Pragmatic Approach to In Situ Simulation to Identify Latent Safety Threats Before Moving to a Newly Built ICU.

OBJECTIVES: Transitions to new care environments may have unexpected consequences that threaten patient safety. We undertook a quality improvement project using in situ simulation to learn the new patient care environment and expose latent safety threats before transitioning patients to a newly built adult ICU. DESIGN: Descriptive review of a patient safety initiative. SETTING: A newly built 24-bed neurocritical care unit at a tertiary care academic medical center. SUBJECTS: Care providers working in neurocritical care unit. INTERVENTIONS: We implemented a pragmatic three-stage in situ simulation program to learn a new patient care environment, transitioning patients from an open bay unit to a newly built private room-based ICU. The project tested the safety and efficiency of new workflows created by new patient- and family-centric features of the unit. We used standardized patients and high-fidelity mannequins to simulate patient scenarios, with "test" patients created through all electronic databases. Relevant personnel from clinical and nonclinical services participated in simulations and/or observed scenarios. We held a debriefing after each stage and scenario to identify safety threats and other concerns. Additional feedback was obtained via a written survey sent to all participants. We prospectively surveyed for missed latent safety threats for 2 years following the simulation and fixed issues as they arose. MEASUREMENTS AND MAIN RESULTS: We identified and addressed 70 latent safety threats, including issues concerning physical environment, infection prevention, patient workflow, and informatics before the move into the new unit. We also developed an orientation manual that highlighted new physical and functional features of the ICU and best practices gleaned from the simulations. All participants agreed or strongly agreed that simulations were beneficial. Two-year follow-up revealed only two missed latent safety threats. CONCLUSIONS: In situ simulation effectively identifies latent safety threats surrounding the transition to new ICUs and should be considered before moving into new units.

Can butyrate prevent colon cancer? The AusFAP study: A randomised, crossover clinical trial.

Increased colonic butyrate from microbial fermentation of fibre may protect from colorectal cancer (CRC). Dietary butyrylated high amylose maize starch (HAMSB) delivers butyrate to the large bowel. The objective of this clinical trial (AusFAP) is to evaluate potential chemoprotective effects of HAMSB on polyposis in individuals with a genetic form of colon cancer, Familial Adenomatous Polyposis (FAP). The study is a multi-site, double blind, randomised, placebo-controlled crossover trial undertaken at major hospitals in Australia. After a baseline endoscopy participants consume either 40g/day of HAMSB or placebo (low amylose maize) starch for 26 weeks. After another endoscopic examination participants consume the alternate starch for 26 weeks. A third endoscopy at 52 weeks is followed by 26 weeks' washout and a final endoscopy at 78 weeks. Primary outcome measure is the global large bowel polyp number. Secondary measures include global polyp size counts, and number and size of polyps at two tattoo sites: one cleared of polyps at baseline, and another safely chosen with polyps left in situ during the study. Other secondary outcome measures include the effects of intervention on cellular proliferation in colonic biopsies, faecal measures including short chain fatty acid concentrations, and participants' dietary intakes. Generalized linear mixed models analysis will be used to estimate differences in primary outcomes between intervention and placebo periods. This study represents the first clinical evaluation of the effects of increased colonic butyrate on polyp burden in FAP which, if effective, may translate to lower risk of sporadic CRC in the community. Australian New Zealand Clinical Trials Registry Number: 12612000804886.

Emodin inhibits colon cancer by altering BCL-2 family proteins and cell survival pathways.

BACKGROUND: Currently offered therapeutics to treat colon cancer (CoCa) are toxic when given at maximum tolerated dose to achieve optimal clinical response. Hence, less toxic therapeutic intervention is needed to treat CoCa. In this study, we investigated the effect of a natural agent, Emodin, on CoCa. METHODS: Cell viability (MTT) assay was used to determine the effect of Emodin on human CoCa and colon epithelial cells. Flow cytometric analysis was used to determine Emodin induced cell death. Antibody microarray and western blot analyses were used to determine Emodin induced molecular changes involved in cell death. Change in mitochondrial membrane potential in response to Emodin was determined by flow cytometric analysis. Expression and localization of Bcl-2 family proteins were assessed by western blot analysis. RESULTS: Emodin decreased viability of CoCa cells and induced apoptosis in a time and dose-dependent manner compared to vehicle-treated control without significantly impacting normal colon epithelial cells. Emodin activated caspases, modulated Bcl-2 family of proteins and reduced mitochondrial membrane potential to induce CoCa cell death. Further, changes in Bcl-2 family protein expression and localization correlated with loss in mitochondrial membrane potential. Signaling (MAPK/JNK, PI3K/AKT, NF-κß and STAT) pathways associated with cell growth, differentiation, and Bcl-2 family expression or function were negatively regulated by Emodin. CONCLUSIONS: Ability of Emodin to impact molecular pathways involved in cell survival and apoptosis highlight the potential of this agent as a new and less toxic alternative for CoCa treatment.

