti-helicase therapies.

Implementing risk-stratified screening for common cancers: a review of potential ethical, legal and social issues

BACKGROUND

The identification of common genetic variants associated with common cancers including breast, prostate and ovarian cancers would allow population stratification by genotype to effectively target screening and treatment. As scientific, clinical and economic evidence mounts there will be increasing pressure for risk-stratified screening programmes to be implemented.

METHODS

This paper reviews some of the main ethical, legal and social issues (ELSI) raised by the introduction of genotyping into risk-stratified screening programmes, in terms of Beauchamp and Childress's four principles of biomedical ethics--respect for autonomy, non-maleficence, beneficence and justice. Two alternative approaches to data collection, storage, communication and consent are used to exemplify the ELSI issues that are likely to be raised.

RESULTS

Ultimately, the provision of risk-stratified screening using genotyping raises fundamental questions about respective roles of individuals, healthcare providers and the state in organizing or mandating such programmes, and the principles, which underpin their provision, particularly the requirement for distributive justice.

CONCLUSIONS

The scope and breadth of these issues suggest that ELSI relating to risk-stratified screening will become increasingly important for policy-makers, healthcare professionals and a wide diversity of stakeholders.

Astronomical algorithms for automated analysis of tissue protein expression in breast cancer

BACKGROUND

High-throughput evaluation of tissue biomarkers in oncology has been greatly accelerated by the widespread use of tissue microarrays (TMAs) and immunohistochemistry. Although TMAs have the potential to facilitate protein expression profiling on a scale to rival experiments of tumour transcriptomes, the bottleneck and imprecision of manually scoring TMAs has impeded progress.

METHODS

We report image analysis algorithms adapted from astronomy for the precise automated analysis of IHC in all subcellular compartments. The power of this technique is demonstrated using over 2000 breast tumours and comparing quantitative automated scores against manual assessment by pathologists.

RESULTS

All continuous automated scores showed good correlation with their corresponding ordinal manual scores. For oestrogen receptor (ER), the correlation was 0.82, P<0.0001, for BCL2 0.72, P<0.0001 and for HER2 0.62, P<0.0001. Automated scores showed excellent concordance with manual scores for the unsupervised assignment of cases to 'positive' or 'negative' categories with agreement rates of up to 96%.

CONCLUSION

The adaptation of astronomical algorithms coupled with their application to large annotated study cohorts, constitutes a powerful tool for the realisation of the enormous potential of digital pathology.

Stratified cancer screening: the practicalities of implementation

BACKGROUND

Improving understanding of the genetic basis of disease susceptibility enables us to estimate individuals' risk of developing cancer and offer them disease prevention, including screening, stratified to reflect that risk. Little attention has so far been given to the implementation of stratified screening. This article reviews the issues that would arise in delivering such tailored approaches to prevention in practice.

RESULTS

Issues analysed include the organisational context within which implementation of stratified prevention would occur, how the offer of screening would be made, making sure consent is adequately informed, how individuals' risk would be assessed, the age at which risk estimation should occur, and the potential use of genetic data for other purposes. The review also considers how management might differ depending on individuals' risk, how their results would be communicated and their follow-up arranged, and the different issues raised by modification of an existing screening programme, such as that for breast cancer, and the establishment of a new one, for example for prostate cancer.

CONCLUSION

Stratified screening based on genetic testing is a radically new approach to prevention. Various organisational issues would need to be considered before it could be introduced, and a number of questions require further research.

Abstract P3-08-02: Common variants at 10p14 and 1p11.2 display heterogeneity in breast cancer associations by E-cadherin tumor tissue expression in two independent datasets

Background: E-cadherin is a tumor suppressor gene involved in cell-cell adhesion, epithelial-to-mesenchymal transitions (EMT) and invasion. Loss of E-cadherin expression is strongly associated with lobular breast cancers, which exhibit single cell patterns of infiltration and are often estrogen receptor positive. We sought to determine if relative risk estimates for 19 established breast cancer susceptibility loci were modified by E-cadherin breast tumor tissue expression.

Methods: Case-control analyses included up to 1885 invasive breast cancer cases and 2366 age and site matched controls aged 20–74 years from the Polish Breast Cancer Study (PBCS), a population based case-control study conducted in Poland from 2000–2003. Genotyping of the 19 single nucleotide polymorphisms (SNPs) was performed using TaqMan® assays. Tissue expression of E-cadherin was assessed using immunohistochemical (IHC) staining of tissue microarrays and IHC results were scored as the product of percent positive tumor cells × intensity. Tumors having a score of &lt;10 were classified as E-cadherin low and those with a score ≥10 as E-cadherin high. Polytomous logistic regression models adjusted for age and study site were used to estimate odds ratios (OR) and 95% confidence intervals (95% CI) for each breast cancer subtype, defined by E-cadherin expression levels, compared to controls. Case-only data from the PBCS (N = 797) and the Study of Epidemiology and Risk Factors in Cancer Heredity, SEARCH (N = 2155) was used in logistic regression models to test for heterogeneity of SNPs by E-cadherin expression.

