Cost analysis of biomarker testing for mismatch repair deficiency in node-positive colorectal cancer

Background

Microsatellite instability (MSI) in colorectal cancer is caused by defective DNA mismatch repair (MMR). It is present in 15 per cent of sporadic colorectal cancers owing to epigenetic mutL homologue 1 (MLH1) inactivation. The evidence suggests that patients with tumours caused by defective DNA MMR do not benefit from 5-fluorouracil (5-FU)-based chemotherapy.

Methods

The proportion of cancers with defective DNA MMR identified by MSI analysis or immunohistochemistry was calculated from published data. The cost of analysis was compared with the potential savings if 5-FU-based chemotherapy was not administered to these patients.

Results

Some 16·3 per cent of sporadic colorectal cancers had defective DNA MMR. Immunostaining for MLH1 and mutS homologue 2 (MSH2) had a sensitivity of 92·4 per cent and a specificity of 99·6 per cent for identifying MSI-high tumours. The strongest predictive variable was right-sidedness, with positive and negative predictive values of 0·329 and 0·948 respectively. If 5-FU-based chemotherapy were not administered, potential savings of up to £1·2 million per 1000 patients tested could be made. Costs would be higher if alternative chemotherapeutic regimens were substituted as a result of testing.

Conclusion

Knowledge of MMR status may enable participation in trials of non-5-FU-based chemotherapy. The cost of MMR testing may be offset by more efficient use of chemotherapy.

Predicting the likelihood of carrying a BRCA1 or BRCA2 mutation: validation of BOADICEA, BRCAPRO, IBIS, Myriad and the Manchester scoring system using data from UK genetics clinics

OBJECTIVES

Genetic testing for the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2 has important implications for the clinical management of people found to carry a mutation. However, genetic testing is expensive and may be associated with adverse psychosocial effects. To provide a cost-efficient and clinically appropriate genetic counselling service, genetic testing should be targeted at those individuals most likely to carry pathogenic mutations. Several algorithms that predict the likelihood of carrying a BRCA1 or a BRCA2 mutation are currently used in clinical practice to identify such individuals.

DESIGN

We evaluated the performance of the carrier prediction algorithms BOADICEA, BRCAPRO, IBIS, the Manchester scoring system and Myriad tables, using 1934 families seen in cancer genetics clinics in the UK in whom an index patient had been screened for BRCA1 and/or BRCA2 mutations. The models were evaluated for calibration, discrimination and accuracy of the predictions.

RESULTS

Of the five algorithms, only BOADICEA predicted the overall observed number of mutations detected accurately (ie, was well calibrated). BOADICEA also provided the best discrimination, being significantly better (p<0.05) than all models except BRCAPRO (area under the receiver operating characteristic curve statistics: BOADICEA = 0.77, BRCAPRO = 0.76, IBIS = 0.74, Manchester = 0.75, Myriad = 0.72). All models underpredicted the number of BRCA1 and BRCA2 mutations in the low estimated risk category.

CONCLUSIONS

Carrier prediction algorithms provide a rational basis for counselling individuals likely to carry BRCA1 or BRCA2 mutations. Their widespread use would improve equity of access and the cost-effectiveness of genetic testing.

The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions

Multiple genetic loci confer susceptibility to breast and ovarian cancers. We have previously developed a model (BOADICEA) under which susceptibility to breast cancer is explained by mutations in BRCA1 and BRCA2, as well as by the joint multiplicative effects of many genes (polygenic component). We have now updated BOADICEA using additional family data from two UK population-based studies of breast cancer and family data from BRCA1 and BRCA2 carriers identified by 22 population-based studies of breast or ovarian cancer. The combined data set includes 2785 families (301 BRCA1 positive and 236 BRCA2 positive). Incidences were smoothed using locally weighted regression techniques to avoid large variations between adjacent intervals. A birth cohort effect on the cancer risks was implemented, whereby each individual was assumed to develop cancer according to calendar period-specific incidences. The fitted model predicts that the average breast cancer risks in carriers increase in more recent birth cohorts. For example, the average cumulative breast cancer risk to age 70 years among BRCA1 carriers is 50% for women born in 1920-1929 and 58% among women born after 1950. The model was further extended to take into account the risks of male breast, prostate and pancreatic cancer, and to allow for the risk of multiple cancers. BOADICEA can be used to predict carrier probabilities and cancer risks to individuals with any family history, and has been implemented in a user-friendly Web-based program (http://www.srl.cam.ac.uk/genepi/boadicea/boadicea_home.html).