Choice architecture modifies fruit and vegetable purchasing in a university campus grocery store: time series modelling of a natural experiment.

BACKGROUND: In developed countries, adolescent and young adult diets have been found to be nutritionally poor. The aim of this study was to examine whether a choice architecture intervention, re-arrangement of produce within a grocery store to increase the accessibility of fruit and vegetables, affected purchasing behaviour on a university campus. METHODS: A database of daily sales data from January 2012 to July 2017 was obtained from a campus grocery store. Two changes to the layout were made during this time period. In January 2015, fruit and vegetables were moved from the back of the store, furthest from the entrance, to the aisle closest to the entrance and an entrance-facing display increasing their accessibility. In April 2016, the entrance-facing display of fruit and vegetables was replaced with a chiller cabinet so that fruit and vegetables remained more accessible than during the baseline period, but less accessible than in the period immediately previously. A retrospective interrupted time series analysis using dynamic regression was used to model the data and to examine the effect of the store re-arrangements on purchasing. All analyses were carried out both for sales-by-quantity and for sales-by-money. RESULTS: The first shop re-arrangement which made fruit and vegetables more prominent, increased the percentage of total sales that were fruit and vegetables, when analysed by either items purchased or money spent. The second rearrangement also had a positive effect on the percentage of total sales that were fruit and vegetables compared to baseline, however this was not significant at the 5% level. Over the five year period, the percentage of sales that were fruit and vegetables declined both in terms of items purchased, and money spent. CONCLUSIONS: Increasing accessibility of fruit and vegetables in a grocery store is a feasible way to improve the diet of students in tertiary education. There is evidence of declining fruit and vegetable consumption among the studied population, which should be further investigated.

Association of a Surgical Task During Training With Team Skill Acquisition Among Surgical Residents: The Missing Piece in Multidisciplinary Team Training.

IMPORTANCE: The human patient simulators that are currently used in multidisciplinary operating room team training scenarios cannot simulate surgical tasks because they lack a realistic surgical anatomy. Thus, they eliminate the surgeon's primary task in the operating room. The surgical trainee is presented with a significant barrier when he or she attempts to suspend disbelief and engage in the scenario. OBJECTIVE: To develop and test a simulation-based operating room team training strategy that challenges the communication abilities and teamwork competencies of surgeons while they are engaged in realistic operative maneuvers. DESIGN, SETTING, AND PARTICIPANTS: This pre-post educational intervention pilot study compared the gains in teamwork skills for midlevel surgical residents at Wake Forest Baptist Medical Center after they participated in a standardized multidisciplinary team training scenario with 3 possible levels of surgical realism: (1) SimMan (Laerdal) (control group, no surgical anatomy); (2) "synthetic anatomy for surgical tasks" mannequin (medium-fidelity anatomy), and (3) a patient simulated by a deceased donor (high-fidelity anatomy). INTERVENTIONS: Participation in the simulation scenario and the subsequent debriefing. MAIN OUTCOMES AND MEASURES: Teamwork competency was assessed using several instruments with extensive validity evidence, including the Nontechnical Skills assessment, the Trauma Management Skills scoring system, the Crisis Resource Management checklist, and a self-efficacy survey instrument. Participant satisfaction was assessed with a Likert-scale questionnaire. RESULTS: Scenario participants included midlevel surgical residents, anesthesia providers, scrub nurses, and circulating nurses. Statistical models showed that surgical residents exposed to medium-fidelity simulation (synthetic anatomy for surgical tasks) team training scenarios demonstrated greater gains in teamwork skills compared with control groups (SimMan) (Nontechnical Skills video score: 95% CI, 1.06-16.41; Trauma Management Skills video score: 95% CI, 0.61-2.90) and equivalent gains in teamwork skills compared with high-fidelity simulations (deceased donor) (Nontechnical Skills video score: 95% CI, -8.51 to 6.71; Trauma Management Skills video score: 95% CI, -1.70 to 0.49). CONCLUSIONS AND RELEVANCE: Including a surgical task in operating room team training significantly enhanced the acquisition of teamwork skills among midlevel surgical residents. Incorporating relatively inexpensive, medium-fidelity synthetic anatomy in human patient simulators was as effective as using high-fidelity anatomies from deceased donors for promoting teamwork skills in this learning group.