Results: Three SNPs suggested significant heterogeneity by E-cadherin expression in the PBCS: rs2046210 at 6q25.1(ESR1) [per-allele ORs (95% CI); 1.53 (1.19–1.98) for E-cadherin low tumors and 0.99 (0.86–1.14) for E-cadherin high tumors, P-heterogeneity = 0.002]; rs1045485 at 10p14 (CASP8) [per-allele ORs (95% CI); 0.62 (0.41–0.93) for E-cadherin low tumors and 0.98 (0.81–1.18) for E-cadherin high tumors, P-heterogeneity = 0.04]; and rs11249433 at 1p11.2 (NOTCH2/FCGR1B) [per-allele ORs (95% CI); 1.29 (1.02–1.64) for E-cadherin low tumors and 1.01 (0.88–1.15) for E-cadherin high tumors, P-heterogeneity = 0.06]. Combined case-only analysis of PBCS and SEARCH for these three SNPs showed significant heterogeneity by E-cadherin expression for rs11249433 [Interaction OR (95% CI); 1.19 (1.05–1.36), P-heterogeneity = 0.007] and rs1045485 [Interaction OR (95% CI); 0.69 (0.53–0.90), P-heterogeneity = 0.007]. The association with rs2046210 [Interaction OR (95% CI); 1.12 (0.61–2.03), P-heterogeneity = 0.73] did not remain significant in combined analyses.

Conclusion: Our findings provide evidence that associations for breast cancer susceptibility loci vary by E-cadherin tumor tissue expression, which has not been described previously. Specifically, our results suggest that the genetic markers rs11249433 and rs1045485 may preferentially modify risk for tumors with low or absent E-cadherin expression in two independent data sets.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-08-02.

Abstract P3-08-05: Title: Copy number variation and risk of chemotherapy-related infection

Background: Copy-number variations (CNVs) are DNA changes that result in regions of the genome being either duplicated (copy number gains) or deleted (copy number losses). CNVs have been identified in 12% of the human genome. Although CNVs do not appear to have a major role in disease susceptibility, it is known that they are involved in drug metabolism, toxicity and response. Infection is a common dose and/or treatment limiting chemotherapy-related toxicity. Infections can be a major cause of morbidity and mortality. Although a limited number of studies have investigated the association of single nucleotide polymorphisms (SNPs) with severity of infection, no studies so far have identified CNV associations with chemotherapy-related infection. In a non-oncological setting, CNVs have been noted to be associated with altered risk of certain types of infections and severe sepsis. This study aims to evaluate whether CNV are associated with the risk of chemotherapy-related infection in a genome wide association study (GWAS) of breast cancer patients recruited to clinical trials and treated with chemotherapy regimens including paclitaxel, epirubicin, cyclophosphamide, gemcitabine, 5fluorouracil and methotrexate.

Method: DNA from blood and saliva samples were collected as part of the pharmacogenetics GWAS, PGSNPS. Chemotherapy-related infection was assessed using the NCI Common Toxicity Criteria (CTC). Patients (n = 1921 samples) were classified as cases (NCI CTC grades 2–4) or as controls (NCI CTC grades 0–1). The Affymetrix SNP6.0 array, which contains more than 946,000 probes for the detection of CNVs and more than 906,600 SNPs, was used as the copy number estimation platform. DNA was segmented using DNAcopy (circular binary segmentation). CNVs were called based on their median and standard deviation. Log-ratios larger than the median plus 2 times the standard deviation were considered gains and log-ratios with values smaller than 2.5 times the standard deviation were considered as losses. Only regions with a copy number alteration present in at least a 10% of the samples were considered for the analysis. Fisher's exact test was performed on each of these regions and the variable ‘infection’. 2-side p-values were obtained and adjusted using Benjamin-Hochberg correction.

Results: One CNV region (frequency of gain 0.16) showed an association with increased risk of infection (Odds Ratio=1.79, 95% Confidence Interval [1.34–2.40], P = 6.37 × 10−5). Five other CNV regions demonstrated copy number gains and three CNV regions showed copy number losses that were associated with an increased risk of infection (P = 10−4). All regions had a frequency of gain or loss &gt; 0.10 and were therefore not rare variants.

Conclusion: These data suggest that CNVs may play a role in increased risk of chemotherapy-related toxicity. The most significant CNVs associated with infection are currently undergoing validation using an independent cohort of adjuvant breast cancer patients with similar exposure to chemotherapy and comparable documentation of chemotherapy-related infection.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-08-05.

Aurora kinase A outperforms Ki67 as a prognostic marker in ER-positive breast cancer

Background:

Proliferation has emerged as a major prognostic factor in luminal breast cancer. The immunohistochemical (IHC) proliferation marker Ki67 has been most extensively investigated but has not gained widespread clinical acceptance.

Methods:

We have conducted a head-to-head comparison of a panel of proliferation markers, including Ki67. Our aim was to establish the marker of the greatest prognostic utility. Tumour samples from 3093 women with breast cancer were constructed as tissue microarrays. We used IHC to detect expression of mini-chromosome maintenance protein 2, Ki67, aurora kinase A (AURKA), polo-like kinase 1, geminin and phospho-histone H3. We used a Cox proportional-hazards model to investigate the association with 10-year breast cancer-specific survival (BCSS). Missing values were resolved using multiple imputation.

Results:

The prognostic significance of proliferation was limited to oestrogen receptor (ER)-positive breast cancer. Aurora kinase A emerged as the marker of the greatest prognostic significance in a multivariate model adjusted for the standard clinical and molecular covariates (hazard ratio 1.3; 95% confidence interval 1.1–1.5; P=0.005), outperforming all other markers including Ki67.

Conclusion:

Aurora kinase A outperforms other proliferation markers as an independent predictor of BCSS in ER-positive breast cancer. It has the potential for use in routine clinical practice.

