Survival in breast cancer is familial

Role of germline variants in the metastasis of breast carcinomas

Most cancer-related deaths in breast cancer patients are associated with metastasis, a multistep, intricate process that requires the cooperation of tumour cells, tumour microenvironment and metastasis target tissues. It is accepted that metastasis does not depend on the tumour characteristics but the host’s genetic makeup. However, there has been limited success in determining the germline genetic variants that influence metastasis development, mainly because of the limitations of traditional genome-wide association studies to detect the relevant genetic polymorphisms underlying complex phenotypes. In this work, we leveraged the extreme discordant phenotypes approach and the epistasis networks to analyse the genotypes of 97 breast cancer patients. We found that the host’s genetic makeup facilitates metastases by the dysregulation of gene expression that can promote the dispersion of metastatic seeds and help establish the metastatic niche—providing a congenial soil for the metastatic seeds.

From Oncological Paradigms to Non-Communicable Disease Pandemic. The Need of Recovery Human Biology Evolution

The paradigm of the Somatic Mutation Theory (SMT) is failing, and a new paradigm is underway but not yet established. What is being challenged is a conceptual approach that involves the entire human biology and the development of chronic diseases. The behavior of breast and other solid cancers is compatible with the concept that the primary tumor is able to control its microscopic metastases, in the same way that an organ (e.g., the liver) is able to control its physiological size. This finding suggested that cancer and its metastases may behave as an organoid. The new paradigm under construction considers the origin of tumors as a disturbance in the communication network between tissue cell populations and between cells and extracellular matrix, and supports a systemic approach to the study of both healthy and pathologic tissues. The commentary provides a rationale for the role of physical exercise in the control of tumor dormancy according to a human evolutionary perspective.

Late Recurrence in Breast Cancer: To Run after the Oxen or to Try to Close the Barn?

Simple Summary

The initial treatment of early breast cancer has achieved important clinical results over time. However, late recurrences after many years of disease-free survival remain an open question, which has recently attracted the attention of a few researchers. The authors of this commentary suggest that the approach emerging from scientific meetings regarding this subject is marred by the lack of attention to recent clinical and laboratory data. The role of tumor dormancy and the dynamics of disease recurrence are presented here and a more general reflection on therapeutic approaches to cancer is proposed.

Abstract

The problem of late recurrence in breast cancer has recently gained attention and was also addressed in an international workshop held in Toronto (ON, Canada), in which several aspects of the question were examined. This Commentary offers a few considerations, which may be useful for the ongoing investigations. A few premises are discussed: (a) clinical recurrences, especially the late ones, imply periods of tumor dormancy; (b) a structured pattern of distant metastases appearance is detectable in both early and late follow-up times; (c) the current general paradigm underlying neoplastic treatments, i.e., that killing all cancer cells is the only way to control the disease, which is strictly sprouting from the somatic mutation theory, should be re-considered. Finally, a few research approaches are suggested.

Genetic insights into the morass of metastatic heterogeneity

Tumour heterogeneity poses a substantial problem for the clinical management of cancer. Somatic evolution of the cancer genome results in genetically distinct subclones in the primary tumour with different biological properties and therapeutic sensitivities. The problem of heterogeneity is compounded in metastatic disease owing to the complexity of the metastatic process and the multiple biological hurdles that the tumour cell must overcome to establish a clinically overt metastatic lesion. New advances in sequencing technology and clinical sample acquisition are providing insights into the phylogenetic relationship of metastases and primary tumours at the level of somatic tumour genetics while also illuminating fundamental mechanisms of the metastatic process. In addition to somatically acquired genetic heterogeneity in the tumour cells, inherited population-based genetic heterogeneity can profoundly modify metastatic biology and further complicate the development of effective, broadly applicable antimetastatic therapies. Here, we examine how genetic heterogeneity impacts metastatic disease and the implications of current knowledge for future research endeavours and therapeutic interventions.