Morphological and chemical changes of aerosolized E. coli treated with a dielectric barrier discharge.

This study presents the morphological and chemical modification of the cell structure of aerosolized Escherichia coli treated with a dielectric barrier discharge (DBD). Exposure to DBD results in severe oxidation of the bacteria, leading to the formation of hydroxyl groups and carbonyl groups and a significant reduction in amine functionalities and phosphate groups. Near edge x-ray absorption fine structure (NEXAFS) measurements confirm the presence of additional oxide bonds upon DBD treatment, suggesting oxidation of the outer layer of the cell wall. Electron microscopy images show that the bacteria undergo physical distortion to varying degrees, resulting in deformation of the bacterial structure. The electromagnetic field around the DBD coil causes severe damage to the cell structure, possibly resulting in leakage of vital cellular materials. The oxidation and chemical modification of the bacterial components are evident from the Fourier transform infrared spectroscopy and NEXAFS results. The bacterial reculture experiments confirm inactivation of airborne E. coli upon treating with DBD.

Little evidence for association between the TGFBR1*6A variant and colorectal cancer: a family-based association study on non-syndromic family members from Australia and Spain.

BACKGROUND: Genome-wide linkage studies have identified the 9q22 chromosomal region as linked with colorectal cancer (CRC) predisposition. A candidate gene in this region is transforming growth factor ß receptor 1 (TGFBR1). Investigation of TGFBR1 has focused on the common genetic variant rs11466445, a short exonic deletion of nine base pairs which results in truncation of a stretch of nine alanine residues to six alanine residues in the gene product. While the six alanine (*6A) allele has been reported to be associated with increased risk of CRC in some population based study groups this association remains the subject of robust debate. To date, reports have been limited to population-based case-control association studies, or case-control studies of CRC families selecting one affected individual per family. No study has yet taken advantage of all the genetic information provided by multiplex CRC families. METHODS: We have tested for an association between rs11466445 and risk of CRC using several family-based statistical tests in a new study group comprising members of non-syndromic high risk CRC families sourced from three familial cancer centres, two in Australia and one in Spain. RESULTS: We report a finding of a nominally significant result using the pedigree-based association test approach (PBAT; p = 0.028), while other family-based tests were non-significant, but with a p-value <; 0.10 in each instance. These other tests included the Generalised Disequilibrium Test (GDT; p = 0.085), parent of origin GDT Generalised Disequilibrium Test (GDT-PO; p = 0.081) and empirical Family-Based Association Test (FBAT; p = 0.096, additive model). Related-person case-control testing using the "More Powerful" Quasi-Likelihood Score Test did not provide any evidence for association (MQLS; p = 0.41). CONCLUSIONS: After conservatively taking into account considerations for multiple hypothesis testing, we find little evidence for an association between the TGFBR1*6A allele and CRC risk in these families. The weak support for an increase in risk in CRC predisposed families is in agreement with recent meta-analyses of case-control studies, which estimate only a modest increase in sporadic CRC risk among 6*A allele carriers.

Features predicting weight loss in overweight or obese participants in a web-based intervention: randomized trial.