Prognosis by breast cancer subtypes in patients treated with adjuvant chemotherapy in a clinical trial

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Background: Breast cancer can be classified into molecular subtypes that have distinct survival patterns. The purpose of this study was i) to evaluate the prognostic significance of breast cancer subtypes in a cohort of women taking part in the NEAT and BR9601 clinical trials comparing CMF with ECMF, and ii) to evaluate whether the subtypes were predictive of the added benefit of epirubicin in these trials.

Methods: Tumor tissue microarrays were stained and scored for ER, PR, HER2, EGFR and CK5/6. These were used to classify the tumors into six intrinsic subtypes (1). We used Cox regression to compare overall survival (OS), breast cancer specific survival (BSS) and relapse free survival (RFS) in the different subgroups. We also compared the effect of ECMF with CMF by subgroup.

Results: IHC data were available for 1725 cases of whom 805 were Luminal 1-basal negative, 153 were Luminal 1-basal positive, 174 were Luminal 2, 192 were HER2-like, 230 were core basal phenotype and 171 were 5-negative phenotype. Median follow-up time was 7 years. The prognostic effects of the subtypes were similar to those reported for unselected breast cancer cases irrespective of adjuvant therapy (Blows FM, et al. PLoS Med 2010;75:e1000279.). In particular, the luminal 1-basal negative tumors were associated with the best prognosis in five years after surgery and the HER2-like tumors were associated with the poorest prognosis. ECMF has previously shown to be associated with a 33% relative risk reduction for OS compared to CMF (Poole CJ et al. N Engl J Med 2006;35518:1851-62.). There was little evidence for significant heterogeneity of effect by tumor subtype for any end point (OS P= 0.40, BSS P=0.53 RFS P=0.50). However, there was an observed trend towards the largest additional benefit from ECMF being in women with tumors of the 5-negative phenotype (OS HR=0.39 95% CI 0.21-0.73) and the smallest being in Luminal 1-basal negative tumors (OS HR=0.86 95% CI 0.64-1.16).

Conclusions: In a clinical trial in which all patients received chemotherapy, we confirmed that breast cancer subtypes show distinct behaviour with differences in short and long term survival. The benefit of ECMF over CMF was statistically similar in all disease subtypes.

Patient and tumour characteristics, management, and age-specific survival in women with breast cancer in the East of England

BACKGROUND

Breast cancer relative survival (BCRS), which compares the observed survival of women with breast cancer with the expected survival of women for the whole population of the same age, time period, and geographical region, tends to be poorer in older women, but the reasons for this are not clear. We examined the influence of patient and tumour characteristics, and treatment on BCRS to see whether these could explain the age-specific effect.

METHODS

Data for 14,048 female breast cancer patients diagnosed from 1999 to 2007, aged 50 years or over were obtained from the Eastern Cancer Registration and Information Centre. We estimated relative 5- and 10-year survival for patients in four age groups (50-69, 70-74, 75-79, and 80+ years). We also modelled relative excess mortality (REM) rate using Poisson regression adjusting for patient characteristics and treatment. The REMs derived from these models quantify the extent to which the hazard of death differs from the hazard in the reference category, after taking into account the background risk of death in the general population. We compared the results with those obtained for breast cancer-specific mortality, analysed using multivariate Cox regression.

RESULTS

Median follow-up time was 4.7 years. Relative 5-year survival was 89, 81, 76, and 70% for patients aged 50-69, 70-74, 75-79, and 80+ years, respectively. Corresponding relative 10-year survival was 84, 77, 67, and 66%. Unadjusted REM was 1.93, 2.74, and 3.88 for patients aged 70-74, 75-79, and 80+ years, respectively, (50-69 years as reference). The equivalent hazard ratios from the Cox model were 1.88, 2.45, and 3.81. These were attenuated after adjusting for confounders (REM - 1.49, 1.36, and 1.23; Cox - 1.47, 1.50, and 1.76).

CONCLUSION

We confirmed poorer BCRS in older women in our region. This was partially explained by known prognostic factors. Further research is needed to determine whether biological differences or suboptimal management can explain the residual excess mortality.

Comparison of methods for handling missing data on immunohistochemical markers in survival analysis of breast cancer

BACKGROUND

Tissue micro-arrays (TMAs) are increasingly used to generate data of the molecular phenotype of tumours in clinical epidemiology studies, such as studies of disease prognosis. However, TMA data are particularly prone to missingness. A variety of methods to deal with missing data are available. However, the validity of the various approaches is dependent on the structure of the missing data and there are few empirical studies dealing with missing data from molecular pathology. The purpose of this study was to investigate the results of four commonly used approaches to handling missing data from a large, multi-centre study of the molecular pathological determinants of prognosis in breast cancer.

PATIENTS AND METHODS

We pooled data from over 11,000 cases of invasive breast cancer from five studies that collected information on seven prognostic indicators together with survival time data. We compared the results of a multi-variate Cox regression using four approaches to handling missing data - complete case analysis (CCA), mean substitution (MS) and multiple imputation without inclusion of the outcome (MI-) and multiple imputation with inclusion of the outcome (MI+). We also performed an analysis in which missing data were simulated under different assumptions and the results of the four methods were compared.

RESULTS

Over half the cases had missing data on at least one of the seven variables and 11 percent had missing data on 4 or more. The multi-variate hazard ratio estimates based on multiple imputation models were very similar to those derived after using MS, with similar standard errors. Hazard ratio estimates based on the CCA were only slightly different, but the estimates were less precise as the standard errors were large. However, in data simulated to be missing completely at random (MCAR) or missing at random (MAR), estimates for MI+ were least biased and most accurate, whereas estimates for CCA were most biased and least accurate.

