Testing for BRCA1 mutations: a cost-effectiveness analysis

Molecular Profile and Clinical Variables in Brca1-Positive Breast Cancers. A Population-Based Study

Purpose

To evaluate the clinical features of breast cancer patients with genetic susceptibility to this disease and to investigate the contribution of BRCA1 germline mutations to the phenotype of these tumors.

Patients and Methods

We reviewed the clinical and pathological records of 102 women with suspected inherited susceptibility to breast cancer consecutively seen at the Genetic Oncology Service of Parma, Italy. Sixty-two patients with a high probability of harboring a germline, cancer-predisposing mutation were tested for BRCA1 mutations. Exon 11 was screened using the protein truncation test and detected mutations were confirmed by direct sequencing (DS). All other exons were analyzed by DS.

Results

Among the 62 patients with a completed mutation analysis, 48 (77.4%) had wild-type BRCA1, six (9.6%) had variants of unclear significance, eight (13%) had deleterious mutations. BRCA1-associated breast cancers (BABC) were significantly less likely to be diagnosed at stage I than breast cancers in women without mutations (12.5% vs 51%; P = 0.045), more likely to have a high proliferation rate (100% vs 24%, P<0.001), and more likely to be histological grade 3 (100% vs 14%, P<0.001), estrogen and progesterone receptor negative (87.5% vs 13%, P<0.001; 75% vs 23%, P = 0.004), and p53 positive (87.5% vs 30%, P = 0.023). All tumors with BRCA1 mutations were HER-2/neu negative compared with 57% of the non-BRCA1 tumors ( P = 0.04). There were no significant differences between BABC and non-BABC in 20-year relapse-free survival, 20-year event-free survival, and 20-year overall survival.

Conclusion

In this population-based study, BABC seems to present with adverse molecular features when compared with non-BABC, although the prognosis appears to be similar.

Cost-minimization analysis of GSTP1c.313A>G genotyping for the prevention of cisplatin-induced nausea and vomiting: A Bayesian inference approach

Background

Chemotherapy-induced nausea and vomiting are concerning adverse events resulting from cancer treatment, and current guidelines recommend the use of neurokinin-1-selective antagonists, such as fosaprepitant, in highly emetogenic schemes. However, the implementation of this strategy may be limited by the cost of treatment. GSTP1 c.313A>G genotype was recently described as a predictor of vomiting related to high-dose cisplatin. We hypothesized that the inclusion of routine GSTP1 c.313A>G screening may be promising in financial terms, in contrast to the wide-spread use of fosaprepitant.

Methods

A cost-minimization analysis was planned to compare GSTP1 c.313A>G genotyping versus overall fosaprepitant implementation for patients with head and neck cancer under chemoradiation therapy with high-dose cisplatin. A decision analytic tree was designed, and conditional probabilities were calculated under Markov chain Monte Carlo simulations using the Metropolis-Hastings algorithm. The observed data included patients under treatment without fosaprepitant, while priors were derived from published studies.

Results

To introduce screening with real-time polymerase chain reaction, an initial investment of U$ 39,379.97 would be required, with an amortization cost of U$ 7,272.97 per year. The mean cost of standard therapy with fosaprepitant is U$ 243.24 per patient, and although the initial cost of routine genotyping is higher, there is a tendency of progressive minimization at a threshold of 155 patients (Credible interval–CI: 119 to 216), provided more than one sample is incorporated for simultaneous analysis. A resulting reduction of 35.83% (CI: 30.31 to 41.74%) in fosaprepitant expenditures is then expected with the implementation of GSTP1 c.313A>G genotyping.

Conclusion

GSTP1 c.313A>G genotyping may reduce the use of preventive support for chemotherapy induced nausea and lower the overall cost of treatment. Despite the results of this simulation, randomized, interventional studies are required to control for known and unknown confounders as well as unexpected expenses.

Commercial landscape of noninvasive prenatal testing in the United States

Cell-free fetal DNA-based noninvasive prenatal testing (NIPT) could significantly change the paradigm of prenatal testing and screening. Intellectual property (IP) and commercialization promise to be important components of the emerging debate about clinical implementation of these technologies. We have assembled information about types of testing, prices, turnaround times, and reimbursement of recently launched commercial tests in the United States from the trade press, news articles, and scientific, legal, and business publications. We also describe the patenting and licensing landscape of technologies underlying these tests and ongoing patent litigation in the United States. Finally, we discuss how IP issues may affect clinical translation of NIPT and their potential implications for stakeholders. Fetal medicine professionals (clinicians and researchers), genetic counselors, insurers, regulators, test developers, and patients may be able to use this information to make informed decisions about clinical implementation of current and emerging noninvasive prenatal tests.

A novel high-resolution melting analysis-based method for Yersinia pseudotuberculosis genotyping

Yersinia pseudotuberculosis is an enteric pathogen that is environmentally widespread and is known to cause human and animal infections. The development of a fast and inexpensive typing system is necessary to facilitate epidemiological studies of Y. pseudotuberculosis infections. In this study, we aimed to develop a method of Y. pseudotuberculosis genotyping based on determining differences in single-nucleotide polymorphisms (SNPs) using a high-resolution melting analysis (HRMA). Using a set of nine primer pairs, ten SNPs were screened from sequences in the 16S rRNA, glnA, gyrB and recA sequences of 12 Y. pseudotuberculosis strains that were deposited in the GenBank database. The genetic diversity of a collection of 40 clinical Y. pseudotuberculosis strains was determined using the HRMA method and the multilocus sequence typing (MLST) technique was used for comparison. Different melting profiles were found in five out of a total of nine analyzed fragments. A phylogenetic tree was constructed from the nucleotides that were identified in the nine analyzed fragments, and the tree demonstrated that Y. pseudotuberculosis strains were separated into two groups. The first cluster was composed of strains from the 1/O:1a serogroup and the second of strains from the 2/O:3 serogroup. The separation into two clusters based on distinct bio-serogroups of Y. pseudotuberculosis was consistent with the results in the MLST database. The simple and highly reproducible HRMA assay developed by us may be used as a rapid and cost-effective method to genotype Y. pseudotuberculosis strains of O:1 and O:3 serogroups and it can complement sequence-based methods facilitating epidemiological studies of this Yersinia species.