BACKGROUND: Obesity remains a serious issue in many countries. Web-based programs offer good potential for delivery of weight loss programs. Yet, many Internet-delivered weight loss studies include support from medical or nutritional experts, and relatively little is known about purely web-based weight loss programs. OBJECTIVE: To determine whether supportive features and personalization in a 12-week web-based lifestyle intervention with no in-person professional contact affect retention and weight loss. METHODS: We assessed the effect of different features of a web-based weight loss intervention using a 12-week repeated-measures randomized parallel design. We developed 7 sites representing 3 functional groups. A national mass media promotion was used to attract overweight/obese Australian adults (based on body mass index [BMI] calculated from self-reported heights and weights). Eligible respondents (n = 8112) were randomly allocated to one of 3 functional groups: information-based (n = 183), supportive (n = 3994), or personalized-supportive (n = 3935). Both supportive sites included tools, such as a weight tracker, meal planner, and social networking platform. The personalized-supportive site included a meal planner that offered recommendations that were personalized using an algorithm based on a user's preferences for certain foods. Dietary and activity information were constant across sites, based on an existing and tested 12-week weight loss program (the Total Wellbeing Diet). Before and/or after the intervention, participants completed demographic (including self-reported weight), behavioral, and evaluation questionnaires online. Usage of the website and features was objectively recorded. All screening and data collection procedures were performed online with no face-to-face contact. RESULTS: Across all 3 groups, attrition was high at around 40% in the first week and 20% of the remaining participants each week. Retention was higher for the supportive sites compared to the information-based site only at week 12 (P = .01). The average number of days that each site was used varied significantly (P = .02) and was higher for the supportive site at 5.96 (SD 11.36) and personalized-supportive site at 5.50 (SD 10.35), relative to the information-based site at 3.43 (SD 4.28). In total, 435 participants provided a valid final weight at the 12-week follow-up. Intention-to-treat analyses (using multiple imputations) revealed that there were no statistically significant differences in weight loss between sites (P = .42). On average, participants lost 2.76% (SE 0.32%) of their initial body weight, with 23.7% (SE 3.7%) losing 5% or more of their initial weight. Within supportive conditions, the level of use of the online weight tracker was predictive of weight loss (model estimate = 0.34, P < .001). Age (model estimate = 0.04, P < .001) and initial BMI (model estimate = -0.03, P < .002) were associated with frequency of use of the weight tracker. CONCLUSIONS: Relative to a static control, inclusion of social networking features and personalized meal planning recommendations in a web-based weight loss program did not demonstrate additive effects for user weight loss or retention. These features did, however, increase the average number of days that a user engaged with the system. For users of the supportive websites, greater use of the weight tracker tool was associated with greater weight loss.

A simulation study to assess a variable selection method for selecting single nucleotide polymorphisms associated with disease.

In genome-wide association studies, where hundreds of thousands of single nucleotide polymorphisms (SNPs) are genotyped, the potential for false positives is high and methods for selecting models with only a few SNPs are required. Methods for variable selection giving sets of SNPs associated with disease have been developed, but are still less common than evaluation of individual SNPs one at a time. To assess the potential improvement available from multi-SNP approaches, we examined the performance of the software GeneRaVE as a variable selection method when applied to SNP data in case-control studies. The method was assessed via simulations, in which a haplotype identified by three SNPs was taken to be associated with the disease. Simulated data sets reflecting different levels and patterns of genetic association with the disease were generated. In order to have a baseline level of performance to assess the method against, we used a generalized linear model using only the three disease susceptibility SNPs to provide an upper bound on the possible performance of the selection methods. To investigate the advantage of using variable selection method as a multivariate method over a single SNP approach, we used chi-squared tests for each of the disease susceptibility (DS) SNPs with correction for multiple testing. Simulation results showed that GeneRaVE performed well and outperformed single SNP analysis using the chi-squared method in identifying disease-related SNPs. In application to a large dataset, it identified SNPs known to be associated with disease that were not identified by single SNP methods.

Continuous evolution of statistical estimators for optimal decision-making.

In many everyday situations, humans must make precise decisions in the presence of uncertain sensory information. For example, when asked to combine information from multiple sources we often assign greater weight to the more reliable information. It has been proposed that statistical-optimality often observed in human perception and decision-making requires that humans have access to the uncertainty of both their senses and their decisions. However, the mechanisms underlying the processes of uncertainty estimation remain largely unexplored. In this paper we introduce a novel visual tracking experiment that requires subjects to continuously report their evolving perception of the mean and uncertainty of noisy visual cues over time. We show that subjects accumulate sensory information over the course of a trial to form a continuous estimate of the mean, hindered only by natural kinematic constraints (sensorimotor latency etc.). Furthermore, subjects have access to a measure of their continuous objective uncertainty, rapidly acquired from sensory information available within a trial, but limited by natural kinematic constraints and a conservative margin for error. Our results provide the first direct evidence of the continuous mean and uncertainty estimation mechanisms in humans that may underlie optimal decision making.

Evidence of linkage to chromosomes 10p15.3-p15.1, 14q24.3-q31.1 and 9q33.3-q34.3 in non-syndromic colorectal cancer families.

