Validation of an RNA cell cycle progression score for predicting death from prostate cancer in a conservatively managed needle biopsy cohort.

BACKGROUND: The natural history of prostate cancer is highly variable and difficult to predict accurately. Better markers are needed to guide management and avoid unnecessary treatment. In this study, we validate the prognostic value of a cell cycle progression score (CCP score) independently and in a prespecified linear combination with standard clinical variables, that is, a clinical-cell-cycle-risk (CCR) score. METHODS: Paraffin sections from 761 men with clinically localized prostate cancer diagnosed by needle biopsy and managed conservatively in the United Kingdom, mostly between 2000 and 2003. The primary end point was prostate cancer death. Clinical variables consisted of centrally reviewed Gleason score, baseline PSA level, age, clinical stage, and extent of disease; these were combined into a single predefined risk assessment (CAPRA) score. Full data were available for 585 men who formed a fully independent validation cohort. RESULTS: In univariate analysis, the CCP score hazard ratio was 2.08 (95% CI (1.76, 2.46), P<10(-13)) for one unit change of the score. In multivariate analysis including CAPRA, the CCP score hazard ratio was 1.76 (95% CI (1.44, 2.14), P<10(-6)). The predefined CCR score was highly predictive, hazard ratio 2.17 (95% CI (1.83, 2.57), χ(2)=89.0, P<10(-20)) and captured virtually all available prognostic information. CONCLUSIONS: The CCP score provides significant pretreatment prognostic information that cannot be provided by clinical variables and is useful for determining which patients can be safely managed conservatively, avoiding radical treatment.

A telephone reminder intervention to improve breast screening information and access.

OBJECTIVES: In the UK, women aged 50-70 are offered breast cancer screening every three years. Screening participation rates in London have been particularly low. Low rates have been associated with low socio-economic status, and some ethnic groups have been observed to be underserved by cancer screening. This paper reports on a telephone reminder intervention in London Newham, an area of high deprivation and ethnic diversity. STUDY DESIGN: Observational study of planned intervention. METHODS: Women invited for breast screening were telephoned to confirm receipt of the invitation letter, remind invitees of their upcoming appointment, and to provide further information. Aggregate data at general practice level on invitation to and attendance at breast screening and on numbers reached by telephone were analysed by logistic regression. RESULTS: For the 29 participating GP practices (10,928 invitees) overall uptake in 2010 was higher compared to the previous screening round in 2007 (67% vs. 51%; p < 0.001). On average 59% of invitees were reached by the reminder calls. A 10% increase in women reached resulted in an 8% increase in the odds of women attending their screening appointment (95% CI: 5%-11%), after adjusting for 2007 attendance rates. Practices with a higher proportion of South Asian women were associated with a larger uptake adjusted for 2007 uptake and population reached by the telephone intervention, (4% increase in odds of attendance per 10% increase in South Asian population, CI 1%-7%, p = 0.003) while practices with a higher proportion of black women were associated with a smaller uptake similarly adjusted. (11% decrease in odds of attendance per 10% increase in black population, CI 9%-16%, p < 0.001). CONCLUSIONS: A language- and culture-sensitive programme of reminder calls substantially improved breast cancer screening uptake.

A novel, externally validated inflammation-based prognostic algorithm in hepatocellular carcinoma: the prognostic nutritional index (PNI).