Genetic testing in the European Union: does economic evaluation matter?

OBJECTIVE

We review the published economic evaluation studies applied to genetic technologies in the EU to know the main diseases addressed by these studies, the ways the studies were conducted and to assess the efficiency of these new technologies. The final aim of this review was to understand the possibilities of the economic evaluations performed up to date as a tool to contribute to decision making in this area.

METHODS

We have reviewed a set of articles found in several databases until March 2010. Literature searches were made in the following databases: PubMed; Euronheed; Centre for Reviews and Dissemination of the University of York-Health Technology Assessment, Database of Abstracts of Reviews of Effects, NHS Economic Evaluation Database; and Scopus. The algorithm was "(screening or diagnosis) and genetic and (cost or economic) and (country EU27)". We included studies if they met the following criteria: (1) a genetic technology was analysed; (2) human DNA must be tested for; (3) the analysis was a real economic evaluation or a cost study, and (4) the articles had to be related to any EU Member State.

RESULTS

We initially found 3,559 papers on genetic testing but only 92 articles of economic analysis referred to a wide range of genetic diseases matched the inclusion criteria. The most studied diseases were as follows: cystic fibrosis (12), breast and ovarian cancer (8), hereditary hemochromatosis (6), Down's syndrome (7), colorectal cancer (5), familial hypercholesterolaemia (5), prostate cancer (4), and thrombophilia (4). Genetic tests were mostly used for screening purposes, and cost-effectiveness analysis is the most common type of economic study. The analysed gene technologies are deemed to be efficient for some specific population groups and screening algorithms according to the values of their cost-effectiveness ratios that were below the commonly accepted threshold of 30,000€.

CONCLUSIONS

Economic evaluation of genetic technologies matters but the number of published studies is still rather low as to be widely used for most of the decisions in different jurisdictions across the EU. Further, the decision bodies across EU27 are fragmented and the responsibilities are located at different levels of the decision process for what it is difficult to find out whether a given decision on genetic tests was somehow supported by the economic evaluation results.

Developing national guidance on genetic testing for breast cancer predisposition: the role of economic evidence?

Advancements in genetic testing to identify predisposition for hereditary breast cancer (HBC) mean that it is important to understand the incremental costs and benefits of the new technologies compared with current testing strategies. This study aimed to (1) identify and critically appraise existing economic evidence for BRCA1/2 mutation testing for HBC and (2) establish whether economic evidence was used to inform national guidance in England and Wales. A telephone interview with diagnostic laboratories (n=14) offering BRCA1/2 mutation testing identified that 9 (64%) used Sanger DNA sequencing with multiplex ligation-dependent probe amplification and two offered next generation sequencing. A systematic review identified 15 economic studies that evaluated: genetic testing for HBC (5 studies); preventive management options for women at risk of HBC (8 studies); and different laboratory approaches for BRCA1 testing (2 studies). These evaluations were not relevant to U.K. practice, and therefore the development of national guidance using a risk threshold to trigger BRCA1/2 testing has not been informed by existing economic evidence. The lack of economic evidence supporting the current risk threshold for national guidance has implications for the efficient use of healthcare resources and the design of economic evaluations of new technologies for BRCA1/2 testing.

EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients

The detection of unknown mutations remains a serious challenge and, despite the expected benefits for the patient's health, a large number of genes are not screened on a routine basis. We present the diagnostic application of EMMA (Enhanced Mismatch Mutation Analysis(®) , Fluigent, Paris, France), a novel method based on heteroduplex analysis by capillary electrophoresis using innovative matrices. BRCA1 and BRCA2 were screened for point mutations and large rearrangements in 1,525 unrelated patients (372 for the validation step and 1,153 in routine diagnosis) using a single analytical condition. Seven working days were needed for complete BRCA1/2 screening in 30 patients by one technician (excluding DNA extraction and sequencing). A total of 137 mutations were found, including a BRCA2 duplication of exons 19 and 20, previously missed by Comprehensive BRACAnalysis(®) . The mutation detection rate was 11.9%, which is consistent with patient inclusions. This study therefore suggests that EMMA represents a valuable short-term and midterm option for many diagnostic laboratories looking for an easy, reliable, and affordable strategy, enabling fast and sensitive analysis for a large number of genes.

Advantage of high-resolution melting curve analysis over conformation-sensitive gel electrophoresis for mutational screening of BRCA1 and BRCA2 genes

BACKGROUND

Mutation screening of BRCA1 and BRCA2 (BRCAs) genes is a time-consuming and costly procedure that demands faster and cheaper alternative methods for routine diagnostics. The present study is aimed at comparing the results obtained with screening mutations methods, conformation sensitive gel electrophoresis (CSGE) and high-resolution melting analysis (HRMA), for BRCAs attending to their specificity, sensitivity, reliability and cost-efficiency.

METHODS

We included 52 DNA samples of index patients from high-risk families. The mutational screening was performed by CSGE according to the Ganguly (1993) method and HRMA according to a modified De Leeneer (2008) method. The assays were performed in 384 well plates in the LightCycler 480 (Roche). All PCR products showing altered patterns were confirmed by sequencing.

RESULTS

The results obtained with the mutational study of BRCAs genes showed that HRMA exhibited higher sensitivity than CSGE as it was able to detect a wide mutational spectra of genetic variants in a larger number of samples. Aditionally, the combination of HRMA with hybiridization probes in a second step of the assay allows the specific confirmation of mutations. Furthermore, HRMA use less time, allowing the reduction of analysis time.

CONCLUSIONS

HRMA offers clear advantages over CSGE for the mutation screening of BRCAs genes as it has greater sensitivity and higher efficiency and it is less time-consuming.