Defining the Influence of Germline Variation on Metastasis Using Systems Genetics Approaches

Cancer is estimated to be responsible for 8 million deaths worldwide and over half a million deaths every year in the United States. The majority of cancer-related deaths in solid tumors is directly associated with the effects of metastasis. While the influence of germline factors on cancer risk and development has long been recognized, the contribution of hereditary variation to tumor progression and metastasis has only gained acceptance more recently. A variety of approaches have been used to define how hereditary variation influences tumor progression and metastasis. One approach that garnered much early attention was epidemiological studies of cohorts of cancer patients, which demonstrated that specific loci within the human genome are associated with a differential propensity for aggressive tumor development. However, a powerful, and somewhat underutilized approach has been the use of systems genetics approaches in transgenic mouse models of human cancer. Such approaches are typically multifaceted, and involve integration of multiple lines of evidence derived, for example, from genetic and transcriptomic screens of genetically diverse mouse models of cancer, coupled with bioinformatics analysis of human cancer datasets, and functional analysis of candidate genes. These methodologies have allowed for the identification of multiple hereditary metastasis susceptibility genes, with wide-ranging cellular functions including regulation of gene transcription, cell proliferation, and cell-cell adhesion. In this chapter, we review how each of these approaches have facilitated the identification of these hereditary metastasis modifiers, the molecular functions of these metastasis-associated genes, and the implications of these findings upon patient survival.

Cancer as a changed tissue's way of life (when to treat, when to watch and when to think)

The profound scientific and commercial success of molecular biology, the progress of 'cancer gene' investigation technologies, together, pushed forward the postulate that genes explain 'everything'. Yet, during the last few years the microenvironments of solid tumors have emerged as key modulators of initiation, progression and metastasis and as essential to the therapeutic response. In the present review, we provide a synthetic examination of the main traits of cells embedded into the cancer stroma and emphasize several evidences that all components of the tumor tissue cooperate in space and time. Then we turn to discuss the epitheliocentric somatic mutational view and other new paradigms assuming that disturbed tissue interactions among cell populations are critical to cancer causation, growth and spread.

RELATIVE EFFECTIVENESS IN BREAST CANCER TREATMENT: A HEALTH PRODUCTION APPROACH

Background: Pharmaceuticals’ relative effectiveness has come to the fore in the policy arena, reflecting the need to understand how relative efficacy (what can work) translates into added benefit in routine clinical use (what does work). European payers and licensing authorities assess value for money and post-launch benefit–risk profiles, and efforts to standardize assessments of relative effectiveness across the European Union (EU) are under way. However, the ways that relative effectiveness differs across EU healthcare settings are poorly understood.

Methods: To understand which factors influence differences in relative effectiveness, we developed an analytical framework that treats the healthcare system as a health production function. Using evidence on breast cancer from England, Spain, and Sweden as a case study, we investigated the reasons why the relative effectiveness of a new drug might vary across healthcare systems. Evidence was identified from a literature review and national clinical guidance.

Results: The review included thirteen international studies and thirty country-specific studies. Cross-country differences in population age structure, deprivation, and educational attainment were consistently associated with variation in outcomes. Screening intensity appeared to drive differences in survival, although the impact on mortality was unclear.

Conclusions: The way efficacy translates into relative effectiveness across health systems is likely to be influenced by a range of complex and interrelated factors. These factors could inform government and payer policy decisions on ways to optimize relative effectiveness, and help increase understanding of the potential transferability of data on relative effectiveness from one health system to another.

Survival in familial and non-familial breast cancer by age and stage at diagnosis

We aimed to compare the survival in familial and sporadic breast cancer (BC) patients who were diagnosed at an identical age and TNM stage. The Nationwide Swedish Family-Cancer Database including all Swedes born after 1931 and their biological parents, totalling >14.7 million individuals, was used. Hazard ratios (HRs) were calculated for women with BC in a first-degree relative (FDR) versus BC patients without positive family history. There was no difference in survival of familial BC patients who were diagnosed at higher TNM status or older age (>40) compared to sporadic BC cases diagnosed at the same late TNM stage. Young BC patients (age <40) in early stages had the worst survival when their FDR was diagnosed with single (HR: 2.0-3.7) or multiple (HR: 2.4-7.1) BC at any age. We concluded that there is no difference in survival of familial and non-familial BC patients who are diagnosed at higher TNM status or older ages (>40). Young familial BC patients (age <40), diagnosed at early stage, have the poorer survival compared to sporadic cases. Our results urge the need for identifying the underling genetic component for such a difference in survival of familial BC.