BACKGROUND: There is increasing evidence that the presence of an ongoing systemic inflammatory response is a stage-independent predictor of poor outcome in patients with cancer. The aim of this study was to investigate whether an inflammation-based prognostic score, the prognostic nutritional index (PNI), is associated with overall survival (OS) in patients with hepatocellular carcinoma (HCC). METHODS: All patients with a new diagnosis of HCC presenting to the Medical Oncology Department, Hammersmith Hospital between 1993 and 2011 (n=112) were included. Demographic and clinical data were collected. Patients in whom the combined albumin (g l(-1)) × total lymphocyte count × 10(9) l(-1) was ≥45, at presentation, were allocated a PNI score of 0. Patients in whom this total score was <45 were allocated a score of 1. Univariate and multivariate analyses were performed to identify clinicopathological variables associated with OS. Independent predictors of survival identified on multivariate analysis were validated in an independent, stage-matched cohort of 68 patients. RESULTS: Univariate analyses showed that PNI (P=0.003), intrahepatic spread (P<0.001), the presence of extrahepatic disease (P=0.006), portal vein thrombosis (P=0.02), tumour multifocality (P=0.003), alfa-fetoprotein >400 ng ml(-1) (P<0.001) and Barcelona Clinic Liver Cancer score (P<0.01) were all predictors of OS in the training set. Multivariate analysis revealed the PNI (P=0.05), presence of extrahepatic disease (P<0.001) and degree of intrahepatic spread (P<0.001) as independent predictors of worse OS in this population. The PNI retained independent prognostic value in the validation set (P<0.001). CONCLUSION: The presence of a systemic inflammatory response, as measured by the PNI, is an independent and externally validated predictor of poor OS in patients with HCC.

A metabolic phenotyping approach to understanding relationships between metabolic syndrome and breast tumour responses to chemotherapy.

PURPOSE: Breast cancer is associated with adverse outcomes in patients with the metabolic syndrome phenotype. To study this further, we examined the relationship between serum metabolite levels and the components of metabolic syndrome with treatment outcomes in breast cancer. METHODS: A total of 88 women with measurable breast cancer were studied; their serum metabolites as assessed by (1)H nuclear magnetic resonance spectroscopy, blood pressure, lipids, glucose, body mass index and waist circumference were recorded and correlated with treatment response. RESULTS: We identified metabolic syndrome in approximately half of our cohort (42 patients) and observed a significant trend (P = 0.03) of increased incidence of metabolic syndrome in partial response (33.3%), stable disease (42.9%) and progressive disease groups (66.1%). High blood sugar predicted a poor response (P < 0.001). Logistic regression of metabonomic data demonstrated that high lactate (P = 0.03) and low alanine (P = 0.01) combined with high glucose (P = 0.01) were associated with disease progression. CONCLUSIONS: Metabolic syndrome is commonly observed in metastatic breast cancer and these patients have poorer outcomes. These data, which support our previous findings, suggest that high blood glucose as part of metabolic syndrome is associated with a poor response in breast cancer. They also validate new therapeutic approaches that focus on metabolism.

Simple indices of inflammation as predictors of death from cancer or cardiovascular disease in a prospective cohort after two decades of follow-up.

BACKGROUND: Previous studies have identified sub-clinical inflammation as a potential factor in the pathogenesis of cancer and cardiovascular disease (CVD) but the possibility that simple, readily measured indices of sub-clinical inflammation might predict both CVD and cancer has not been tested in the context of a single, prospective analysis. AIM: To evaluate simply measured indices of inflammation as long-term predictors of death from either cancer or CVD. DESIGN: Prospective open cohort study. METHODS: A total of 1192 white males received measurements of a range of risk markers including the inflammation indices white blood cell count (WBC), erythrocyte sedimentation rate (ESR) and serum globulin concentrations. Inflammation marker clustering was quantified as a factor-analysis-derived inflammation score and survival time to death from any cancer or CVD was modeled on baseline measures using the Cox proportional hazards model. RESULTS: A total of 1010 participants met inclusion criteria, of whom 94 died of cancer and 67 of CVD. Mean follow-up times among cases and survivors ranged from 18.2-21.9 years. Independently of established risk factors [age, body mass index (BMI), smoking, alcohol and exercise], WBC, ESR and globulin levels were all individually predictive of both cancer (hazard ratio 1.43, P = 0.002; 1.27, P = 0.02; 1.26, P = 0.02, respectively) and CVD mortality (1.29, P = 0.06; 1.43, P = 0.007; 1.50, P = 0.001). The inflammation score predicted both cancer mortality (1.35, P = 0.003) and CVD mortality (1.46, P = 0.002). Risks associated with high inflammation score were equivalent to and independent of smoking cigarettes for cancer or, for CVD, having a serum cholesterol concentration ≥6.2 mmol/l. CONCLUSIONS: Simple indices of inflammation predict death from cancer or CVD two decades later as strongly as smoking predicts cancer or cholesterol predicts CVD. Their measurement could contribute to evaluation of both cancer and CVD risk.