Germline and somatic NF1 gene mutation spectrum in NF1-associated malignant peripheral nerve sheath tumors (MPNSTs)

About 10% of neurofibromatosis type 1 (NF1) patients develop malignant peripheral nerve sheath tumors (MPNSTs) and represent considerable patient morbidity and mortality. Elucidation of the genetic mechanisms by which inherited and acquired NF1 disease gene variants lead to MPNST development is important. A study was undertaken to identify the constitutional and somatic NF1 mutations in 34 MPNSTs from 27 NF1 patients. The NF1 germline mutations identified in 22 lymphocytes DNA from these patients included seven novel mutations and a large 1.4-Mb deletion. The NF1 germline mutation spectrum was similar to that previously identified in adult NF1 patients without MPNST. Somatic NF1 mutations were identified in tumor DNA from 31 out of 34 MPNSTs, of which 28 were large genomic deletions. The high prevalence (>90%) of such deletions in MPNST contrast with the =or<20% found in benign neurofibromas and is indicative of the involvement of different mutational mechanisms in these tumors. Coinactivation of the TP53 gene by deletion, or by point mutation along with NF1 gene inactivation, is known to exacerbate disease symptoms in NF1, therefore TP53 gene inactivation was screened. DNA from 20 tumors showed evidence for loss of heterozygosity (LOH) across the TP53 region in 11 samples, with novel TP53 point mutations in four tumors.

Desmoid tumours in patients with familial adenomatous polyposis and desmoid region adenomatous polyposis coli mutations

BACKGROUND

:The aim of this study was to determine the proportion of patients with familial adenomatous polyposis (FAP) who had mutations in the desmoid region of the adenomatous polyposis coli (APC) gene that phenotypically expresses desmoid disease, and to determine the role for surgery in these patients.

METHODS

Data from the North West Region FAP database and case notes were analysed retrospectively.

RESULTS

Of 363 patients with FAP, 47 from ten families had APC mutations in the desmoid region 3' to codon 1399. Of 22 patients undergoing surgery, 16 developed desmoids, and of these 12 had mesenteric desmoid disease. Complications from mesenteric desmoids were death (two patients), enterectomy (three), local resection (three), fistula (one), cholangitis and local resection (one), bowel obstruction (one) and bowel and ureteric obstruction (one). Preoperative polyp burden ranged from 0 to 100 in eight patients (median age 24.5 (range 16-39) years) and more than 100 in seven (median age 39 (range 31-64) years). One patient had no record of polyp burden.

CONCLUSION

In individuals with 3' APC mutations, abdominal surgery is associated with a 65 per cent risk of developing mesenteric desmoids. An alternative strategy might be to attempt to manage the polyps endoscopically.

News on the genetics, epidemiology, medical care and translational research of Schwannomas

Recent years have seen substantial news and updates in the genetics and diagnosis of schwannomas, even a new hereditary disease with schwannomas; Schwannomatosis has been defined. These developments have consequently led to better evaluation of the incidence of schwannomas. Although there has also been progress in the treatment of schwannomas especially in the field of radiation therapy, hereditary diseases with multiple tumours still represent a therapeutic dilemma. NF2 in particular still causes major morbidity and mortality owing to the neurological deficit of multiple tumour disease and deafness caused by vestibular nerve involvement. Thus there has been great enthusiasm about disease models in the hope that translational research will give rise to new therapies.