CONCLUSION

In this study, empirical results from analyses using CCA, MS, MI- and MI+ were similar, although results from CCA were less precise. The results from simulations suggest that in general MI+ is likely to be the best. Given the ease of implementing MI in standard statistical software, the results of MI+ and CCA should be compared in any multi-variate analysis where missing data are a problem.

A large-scale meta-analysis to refine colorectal cancer risk estimates associated with MUTYH variants

Background:

Defective DNA repair has a causal role in hereditary colorectal cancer (CRC). Defects in the base excision repair gene MUTYH are responsible for MUTYH-associated polyposis and CRC predisposition as an autosomal recessive trait. Numerous reports have suggested MUTYH mono-allelic variants to be low penetrance risk alleles. We report a large collaborative meta-analysis to assess and refine CRC risk estimates associated with bi-allelic and mono-allelic MUTYH variants and investigate age and sex influence on risk.

Methods:

MUTYH genotype data were included from 20 565 cases and 15 524 controls. Three logistic regression models were tested: a crude model; adjusted for age and sex; adjusted for age, sex and study.

Results:

All three models produced very similar results. MUTYH bi-allelic carriers demonstrated a 28-fold increase in risk (95% confidence interval (CI): 6.95–115). Significant bi-allelic effects were also observed for G396D and Y179C/G396D compound heterozygotes and a marginal mono-allelic effect for variant Y179C (odds ratio (OR)=1.34; 95% CI: 1.00–1.80). A pooled meta-analysis of all published and unpublished datasets submitted showed bi-allelic effects for MUTYH, G396D and Y179C (OR=10.8, 95% CI: 5.02–23.2; OR=6.47, 95% CI: 2.33–18.0; OR=3.35, 95% CI: 1.14–9.89) and marginal mono-allelic effect for variants MUTYH (OR=1.16, 95% CI: 1.00–1.34) and Y179C alone (OR=1.34, 95% CI: 1.01–1.77).

Conclusions:

Overall, this large study refines estimates of disease risk associated with mono-allelic and bi-allelic MUTYH carriers.

BCL2 in breast cancer: a favourable prognostic marker across molecular subtypes and independent of adjuvant therapy received

BACKGROUND

Breast cancer is heterogeneous and the existing prognostic classifiers are limited in accuracy, leading to unnecessary treatment of numerous women. B-cell lymphoma 2 (BCL2), an antiapoptotic protein, has been proposed as a prognostic marker, but this effect is considered to relate to oestrogen receptor (ER) status. This study aimed to test the clinical validity of BCL2 as an independent prognostic marker.

METHODS

Five studies of 11 212 women with early-stage breast cancer were analysed. Individual patient data included tumour size, grade, lymph node status, endocrine therapy, chemotherapy and mortality. BCL2, ER, progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) levels were determined in all tumours. A Cox model incorporating the time-dependent effects of each variable was used to explore the prognostic significance of BCL2.

RESULTS

In univariate analysis, ER, PR and BCL2 positivity was associated with improved survival and HER2 positivity with inferior survival. For ER and PR this effect was time dependent, whereas for BCL2 and HER2 the effect persisted over time. In multivariate analysis, BCL2 positivity retained independent prognostic significance (hazard ratio (HR) 0.76, 95% confidence interval (CI) 0.66-0.88, P<0.001). BCL2 was a powerful prognostic marker in ER- (HR 0.63, 95% CI 0.54-0.74, P<0.001) and ER+ disease (HR 0.56, 95% CI 0.48-0.65, P<0.001), and in HER2- (HR 0.55, 95% CI 0.49-0.61, P<0.001) and HER2+ disease (HR 0.70, 95% CI 0.57-0.85, P<0.001), irrespective of the type of adjuvant therapy received. Addition of BCL2 to the Adjuvant! Online prognostic model, for a subset of cases with a 10-year follow-up, improved the survival prediction (P=0.0039).

CONCLUSIONS

BCL2 is an independent indicator of favourable prognosis for all types of early-stage breast cancer. This study establishes the rationale for introduction of BCL2 immunohistochemistry to improve prognostic stratification. Further work is now needed to ascertain the exact way to apply BCL2 testing for risk stratification and to standardise BCL2 immunohistochemistry for this application.

Common germ-line polymorphism of C1QA and breast cancer survival

BACKGROUND

A synonymous single nucleotide polymorphism (SNP) rs172378 (A>G, Gly->Gly) in the complement component C1QA has been proposed to be associated with distant breast cancer metastasis. We previously reported overexpression of this gene to be significantly associated with better prognosis in oestrogen-receptor-negative tumours. The purpose of this study was to investigate the association of rs172378 with expression of C1QA and breast cancer survival.

METHODS

We analysed the gene expression pattern of rs172378 in normal and tumour tissue samples, and further explored its involvement in relation to mortality in 2270 women with breast cancer participating in Studies of Epidemiology and Risk factors in Cancer Heredity, a population-based case-control study.

RESULTS

We found that although rs172378 showed differential allelic expression significantly different between normal (preferentially expressing the G allele) and tumour tissue samples (preferentially expressing the A allele), there was no significant difference in survival by rs172378 genotype (per allele hazard ratio (HR) 1.02, 95% CI: 0.88-1.19, P=0.78 for all-cause mortality; HR 1.03, 95% CI: 0.87-1.22, P=0.72 for breast-cancer-specific mortality).