Natural history of Ullrich congenital muscular dystrophy.

OBJECTIVE: To describe the course, complications, and prognosis of Ullrich congenital muscular dystrophy (UCMD), with special reference to life-changing events, including loss of ambulation, respiratory insufficiency, and death. METHODS: Review of the case notes of 13 patients with UCMD, aged 15 years or older at last visit, followed up at a tertiary neuromuscular centre, London, UK, from 1977 to 2007. Data collected were age at onset of symptoms, presenting symptoms, mobility, contractures, scoliosis, skin abnormalities, respiratory function, and feeding difficulties. RESULTS: The mean age at onset of symptoms was 12 months (SD 14 months). Eight patients (61.5%) acquired independent ambulation at a mean age of 1.7 years (SD 0.8 years). Nine patients (69.2%) became constant wheelchair users at a mean age of 11.1 years (SD 4.8 years). Three patients continued to ambulate indoors with assistance. Forced vital capacity (FVC) values were abnormal in all patients from age 6 years. The mean FVC (% predicted) declined at a mean rate of 2.6% (SD 4.1%) yearly. Nine patients (69.2%) started noninvasive ventilation at a mean age of 14.3 years (SD 5.0 years). Two patients died of respiratory insufficiency. CONCLUSION: In Ullrich congenital muscular dystrophy (UCMD), the decline in motor and respiratory functions is more rapid in the first decade of life. The deterioration is invariable, but not always correlated with age or severity at presentation. This information should be of help to better anticipate the difficulties encountered by patients with UCMD and in planning future therapeutic trials in this condition.

Neuroleptics in the treatment of aggressive challenging behaviour for people with intellectual disabilities: a randomised controlled trial (NACHBID).

OBJECTIVE(S): To assess the effects and cost-effectiveness of haloperidol, risperidone and placebo on aggressive challenging behaviour in adults with intellectual disability. DESIGN: A double-blind randomised controlled trial of two drugs and placebo administered in flexible dosage, with full, independent assessments of aggressive and aberrant behaviour, global improvement, carer burden, quality of life and adverse drug effects at baseline, 4, 12 and 26 weeks, and comparison of total care costs in the 6 months before and after randomisation. At 12 weeks, patients were given the option of leaving the trial or continuing until 26 weeks. Assessments of observed aggression were also carried out with key workers at weekly intervals throughout the trial. SETTING: Patients were recruited from all those being treated by intellectual disability services in eight sites in England, one in Wales and one in Queensland, Australia. PARTICIPANTS: Patients from all severity levels of intellectual disability; recruitment was extended to include those who may have been treated with neuroleptic drugs in the past. EXCLUSION CRITERIA: treatment with depot neuroleptics/another form of injected neuroleptic medication within the last 3 months; continuous oral neuroleptic medication within the last week; those under a section of the Mental Health Act 1983 or Queensland Mental Health Act 2000. INTERVENTIONS: Randomisation to treatment with haloperidol (a typical neuroleptic drug), risperidone (an atypical neuroleptic drug) or placebo using a permuted blocks procedure. Dosages were: haloperidol 1.25-5.0 mg daily; risperidone 0.5-2.0 mg daily. MAIN OUTCOME MEASURES: Primary: reduction in aggressive episodes between baseline and 4 weeks using Modified Overt Aggression Scale. Secondary: Aberrant Behaviour Checklist; Uplift/Burden Scale; 40-item Quality of Life Questionnaire; Udvalg for Kliniske Undersøgelser scale; Clinical Global Impressions scale. Economic costs recorded using a modified version of Client Service Receipt Inventory for 6 months before and after randomisation. RESULTS: There were considerable difficulties in recruitment because of ethical and consent doubts. Twenty-two clinicians recruited a total of 86 patients. Mean daily dosages were 1.07 mg rising to 1.78 mg for risperidone and 2.54 mg rising to 2.94 mg for haloperidol. Aggression declined dramatically with all three treatments by 4 weeks, with placebo showing the greatest reduction (79%, versus 57% for combined drugs) (p = 0.06). Placebo-treated patients showed no evidence of inferior response in comparison to patients receiving neuroleptic drugs. An additional study found that clinicians who had not participated in clinical trials before were less likely to recruit. Mean total cost of accommodation, services, informal care and treatment over the 6 months of the trial was 16,336 pounds for placebo, 17,626 pounds for haloperidol and 18,954 pounds for risperidone. CONCLUSIONS: There were no significant important benefits conferred by treatment with risperidone or haloperidol, and treatment with these drugs was not cost-effective. While neuroleptic drugs may be of value in the treatment of aggressive behaviour in some patients with intellectual disability, the underlying pathology needs to be evaluated before these are given. The specific diagnostic indications for such treatment require further investigation. Prescription of low doses of neuroleptic drugs in intellectual disability on the grounds of greater responsiveness and greater liability to adverse effects also needs to be re-examined.

