Review of non-clinical risk models to aid prevention of breast cancer.

A disease risk model is a statistical method which assesses the probability that an individual will develop one or more diseases within a stated period of time. Such models take into account the presence or absence of specific epidemiological risk factors associated with the disease and thereby potentially identify individuals at higher risk. Such models are currently used clinically to identify people at higher risk, including identifying women who are at increased risk of developing breast cancer. Many genetic and non-genetic breast cancer risk models have been developed previously. We have evaluated existing non-genetic/non-clinical models for breast cancer that incorporate modifiable risk factors. This review focuses on risk models that can be used by women themselves in the community in the absence of clinical risk factors characterization. The inclusion of modifiable factors in these models means that they can be used to improve primary prevention and health education pertinent for breast cancer. Literature searches were conducted using PubMed, ScienceDirect and the Cochrane Database of Systematic Reviews. Fourteen studies were eligible for review with sample sizes ranging from 654 to 248,407 participants. All models reviewed had acceptable calibration measures, with expected/observed (E/O) ratios ranging from 0.79 to 1.17. However, discrimination measures were variable across studies with concordance statistics (C-statistics) ranging from 0.56 to 0.89. We conclude that breast cancer risk models that include modifiable risk factors have been well calibrated but have less ability to discriminate. The latter may be a consequence of the omission of some significant risk factors in the models or from applying models to studies with limited sample sizes. More importantly, external validation is missing for most of the models. Generalization across models is also problematic as some variables may not be considered applicable to some populations and each model performance is conditioned by particular population characteristics. In conclusion, it is clear that there is still a need to develop a more reliable model for estimating breast cancer risk which has a good calibration, ability to accurately discriminate high risk and with better generalizability across populations.

Biobanking for Europe.

Biobanks are well-organized resources comprising biological samples and associated information that are accessible to scientific investigation. Across Europe, millions of samples with related data are held in different types of collections. While individual collections can be well organized and accessible, the resources are subject to fragmentation, insecurity of funding and incompleteness. To address these issues, a Biobanking and BioMolecular Resources Infrastructure (BBMRI) is to be developed across Europe, thereby implementing a European 'roadmap' for research infrastructures that was developed by a forum of EU member states and that has been received by the European Commission. In this review, we describe the work involved in preparing for the construction of BBMRI in a European and global context.

Impaired glucose tolerance and insulin resistance in heart failure: underrecognized and undertreated?

BACKGROUND: A link between diabetes mellitus (DM) and heart failure (HF) has been well-recognized for more than a century. HF is also closely linked to abnormal glucose regulation (AGR) and insulin resistance (IR) in patients without DM and, similarly, these conditions commonly coexist. In epidemiological studies, each condition appears to predict the other. The prevalence of AGR/IR in HF patients without DM is significantly underrecognized and, as yet, the optimal method for screening for these abnormalities in the outpatient setting is unclear. METHODS AND RESULTS: The purpose of this review is to overview the prevalence and prognostic impact of AGR and IR in HF patients without DM and discuss potential pathophysiological pathways that link these conditions with HF. The severity of glucose intolerance in patients with HF correlates with functional and clinical severity of HF and is an independent predictor of an adverse outcome. It is thought that changes in cardiac metabolism, including a switch from glucose metabolism toward fatty acid metabolism, may in part contribute to the pathophysiological processes associated with HF patients with AGR/IR. CONCLUSIONS: We discuss how pharmacological targeting of metabolic pathways in the myocardium of these patients with HF may represent novel therapeutic strategies in these at-risk patients.

Familial chronic lymphocytic leukemia in Norway and Denmark. Comments on pleiotropy and birth order.