Myriad Genetics: In the eye of the policy storm

From the late 1980s, a storm surrounding the wisdom, ethics, and economics of human gene patents has been brewing. The various winds of concern in this storm touched on the impact of gene patents on basic and clinical research, on health care delivery, and on the ability of public health care systems to provide equal access when faced with costly patented genetic diagnostic tests. Myriad Genetics, Inc., along with its subsidiary, Myriad Genetic Laboratories, Inc., a small Utah-based biotechnology company, found itself unwittingly in the eye of this storm after a series of decisions it made regarding the commercialization of a hereditary breast cancer diagnostic test. This case study examine the background to Myriad's decisions, the context in which these decisions were made and the policy, research and business response to them.

Impact of gene patents and licensing practices on access to genetic testing for inherited susceptibility to cancer: comparing breast and ovarian cancers with colon cancers

Genetic testing for inherited susceptibility to breast and ovarian cancer can be compared with similar testing for colorectal cancer as a "natural experiment." Inherited susceptibility accounts for a similar fraction of both cancers and genetic testing results guide decisions about options for prophylactic surgery in both sets of conditions. One major difference is that in the United States, Myriad Genetics is the sole provider of genetic testing, because it has sole control of relevant patents for BRCA1 and BRCA2 genes, whereas genetic testing for familial colorectal cancer is available from multiple laboratories. Colorectal cancer-associated genes are also patented, but they have been nonexclusively licensed. Prices for BRCA1 and 2 testing do not reflect an obvious price premium attributable to exclusive patent rights compared with colorectal cancer testing, and indeed, Myriad's per unit costs are somewhat lower for BRCA1/2 testing than testing for colorectal cancer susceptibility. Myriad has not enforced patents against basic research and negotiated a Memorandum of Understanding with the National Cancer Institute in 1999 for institutional BRCA testing in clinical research. The main impact of patenting and licensing in BRCA compared with colorectal cancer is the business model of genetic testing, with a sole provider for BRCA and multiple laboratories for colorectal cancer genetic testing. Myriad's sole-provider model has not worked in jurisdictions outside the United States, largely because of differences in breadth of patent protection, responses of government health services, and difficulty in patent enforcement.

Gene patents and personalized medicine - what lies ahead?

Gene patents have generally not impeded biomedical research, but some problems that arise in genetic diagnostics can be attributed to exclusively licensed gene patents. Gene patents for therapeutics have often been litigated but have received surprisingly little public outcry. In stark contrast, genetic diagnostics have been highly controversial but rarely litigated: no case has gone to trial and there is little case law to guide policy. Most recently the Secretary's Advisory Committee for Genetics Health and Society (SACGHS) released a draft report examining how patenting and licensing affect access to clinical genetic testing in the US. The SACGHS reported that patents neither greatly hindered nor facilitated patient access to genetic testing; both the harms and the benefits of patents on genetic diagnostics have been exaggerated. Problems do occur when patents are exclusively licensed to a single provider and no alternative is available. Courts have been changing the thresholds for what can be patented, and how strongly patents can be enforced. Technologies for sequencing, genotyping and gene expression profiling promise to guide clinical decisions in managing common chronic diseases and infectious diseases, and will likely be an integral part of personalized medicine. Developing such genomic tests may require mapping a complex intellectual property landscape and cutting through thickets of patented DNA sequences and related methods. Our preliminary studies have found patent claims that, if strictly enforced, might block the use of multi-gene tests or full-genome sequence data. Yet new technologies promise to reduce the costs of complete genomic sequencing to prices that are comparable to current genetic tests for a single condition. Courts, companies, and policy makers seem unlikely to allow intellectual property to obstruct such technological advance, but prudent policy will depend on careful analysis and foresight. The SACGHS report signals that the US government is paying attention, and increases the odds that policy will foster socially beneficial uses of genetic testing while preserving intellectual property incentives and mitigating the problems that arise from legal monopolies.

Description and validation of high-throughput simultaneous genotyping and mutation scanning by high-resolution melting curve analysis

Mutation scanning using high-resolution melting curve analysis (HR-melt) is an effective and sensitive method to detect sequence variations. However, the presence of a common SNP within a mutation scanning amplicon may considerably complicate the interpretation of results and increase the number of samples flagged for sequencing by interfering with the clustering of samples according to melting profiles. A protocol describing simultaneous high-resolution gene scanning and genotyping has been reported. Here, we show that it can improve the sensitivity and the efficiency of large-scale case-control mutation screening. Two exons of ATM, both containing an SNP interfering with standard mutation scanning, were selected for screening of 1,356 subjects from an international breast cancer genetics study. Asymmetric PCR was performed in the presence of an SNP-specific unlabeled probe. Stratification of the samples according to their probe-target melting was aided by customized HR-melt software. This approach improved identification of rare known and unknown variants, while dramatically reducing the sequencing effort. It even allowed genotyping of tandem SNPs using a single probe. Hence, HR-melt is a rapid, efficient, and cost-effective tool that can be used for high-throughput mutation screening for research, as well as for molecular diagnostic and clinical purposes.

"Sequencing-grade" screening for BRCA1 variants by oligo-arrays

The need for fast, efficient, and less costly means to screen genetic variants associated with disease predisposition led us to develop an oligo-nucleotide array-based process for gene-specific single nucleotide polymorphism (SNP) genotyping. This cost-effective, high-throughput strategy has high sensitivity and the same degree of accuracy as direct sequencing, the current gold standard for genetic screening. We used the BRCA1 breast and ovarian cancer predisposing gene model for the validation of the accuracy and efficiency of our strategy. This process could detect point mutations, insertions or deletions of any length, of known and unknown variants even in heterozygous conditions without affecting sensitivity and specificity. The system could be applied to other disorders and can also be custom-designed to include a number of genes related to specific clinical conditions. This system is particularly useful for the screening of long genomic regions with relatively infrequent but clinically relevant variants, while drastically cutting time and costs in comparison to high-throughput sequencing.

Evaluating the performance of models for predicting the BRCA germline mutations in Han Chinese familial breast cancer patients

PURPOSE

Established models (Penn, Myraid and BRCApro) are useful of estimating the probability that a person has a BRCA mutation. But the value of these models in Chinese population is unclear. The aim of the study is to evaluate the performance of three models on the assisting in pre-test genetic risk counseling.