Inbreeding and homozygosity in breast cancer survival

Genome-wide association studies (GWASs) help to understand the effects of single nucleotide polymorphisms (SNPs) on breast cancer (BC) progression and survival. We performed multiple analyses on data from a previously conducted GWAS for the influence of individual SNPs, runs of homozygosity (ROHs) and inbreeding on BC survival. (I.) The association of individual SNPs indicated no differences in the proportions of homozygous individuals among short-time survivors (STSs) and long-time survivors (LTSs). (II.) The analysis revealed differences among the populations for the number of ROHs per person and the total and average length of ROHs per person and among LTSs and STSs for the number of ROHs per person. (III.) Common ROHs at particular genomic positions were nominally more frequent among LTSs than in STSs. Common ROHs showed significant evidence for natural selection (iHS, Tajima's D, Fay-Wu's H). Most regions could be linked to genes related to BC progression or treatment. (IV.) Results were supported by a higher level of inbreeding among LTSs. Our results showed that an increased level of homozygosity may result in a preference of individuals during BC treatment. Although common ROHs were short, variants within ROHs might favor survival of BC and may function in a recessive manner.

The role of individual inheritance in tumor progression and metastasis

Metastasis, the dissemination and growth of tumor cells at secondary sites, is the primary cause of patient mortality from solid tumors. Metastasis is an extremely complex, inefficient process requiring contributions of not only the tumor cell but also local and distant environmental factors, at both the cellular and molecular level. Variation in the function of any of the steps in the metastatic cascade may therefore have profound implications for the ultimate course of the disease. In addition to the somatic and cellular heterogeneity that can affect cancer outcome, an individual's specific ancestry or genetic background can also significantly influence metastatic progression. These inherited variants not only encoded for metastatic susceptibility but also provided a window to study critical factors that are not easily accessible with current technologies. Furthermore, investigations into inherited metastatic susceptibility enable identification of important molecular and cellular processes that are not subject to mutation and are consequently not detectable by standard cancer genome sequencing strategies. Incorporation of inherited variation into metastasis research therefore provides methods to more comprehensively investigate the etiology of the lethal consequences of tumor progression.

Therogenetics: transferring GWAS technology to the clinic

Molecular characteristics of breast tumours have been used for the last decades to guide clinicians in treating this devastating disease. More recent information has led to further refinement of molecular characteristics of breast tumours, and subsequent indications for specific treatments. However, evidence exists that factors independent of the primary tumour type, potentially germline genetics, may influence progression to metastasis. In this review, we expose some of this evidence, and propose tools needed to overcome current limitations to the identification of specific germline variants that influence risk of metastases in breast cancer patients.

Systematic pathway enrichment analysis of a genome-wide association study on breast cancer survival reveals an influence of genes involved in cell adhesion and calcium signaling on the patients' clinical outcome

Genome-wide association studies (GWASs) may help to understand the effects of genetic polymorphisms on breast cancer (BC) progression and survival. However, they give only a focused view, which cannot capture the tremendous complexity of this disease. Therefore, we investigated data from a previously conducted GWAS on BC survival for enriched pathways by different enrichment analysis tools using the two main annotation databases Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The goal was to identify the functional categories (GO terms and KEGG pathways) that are consistently overrepresented in a statistically significant way in the list of genes generated from the single nucleotide polymorphism (SNP) data. The SNPs with allelic p-value cut-offs 0.005 and 0.01 were annotated to the genes by excluding or including a 20 kb up-and down-stream sequence of the genes and analyzed by six different tools. We identified eleven consistently enriched categories, the most significant ones relating to cell adhesion and calcium ion binding. Moreover, we investigated the similarity between our GWAS and the enrichment analyses of twelve published gene expression signatures for breast cancer prognosis. Five of them were commonly used and commercially available, five were based on different aspects of metastasis formation and two were developed from meta-analyses of published prognostic signatures. This comparison revealed similarities between our GWAS data and the general and the specific brain metastasis gene signatures as well as the Oncotype DX signature. As metastasis formation is a strong indicator of a patient’s prognosis, this result reflects the survival aspect of the conducted GWAS and supports cell adhesion and calcium signaling as important pathways in cancer progression.