The prevalence of personality disorder in schizophrenia and psychotic disorders: systematic review of rates and explanatory modelling.

BACKGROUND: Personality disorder (PD) in psychosis is poorly studied. As PD can affect outcome in mental disorders, it is important to understand its prevalence in order to plan services, understand prognosis more fully and maximize management options. MethodLiterature searching revealed 3972 potential papers. Twenty papers including 6345 patients were included in the final analysis. There was great variation in prevalence and multilevel modelling was used to identify possible reasons for this heterogeneity. RESULTS: The prevalence of PD varied from 4.5% to 100%. Multilevel analysis suggested country of study, study type, the instruments used to diagnose PD and patient care correlated with the prevalence data explaining the study level heterogeneity, with 34.2, 33.4, 17.0 and 4.5% by each variable respectively. Personality studies in Canada and Sweden reported lower PD prevalence, whereas in Spain it was higher than the multinational study. Compared with randomized controlled trials, case-control studies reported lower prevalence [odds ratio (OR)=0.35, 95% confidence interval (CI) 0.15-0.79] and observational studies higher prevalence (OR 70.5, 95% CI 8.5-583). Primary-care patients were less likely to be diagnosed (OR 0.02, 95% CI 0-0.19) than hospital patients, and out-patients had higher prevalence (OR 12.5, 95% CI 1.77-88.6). CONCLUSIONS: The reported prevalence of PD in schizophrenia varies significantly. Statistical modelling suggests care, country, study type and diagnostic tools for PD all bias prevalence rates. The number of papers reaching the inclusion criteria, the relative paucity of information and the difficulties in developing an accurate statistical model limited interpretation from the study.

The influence of ploidy on saltwater adaptation, acute stress response and immune function following seawater transfer in non-smolting rainbow trout.

We investigated the effect of ploidy on osmoregulatory, stress and immune responses in non-smolting rainbow trout during saltwater adaptation. Sibling groups of diploid and triploid trout were acclimated in freshwater (FW) and then subjected to abrupt transfer to full strength (35ppt) saltwater (SW) or back to FW. Fish were sampled pre-stress, and 1, 3, 6, 12, 24, 48, 72 and 168h post-stress. Overall mortality in SW was less than 5% in either ploidy, with no mortality in FW. Significant elevations in plasma osmolality and gill ATPase were observed within 1-3h of SW transfer, but retuned to basal levels within 72h indicative of rapid saltwater adaptation and did not differ between ploidy. Furthermore, FW-SW transfer also caused significant and sustained elevations in total blood haemoglobin, plasma IGF-I, cortisol, glucose, total white blood cell counts, increased plasma but decreased mucus lysozyme, and enhanced head kidney macrophage respiratory burst activity. Conversely, FW-FW transfer evoked more transient and less elevated responses, more typical of primary and secondary responses to a single stressor. We conclude that the more elevated levels in these parameters are a function of saltwater adaptation as well as the generic stress response, and that this did not differ between ploidy. Strong positive correlations were found between plasma IGF-I and cortisol, and with osmolality, glucose and WBC, while a negative correlation was found with plasma lysozyme irrespective of ploidy. Overall, the current results suggest that triploidy does not affect the ability of non-smolting trout to adapt to full strength seawater under optimum conditions, and that the osmotic and stress response to such transfer is similar to diploids.