CONCLUSION

Our study results show that rs172378 is linked to a cis-regulatory element affecting gene expression and that allelic preferential expression is altered in tumour samples, but do not support an association between genetic variation in C1QA and breast cancer survival.

COGENT (COlorectal cancer GENeTics): an international consortium to study the role of polymorphic variation on the risk of colorectal cancer

It is now recognised that a part of the inherited risk of colorectal cancer (CRC) can be explained by the co-inheritance of low-penetrance genetic variants. The accumulated experience to date in identifying these variants has served to highlight difficulties in conducting statistically and methodologically rigorous studies and follow-up analyses. The COGENT (COlorectal cancer GENeTics) consortium includes 20 research groups in Europe, Australia, the Americas, China and Japan. The overarching goal of COGENT is to identify and characterise low-penetrance susceptibility variants for CRC through association-based analyses. In this study, we review the rationale for identifying low-penetrance variants for CRC and our proposed strategy for establishing COGENT.

Adjuvant UK: A UK Prognostic Model for Early Breast Cancer That Includes Mode of Detection

AIM: To develop and validate a prognostication model to predict overall survival for women treated for early breast cancer in the UK based on cancer registry data. Unlike SEER, this dataset includes accurate information on mode of detection as well as systemic therapy.METHOD: Using the Eastern Cancer Registration & Information Centre (ECRIC) dataset, information was collated for 5818 women diagnosed with invasive breast cancer in East Anglia from 1999-2003. All patients underwent surgery, had records of pathological staging (tumour size, grade, lymph node status, ER status), systemic treatment (chemotherapy, hormone therapy, both), mode of detection (screen-detected, symptomatic) and follow up, censored on 31 December 2007. A model was derived from these data using Cox proportional hazards, with ER positive and ER negative tumours modelled separately, and this was subsequently validated in an external dataset of 5468 patients from the West Midlands Cancer Intelligence Unit (WMCIU). Validation was performed by comparing (a) observed and expected mortality (overall & breast cancer specific) at 5 & 8 years and (b) receiver operating characteristic (ROC) curves in both ECRIC & WMCIU datasets.RESULTS:ECRIC datasetDifference in overall observed/expected mortality &lt;1% at 5 years (14.8% vs 14.9%) and 8 years (18.9% vs 18.9%). Area under ROC curve (AUC) was 0.81.Difference in breast cancer specific observed/expected mortality &lt;1% at 5 years (10.6% vs 11.0%) and 8 years (12.9% vs 13.5%). AUC was 0.84.WMCIU dataset:Difference in overall observed/expected mortality &lt; 1% at 5 years (15.8% vs 16.5%) and 8 years (17.5% vs 17.8%). AUC was 0.79.Difference in breast cancer specific observed/expected mortality &lt;2% at 5 years (11.0% vs 12.6%) and 8 years (12.2% vs 13.6%). AUC was 0.82.Overall model fit was good across all subgroups although the ER positive model provided better discrimination (AUC 0.82) than ER negative (AUC 0.75). There was no significant difference between the ROC curves generated with ECRIC and WMCIU data (ER positive X2 = 0.17, p=0.68; ER negative X2 =0.00, P=0.95).CONCLUSION: We have developed a prognostication model for early breast cancer based on data from a UK cancer registry that has included mode of detection for the first time. The model is well calibrated, provides a high degree of discrimination and has been validated in a second patient cohort. This model will underpin a new web-based prognostication and treatment benefit tool for early breast cancer based on UK data (Adjuvant UK).

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4033.

Adjuvant UK: Validation of a UK prognostic model for early breast cancer

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Background: To develop and validate a prognostication model to predict overall survival for women treated for early breast cancer in the UK based on cancer registry data. The main advantages are that unlike SEER, this dataset includes accurate information on mode of detection as well as systemic therapy. Methods: Using the Eastern Cancer Registration & Information Centre (ECRIC) dataset, information was collated for 5,818 women diagnosed with invasive breast cancer in East Anglia from 1999–2003. All patients underwent surgery, had records of pathological staging (tumour size, grade, lymph node status, ER status) and systemic treatment (chemotherapy, hormone therapy, both), mode of detection (screen-detected, symptomatic) and were followed up to December 2007. A model was derived from these data using Cox proportional hazards and this was subsequently validated in an external dataset of 5,468 patients from the West Midlands Cancer Intelligence Unit (WMCIU). Validation was performed by comparing (a) observed and predicted mortality - overall and by risk group decile - and (b) receiver operating characteristic (ROC) curves in both ECRIC & WMCIU datasets. Results: ECRIC dataset: Observed/predicted deaths were: 2 years (262/267), 5 years (868/867), 8 years (1108/1093). Area under ROC curve was 0.800WMCIU dataset: Observed/predicted deaths were: 2 years (317/298), 5 years (862/919), 8 years (955/999). Area under ROC curve was 0.783. The model and validation worked equally well at all time points (2, 5, 8 years) and in all risk group deciles. In the validation dataset the observed and predicted 8-year OS was within 1% (17.5% versus 18.3%). There was no significant statistical difference between the ROC curves (X2 = 2.35, P=.12) for prediction at 8 years in ECRIC and WMCIU data. Conclusions: We have developed a prognostication model for early breast cancer based on data from a UK cancer registry and validated the model using data from another UK registry. The model was well calibrated and provides a high degree of discrimination. This model will underpin the first web-based prognostication and treatment benefit tool for early breast cancer in the UK (Adjuvant UK).