AIM: To investigate the genetics of chronic lymphocytic leukemia (CLL). MATERIALS AND METHODS: In 56 (7%) out of 800 CLL patients with concomitant malignant hematological disease, 51 families and 141 cases were ascertained. RESULT: 106 cases (75%) of CLL, 27 cases (19%) of nonCLL and 8 cases (6%) of myeloproliferative disorders. Paternal disease was transmitted primarily to the youngest sons in the sibship while maternal disease was transmitted equally to all sibs, demonstrated by means of matrix conjugation and confirmed with Cox regression on parity and birth order (maternal-offspring combination: relative risk (RR), 95% confidence interval (CI)=1.47 (0.89 - 2.43), p=0.12, compared with paternal-offspring combination: RR=3.25, 95% CI=(1.57-6.72), p<0.001). The B-cell expression in familial and sporadic CLL was indistinguishable. CONCLUSION: Parental genomic imprinting is pointed out as one possible mechanism behind this non-Mendelian genomic output.

The UK DNA banking network: a "fair access" biobank.

The UK DNA Banking Network (UDBN) is a secondary biobank: it aggregates and manages resources (samples and data) originated by others. The network comprises, on the one hand, investigator groups led by clinicians each with a distinct disease specialism and, on the other hand, a research infrastructure to manage samples and data. The infrastructure addresses the problem of providing secure quality-assured accrual, storage, replenishment and distribution capacities for samples and of facilitating access to DNA aliquots and data for new peer-reviewed studies in genetic epidemiology. 'Fair access' principles and practices have been pragmatically developed that, unlike open access policies in this area, are not cumbersome but, rather, are fit for the purpose of expediting new study designs and their implementation. UDBN has so far distributed >60,000 samples for major genotyping studies yielding >10 billion genotypes. It provides a working model that can inform progress in biobanking nationally, across Europe and internationally.

Risk biomarkers enable precision in public health.

Precision medicine uses biomarkers to diagnose disease. However, they can also be used to measure risk of disease. Thus, biomarkers herald a new addition to public health - Precision Public Health. We examine the implications. Risk biomarkers are identified by analyzing population cohorts. They constitute risk factors in mathematical 'Disease Risk Models'. The risk may be fixed as in a genetic biomarker or variable as in some protein biomarkers. They help monitor current risk of disease in an individual, thereby aiding efforts to reduce risk. In the UK, the NHS Health Check system is a universal system for assessing risk and for risk reduction. The system can now make use of modern biomarkers once appropriate infrastructure and governance are in place.

Birth order pattern in the inheritance of chronic lymphocytic leukaemia and related lymphoproliferative disease.

Rank order of affected offspring in a sibship can inform on epigenetic factors in disease susceptibility. Here we report an analysis of birth order in 32 families segregating chronic lymphocytic leukaemia (CLL) and other B-cell lymphoproliferative disorders. A paternal-offspring, but not a maternal-offspring birth rank order was observed. Cox regression analysis provided relative risks (RR) for paternal and maternal transmission of 3.60 (CI 95%: 1.54 - 8.42; P = 0.0005) and 1.64 (CI 95%: 0.90 - 3.01; P = 0.096), respectively. The significance of paternal and maternal transmission of CLL-CLL pairs employing Haldane and Smith's test were 0.006 and 0.63, respectively. There was no evidence of a relationship between parental age and birth order. The genetic mechanism behind the birth order effect observed is discussed in the light of non-Mendelian imprinting and pregnancy related microchimerism.

Breakpoints in the ataxia telangiectasia gene arise at the RGYW somatic hypermutation motif.

The mature sporadic T-cell malignancy, T-cell prolymphocytic leukemia (T-PLL) is remarkable for frequently harbouring somatic mutations of the Ataxia Telangiectasia (A-T) gene, ATM. Because some data suggest ATM is frequently rearranged in T-PLL, it was decided to investigate such rearrangements in detail by cloning breakpoints. Among 17 T-PLL tumour samples, three rearrangements were detected by Southern blotting. Two cases harboured a unique type of intragenic duplication in which breakpoints arose at the consensus sequence RGYW/WRCY. The third case harboured a large deletion terminating within the ATM gene. Also, 13 T-cell acute lymphoblastic leukemia (T-ALL) samples were examined and one sample harboured a deletion- insertion with the RGYW motif at the breakpoint in ATM. This is the first known deleterious mutation detected in ATM in T-ALL. Interestingly, the RGYW motif is the signal for a cell-cycle regulated DNA double strand break (DSB) that initiates somatic hypermutation of immunoglobulin and, probably, T-cell receptor genes. The structures of the ATM duplications suggest they may arise from an error in somatic hypermutation. We suggest that aberrant components of somatic hypermutation may contribute to the defective DSB repair characteristic of cancer.