METHODS

Three risk assessment models, Penn II, Myriad and BRCApro, were applied to 212 familial breast cancer patients who had undergone BRCA1/2 mutation analysis. Sensitivity, specificity, positive and negative predictive values, likelihood ratios and area under the receiver operator characteristic (ROC) curve were calculated for each model.

RESULTS

Myriad showed a better ROC curve than BRCApro either for BRCA1 or BRCA1/2 combination mutation prediction, but BRCApro had a higher positive likelihood ratio when using 10% as the probability threshold. The performance of three models improved when they were evaluated in 66 patients from high risk families, presenting increased ROC and positive likelihood ratio. Especially that of BRCApro for BRCA2, the ROC was increased to 0.716 and its positive likelihood was 5.6.

CONCLUSION

Three models had the similar impact on the pre-test probability of BRCA mutation. But at a 10% cutoff point, BRCApro had the best BRCA mutation carrier prediction value. The performance of BRCApro for BRCA2 mutation prediction was improved when it was restricted in patients from high risk families.

NF2 mutation screening by denaturing high-performance liquid chromatography and high-resolution melting analysis

Neurofibromatosis type 2 (NF2) is an autosomal-dominant disorder caused by mutations in the NF2 gene and predisposing to the development of nervous system. Identification of germline mutations is essential to provide appropriate genetic counseling in NF2 patients, but it represents an extremely challenging task because the vast majority of mutations are unique and spread over the entire coding sequence. Moreover, about 30% of de novo patients are indeed mosaic, and direct sequencing can undetect mutated alleles present in a minority of cells. As most screening techniques do not meet the requirements for efficient NF2 testing, we have developed a semi-automated denaturing high-performance liquid chromatography (DHPLC) method for point mutation detection combined with a multiplex ligation-dependent probe amplification approach to screen for gene rearrangements. In addition, we have evaluated high-resolution melting analysis (HRMA) as an exon scanning procedure to identify point mutations in the NF2 gene. The results obtained in 92 NF2 patients expand the NF2 mutational spectrum and indicate DHPLC and HRMA as good systems to screen for point mutations in diseases with a heterogeneous spectrum of alterations.

A comparison of CDKN2A mutation detection within the Melanoma Genetics Consortium (GenoMEL)

CDKN2A is the major melanoma susceptibility gene so far identified, but only 40% of three or more case families have identified mutations. A comparison of mutation detection rates was carried out by "blind" exchange of samples across GenoMEL, the Melanoma Genetics Consortium, to establish the false negative detection rates. Denaturing high performance liquid chromatography (DHPLC) screening results from 451 samples were compared to screening data from nine research groups in which the initial mutation screen had been done predominantly by sequencing. Three samples with mutations identified at the local centres were not detected by the DHPLC screen. No additional mutations were detected by DHPLC. Mutation detection across groups within GenoMEL is carried out to a consistently high standard. The relatively low rate of CDKN2A mutation detection is not due to failure to detect mutations and implies the existence of other high penetrance melanoma susceptibility genes.

Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations

Germline mutations in the BRCA1 or BRCA2 tumour-suppressor genes are strong predictors of breast and/or ovarian cancer development. The contribution of these mutations to breast cancer risk within any specific population is a function of both their prevalence and their penetrance. Mutation prevalence varies among ethnic groups and may be influenced by founder mutations. Penetrance can be influenced by mutation-specific phenotypes and the potential modifying effects of the patient's own genetic and environmental background. Although estimates of both mutation prevalence and mutation penetrance rates are inconsistent and occasionally controversial, understanding them is crucial for providing accurate risk information to each patient.

Humoral immune responses to MUC1 in women with a BRCA1 or BRCA2 mutation

INTRODUCTION

Breast cancer patients with early disease and a natural humoral response to MUC1 have a favourable prognosis, suggesting a possible role of MUC1 antibodies (ab) in controlling haematogenous tumour dissemination and outgrowth. The aim of the study was to evaluate humoral immune responses to MUC1 in women at hereditary high risk of breast cancer to investigate whether this immune response could play a role in the prevention of disease.

MATERIALS AND METHODS

CA15.3 (U/mL), and IgG and IgM ab to MUC1 (arbitrary units per mL, Arb-U/mL) were measured in serum samples obtained from 422 women at hereditary high risk of breast/ovarian cancer, of whom 127 BRCA1/2 carriers, attending the Familial Cancer Clinic of the VU University Medical Centre, and from 370 age-matched healthy controls. Serum samples obtained from women who developed breast cancer (N=12) or breast cancer recurrence (N=17), and from women who underwent prophylactic mastectomy (N=12) and had no breast lesions were also tested.

RESULTS

CA15.3 ranked significantly higher in mutation carriers than in controls (P=0.03). MUC1 IgG ab levels ranked significantly lower in BRCA1/2 mutation carriers than in controls (P=0.003). MUC1 IgG levels were not significantly different (P=0.53) between women who developed primary breast cancer (median 0.72Arb-U/ml, range 0.52-2.44Arb-U/ml) and women who underwent prophylactic mastectomy and had no breast lesions (median 1.04Arb-U/ml, range 0.43-2.88Arb-U/ml).

CONCLUSION

Serum levels of natural IgG ab to MUC1 are lower in BRCA1/2 mutation carriers than in healthy controls. Furthermore, in contrast to previous results in women with sporadic breast cancer, no elevated MUC1 IgG ab were seen in women at hereditary high risk who developed breast cancer. Prophylactic immunotherapy with MUC1 substrates may be a strategy to reduce the risk of breast cancer in BRCA1/2 mutation carriers, strengthening tumour immune surveillance.

Serum CA-125 in relation to adnexal dysplasia and cancer in women at hereditary high risk of ovarian cancer

PURPOSE

Serum CA-125 level is commonly used as indicator for ovarian cancer recurrence. However, its value for the prediction of neoplastic lesions is unknown. The aim of this study was to investigate whether CA-125 concentrations are indicative of adnexal dysplasia and cancer in women at hereditary high risk of ovarian/tubal cancer.