Fin erosion on rainbow trout on commercial trout farms in the United Kingdom.

Fish weighing less than 30 g and more than 100 g were sampled from 38 rearing units on 10 commercial farms growing rainbow trout for the table market. A fin index was calculated for each of the eight rayed fins on 949 trout by dividing their length by the standard length of the fish. There was a large range in the indices of all eight fins. The fin indices of the small and large fish were compared, controlling for farm effect. With the exception of the dorsal fin, all the indices were larger for the small fish than for the large fish, but the magnitude of the difference was greater for some fins than others. In comparison with the fins of wild fish, the pectoral and dorsal fins appeared to be most eroded and the damage to these fins was evident even in the small fish. The erosion of the caudal, anal and ventral (or pelvic) fins was more prominent in the larger fish. Variations in the fin indices of the caudal, anal and ventral fins suggested that there was little variation between rearing units on the same farm, but that there was significant variation between individual fish in the same rearing units, and between fish on different farms.

Investigation of the ability of haplotype association and logistic regression to identify associated susceptibility loci.

While finely spaced markers are increasingly being used in case-control association studies in attempts to identify susceptibility loci, not enough is yet known as to the optimal spacing of such markers, their likely power to detect association, the relative merits of single marker versus multimarker analysis, or which methods of analysis may be optimal. Some investigations of these issues have used markers simulated under different theoretical models of population evolution. However the HapMap project and other sources provide real datasets which can be used to obtain a more realistic view of the performance of these approaches. SNPs around APOE and from two HapMap regions were used to obtain information regarding linkage disequilibrium (LD) relationships between polymorphisms, and these real patterns of LD were used to simulate datasets such as would be obtained in case-control studies were these SNPs to influence susceptibility to disease. The datasets obtained were analysed using tests for heterogeneity of estimated haplotype frequencies and using logistic regression analyses in which only main effects from each marker were considered. All markers surrounding the putative susceptibility locus were analysed, using sets of either 1, 2, 3 or 4 markers at a time. Some markers within 150 kb of the susceptibility locus were able to detect association. At distances less than 100 kb there was no correlation between the distance from the susceptibility locus and the strength of evidence for association. When the average inter-locus spacing is 25 kb many loci would not be detected, while when the spacing is as low as 2 kb one can be fairly confident that at least one marker will be in strong enough LD with the susceptibility locus to enable association to be detected, if the susceptibility locus has a strong enough effect relative to the sample size. With an inter-locus spacing of 4 kb some susceptibility loci did not have a marker locus in strong LD, potentially undermining the ability to detect association. There was little difference in the performance of haplotype-based analysis compared with logistic regression considering effects of each marker as separate. Multimarker analysis on occasion produced results which were much more highly significant than single marker analysis, but only very rarely. Our results support the view that if markers are randomly selected then a spacing as low as 2 kb is desirable. Multimarker analysis can sometimes be more powerful than single marker analysis so both should be performed. However, because it is rare for multimarker analysis to be much more highly significant than single marker analysis one should strongly suspect that when such results occur they may be due to mistakes in genotyping or through some other artefact. Haplotype analysis may be more prone to such problems than logistic regression, suggesting that the latter method might be preferred.

Screening of histone deacetylases (HDAC) expression in human prostate cancer reveals distinct class I HDAC profiles between epithelial and stromal cells.