The seed and soil hypothesis revisited: current state of knowledge of inherited genes on prognosis in breast cancer

The crucial event in the course of malignancies such as breast cancer is its metastatic spread from the primary tumor of origin to distant organs. The natural history of a tumor is determined by the expression of its genes, and in this sense, knowledge has advanced dramatically in recent decades. However, much less is known about the role that the patient plays in the behavior of a tumor. In this article, we review the evidence regarding the genetic background of the host in metastatic tumor dissemination, providing information from epidemiological studies as well as from animal models and human studies. Undoubtedly, the elucidation of possible interpersonal variability in susceptibility to developing metastases would significantly contribute to improve management of cancer patients.

Subsequent cancers in patients diagnosed with cancer of unknown primary (CUP): etiological insights?

BACKGROUND

Patterns of subsequent malignancies in patients with cancer of unknown primary (CUP) may provide etiological insight into the primary tumor. The objective of the present study is to quantify risks of the subsequent cancers in CUP patients since such studies are lacking.

PATIENTS AND METHODS

A population-based cohort of CUP was identified from the Swedish Family-Cancer Database of year 2008. Standardized incidence ratios (SIRs) were calculated for developing the following malignancies in 31,357 CUP patients from 1975 to 2008.

RESULTS

A total of 755 CUP patients developed subsequent cancers, showing a significantly increased overall SIR of 1.69 (95% confidence interval 1.57-1.81). Among the most common 32 malignancies, increased SIRs were noted for 16 sites. Over 10-fold increases were observed for squamous cell carcinoma at four sites, possibly as a result of uncontrolled human papillomavirus infection due to faltering immune surveillance. The highest SIRs were observed among CUP patients diagnosed at a younger age and during the first follow-up year.

CONCLUSIONS

Swedish CUP survivors had a higher risk of developing many subsequent cancers. Different patterns of risk excess may be suggestive of possible roles for disease- and therapy-related immunosuppression, reappearance of hidden primary tumors, or genetic predisposition.

Prognostic impact of polymorphisms in the MYBL2 interacting genes in breast cancer

MYBL2 is a transcription factor, which regulates the expression of genes involved in cancer progression. In this study, we investigated whether putative functional variants in genes regulating MYBL2 (E2F1, E2F3 and E2F4) or in genes, which are regulated by MYBL2 (BCL2, BIRC5, COL1A1, COL1A2, COL5A2, ERBB2, CLU, LIN9 and TOP2A) affect breast cancer (BC) susceptibility and clinical outcome. Twenty-eight SNPs were genotyped in a population-based series of 782 Swedish BC cases and 1,559 matched controls. BC-specific survival analysis of BIRC5 suggested that carriers of the minor allele of rs8073069 and rs1042489 have a worse survival compared with the major homozygotes (HR 2.46, 95% CI 1.39-4.36 and HR 1.81, 95% CI 1.01-3.25, respectively). The poor survival was observed especially in women with aggressive tumours. Multivariate analysis supported the role of rs8073069 as an independent prognostic marker. For BCL2, minor allele carriers of rs1564483 were more likely to have hormone receptor-positive tumours than the major homozygotes. Another SNP in BCL2, rs4987852, was associated with tumour stages II-IV and histologic grade 3. In CLU, the minor allele carriers of rs9331888 were more likely to have tumours with regional lymph node metastasis and stages II-IV than the major homozygotes. In conclusion, our study suggests a role of genetic variation in BIRC5, BCL2 and CLU as progression and prognostic markers for BC, supporting previous studies based on the expression of the genes.

Single nucleotide polymorphisms in the 20q13 amplicon genes in relation to breast cancer risk and clinical outcome