PATIENTS AND METHODS

CA-125 was obtained from 424 women at hereditary high risk of ovarian/tubal cancer attending the VU University Medical Center (Amsterdam, the Netherlands) between 1993 and 2005. Serum samples obtained at the second-to-last (n = 64) and last (n = 98) visit before surgery were tested in women who underwent adnexal surgery for diagnostic (n = 9) or prophylactic (n = 89) reasons. Serum samples obtained from 370 age-matched healthy women were used as controls.

RESULTS

Both the absolute value (P < .0001) and the serial change (P < .0001) of CA-125 were predictive for ovarian cancer (n = 8). For adnexal dysplasia (n = 23), the absolute value of CA-125 (P = .003) was predictive, but the serial change in CA-125 was not (P = .32). The odds ratio for adnexal dysplasia versus nondysplasia in the highest tertile (CA-125 levels 14 U/mL) compared with the lowest tertile (CA-125 < 10 U/mL) was 6 (95% CI, 1.32 to 36.66).

CONCLUSION

In patients at hereditary high risk for adnexal cancer, both the absolute value of serum CA-125 and the change in serial CA-125 are predictors for ovarian cancer. Remarkably, the absolute value of CA-125 is also predictive for adnexal dysplasia. CA-125 values should, therefore, be taken into account in the decision toward prophylactic bilateral salpingo-oophorectomy.

Management of BRCA1/2 associated breast cancer: a systematic qualitative review of the state of knowledge in 2006

INTRODUCTION

The optimal clinical management of breast cancer (BC) arising in BRCA1/2 mutations carriers is a difficult issue complicated by the risk of subsequent malignancies and by the potential differences in response to local and systemic therapies.

AIM

Systematically review the difference in outcome after breast conservation therapy (BCT) and uni-or bilateral mastectomy in BRCA1/2 related BC.

MATERIAL AND METHODS

We selected 20 studies, for which we evaluated the methodology, the characteristics of the populations, biases, confounding risk factors and outcomes.

RESULTS

All studies are retrospective, entailed by numerous biases. They varied with respect to patients' number, selection, and confounding factors. Hereditary BC patients carried an increased risk of ipsilateral recurrence in 5/17 studies, a worse survival in 4/14, an increased risk of contralateral BC in 14/16.

CONCLUSION

Except for contralateral risk, the presence of a BRCA mutation does not seem to offer additional prognostic information. Large prospective trials, stratified for risk reduction strategies are warranted.

Extensive scanning of the calpain-3 gene broadens the spectrum of LGMD2A phenotypes

BACKGROUND

The limb girdle muscular dystrophies (LGMD) are a heterogeneous group of Mendelian disorders highlighted by weakness of the pelvic and shoulder girdle muscles. Seventeen autosomal loci have been so far identified and genetic tests are mandatory to distinguish among the forms. Mutations at the calpain 3 locus (CAPN3) cause LGMD type 2A.

OBJECTIVE

To obtain unbiased information on the consequences of CAPN3 mutations.

PATIENTS

530 subjects with different grades of symptoms and 300 controls.

METHODS

High throughput denaturing HPLC analysis of DNA pools.

RESULTS

141 LGMD2A cases were identified, carrying 82 different CAPN3 mutations (45 novel), along with 18 novel polymorphisms/variants. Females had a more favourable course than males. In 94% of the more severely affected patient group, the defect was also discovered in the second allele. This proves the sensitivity of the approach. CAPN3 mutations were found in 35.1% of classical LGMD phenotypes. Mutations were also found in 18.4% of atypical patients and in 12.6% of subjects with high serum creatine kinase levels.

CONCLUSIONS

A non-invasive and cost-effective strategy, based on the high throughput denaturing HPLC analysis of DNA pools, was used to obtain unbiased information on the consequences of CAPN3 mutations in the largest genetic study ever undertaken. This broadens the spectrum of LGMD2A phenotypes and sets the carrier frequency at 1:103.

Improving sensitivity of electrophoretic heteroduplex analysis using nucleosides as additives: Application to the breast cancer predisposition geneBRCA2

A new method for the detection of unknown mutations, enhanced mismatch mutation analysis (EMMA), is proposed. It is based on electrophoretic heteroduplex analysis (HDA). The resolution is considerably improved, thanks to the combination of high-resolution block-copolymer sieving matrix, and nucleosides as additives in the electrophoretic medium. The EMMA method is compared to denaturing HPLC (DHPLC) in a large-scale study of mutations in the breast cancer-associated gene BRCA2, involving 4655 DNA amplicons from 94 patients. The rate of false positives was 0.09%. The raw success rate, without optimization of the amplicons tiling, was 94%, a value much higher than that achieved earlier with HDA, and comparable with that obtained with DHPLC. An analysis of the missed mutations suggest that the success rate could be improved up to about 97%, simply by redesigning the amplicons, while retaining the speed, cost effectiveness, and simplicity of the method.

Low prevalence of (pre) malignant lesions in the breast and high prevalence in the ovary and Fallopian tube in women at hereditary high risk of breast and ovarian cancer

To analyse the prevalence of (pre) malignant lesions occurring in breast and adnexal tissue at prophylactic surgery in women at hereditary high risk of breast and/or ovarian cancers. Tissue was obtained from 85 women who underwent prophylactic bilateral salpingo-oophorectomy (pBSO) and from 59 women who underwent prophylactic mastectomy (pM). Control tissue samples were obtained from women undergoing breast reduction surgery (N = 99) or adnexal surgery for benign reasons (N = 72). In women with a BRCA1/2 mutation, the prevalence of a (pre) malignant adnexal lesion was 50% (95% CI 26-74) if older than 40 years and 14% (95% CI 0-58) if younger. The prevalences of (pre) malignant breast lesions in women older than 40 years, with and without a BRCA1/2 mutation, were 0% (95% CI 0-16) and 47% (95% CI 21-73), respectively. No association was found between (pre) malignant lesions in breast and adnexal tissue occurring in 28 women who underwent surgery on both organs (R = 0.155, p = 0.432), but the prevalence of lesions was significantly higher in adnexal tissue than in the breast (p = 0.023). Compared to controls, women at hereditary high risk had a higher chance of (pre) malignant lesions in the breast and an even higher chance of such lesions in the adnexal tissue. There was no indication for concomitant presence of such lesions in both organs at the time of prophylactic surgery. The high frequency of (pre) malignant lesions in the adnexal tissue stresses further the importance of pBSO from the age of 40 onwards in women at hereditary high risk.