Treatment of high fluoride concentration water by MgAl-CO3 layered double hydroxides: kinetic and equilibrium studies

MgAl-CO(3) layered double hydroxides (LDHs) have been employed to treat high fluoride concentration solution. The influences of solution pH, initial fluoride concentration and other anions in the solution were investigated by a series of batch experiments. A marked decrease in the amount of adsorbed fluoride by LDHs is observed with increasing pH. The extent of fluoride removal in the presence of other anions decreases in the order HCO(3)(-)>Cl(-)>H(2)PO(4)(-)>SO(4)(2-). The equilibrium isotherm for fluoride uptake corresponds closely to the Langmuir-Freundlich (L-F) model. The maximum capacity of LDHs for fluoride ions and the Gibbs free energy (DeltaG(0)) for the defluoridation process were calculated to be 319.8+/-5.7mg/g and -9.0+/-0.66kJ/mol, respectively. The negative value of DeltaG(0) indicates the spontaneous nature of the treatment process. Four kinetic models have been evaluated in order to attempt to fit the experimental data, namely the pseudo-first order, the pseudo-second order, the modified multiplex and the double exponential models. It was found that the modified multiplex model, involving a rapid first order step and a slow second order step most closely described the kinetics. The activation energies for the two steps are 37.2+/-5.26 and 72.6+/-4.52kJ/mol, respectively, suggesting that the rapid step is controlled by diffusion processes, whilst the second step is controlled by the reaction of fluoride with the LDHs.

Radiation-induced brain tumours in nevoid basal cell carcinoma syndrome: implications for treatment and surveillance

INTRODUCTION

We report two cases of radiation-induced intracranial tumours after treatment for medulloblastoma presenting in children with nevoid basal cell carcinoma syndrome.

DISCUSSION

These cases illustrate the need for judicious use of post-operative radiotherapy as secondary tumors are commonly reported. This is particularly important as the initial tumour in this cohort is of the 'less aggressive' desmoplastic subtype.

An absence of cutaneous neurofibromas associated with a 3-bp inframe deletion in exon 17 of the NF1 gene (c.2970-2972 delAAT): evidence of a clinically significant NF1 genotype-phenotype correlation

Neurofibromatosis type 1 (NF1) is characterized by cafe-au-lait spots, skinfold freckling, and cutaneous neurofibromas. No obvious relationships between small mutations (<20 bp) of the NF1 gene and a specific phenotype have previously been demonstrated, which suggests that interaction with either unlinked modifying genes and/or the normal NF1 allele may be involved in the development of the particular clinical features associated with NF1. We identified 21 unrelated probands with NF1 (14 familial and 7 sporadic cases) who were all found to have the same c.2970-2972 delAAT (p.990delM) mutation but no cutaneous neurofibromas or clinically obvious plexiform neurofibromas. Molecular analysis identified the same 3-bp inframe deletion (c.2970-2972 delAAT) in exon 17 of the NF1 gene in all affected subjects. The Delta AAT mutation is predicted to result in the loss of one of two adjacent methionines (codon 991 or 992) ( Delta Met991), in conjunction with silent ACA-->ACG change of codon 990. These two methionine residues are located in a highly conserved region of neurofibromin and are expected, therefore, to have a functional role in the protein. Our data represent results from the first study to correlate a specific small mutation of the NF1 gene to the expression of a particular clinical phenotype. The biological mechanism that relates this specific mutation to the suppression of cutaneous neurofibroma development is unknown.

Cost-effectiveness of screening with contrast enhanced magnetic resonance imaging vs X-ray mammography of women at a high familial risk of breast cancer

Contrast enhanced magnetic resonance imaging (CE MRI) is the most sensitive tool for screening women who are at high familial risk of breast cancer. Our aim in this study was to assess the cost-effectiveness of X-ray mammography (XRM), CE MRI or both strategies combined. In total, 649 women were enrolled in the MARIBS study and screened with both CE MRI and mammography resulting in 1881 screens and 1–7 individual annual screening events. Women aged 35–49 years at high risk of breast cancer, either because they have a strong family history of breast cancer or are tested carriers of a BRCA1, BRCA2 or TP53 mutation or are at a 50% risk of having inherited such a mutation, were recruited from 22 centres and offered annual MRI and XRM for between 2 and 7 years. Information on the number and type of further investigations was collected and specifically calculated unit costs were used to calculate the incremental cost per cancer detected. The numbers of cancer detected was 13 for mammography, 27 for CE MRI and 33 for mammography and CE MRI combined. In the subgroup of BRCA1 (BRCA2) mutation carriers or of women having a first degree relative with a mutation in BRCA1 (BRCA2) corresponding numbers were 3 (6), 12 (7) and 12 (11), respectively. For all women, the incremental cost per cancer detected with CE MRI and mammography combined was £28 284 compared to mammography. When only BRCA1 or the BRCA2 groups were considered, this cost would be reduced to £11 731 (CE MRI vs mammography) and £15 302 (CE MRI and mammography vs mammography). Results were most sensitive to the unit cost estimate for a CE MRI screening test. Contrast-enhanced MRI might be a cost-effective screening modality for women at high risk, particularly for the BRCA1 and BRCA2 subgroups. Further work is needed to assess the impact of screening on mortality and health-related quality of life.