Concomitant inactivation of p53 and Chk2 in breast cancer.

The structure and expression of the human Rad53 homologue Chk2 was analysed in breast cancer. The previously described silent polymorphism at nucleotide 252 in codon 84 (GAA>GAG) was observed in 5/141 cases. Somatic Chk2 coding mutations were detected in 7/141 cases, these occurring in 4/18 BRCA1-associated breast cancers, 1/78 sporadic breast cancers and 2/25 typical medullary carcinomas. Each of the BRCA1-associated cancers with Chk2 mutations also contained mutations in p53, whereas the single sporadic cancer with Chk2 mutation was wild-type for p53. Expression of Chk2 was ubiquitously detected in normal ductal epithelium of the breast, but there was loss of expression in a significant proportion of breast carcinomas, and this occurred in cancers both with and without p53 mutation. A CpG island was identified 5' of the Chk2 transcriptional start site, but there was no evidence of cytosine methylation in any of the cancers with down-regulated Chk2 expression. Analysis of the germ-line of 45 individuals with hereditary or early onset breast cancer revealed wild-type Chk2 sequence in all cases. Thus, despite the rarity of somatic mutations in Chk2 in sporadic breast carcinomas, our results nevertheless reveal that concomitant loss of function in Chk2 (via down-regulation of expression) and p53 (via mutation) occurs in a proportion of sporadic cases. However, consistent with other studies, we show that germ-line mutations in Chk2 are unlikely to account for a significant proportion of non BRCA1-, non BRCA2-associated hereditary breast cancers.

Biobank Finances: A Socio-Economic Analysis and Review.

This socio-economic study is based on the widely held view that there is an inadequate supply of human biological samples that is hampering biomedical research development and innovation (RDI). The potential value of samples and the associated data are thus not being realized. We aimed to examine whether the financing of biobanks contributes to this problem and then to propose a national solution. We combined three methods: a qualitative case study; literature analysis; and informal consultations with experts. The case study enabled an examination of the complex institutional arrangements for biobanks, with a particular focus on cost models. For the purposes of comparison, a typology for biobanks was developed using the three methods. We found that it is not possible to apply a standard cost model across the diversity of biobanks, and there is a deficit in coordination and sustainability and an excess of complexity. We propose that coordination across this diversity requires dedicated resources for a national biobanking distributed research infrastructure. A coordination center would establish and improve standards and support a national portal for access. This should be financed centrally by public funds, possibly supplemented by industrial funding. We propose that: a) sample acquisition continues to be costed into projects and project proposals to ensure biobanking is driven by research needs; b) core biobanking activities and facilities be supported by central public funds distributed directly to host public institutions; and c) marginal costs for access be paid for by the user.

A robust method for detecting CHK2/RAD53 mutations in genomic DNA.

While screening for germline CHK2 mutations in cancer cases by heteroduplex CSGE, we observed that additional PCR fragments were generated from the 3' end region of the gene that includes exons 11-14. Direct sequencing of these fragments suggested that homologous loci (possibly pseudogenes) were concomitantly being amplified. Searches of public sequence databases showed that a number of areas of the genome show a high degree of homology to exons 10-14 of the CHK2 gene. The presence of these homologous regions means that standard screening methods for detecting mutations in CHK2, based on PCR of genomic DNA, are prone to error. To circumvent this problem, we have developed a strategy, based on long-range PCR, to screen the functional copy of CHK2. Using this approach it is possible to carry out a comprehensive mutational analysis of CHK2 from genomic DNA.

Causation of chronic lymphocytic leukemia--insights from familial disease.