Genetic health technology and economic evaluation: a critical review

The aim of the review is to establish whether, on the basis of previous published evidence, current accepted guidance for health economic evaluation needs to be adapted to evaluate healthcare based on use of genetic information. Online literature search strategies were designed (using PubMed and the NHS Economic Evaluation Database [NHS EED], among others) to gather papers carrying out or discussing economic evaluation and genetics. Papers meeting the inclusion criteria were obtained and reviewed. The papers purporting to be economic analyses were classified using the criteria of the NHS EED and the British Medical Journal (BMJ) working party on peer review of health economic literature. Of 120 English-language papers that met the criteria for review, only 37 were economic evaluations according to the criteria set out by the NHS EED and BMJ working party on economic evaluations. Of these 37, only 33 papers discussed economic evaluation methodologies in the genetics context. The economic evaluation papers did not seem to tackle any of the problems discussed in the methodological papers. Economic evaluation methods offer a structured approach for evaluation of changes but may need to change in order to assess the new technologies. We have found that such studies have not been widely reported, and that those that have been reported do not depart from current economic methods. We have identified a need for better skills and guidance in health economics within this growing area of research.

Analysing DNA patents in relation with diagnostic genetic testing

In the ongoing debate concerning DNA patents, there is a need for empirical data. We aim at creating this data set for DNA patents related to diagnostic genetic testing. To this end we developed two tools to facilitate this process. First, we set up a search strategy to find the relevant patents. Second, we provide a claim classification template to assist the user in the assessment of the subject matter covered by the patent claims and in creating a comprehensive overview of the patent situation within this field. These tools have been used in a pilot study on 11 selected hereditary disorders. In addition, a detailed analysis of the familial breast and ovarian cancer genes patents retrieved by the developed search strategy and their claim classification, after meticulous reading of the documents, allowed us to better describe the problems which medical geneticists and researchers might face when dealing with the patented technology.

Retinoblastoma: genetic testing versus conventional clinical screening in India

INTRODUCTION

Genetic testing is increasingly being used to evaluate susceptibility to hereditary diseases because it is a cost effective screening method. Predictive testing for retinoblastoma can help to save the vision and avoid unnecessary (and invasive) eye examinations for probands and their close relatives. This study was undertaken to evaluate the cost effectiveness of the retinoblastoma genetic screening strategy established in our hospital.

STUDY DESIGN

Cytogenetic study of peripheral blood, mutational, and methylation analyses from the tumor DNA of 25 patients with retinoblastoma was undertaken. The cost for retinoblastoma (RB1) gene screening was calculated based on the cost of the chemicals and consumables used and the clinical examination charges at our hospital. A comparison was made between the cost of genetic screening and clinical testing for retinoblastoma. Retinoblastoma patients underwent clinical management and genetic testing at Sankara Nethralaya, Chennai, India.

RESULTS

By adopting a genetic screening strategy, a 3.5-fold cost saving was seen for a proband while a 6-fold saving was seen for a family with two sibs compared to the cost of clinical examination. The clinical examination fee and cost of genetic screening for a proband was dollarUS536 and dollarUS152, respectively, while for a nuclear family with two sibs the costs were dollarUS1071 and dollarUS175, respectively.

DISCUSSION

Savings for a family will be higher if indirect costs, such as savings in travel times to and from the hospital and labor savings, were taken into account. Cost will be a major factor in determining the implementation of genetic screening for RB1 gene in the clinical practice.

CONCLUSION

In our study in India, genetic screening for retinoblastoma was cheaper than conventional screening and was useful in the genetic counseling of the families.

Contribution of BRCA1 and BRCA2 germ-line mutations to the incidence of breast cancer in young women: results from a prospective population-based study in France

The prevalence of BRCA1/2 germ-line mutations was assessed in a prospective population-based series of early-onset breast cancer (BC) patients in France, and the usefulness of a clinical assessment of hereditary BC risk, based on multiple criteria including pedigree structure, was evaluated. Through the Rhone region BC registry, 232 women diagnosed with BC before 46 years of age were included. They were tested for BRCA1/2 mutations an average of 10 months after diagnosis. All the women were classified according to their family history of cancer: high risk of hereditary breast cancer (HBC), low risk of HBC, isolated BC, and unknown HBC risk. Deleterious mutations were observed in 21 women (9.1%): 15 (6.5%) BRCA1 and 6 (2.6%) BRCA2. Mutations were more prevalent in women who developed BC before age 41 than in women who developed BC between ages 41 and 45 (12.8% versus 5.2%, respectively, P = 0.04). A high prevalence of BRCA1/2 mutations was found among women in the high-risk category with particular family features (i.e., small family size, predominantly male pedigree, specific cancers; 23.5%) and among women with isolated BC before age 41 and with five or fewer close adult female relatives (16.6%). According to the 10% probability level recommended by the American Society of Clinical Oncology guidelines for genetic testing of cancer, BRCA1/2 mutation screening should be considered for all women diagnosed before age 41, except for those with isolated BC in a large pedigree including multiple unaffected female relatives. The clinical assessment of HBC risk that we have developed should help in the decision to perform genetic testing.

Rapid mutation detection in complex genes by heteroduplex analysis with capillary array electrophoresis

Mutational analysis of large multiexon genes without prevalent mutations is a laborious undertaking that requires the use of a high-throughput scanning technique. The Human Genome Project has enabled the development of powerful techniques for mutation detection in large multiexon genes. We have transferred heteroduplex analysis (HA) by conformation-sensitive gel electrophoresis of the two major breast cancer (BC) predisposing genes, BRCA1 and BRCA2, to a multicapillary DNA sequencer in order to increase the throughput of this technique. This new method that we have called heteroduplex analysis by capillary array electrophoresis (HA-CAE) is based on the use of multiplex-polymerase chain reaction (PCR), different fluorescent labels and HA in a 16-capillary DNA sequencer. To date, a total of 114 different DNA sequence variants (19 insertions/deletions and 95 single-nucleotide substitutions - SNS) of BRCA1 and BRCA2 from 431 unrelated BC families have been successfully detected by HA-CAE. In addition, we have optimized the multiplex-PCR conditions for the colorectal cancer genes MLH1 and MSH2 in order to analyze them by HA-CAE. Both genes have been amplified in 13 multiplex groups, which contain the 35 exons, and their corresponding flanking intronic sequences. MLH1 and MSH2 have been analyzed in nine hereditary nonpolyposis colorectal cancer patients, and we have found six different DNA changes: one complex deletion/insertion mutation in MLH1 exon 19 and another five SNS. Only the complex mutation and one SNS may be classified as cancer-prone mutations. Our experience has revealed that HA-CAE is a simple, fast, reproducible and sensitive method to scan the sequences of complex genes.