Histone deacetylases (HDACs) represent a large family of enzymes identified as key regulators of nucleosomal histone acetylation, a major epigenetic event that controls eukaryotic gene transcription. Inappropriate deacetylation mediated by HDACs has been associated with profound alterations in cellular biology. We have thus hypothesized that an altered HDAC expression may favor cancer development/progression. To test this possibility, we have sought to screen the expression profiles of several class I and class II HDACs (HDAC1-8) in DU-145, PC-3 and LNCaP human prostate cancer cell lines as well as in matched malignant and non-malignant prostate tissues by use of real time RT-PCR, immunoblot and immunohistochemistry. All HDAC transcripts tested were detected at various levels in all prostate cancer cell lines and tissue samples analyzed. In prostate tissues, the abundance of HDAC1 protein, which was exclusively expressed in the cell nucleus, was similar in normal and malignant epithelial cells, but was usually lower in stromal cells. Unexpectedly, HDAC8, another class I HDAC, was not detected in epithelial cells but was uniquely expressed in the cytoplasm of stromal cells. HDAC5, a class II HDAC involved in myogenesis, was not detected in the tissues. Altogether, our findings indicate that epithelial and stromal cells exhibit distinct class I HDAC expression profiles, and the abundance of HDAC1 is not altered in human prostate cancer. In addition, our observations are the first to demonstrate the prominently cytosolic distribution of a class I HDAC, HDAC8.

The EIF2AK3 gene region and type I diabetes in subjects from South India.

Mutations in the EIF2AK3 gene underlie susceptibility to the Wolcott-Rallison syndrome, which is a monogenic disease associated with insulin-deficient neonatal diabetes. Furthermore, suggestive evidence of linkage between type 1 diabetes (T1DM) and the EIF2KA3 chromosomal region has been reported in Scandinavian families. We have investigated the hypothesis that polymorphic variants in and around the EIF2AK3 gene might partially account for susceptibility to T1DM in South Indian subjects. Excess transmission of the common alleles of two polymorphic markers (D2S1786 and 15INDEL, located within the gene) downstream of EIF2AK3, either singly (D2S1786, P = 0.01) and 15INDEL (P = 0.02) or as a combination (P < 0.001), were found in 234 families with a T1DM proband. There was also a clear paternal effect for the 15INDEL marker (P = 0.005) on disease susceptibility. The presence of the common allele of both markers was found in decreased frequency in the subjects with normal glucose tolerance compared to probands with T1DM (both P

Further investigation of linkage disequilibrium SNPs and their ability to identify associated susceptibility loci.

There is currently considerable interest in the use of single-nucleotide polymorphisms (SNPs) to map disease susceptibility genes. The success of this method will depend on a number of factors including the strength of linkage disequilibrium (LD) between marker and disease loci. We used a data set of SNP genotypings in the region of the APOE disease susceptibility locus to investigate the likely usefulness of SNPs in case-control studies. Using the estimated haplotype structure surrounding and including the APOE locus, and assuming a codominant disease model, we treated each SNP in turn as if it were a disease susceptibility locus and obtained, for each disease locus and markers, the expected likelihood ratio test (LRT) to assess disease association. We were particularly interested in the power to detect association with the susceptibility polymorphism itself, the power of nearby markers to detect association, and the ability to distinguish between the susceptibility polymorphism and marker loci also showing association. We found that the expected LRT depended critically on disease allele frequencies. For disease loci with a reasonably common allele we were usually able to detect association. However, for only a subset of markers in the close neighbourhood of the disease locus was association detectable. In these cases we were usually, but not always, able to distinguish the disease locus from nearby associated marker loci. For some disease loci, no other loci demonstrated detectable association with the disease phenotype. We conclude that one may need to use very dense SNP maps in order to avoid overlooking polymorphisms affecting susceptibility to a common phenotype.

Haplotype association analysis of discrete and continuous traits using mixture of regression models.

We present a regression-based method of haplotype association analysis for quantitative and dichotomous traits in samples consisting of unrelated individuals. The method takes account of uncertain phase by initially estimating haplotype frequencies and obtaining the posterior probabilities of all possible haplotype combinations in each individual, then using these as weights in a finite mixture of regression models. Using this method, different combinations of marker loci can be modeled, to find a parsimonious set of marker loci that are most predictive and therefore most likely to be closely associated with the a quantitative trait locus. The method has the additional advantage of being able to use individuals with some missing genotype data, by considering all possible genotypes at the missing markers. We have implemented this method using the SNPHAP and Mx programs and illustrated its use on published data on idiopathic generalized epilepsy.

Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.

Biallelic markers, such as single nucleotide polymorphisms (SNPs), provide greater information for localising disease loci when treated as multilocus haplotypes, but often haplotypes are not immediately available from multilocus genotypes in case-control studies. An artificial neural network allows investigation of association between disease phenotype and tightly linked markers without requiring haplotype phase and without modelling any evolutionary history for the disease-related haplotypes. The network assesses whether marker haplotypes differ between cases and controls to the extent that classification of disease status based on multi-marker genotypes is achievable. The network is "trained" to "recognise" affection status based on supplied marker genotypes, and then for each multi-marker genotype it produces outputs which aim to approximate the associated affection status. Next, the genotypes are permuted relative to affection status to produce many random datasets and the process of training and recording of outputs is repeated. The extent to which the ability to predict affection for the real dataset exceeds that for the random datasets measures the statistical significance of the association between multi-marker genotype and affection. This permutation test performs well with simulated case-control datasets, particularly when major gene effects are present. We have explored the effects of systematically varying different network parameters in order to identify their optimal values. We have applied the permutation test to 4 SNPs of the calpain 10 (CAPN10) gene typed in a case-control sample of subjects with type 2 diabetes, impaired glucose tolerance, and controls. We show that the neural network produces more highly significant evidence for association than do single marker tests corrected for the number of markers genotyped. The use of a permutation test could potentially allow conditional analyses which could incorporate known risk factors alongside marker genotypes. Permuting only the marker genotypes relative to affection status and these risk factors would allow the contribution of the markers to disease risk to be independently assessed.

A quick and simple method for detecting subjects with abnormal genetic background in case-control samples.

It is important that case-control samples be drawn from a genetically homogeneous population in order to avoid artefactual false positive results and to enhance power to detect disease mutations and markers in linkage disequilibrium with them. Tests which simply compare overall marker allele frequencies between cases and controls will fail to identify a relatively small number of subjects drawn from a different genetic background who could usefully be discarded from the sample. Such subjects can be identified using multilocus tests, but previously described tests have been unnecessarily complex and cumbersome for this simple application. We describe a straightforward test, implemented in the CHECKHET program, which uses a measure of genetic difference and permutation procedures to rapidly identify such subjects using genotypes from multiple unlinked markers. It seems to perform reasonably well on simulated data, and with real data appears to identify two abnormal subjects within a case-control sample. We recommend that such tests be routinely applied to case-control samples once sufficient numbers of markers have been genotyped within them.

Extension of conditional model-free likelihood-based linkage analysis to additive and other models.

We have previously described extending our method of 'model-free' linkage analysis, implemented in the MFLINK program, in order to deal with liability classes. This allows a new form of conditional two-locus linkage analysis, meaning that the genotypes of a known risk locus can be used to define liability classes so that their effects can be incorporated in tests for linkage at additional loci. In this method, relationships between transmission models for different liability classes were constrained so that there was a constant multiplicative effect on penetrance values. Here we present further extensions to the method to allow for different relationships. In particular, rather than only having a multiplicative effect on risk of affection we now allow specification of a multiplicative effect on risk of non-affection, or a combination of both relationships, across liability classes. We now also allow specification of an additive effect on penetrance. By way of example, we apply these methods to genome scan data for Alzheimer's disease using apolipoprotein E genotype to define liability classes. We show that, although in general the different methods produce results which tend to be quite highly correlated, certain markers can produce quite different results according to the method applied and that these could well lead to differences of interpretation. Without knowing a priori which relationship is likely to be most appropriate to describe the overall combined effect of the two loci one might be obliged to apply a number of different methods. This in turn may lead to the familiar difficulties associated with multiple testing. Nevertheless, the new method allows researchers greater flexibility in analysing linkage data for diseases in which one or more risk polymorphisms have already been identified.