No significant financial relationships to disclose.

Mean sojourn time, overdiagnosis, and reduction in advanced stage prostate cancer due to screening with PSA: implications of sojourn time on screening

This study aimed to assess the mean sojourn time (MST) of prostate cancer, to estimate the probability of overdiagnosis, and to predict the potential reduction in advanced stage disease due to screening with PSA. The MST of prostate cancer was derived from detection rates at PSA prevalence testing in 43 842 men, aged 50–69 years, as part of the ProtecT study, from the incidence of non-screen-detected cases obtained from the English population-based cancer registry database, and from PSA sensitivity obtained from the medical literature. The relative reduction in advanced stage disease was derived from the expected and observed incidences of advanced stage prostate cancer. The age-specific MST for men aged 50–59 and 60–69 years were 11.3 and 12.6 years, respectively. Overdiagnosis estimates increased with age; 10–31% of the PSA-detected cases were estimated to be overdiagnosed. An interscreening interval of 2 years was predicted to result in 37 and 63% reduction in advanced stage disease in men 65–69 and 50–54 years, respectively. If the overdiagnosed cases were excluded, the estimated reductions were 9 and 54%, respectively. Thus, the benefit of screening in reducing advanced stage disease is limited by overdiagnosis, which is greater in older men.

Proliferation markers and survival in early breast cancer: a systematic review and meta-analysis of 85 studies in 32,825 patients

We have performed a systematic review and meta-analysis of proliferation markers (Ki-67, mitotic index (MI), proliferating cell nuclear antigen (PCNA) and thymidine or bromodeoxyuridine labelling index (LI)) with respect to survival in early breast cancer. Eighty-five studies involving 32,825 patients were analysed. Ki-67 (43 studies, 15,790 patients), MI (20 studies, 7021 patients), and LI (11 studies, 7337 patients) were associated with significantly shorter overall and disease free survival, using results from univariate and multivariate analyses from the individual studies. PCNA (11 studies, 2677 patients) was associated with shorter overall survival by multivariate analysis only, because of lack of data. There was some evidence for publication bias, but all markers remained significant after allowing for this. Ki-67, MI, PCNA and LI are associated with worse survival outcomes in early breast cancer. However, whether these proliferation markers provide additional prognostic information to commonly used prognostic indices remains unclear.

HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer

ERBB2 is frequently amplified in breast tumours as part of a wide region of amplification on chromosome 17q21. This amplicon contains many candidate genes for breast cancer susceptibility. We used a genetic association study design to determine if common genetic variation (frequency>or=5%) in a 400-kb region surrounding ERBB2 and containing the PPARBP, CRK7, NEUROD2, PPP1R1B, STARD3, TCAP, PNMT, CAB2, ERBB2, C17ORF37, GRB7 and ZNFN1A3 genes, was associated with breast cancer risk. Sixteen tagging single-nucleotide polymorphisms (tSNPs) selected within blocks of linkage disequilibrium from the HapMap database, one HapMap singleton SNP, and six additional SNPs randomly selected from dbSNP were genotyped using Taqman in a large study set of British women (2275 cases, 2280 controls). We observed no association between any of the genotypes or associated haplotypes and disease risk. In order to simulate unidentified SNPs, we performed the leave-one-out cross-validation procedure on the HapMap data; over 90% of the common genetic variation was well represented by tagging polymorphisms. We are therefore likely to have tagged any common variants present in our population. In summary, we found no association between common genetic variation in the 17q21 ERBB2 amplicon and breast cancer risk in British women.

Single-nucleotide polymorphisms in the RB1 gene and association with breast cancer in the British population

A substantial proportion of the familial risk of breast cancer may be attributable to genetic variants each contributing a small effect. pRb controls the cell cycle and polymorphisms within it are candidates for such low penetrance susceptibility alleles, since the gene has been implicated in several human tumours, particularly breast cancer. The purpose of this study was to determine whether common variants in the RB1 gene are associated with breast cancer risk. We assessed 15 tagging single-nucleotide polymorphisms (SNPs) using a case–control study design (n⩽4474 cases and n⩽4560 controls). A difference in genotype frequencies was found between cases and controls for rs2854344 in intron 17 (P-trend=0.007) and rs198580 in intron 19 (P-trend=0.018). Carrying the minor allele of these SNPs appears to confer a protective effect on breast cancer risk (odd ratio (OR)=0.86 (0.76–0.96) for rs2854344 and OR=0.80 (0.66–0.96) for rs198580). However, after adjusting for multiple testing these associations were borderline with an adjusted P-trend=0.068 for the most significant SNP (rs2854344). The RB1 gene is not known to contain any coding SNPs with allele frequencies ⩾5% but several intronic variants are in perfect linkage disequilibrium with the associated SNPs. Replication studies are needed to confirm the associations with breast cancer.

Issues of consent and feedback in a genetic epidemiological study of women with breast cancer

Women (N=21) who had had breast cancer and had been enrolled in a large genetic breast cancer epidemiological study were interviewed about their experience of participation in the study, their attitudes to the confidentiality of data, and the feedback of personal and general research results. Collection of family history information seemed more salient in indicating the genetic nature of the study than the enrolment information sheet. There were no concerns about confidentiality. While participants would have welcomed general feedback about the results of the study and were critical that this had not been provided, the feedback of personal information proved complicated and, sometimes, difficult. It is suggested that individual feedback of genetic test information in epidemiological studies should be undertaken only when there are specific reasons.