The 20q13 region is frequently amplified/overexpressed in breast tumours. However, the nature of this amplification/overexpression is unknown. Here, we investigated genetic variation in five 20q13 amplicon genes (MYBL2, AURKA, ZNF217, STK4 and PTPN1) and its impact on breast cancer (BC) susceptibility and clinical outcome. As a novel finding, four polymorphisms in STK4 (rs6017452, rs7271519) and AURKA (rs2273535, rs8173) associated with steroid hormone receptor status both in a Swedish population-based cohort of 783 BC cases and in a Polish familial/early onset cohort of 506 BC cases. In the joint analysis, the minor allele carriers of rs6017452 had more often hormone receptor positive tumours (OR 0.57, 95% CI 0.40-0.81), while homozygotes for the minor allele of rs7271519, rs2273535 and rs8173 had more often hormone receptor negative tumours (2.26, 1.30-3.39; 2.39, 1.14-5.01; 2.39, 1.19-4.80, respectively) than homozygotes for the common allele. BC-specific survival analysis of AURKA suggested that the Swedish carriers of the minor allele of rs16979877, rs2273535 and rs8173 might have a worse survival compared with the major homozygotes. The survival probabilities associated with the AURKA genotypes depended on the tumour phenotype. In the Swedish case-control study, associations with BC susceptibility were observed in a dominant model for three MYBL2 promoter polymorphisms (rs619289, P = 0.02; rs826943, P = 0.03 and rs826944, P = 0.02), two AURKA promoter polymorphisms (rs6064389, P = 0.04 and rs16979877, P = 0.02) and one 3'UTR polymorphism in ZNF217 (rs1056948, P = 0.01). In conclusion, our data confirmed the impact of the previously identified susceptibility locus and provided preliminary evidence for novel susceptibility variants in BC. We provided evidence for the first time that genetic variants at 20q13 may affect hormone receptor status in breast tumours and influence tumour aggressiveness and survival of the patients. Future studies are needed to confirm the prognostic value of our findings in the clinic.

Survival in cancer patients hospitalized for inflammatory bowel disease in Sweden

BACKGROUND

The increased cancer risk among patients diagnosed with inflammatory bowel disease (IBD) is well reported, whereas studies regarding the cancer prognosis with IBD have shown conflicting results. We aimed at assessing and quantifying the cause-specific and overall mortality among cancer patients with IBD compared to those without IBD.

METHODS

The population-based Swedish registers were used to identify cancer patients diagnosed with or without IBD. We used a Cox regression model to estimate hazard ratios (HRs) for cause-specific and overall mortality, showing the probability of death in the study group compared to the reference.

RESULTS

A total of 2462 cancer patients with IBD and 1,011,894 cancer patients without IBD were ascertained from 1964 to 2006, showing a significant survival disparity (overall HR, 1.26; 95% confidence interval [CI]: 1.20-1.33 versus cause-specific HR, 1.22; 95% CI: 1.15-1.29). Although worse overall cancer mortality with IBD was widely observed, the worse cause-specific mortality was only confined to colorectal cancer (CRC). There was no difference in TNM staging among cancer patients with or without IBD. Stratified analyses showed that a worse prognosis was more pronounced in younger patients (<60 years) and in men. Discordant malignant neoplasms and cardiovascular diseases were noted to be associated with increased mortality in the study group.

CONCLUSIONS

Previously diagnosed IBD worsens the prognosis of cancers, especially for CRC. The more pronounced effect was noted among younger patients and in men. The underlying mechanisms warrant further investigation.

Familial mortality and familial incidence in cancer

PURPOSE

An overwhelming majority of data on familial risk in cancer is based on incident cancer, whereas familiality in cancer mortality is largely unknown. If fatal form of cancer was a highly familial subtype, then familial risk for mortality may exceed that of incidence, which would be particularly relevant for clinical decision making and counseling.

PATIENTS AND METHODS

The individuals in the nationwide Swedish Family-Cancer Database were classified according to family history of fatal and nonfatal cancer. Familial risks of incident and fatal concordant cancer were calculated for offspring based on their parental family history using a Cox model with hazard ratio (HR); offspring without family history were the reference.

RESULTS

Most HRs for offspring incident cancers were somewhat higher for fatal compared with nonfatal parental family history. For breast (HR, 1.87 fatal v 1.66 nonfatal; P < .001) and prostate (HR, 2.30 fatal v 1.84 nonfatal; P < .001) cancers, 51.0% of patients with familial breast cancer and 56.6% of patients with prostate cancer had fatal family history. HRs for death in offspring according to a fatal compared with nonfatal family history were significantly increased for colorectal (HR, 1.76 v 1.47, respectively; P = .02), breast (HR, 1.97 v 1.51, respectively; P = .002), and prostate (HR, 2.03 v 1.59, respectively; P = .002) cancers. TNM classification did not seem to differ between the family histories. We showed also that an overwhelming proportion of offspring were diagnosed after the parental death.

CONCLUSION

Familial breast, prostate, and colorectal cancers might have a yet unidentified genetic component associated with poorer survival. It may be useful to record survival data in family history records.