In Western countries B-cell chronic lymphocytic leukemia (CLL) is the most common form of leukemia. Evidence from epidemiological studies and family studies strongly supports the notion that a subset of CLL involves inherited susceptibility. Identification of genes predisposing to CLL should be useful for diagnosis and treatment, as well as serving as a model for B-cell tumorigenesis in general. Here, we review the current status of knowledge about inherited susceptibility to CLL.

Analysis of the Fanconi anaemia complementation group A gene in acute myeloid leukaemia.

Acute myeloid leukaemia (AML) is the most common acute leukaemia in adults. Around 10-15% of individuals with recessively inherited Fanconi anaemia (FA) develop AML. FA is one of a group of recessive syndromes characterized by excessive spontaneous chromosomal breakage in which heterozygote carriers appear to display an increased risk of cancer and there is some indirect evidence that FA carriers may also be at increased risk of AML. This suggests that FA genes may play a role in the development of AML in the wider context. To examine this proposition, further, we have screened samples from 79 AML patients for mutations in the major FA gene, FANCA. No truncating FANCA mutations were detected. One missense mutation previously designated as pathogenic and five novel missense mutations causing non-conservative amino acid substitutions were detected. The data suggests that while FANCA mutations are rare, FANCA mutations may contribute to the development of the disease in a subset of AML.

Instability of CAG-trinucleotide repeats in chronic lymphocytic leukemia.

Anticipation--earlier onset and more severe disease in the offspring generation--is a well documented feature of familial chronic lymphocytic leukaemia (CLL). In a number of Mendelian diseases, anticipation is caused by expansion of contiguous triplets of nucleotides. The severity of disease expression and penetrance is related to the extent of the triplet expansion. To investigate whether repeat nucleotide repeat expansion is a feature of CLL, the repeat expansion detection (RED) technique was applied to samples from 17 patients with familial disease and 32 patients with early-onset CLL disease. No potentially pathological CAG expansions were detected. We conclude that unstable CAG repeat expansion is not a feature of CLL and that other processes are likely to be involved in generating anticipation in familial forms of the disease.

Course fees and academic ranking: insights from the IMI EMTRAIN on-course® database.

The Innovative Medicines Initiative (IMI) funded project on-course® (http://www.on-course.eu/) lists postgraduate biomedical courses in Europe and is comprehensive for all taught and research master's courses. Using on-course®, new insights into education and training in Europe can be delivered; and here we investigate the relationship between master's course fees and university ranking. We hypothesise that higher master's course fees would be associated with higher university ranking. This was indeed the case for research master's courses and for taught master's courses for non-EU students. However, we observed no correlation between taught master's course fees for EU students and university ranking, meaning EU students are paying on average as much for courses at lower ranked universities as they are for courses at higher ranked universities.

Public biobanks: calculation and recovery of costs.

A calculation grid developed by an international expert group was tested across biobanks in six countries to evaluate costs for collections of various types of biospecimens. The assessment yielded a tool for setting specimen-access prices that were transparently related to biobank costs, and the tool was applied across three models of collaborative partnership.

Sources of variability between biobanks in the estimation of DNA concentration.

In biobank networks, accrual, aggregation, and retrieval of samples and data are impeded if minimal standards are not agreed in advance by the network members. The critical requirement is that outputs be standardized between biobanks. To start to address this problem of minimal standards, we undertook a pilot study and now report a follow-up study with 79 centers to identify sources of variability in a common measurement-the estimation of DNA concentration. Our main findings include confirmation of the results of the pilot study on overall variability between centers; fluorescence spectroscopy yields lower estimates of concentration and has less accuracy than absorption spectroscopy; and the 2 technologies differ in their sensitivity to mixing of the samples before measurement. We found that more recent servicing of liquid handling devices contributes to accuracy (at least when deploying absorption spectroscopy). We conclude that, while further study is required, there is a need to promote the development of complete Standard Operating Procedures in academic and commercial laboratories with the implementation of management systems that ensure full adherence to those procedures. There also needs to be a consensus on how much variability in measurements is acceptable for each downstream platform for technologies, including genotyping, sequencing, and epigenetics.