Development of a protocol for evaluation of mammographic surveillance services in women under 50 with a family history of breast cancer

BACKGROUND

Preliminary retrospective data suggest it is possible to identify impalpable breast cancer in women presenting with a family history of breast cancer under the age of 50, by using regular mammography. In consequence, this service is offered in a number of centres in the UK. The effectiveness of such a service, however, has not been fully evaluated.

METHODS

We propose to perform such an evaluation in a cohort of 20000 women under the age of 50 with a significant family history of breast cancer, given regular mammographic surveillance over 5 years. Comparison of surgical and pathological data with completed and ongoing population screening trials using analysis techniques of varying complexity will be performed to obtain an accurate prediction of future breast-cancer mortality reduction. The formal aims are: i) to estimate the difference in breast-cancer mortality in women under the age of 50 with a significant family history of breast cancer having regular mammography, compared with those not being screened; ii) to estimate the cost-effectiveness of regular mammography in this group of women, compared with no screening. The increase in health service resource use attributable to such a policy will be compared with no screening, and costed. Incremental cost-effectiveness ratios of implementing the standardised mammography strategy compared with no screening will be presented in terms of the additional cost per cancer detected, per life saved and per life-year saved.

Incidence of gastric cancer and breast cancer in CDH1 (E-cadherin) mutation carriers from hereditary diffuse gastric cancer families

BACKGROUND & AIMS

Germline mutations in CDH1 are known to cause hereditary diffuse gastric cancer (HDGC). Breast and colorectal cancer have also been reported in CDH1-associated HDGC. The purpose of this study was to estimate the cumulative risk of gastric and breast cancer in CDH1 mutation carriers.

METHODS

Family data were collected by member groups of the International Gastric Cancer Linkage Consortium. Eligible families had at least 3 cases of diffuse gastric cancer, and at least 1 affected member had tested positive for a mutation in CDH1. Eleven families met these criteria. We used the pedigree information to estimate penetrance using the MENDEL program. The conditional likelihood of the pedigree was maximized given the phenotype of the pedigree and genotype of the index case at ascertainment. We parameterized the model in terms of log relative risks for mutation carriers compared with risks in the general population of the United Kingdom. Noncarriers of the gene were assumed to develop the disease at population incidence rates.

RESULTS

The estimated cumulative risk of gastric cancer by age 80 years was 67% for men (95% confidence interval [95% CI], 39-99) and 83% for women (95% CI, 58-99). For women, the cumulative risk of breast cancer was 39% (95% CI, 12-84). The combined risk of gastric cancer and breast cancer in women was 90% by age 80 years.

CONCLUSIONS

These penetrance estimates should be useful for genetic counseling in multiple-case families. However, they may not apply to individuals with a minimal family history, in whom the risks may be lower.

Polymorphisms in CYP1A1 and smoking: no association with breast cancer risk

Several studies have investigated polymorphisms in CYP1A1 and breast cancer risk with inconsistent results. We have carried out a population based case-control study of the Thr461Asn and Ile462Val polymorphisms in CYP1A1 to clarify their importance in determining breast cancer susceptibility. A total of 1873 cases and 712 controls were genotyped for Thr461Asn and 1948 cases and 1355 controls were genotyped for Ile462Val. We have also investigated a putative interaction between smoking and CYP1A1 genotype and breast cancer risk using a case only study design. The genotype distribution of Thr461Asp in controls was close to that expected under Hardy-Weinberg equilibrium (HWE). We detected no significant differences in genotype frequencies between breast cancer cases and controls (P = 0.68). Compared with the Thr/Thr homozygotes there was no significant risk for either the Thr/Asp heterozygote [OR = 1.1 (95% CI 0.8-1.4)] or the Asp/Asp homozygote [OR = 0.4 (0.02-6.1)]. The genotype distribution of Ile462Val in controls was also close to that expected under HWE with no significant differences between breast cancer cases and the controls (P = 0.44). No significant risk was found for either the Ile/Val heterozygote [OR = 0.8 (0.6-1.1)] or the Val/Val homozygote [OR = 2.7 (0.3-24)] compared with the Ile/Ile homozygotes. Furthermore, subgroup analyses revealed no effect of age or menopausal status on genotypic risks, and we found no evidence for an interaction between genotype and smoking habit or alcohol consumption and susceptibility to breast cancer. We combined our data for the Ile462Val polymorphism with those from four other published studies, but even with >5000 subjects, none of the genotype-associated risks achieved statistical significance, and there was no consistent pattern to the risks associated with increasing Val allele dosage [Ile/Val OR = 0.9 (0.7-1.1), Val/Val OR = 2.3 (0.4-12), and Val carrier OR = 1.0 (0.9-1.1)].

Interleukin 1B and interleukin 1RN polymorphisms are associated with increased risk of gastric carcinoma

BACKGROUND & AIMS

Interleukin (IL)-1 gene cluster proinflammatory polymorphisms have been associated with development of gastric atrophy and with increased risk of gastric carcinoma. We aimed to determine the association between IL-1 loci polymorphisms and increased risk of gastric carcinoma in samples from a Portuguese population, and to find whether there was any relationship with the histologic types of gastric carcinoma.

METHODS

In a case-control study including 220 controls and 152 patients with gastric carcinoma (intestinal, 76; diffuse, 37; and atypical, 39), both the IL-1B-511 biallelic polymorphism and the IL-1RN penta-allelic variable number of tandem repeats were genotyped.