Factors influencing the removal of fluoride from aqueous solution by calcined Mg-Al-CO3 layered double hydroxides

Layered double hydroxides (LDH) calcined at different temperatures (denoted as CLDH) have been demonstrated to recover their original layered structure in the presence of appropriate anions. In the light of this so-called "memory effect", a study of removal of fluoride from aqueous solution by calcined Mg-Al-CO(3)-LDH has been carried out. The LDH calcined at 500 degrees C had the highest capacity of removal of fluoride ion, because of retention of its intrinsic structure. The CLDH with an Mg/Al ratio of 2 has a remarkable ability to adsorb anions. The adsorption loading is higher for the calcined Mg-Al-LDH than for calcined Zn-Al and Ni-Al-LDH. The influence of varying the conditions for removal of fluoride, such as the pH of aqueous solution, the initial fluoride concentration, the dosage of adsorbent, and temperature on removal of fluoride have been investigated. The influence of co-existing anions in fluoride aqueous solution indicates that the percentage of removal of fluoride increased in order PO(4)(3-) < Cl(-) approximately SO(4)(2-) < Br(-) << NO(3)(-). It was found that maximum removal of fluoride from aqueous solutions was obtained in 6h at pH 6.0 with an initial concentration of 50 mg/L, and that the retention of fluoride ions by the CLDH material was 98% or higher. The residual fluoride concentration was found to be 0.4 mg/L with an initial concentration of 20 mg/L, which meets the national standard for drinking water quality. The Freundlich isotherm and Langmuir isotherm were used to fit the data of equilibrium experiments. The results of X-ray diffraction, FT-IR and TG-MS demonstrate that the adsorption phenomenon is accompanied by rehydration with concomitant uptake of fluoride ions to rebuild the initial layered structure.

Breast and ovarian cancer risks to carriers of the BRCA1 5382insC and 185delAG and BRCA2 6174delT mutations: a combined analysis of 22 population based studies

A recent report estimated the breast cancer risks in carriers of the three Ashkenazi founder mutations to be higher than previously published estimates derived from population based studies. In an attempt to confirm this, the breast and ovarian cancer risks associated with the three Ashkenazi founder mutations were estimated using families included in a previous meta-analysis of populatrion based studies. The estimated breast cancer risks for each of the founder BRCA1 and BRCA2 mutations were similar to the corresponding estimates based on all BRCA1 or BRCA2 mutations in the meta-analysis. These estimates appear to be consistent with the observed prevalence of the mutations in the Ashkenazi Jewish population.

Uptake of chloride ion from aqueous solution by calcined layered double hydroxides: equilibrium and kinetic studies

Layered double hydroxides (LDH) calcined within a certain temperature range (denoted as CLDH) have been shown to recover their original layered structure in the presence of appropriate anions. In the light of this so-called "memory effect", uptake of chloride ion from aqueous solution by calcined MgAl-CO3 LDH was investigated in batch mode. The equilibrium isotherm showed that the uptake of chloride ion by CLDH was consistent with the Langmuir and Freundlich equations and that the Langmuir model gave a better fit to the experimental data than the Freundlich model. The maximum uptake capacity of CLDH for chloride ion was 149.5 mg/g, close to the stoichiometric uptake (168 mg/g). The influence of varying pH of solution, initial chloride concentration, adsorbent quantity, and temperature on the kinetics of chloride removal has also been explored. Four kinetic models were used to fit the experimental data, and it was found that the pseudo-second-order kinetics model could be used to describe the uptake process satisfactorily. The calculated value of Ea was found to be 56.8 kJ/mol, which suggests that the process of uptake of chloride ion is controlled by the rate of reaction of chloride ion with the CLDH rather than diffusion. A mechanism for removal of chloride ion has been confirmed by X-ray diffraction, FT-IR spectroscopy and TG-MS measurements.