The Swedish Family-Cancer Database 2009: prospects for histology-specific and immigrant studies

The Swedish Family-Cancer Database comprises a total of 11.8 million individuals covering the Swedish population of the past 100 years. Version VIII of the Database is described in the present article. Cancer cases were retrieved from the Swedish Cancer Registry for the period 1958-2006, including more than 1 million first primary cancers. The number of familial cancers in offspring is 14,000 when a parent was diagnosed with a concordant (same) cancer and the number of concordant siblings was 6,000. From the year 1993 onwards histopathological data according to the SNOMED classification were used, which entails advantages for certain cancers, such as breast cancer. Even though the specific morphological classification only covers a limited number of years, it does cover most familial cancers in the offspring generation. The Database records the country of birth for each subject. A total of 1.79 million individuals were foreign born, Finns and other Scandinavians being the largest immigrant groups. The cancer incidence in the first-generation immigrants was compared to that in native Swedes using standardised incidence ratios (SIRs) to measure relative risk. The SIRs ranged widely between the immigrant groups, from 1.9-fold for myeloma to 25-fold for melanoma. The differences in SIRs were smaller in the second-generation immigrants. The usefulness and the possible applications of the Family-Cancer Database have increased with increasing numbers of cases, and the numerous applications have been described in some 300 publications. Familial cancer studies are in the stimulating interphase of the flourishing disciplines of genetics and epidemiology.

Distinct inherited metastasis susceptibility exists for different breast cancer subtypes: a prognosis study

Introduction

Previous studies in mouse models and pilot epidemiology studies have demonstrated that inherited polymorphisms are associated with inherited risk of tumor progression and poor outcome in human breast cancer. To extend these studies and gain better understanding of the function of inherited polymorphism in breast cancer progression, a validation prognosis study was performed in a large independent breast cancer patient population.

Methods

The study population consisted of 1863 Dutch patients with operable primary breast cancer from Rotterdam, The Netherlands. Genomic DNA was genotyped for the missense Pro436Leu RRP1B single nucleotide polymorphism (SNP) rs9306160 and the intronic SIPA1 SNP rs2448490 by SNP-specific PCR.

Results

A significant association of variants in RRP1B with metastasis-free survival was observed (P = 0.012), validating the role of RRP1B with inherited metastatic susceptibility. Stratification of patients revealed that association with patients' survival was found to be specifically restricted to estrogen receptor positive, lymph node-negative (ER+/LN-) patients (P = 0.011). The specific association with metastasis-free survival only in ER+/LN- patients was replicated for SIPA1, a second metastasis susceptibility gene known to physically interact with RRP1B (P = 0.006). Combining the genotypes of these two genes resulted in the significant ability to discriminate patients with poor metastasis-free survival (HR: 0.40, 95% CI: 0.24 to 0.68, P = 0.001).

Conclusions

These results validate SIPA1 and RRP1B as metastasis susceptibility genes and suggest that genotyping assays may be a useful supplement to other clinical and molecular indicators of prognosis. The results also suggest that lymphatic and hematogeneous metastases are genetically distinct that may involve different mechanisms. If true, these results suggest that metastatic disease, like primary breast cancer, may be multiple diseases and that stratification of late stage patients may therefore be required to fully understand breast cancer progression and metastasis.

Mixture classification model based on clinical markers for breast cancer prognosis

OBJECTIVE

Accurate cancer prognosis prediction is critical to cancer treatment. There have been many prognosis models based on clinical markers, but few of them are satisfied in clinical applications. And with the development of microarray technologies, cancer researchers have discovered many genes as new markers from the gene expression data and have further developed powerful prognosis models based on these so-called genetic biomarkers. However, the application of such biomarkers still suffers from some problems. The first one is there are a great number of genes and a few samples in the gene expression data so that it is difficult to select a unified gene set to establish a stable classifier for prognosis. The second one is that, due to the experimental and technical reasons, there are existing noises and redundancies in gene expression data, which may lead to building a prognosis predictor with poor performance. The last but not the least one is the microarray experiments are so expensive currently that it is hard to obtain abundant samples. Therefore, it is practical to develop prognosis methods mainly based on conventional clinical markers in real cancer treatment applications. This paper aims to establish an accurate classification model for cancer prognosis, in order to make full use of the invaluable information in clinical data, especially which is usually ignored by most of the existing methods when they aim for high prediction accuracies.