RESULTS

We found a significant association between the IL-1 polymorphisms and increased risk for tumor development in patients with intestinal-type gastric carcinoma. A trend towards an increased risk of tumor development was also observed in patients with diffuse-type gastric carcinoma. No significant relationship was observed in patients with atypical carcinoma. Carriers of IL-1B-511T and IL-1RN*2 homozygotes had increased risk for developing intestinal-type gastric carcinoma with odds ratios of 2.7 (95% confidence interval [CI], 1.5-4.9) and 3.1 (95% CI, 1.5-6.5), respectively. Statistical analysis showed an interaction between the 2 loci with the risk conferred by the IL-1B-511T allele substantially increased (odds ratio, 9.0; 95% CI, 3.5-23.0) in individuals homozygous for the IL-1RN*2 allele.

CONCLUSIONS

Our results provide further support to the association between IL-1 gene cluster proinflammatory polymorphisms and increased risk of gastric carcinoma. Furthermore, we found evidence pointing to the existence of a synergistic interaction between the IL-1B and IL-1RN polymorphisms.

Evidence for further breast cancer susceptibility genes in addition to BRCA1 and BRCA2 in a population-based study

We used data from a population based series of breast cancer patients to investigate the genetic models that can best explain familial breast cancer not due to the BRCA1 and BRCA2 genes. The data set consisted of 1,484 women diagnosed with breast cancer under age 55 registered in the East Anglia Cancer registry between 1991-1996. Blood samples taken from the patients were analysed for mutations in BRCA1 and BRCA2. The genetic models were constructed using information on breast and ovarian cancer history in first-degree relatives and on the mutation status of the index patients. We estimated the simultaneous effects of BRCA1, BRCA2, a third hypothetical gene BRCA3, and a polygenic effect. The models were assessed by likelihood comparisons and by comparison of the observed numbers of mutations and affected relatives with the predicted numbers. BRCA1 and BRCA2 could not explain all the familial clustering of breast cancer. The best-fitting single gene model for BRCA3 was a recessive model with a disease allele frequency 24% and penetrance 42% by age 70. However, a polygenic model gave a similarly good fit. The estimated population frequencies for BRCA1 and BRCA2 mutations were similar under both recessive and polygenic models, 0.024 and 0.041%, respectively. A dominant model for BRCA3 gave a somewhat worse fit, although the difference was not significant. The mixed recessive model was identical to the recessive model and the mixed dominant very similar to the polygenic model. The BRCA3 genetic models were robust to the BRCA1 and BRCA2 penetrance assumptions. The overall fit of all models was improved when the known effects of parity on breast and ovarian cancer risks were included in the model-in this case a polygenic model fits best. These findings suggest that a number of common, low-penetrance genes with additive effects may account for the residual non-BRCA1/2 familial aggregation of breast cancer, but Mendelian inheritance of an autosomal recessive allele cannot be ruled out.

Ovarian cancer survival in Ashkenazi Jewish patients with BRCA1 and BRCA2 mutations

PURPOSE

To compare the clinical characteristics and survival of Ashkenazi Jewish ovarian cancer patients with and without BRCA1 and BRCA2 mutations.

METHODS

An unselected series of 118 Ashkenazi Jewish ovarian cancer patients were screened for the three common founder mutations in BRCA1 and BRCA2. Patient survival and other clinical characteristics of the tumours were compared in patients with BRCA1 or BRCA2 mutations and those without mutations.

RESULTS

Twenty-seven individuals with invasive carcinomas were found to have mutations (14 with 185delAG and one with 5382insC in BRCA1 and 12 with 6174delT in BRCA2). No mutations were identified in the 20 patients with borderline tumours. For the invasive carcinomas, there was a survival advantage for BRCA1 and BRCA2 patients compared to patients without mutations, though the differences were not statistically significant. There were no significant differences in the histopathological characteristics of the tumours between the patient groups.

CONCLUSION

These results are similar to those of other studies and suggest that ovarian cancer in BRCA1 and BRCA2 mutation carriers may have a distinct clinical behaviour.

Apparent human BRCA1 knockout caused by mispriming during polymerase chain reaction: implications for genetic testing

We report an apparent BRCA1 homozygous knockout that, on further analysis, was found to be an artefact of the polymerase chain reaction. This finding has two important implications. First, it challenges results of a previous study that reported a homozygous knockout associated with the same BRCA1 mutation. Second, our findings suggest that mispriming caused by mismatched primers at the site of single-nucleotide polymorphisms, leading to preferential amplification of one allele, may represent a significant proportion of instances of mutation-detection insensitivity. This may have major implications for the sensitivity of all polymerase chain reaction-based mutation-detection methods in clinical genetic testing laboratories.

Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers : a new approach for the molecular analysis of paraffin-embedded cancer tissue

We have developed a protocol for degenerate oligonucleotide-primed-polymerase chain reaction-based array comparative genomic hybridization (array CGH) that, when combined with a laser microdissection technique, allows the analysis of cancer cell populations isolated from routine, formalin-fixed, paraffin-embedded tissue samples. Comparison of copy number changes detected by degenerate oligonucleotide-primed-polymerase chain reaction-based array CGH to those detected by conventional array CGH or fluorescence in situ hybridization, demonstrated that amplifications can be reliably detected. Using a genomic microarray containing 57 oncogenes, we screened a total of 28 breast cancer samples and obtained a detailed amplicon profile that is the most comprehensive to date in human breast cancer. The array CGH method described here will allow the genetic analysis of paraffin-embedded human cancer materials for example in the context of clinical trials.