Diagnostic DHPLC Quality Assurance (DDQA): A collaborative approach to the generation of validated and standardized methods for DHPLC-based mutation screening in clinical genetics laboratories

Genetic testing in a clinical diagnostic environment must be subject to rigorous quality control procedures, in order to ensure consistency and accuracy of results. Denaturing high performance liquid chromatography (DHPLC) has become a standard prescreening tool for mutation detection, offering very high efficiency and sensitivity of detection. Despite the relatively simple software-assisted assay setup, DHPLC is a complex assay, and quality control is reliant on ensuring optimal instrument performance, excellent assay design and validation, and sufficient user training and proficiency to interpret results. We describe here a unique collaborative effort by a group of diagnostic clinical genetics laboratories with DHPLC expertise who, together with the manufacturer of one of the most widely used DHPLC platforms, have generated standard operating procedures (SOPs) for instrument operation and maintenance, and for mutation detection by DHPLC. We also describe the validation of a disease-specific SOP for DHPLC assisted mutation screening of the MECP2 gene associated with Rett syndrome. The proposed SOP was validated, and used independently in two laboratories to introduce MECP2 testing. In addition, we provide empirically derived normal ranges for the WAVE System Mutation Standards, which are essential for optimal instrument performance. This effort was initiated to try to standardize DHPLC-based mutation screening procedures across laboratories, and so increase the overall quality of this testing method. This endeavor will thus save each laboratory from having to generate SOPs on their own, which is a lengthy and laborious task. In this respect, we define "generic" SOPs as procedures that are easily adaptable to the individual laboratories' quality systems.

[Molecular alterations in breast cancer: clinical implications and new analytical tools]

PURPOSE

Breast cancer is a complex and heterogeneous disease resulting from various molecular alterations, the identification of which should have profound impact on the management of patients.

CURRENT KNOWLEDGE AND KEY POINTS

The discovery of germline mutations within breast cancer susceptibility genes, such as BRCA1 and BRCA2, which are associated with a major risk of breast cancer during lifetime, has improved the assessment of the individual risk toward the disease, allowing appropriate strategies of screening and prevention. The identification of key molecular actors in the mammary oncogenesis may help to better assess the prognosis of the disease, while providing new therapeutic targets. Large-scale molecular technologies, which allow simultaneous assessment of a high number of molecular parameters in a single assay, should provide new tools to tackle complexity and heterogeneity of breast cancer. Hence, by examining transcriptional profiles of breast cancer using DNA microarrays, it was possible to reveal new prognostic tumor subgroups, previously indistinguishable. Further improvements are awaited with the recent development of high throughput and large-scale technologies investigating the tumor proteome.

PROSPECTS AND PROJECTS

Precise knowledge of molecular alterations involved in each individual breast cancer will allow more effective and less toxic, tailored therapies.

Detection of genomic rearrangements by DHPLC: A prospective study of 90 patients with inherited peripheral neuropathies associated with17p11.2 rearrangements

Large genomic duplications and deletions are increasingly recognized as a cause of human disease. Charcot-Marie-Tooth type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP) result, respectively, from a duplication or deletion of a 1.5 Mb genomic region in 17p11.2-12, containing the PMP22 gene. In routine diagnostic analysis, CMT1A status is inferred from the detection of an imbalanced dosage of two alleles or the presence of three alleles of a polymorphic marker flanking the PMP22 gene. HNPP is suspected if only one allele is seen, but hemizygosity must be confirmed by analyzing allele segregation in the family or by other techniques such as Southern blotting or fluorescence in situ hybridization (FISH). PCR-based methodologies have also been developed that allow single-step determination of the PMP22 gene copy number, wherein amplicons are typically labeled and/or separated by gel electrophoresis. We describe here a fast and reliable PCR-based method for the diagnosis of CMT1A and HNPP in which the PMP22 gene is co-amplified with a reference gene, and the amplicons are separated according to their size and quantified by DHPLC. Our results suggest that this method for quantifying gene dosage could be applied to other genomic rearrangements.

Cancer Genetics Service Provision: A Comparison of Seven European Centres

OBJECTIVE

To conduct a survey in seven European cancer genetics centres to compare service provision, organisation and practices for familial breast and colon cancer consultations and testing. Information was obtained on aspects of services both nationally and locally.

METHODS

A detailed survey questionnaire was adapted collaboratively to obtain the required information. Initial survey data were collected within each centre and interim results were discussed at two European Workshops. Where differences in practice existed, details were clarified to ensure accuracy and adequacy of information. Participating centres were Haifa (Israel), Hannover (Germany), Leiden (The Netherlands), Leuven (Belgium), Manchester (UK), Marseille (France) and Milan (Italy), representing countries with populations ranging from 6.5 to 80 million.