METHODS

First, this paper gives the formal description of general classification problem, and presents a novel mixture classification model to make full use of the invaluable information in clinical data, which is similar to the traditional ensemble classification models except for putting strict constraints on the construction of mapping functions to avoid voting process. Then, a two-layer instance of the proposed model, named as MRS (Mixture of Rough set and Support vector machine), is constructed by integrating rough set and support vector machine (SVM) classification methods, in which, the rough set classifier acts as the first layer to identify some singular samples in data, and the SVM classifier acts as the second layer to classify the remaining samples. Finally, MRS is used to make prognosis prediction on two open breast cancer datasets. One dataset, denoted as BRC-1 hereafter, is a high quality, publicly available dataset of 97 breast cancer tumors of node-negative patients. The other, denoted as BRC-2 hereafter, uses baseline human primary breast tumor data from LBL breast cancer cell collection containing 174 samples.

RESULTS

We have done two experiments on BRC-1 and BRC-2, respectively. In the first experiment, the BRC-1 dataset is divided into train set with 78 patients (34 ones belonging to poor prognosis group and 44 ones belonging to good prognosis group) and test set with 19 patients (12 ones belonging to poor prognosis group and 7 ones belonging to good prognosis). After trained on the train set, the MRS can correctly classify all the 12 patients with poor prognosis, and 6 of 7 patients with good prognosis in the test set. The results are better than previous researches, even better than the 70-gene based biomarkers. And in the second experiment, we construct the classifiers using BRC-2 dataset, and compare MRS with other representative methods in Weka software by 5-fold cross-validation, and comparison results show that MRS has higher prediction accuracy than those methods.

CONCLUSIONS

The proposed mixture classification model can easily integrate methods with different characteristics. It can overcome the shortcomings of traditional voting-based ensemble models and thus can make full use of the information in clinical data. The experimental results illustrate that our implemented MRS classifier can predict the breast cancer prognosis more accurately than previous prognostic methods.

Age of onset in familial breast cancer as background data for medical surveillance

BACKGROUND

Familial breast cancers are known to be of early onset. This article provides differences in the age of onset of breast cancer and death by breast cancer between women with and without a family history.

METHODS

The Swedish Family-Cancer Database was used to estimate the cumulative risk of breast cancer and death by breast cancer according to family history with a stratified Cox model. Family history was defined separately for affected mother or sister considering their diagnostic ages.

RESULTS

The age to reach the same cumulative incidence as women without family history decreased with decreasing diagnostic age of the affected relative. Women with a maternal history reached the risk of women lacking a family history at the age of 50 years between 12.3 (mother affected <40 years) and 3.3 years (mother affected >82 years) earlier. The trend for breast cancer mortality was essentially similar.

CONCLUSIONS

Women with mother or sister affected by breast cancer are diagnosed and die at earlier ages than do women without family history. The differences depend on the diagnostic age of the affected relative. The present data may provide a rationale to derive recommendations for the starting age of screening in women with affected family members.

A systems biology approach to defining metastatic biomarkers and signaling pathways

Metastasis is the final stage of cancer and the primary cause of mortality for most solid malignancies. This terminal phase of cancer progression has been investigated using a variety of high-throughput technologies (i.e., gene expression arrays, array comparative genomic hybridization (aCGH), and proteomics) to identify prognostic expression profiles and better characterize the metastatic process. For decades, the predominant model for the metastatic process has been the 'progression model', yet recent microarray results tend to support an inherent metastatic capability within primary tumors. Moreover, studies using a highly metastatic transgenic mammary tumor model suggest that germline polymorphisms are significant determinants of metastatic efficiency. Likewise, a strong concordance of survival has been observed between family members with cancer, further supporting the link between genetic inheritance and survival. In addition, chromosomal aberrations and signaling pathways related to metastatic capacity have been identified by array comparative genomic hybridization (aCGH) and proteomic studies, respectively. Lastly, carcinoma enzyme activity profiles using activity-based proteomics (ABPP), may be more clinically useful than expression-based proteomics for certain cancers. Most importantly, the application of these high-throughput techniques should expedite the search for additional biomarkers, germline polymorphisms, and expression signatures with greater prognostic value.

Survival in non-Hodgkin's lymphoma by histology and family history

PURPOSE

Although survival has been studied for various subtypes of non-Hodgkin's lymphoma (NHL), there have been few comprehensive studies to quantify the prognosis, including all specific histologies. The effect of family history on survival in NHL has not been examined.