Diagnostic criteria for schwannomatosis

The neurofibromatoses are a diverse group of genetic conditions that share a predisposition to the development of tumors of the nerve sheath. Schwannomatosis is a recently recognized third major form of neurofibromatosis (NF) that causes multiple schwannomas without vestibular tumors diagnostic of NF2. Patients with schwannomatosis represent 2.4 to 5% of all patients requiring schwannoma resection and approximately one third of patients with schwannomatosis have anatomically localized disease with tumors limited to a single limb or segment of spine. Epidemiologic studies suggest that schwannomatosis is as common as NF2, but that familial occurrence is inexplicably rare. Patients with schwannomatosis overwhelmingly present with pain, and pain remains the primary clinical problem and indication for surgery. Diagnostic criteria for schwannomatosis are needed for both clinicians and researchers, but final diagnostic certainly will await the identification of the schwannomatosis locus itself.

Identification of recurrent regions of chromosome loss and gain in vestibular schwannomas using comparative genomic hybridisation

BACKGROUND

Schwannomas are benign tumours of the nervous system that are usually sporadic but also occur in the inherited disorder neurofibromatosis type 2 (NF2). The NF2 gene is a tumour suppressor on chromosome 22. Loss of expression of the NF2 protein product, merlin, is universal in both sporadic and NF2 related schwannomas. The GTPase signalling molecules RhoA and Rac1 regulate merlin function, but to date only mutation in the NF2 gene has been identified as a causal event in schwannoma formation.

METHODS

Comparative genomic hybridisation (CGH) was used to screen 76 vestibular schwannomas from 76 patients (66 sporadic and 10 NF2 related) to identify other chromosome regions that may harbour genes involved in the tumorigenesis.

RESULTS

The most common change was loss on chromosome 22, which was more frequent in sporadic than in NF2 related tumours. Importantly, eight tumours (10%) showed gain of copy number on chromosome 9q34. Each of the two NF2 patients who had received stereotactic radiotherapy had non-chromosome 22 changes, whereas only one of eight non-irradiated NF2 patients had any chromosome changes. Three tumours had gain on 17q, which has also been reported in malignant peripheral nerve sheath tumours that are associated with neurofibromatosis type 1. Other sites that were identified in three or fewer tumours were regions on chromosomes 10, 11, 13, 16, 19, 20, X, and Y.

CONCLUSIONS

These findings should be verified using techniques that can detect smaller genetic changes, such as microarray-CGH.

Evaluation of breast cancer risk assessment packages in the family history evaluation and screening programme

INTRODUCTION

Accurate individualised breast cancer risk assessment is essential to provide risk-benefit analysis prior to initiating interventions designed to lower breast cancer risk. Several mathematical models for the estimation of individual breast cancer risk have been proposed. However, no single model integrates family history, hormonal factors, and benign breast disease in a comprehensive fashion. A new model by Tyrer and Cuzick has addressed these deficiencies. Therefore, this study has assessed the goodness of fit and discriminatory value of the Tyrer-Cuzick model against established models namely Gail, Claus, and Ford.

METHODS

The goodness of fit and discriminatory accuracy of the models was assessed using data from 1933 women attending the Family History Evaluation and Screening Programme, of whom 52 developed cancer. All models were applied to these women over a mean follow up of 5.27 years to estimate risk of breast cancer.

RESULTS

The ratios (95% confidence intervals) of expected to observed numbers of breast cancers were 0.48 (0.37 to 0.64) for Gail, 0.56 (0.43 to 0.75) for Claus, 0.49 (0.37 to 0.65) for Ford, and 0.81 (0.62 to 1.08) for Tyrer-Cuzick. The accuracy of the models for individual cases was evaluated using ROC curves. These showed that the area under the curve was 0.735 for Gail, 0.716 for Claus, 0.737 for Ford, and 0.762 for Tyrer-Cuzick.

CONCLUSION

The Tyrer-Cuzick model is the most consistently accurate model for prediction of breast cancer. The Gail, Claus, and Ford models all significantly underestimate risk, although the accuracy of the Claus model may be improved by adjustments for other risk factors.