RESULTS

The European countries diverged in regard to the number of cancer genetics centres nationally (from 8 in Belgium to 37 in France), and the average population served by each centre (from 0.59 million in Israel to 3.32 million in Italy). All centres offered free care at the point of access, but referral to specialist care varied according to national health care provision. At a centre level, staff roles varied due to differences in training and health care provision. The annual number of counsellees seen in each participating centre ranged from 200 to over 1,700. Access to breast surveillance or bowel screening varied between countries, again reflecting differences in medical care pathways. These countries converged in regard to the wide availability of professional bodies and published guidelines promoting aspects of service provision. Similarities between centres included provision of a multidisciplinary team, with access to psychological support, albeit with varying degrees of integration. All services were dominated (70-90%) by referrals from families with an increased risk of breast cancer despite wide variation in referral patterns. Collection of pedigree data and risk assessment strategies were broadly similar, and centres used comparable genetic testing protocols. Average consultation times ranged between 45 and 90 min. All centres had access to a laboratory offering DNA testing for breast and bowel cancer-predisposing genes, although testing rates varied, reflecting the stage of service development and the type of population. Israel offered the highest number of genetic tests for breast cancer susceptibility because of the existence of specific founder mutations, in part explaining why the cancer genetics service in Haifa differed most from the other six.

CONCLUSION

Despite considerable differences in service organisation, there were broad similarities in the provision of cancer genetic services in the centres surveyed.

L’offre de tests de prédisposition génétique au cancer du sein ou de l’ovaire en France

One example of the recent advances of scientific research on the human genome is the identification of two susceptibility genes to breast/ovarian cancer, BRCA1 and BRCA2, making possible the introduction in medical practices of genetic testing to detect patients with an increased risk of developing such cancers. In this context of diffusion, two surveys were carried out to appraise the activity profiles in 1998 and in 2001 of all the different participants in those new medical practices in France, physicians in charge of genetic counselling, medical centres where consultations take place and laboratories. Results show that over the period 1998-2001, few changes occurred, mainly the reduction of the average waiting time to get the result of a genetic test, the increase in the annual number of BRCA2 families identified to a level similar to the one of BRCA1 and the automation of the biological analyses without noting a considerable increase in the annual output of laboratories till 2001 however. This surprising moderate evolution must be connected to the existence of some particular external factors making the framework of the development of these new medical and biological practices and their future really uncertain. The diffusion of BRCA1/2 genetic testing has been carried out facing the traditional difficulties of any innovating activities, but also the uncertainties related to intellectual property rights on genes and the reimbursement of genetic counselling and biological testing. These uncertainties have certainly restrained the pace of change as many actors in this field have opted for a wait and see strategy bearing in mind the possible future constraints imposed to their future activity, especially if European patents on the BRCA1/2 genes are finally granted by the European patent office (EPO).

Cancer genetics services: a systematic review of the economic evidence and issues

This paper systematically reviews the published economic research upon cancer genetics services for families at risk of having familial breast, ovarian or colorectal cancer. A structured search was made of 15 electronic databases. The search identified 1030 papers, of which 31 fulfilled the inclusion criteria, two were cost–benefit studies, five were cost consequences, four were cost-effectiveness studies, one was a cost analysis, two were cost-minimisation studies, one was a cost–utility study, 10 modelled life years and six were reviews. Modelling studies indicate that surveillance, prophylactic and chemoprevention techniques extend survival for carriers of identified mutations. Genetic testing has been estimated to cost $70–2400 [£48^*–1591] and genetic counselling $129–800 [£89–£551]. The technology of genetic testing has been found to be cost effective. Cost effectiveness was particularly influenced by targeting genetic services for patients with a strong family history of cancer rather than screening the entire population. Future economic evaluation must go beyond merely assessing health outcomes and mutation identification, and account for the impact of genetic services upon the individual, the family and society, establish the value of services to these groups and determine the most effective ways of delivering genetic services.

High-Throughput Mutation Detection Method to Scan BRCA1 and BRCA2 Based on Heteroduplex Analysis by Capillary Array Electrophoresis

Background: Scanning for mutations in BRCA1 and BRCA2 in a large number of samples is hampered by the large sizes of these genes and the scattering of mutations throughout their coding sequences. Automated capillary electrophoresis has been shown to be a powerful system to detect mutations by either single-strand conformation polymorphism or heteroduplex analysis (HA).

Methods: We investigated the adaptation of gel-based HA of BRCA1 and BRCA2 to a fluorescent multicapillary platform to increase the throughput of this technique. We combined multiplex PCR, three different fluorescent labels, and HA in a 16-capillary DNA sequencer and tested 57 DNA sequence variants (11 insertions/deletions and 46 single-nucleotide changes) of BRCA1 and BRCA2.

Results: We detected all 57 DNA changes in a blinded assay, and 2 additional single-nucleotide substitutions (1186 A&gt;G of BRCA1 and 3624 A&gt;G of BRCA2), previously unresolved by conformation-sensitive gel electrophoresis. Furthermore, different DNA changes in the same PCR fragment could be distinguished by their peak patterns.

Conclusions: Capillary-based HA is a fast, efficient, and sensitive method that considerably reduces the amount of “hands-on” time for each sample. By this approach, the entire coding regions of BRCA1 and BRCA2 from two breast cancer patients can be scanned in a single run of 90 min.

Scanning for mutations of the ryanodine receptor (RYR1) gene by denaturing HPLC: detection of three novel malignant hyperthermia alleles

BACKGROUND

Malignant hyperthermia (MH) is a fatal autosomal dominant pharmacogenetic disorder characterized by skeletal muscle hypertonicity that causes a sudden increase in body temperature after exposure to common anesthetic agents. The disease is genetically heterogeneous, with mutations in the gene encoding the skeletal muscle ryanodine receptor (RYR1) at 19q13.1 accounting for up to 80% of the cases. To date, at least 42 RYR1 mutations have been described that cause MH and/or central core disease. Because the RYR1 gene is huge, containing 106 exons, molecular tests have focused on the regions that are more frequently mutated. Thus the causative defect has been identified in only a fraction of families as linked to chromosome 19q, whereas in others it remains undetected.

METHODS

We used denaturing HPLC (DHPLC) to analyze the RYR1 gene. We set up conditions to scan the 27 exons to identify both known and unknown mutations in critical regions of the protein. For each exon, we analyzed members from 52 families with positive in vitro contracture test results, but without preliminary selection by linkage analysis.

RESULTS

We identified seven different mutations in 11 MH families. Among them, three were novel MH alleles: Arg44Cys, Arg533Cys, and Val2117Leu.

CONCLUSION

Because of its sensitivity and speed, DHPLC could be the method of choice for the detection of unknown mutations in the RYR1 gene.