METHODS

We used the Swedish Family-Cancer Database to estimate hazard ratios in NHL by histology and family history.

RESULTS

Using diffuse centroblastic lymphoma as reference (HR 1.0), patients with Waldenström's macroglobulinemia and hairy-cell leukemia had the best survival. Survival advantage was also noted among patients with lymphoplasmacytic lymphoma and different kinds of follicular lymphomas. For T-cell lymphoma, mycosis fungoides showed a favorable prognosis. As for survival by family history, a total of 98 familial cases were noted in our Database with a similar prognosis compared to sporadic cases in both parental and offspring generations. A non-significant familial concordance of either good or poor survival was noted among family members when probands' prognosis was stratified by survival time.

CONCLUSIONS

Our results provide quantitative prognosis data for patients with NHL according to specific histologies. Patients with a familial NHL had a similar prognosis compared to patients with sporadic disease. The data suggest familial concordance in either good or poor survival among family members.

No evidence of familial correlation in breast cancer metastasis

Animal experiments support the hypothesis that the metastatic potential of breast cancer is a heritable trait of the host. Our objective was to evaluate correlations in metastasis occurrence in large families with multiple cases of breast cancer. We evaluated correlation among pairs of relatives in the occurrence and timing of distant metastasis using retrospective cohort data from 743 female breast cancer patients in 242 families. We adjusted for correlation in their age at diagnosis, year of diagnosis, educational level, lymph node involvement, and estrogen receptor status. Distant metastasis occurred in 255 patients (34.3%) during mean followup of 11.7 years. None of the correlation coefficients for metastasis in blood relatives differed significantly from zero. The estimated correlation coefficient in first-degree relatives was -0.03 (95% confidence interval -0.11 to 0.06). These findings suggest that a family history of metastatic breast cancer does not contribute substantially to risk of metastasis for breast cancer patients.

Single nucleotide polymorphisms in chromosomal instability genes and risk and clinical outcome of breast cancer: a Swedish prospective case-control study

Chromosomal instability (CIN) is a major characteristic of many cancers. We investigated whether putatively functional single nucleotide polymorphisms (SNPs) in genes related to CIN (CENPF, ESPL1, NEK2, PTTG1, ZWILCH, ZWINT) affect breast cancer (BC) risk and clinical outcome in a Swedish cohort of 749 incident BC cases with detailed clinical data and up to 15 years of follow-up and 1493 matched controls. As a main observation, carriers of the A allele of the CENPF SNP rs438034 had a worse BC-specific survival compared to the wild type genotype GG carriers (hazard ratio (HR) 2.65, 95% confidence interval (CI) 1.19-5.90), although they were less likely to have regional lymph node metastases (odds ratio (OR) 0.71, 95% CI 0.51-1.01) and tumours of stage II-IV (OR 0.73, 95% CI 0.54-0.99). As there is increasing evidence that CENPF is associated with poor prognosis in patients with primary BC, further independent studies are needed to clarify the importance of genetic variation in the CENPF gene in the clinic.

Concordance of survival in family members with prostate cancer

PURPOSE

Several earlier studies have assessed survival in prostate cancer based on familial risk of this disease. As a novel concept, we posit that factors governing survival in prostate cancer are likely to be different from those governing risk of prostate cancer. To prove this, we searched for familial clustering of survival (ie, concordance of survival among family members).

PATIENTS AND METHODS

We used the nationwide Swedish Family-Cancer Database to estimate hazard rates (HRs) for cause-specific and overall survival in invasive prostate cancer. HRs show the probability of death in the study group compared with the reference group. The study covered 610 sons of affected fathers with median follow-up times for survival ranging from 34 to 76 months.

RESULTS

When the survival in sons was analyzed according to the fathers' length of survival, there was a concordance of prognosis; the HR was 0.62 for sons whose fathers had survived longer than 59 months, compared with sons whose fathers had survived fewer than 24 months (P for trend, .02). On a continuous scale, the sons' survival increased almost linearly with the fathers' survival time. When the analysis was reversed and HRs were derived for fathers, the concordance of good and poor survival remained.

CONCLUSION

The results are consistent in showing that both good and poor survival in prostate cancer aggregate in families. Genetic factors are likely to contribute to the results, which provide the first challenging population-level evidence on heritability in prognosis of prostate cancer.