Protocol for a national multi-centre study of magnetic resonance imaging screening in women at genetic risk of breast cancer

The protocol of the national multicentre study of Magnetic Resonance Imaging (MRI) as a method of screening for breast cancer in women at genetic risk is described. The sensitivity and specificity of contrast-enhanced MRI will be compared with two-view X-ray mammography in a comparative trial. Approximately 500 women below the age of 50 at high genetic risk of breast cancer will be recruited per year for 3 years, with annual MRI and X-ray examination continuing for up to 5 years. A symptomatic cohort will be measured in the initial phase of the study to ensure consistent reporting between centres. The MRI examination will comprise an initial high-sensitivity screening measurement, followed by a high-specificity measurement in equivocal cases. Retrospective analysis will identify the most specific indicators of malignancy. Sensitivity and specificity, together with diagnostic performance, diagnostic impact and therapeutic impact will be assessed with reference to pathology, follow-up and changes in diagnostic certainty and therapeutic decisions. The psychological impact of screening in this high-risk group will be ascertained.

High detection rate for BRCA2 mutations in male breast cancer families from North West England

33 families with a history of male breast cancer aged 60 or less or with a family history of male and female breast cancer were screened for the presence of BRCA2 mutations. 12 pathogenic BRCA2 mutations were identified (36%) in samples from an affected family member. All mutations segregated with disease where it was possible to check. Of the 14 families fulfilling BCLC criteria, 9 (64%) had mutations whilst only 3/16 (19%) of male breast cancer patients with less significant female breast cancer family history having a mutation. All 3 families with ovarian cancer and 3 families with multiple male breast cancer cases had BRCA2 mutations. These data are a further guide to how to prioritise samples for BRCA2 mutation analysis.

Cyril Leslie Oakley, 20 June 1907--27 March 1975

Cyril Leslie Oakley was an eminent immunologist with an international reputation that had been built up at the Wellcome Research Laboratories, Beckenham, by his work on the analysis of the filtrable antigenic factors produced by pathogenic bacteria of the genus Clostridium . Although medically qualified, Oakley never became deeply involved in medical practice, but maintained throughout his life a great fondness for experimental laboratory work, which he always performed with meticulous care and rigorous attention to accuracy.

Helicobacter pylori CagA: analysis of sequence diversity in relation to phosphorylation motifs and implications for the role of CagA as a virulence factor

CagA is transported into host target cells and subsequently phosphorylated. Clearly this is a mechanism by which Helicobacter pylori could take control of one or more host cell signal transduction pathways. Presumably the end result of this interaction favors survival of H. pylori, irrespective of eventual damage to the host cell. CagA is noted for its amino acid (AA) sequence diversity, both within and outside the variable region of the molecule. The primary purpose of this review is to examine how variation in the type and number of CagA phosphorylation sites might determine the outcome of infection by different strains of H. pylori. The answer to this question could help to explain the widely disparate results obtained when H. pylori CagA status has been compared to type and severity of disease outcome in different populations, that is in different countries. Analysis of all available CagA sequences revealed that CagA contains both tyrosine phosphorylation motifs (TPMs) and cyclic-AMP-dependent phosphorylation motifs (CPMs). There are two potential CPMs near the N-terminus of CagA and at least two in the repeat region; these are not all equally well conserved. We also defined a 48-residue AA sequence, which includes the N-terminal TPM at tyrosine (Y)-122, which distinguishes between Eastern (Hong Kong-Taiwan-Japan-Thailand) H. pylori isolates and those from the West (Europe-Africa-the Americas-Australia). All 28 of the Eastern type CagA proteins have a functional N-terminal TPM whereas 11 of 47 (23.4%) of the Western type contain an inactive motif, with threonine (T) replacing the critical aspartic acid (D) residue. Only 13 of 24 (54%) known CagA sequences have an active TPM in the repeat region and only one has two TPMs in this region. The potential TPM near the C-terminus of CagA is not likely to be important since only 3 of 24 (12.5%) sequences were found to be intact. Protein database searches revealed that the AA sequence immediately following the TPM at Y-122 in CagA is homologous with a pair of PDZ domains which are common in signal transducing proteins, particularly tyrosine phosphatases. This provides a theoretical link between CagA and many of the observed responses of host cells to H. pylori. In summary, not all CagA proteins are equal in their potential for initiating host cell responses via signal transduction pathways. The degree of functional diversity of this protein depends upon which phosphorylation motifs are critical to the biological activity of CagA.