Up to 25% of colorectal cancer (CRC) may be caused by inherited genetic variants that have yet to be identified. Previous genome-wide linkage studies (GWLSs) have identified a new loci postulated to contain novel CRC risk genes amongst affected families carrying no identifiable mutations in any of the known susceptibility genes for familial CRC syndromes. To undertake a new GWLS, we recruited members from 54 non-syndromic families from Australia and Spain where at least two first-degree relatives were affected by CRC. We used single-nucleotide polymorphism arrays to genotype 98 concordant affected relative pairs that were informative for linkage analyses. We tested for genome-wide significance (GWS) for linkage to CRC using a quantile statistic method, and we found that GWS was achieved at the 5% level. Independently, using the PSEUDO gene-dropping algorithm, we also found that GWS for linkage to CRC was achieved (P=0.02). Merlin non-parametric linkage analysis revealed significant linkage to CRC for chromosomal region 10p15.3-p15.1 and suggestive linkage to CRC for regions on 14q and 9q. The 10p15.3-p15.1 has not been reported to be linked to hereditary CRC in previous linkage studies, but this region does harbour the Kruppel-like factor 6 (KLF6) gene that is known to be altered in common CRC. Further studies aimed at localising the responsible genes, and characterising their function will give insight into the factors responsible for susceptibility in such families, and perhaps shed further light on the mechanisms of CRC development.

The role of feed-forward and feedback processes for closed-loop prosthesis control.

BACKGROUND: It is widely believed that both feed-forward and feed-back mechanisms are required for successful object manipulation. Open-loop upper-limb prosthesis wearers receive no tactile feedback, which may be the cause of their limited dexterity and compromised grip force control. In this paper we ask whether observed prosthesis control impairments are due to lack of feedback or due to inadequate feed-forward control. METHODS: Healthy subjects were fitted with a closed-loop robotic hand and instructed to grasp and lift objects of different weights as we recorded trajectories and force profiles. We conducted three experiments under different feed-forward and feed-back configurations to elucidate the role of tactile feedback (i) in ideal conditions, (ii) under sensory deprivation, and (iii) under feed-forward uncertainty. RESULTS: (i) We found that subjects formed economical grasps in ideal conditions. (ii) To our surprise, this ability was preserved even when visual and tactile feedback were removed. (iii) When we introduced uncertainty into the hand controller performance degraded significantly in the absence of either visual or tactile feedback. Greatest performance was achieved when both sources of feedback were present. CONCLUSIONS: We have introduced a novel method to understand the cognitive processes underlying grasping and lifting. We have shown quantitatively that tactile feedback can significantly improve performance in the presence of feed-forward uncertainty. However, our results indicate that feed-forward and feed-back mechanisms serve complementary roles, suggesting that to improve on the state-of-the-art in prosthetic hands we must develop prostheses that empower users to correct for the inevitable uncertainty in their feed-forward control.

Butyrate esterified to starch is released in the human gastrointestinal tract.

BACKGROUND: Short-chain fatty acids (SCFAs) maintain human colonic function and may help prevent colonic disease. A study with ileostomists showed that starches acylated with specific SCFAs largely survive passage through the small intestine, but the percentage released in the colon has not been established. OBJECTIVE: The objective was to determine the percentage of ingested esterified butyrate released in the human gastrointestinal tract. DESIGN: The study was a randomized, crossover, controlled trial consisting of baseline and four 2-wk periods during which 16 volunteers consumed diets low in resistant starch plus 20 and 40 g cooked high-amylose maize starch (HAMS: HAMS20 or HAMS40) or butyrylated HAMS (HAMSB20 or HAMSB40) daily. HAMSB20 contained 31.8 mmol esterified butyrate. Complete 48-h fecal collections were made on days 2-3 and 12-13 of each period. RESULTS: Free fecal butyrate concentrations were higher after HAMSB40 than after HAMSB20 (P < 0.005) and HAMS (P < 0.0001) and higher than baseline data (P < 0.0001). Fecal esterified butyrate concentrations were highest in the HAMSB40 (days 12-13; P < 0.0001) group, and concentrations in the HAMSB40 (days 2-3) and HAMSB20 groups were higher than those in the HAMS groups and those at baseline (P < 0.0001). Ingestion of HAMSB20 and HAMSB40 resulted in the release of 26.8 ± 1.0 and 50.2 ± 2.4 mmol butyrate/d (days 12-13) (84.2 ± 3.0% and 79.0 ± 3.1% of total ingested esterified butyrate), respectively, in the gastrointestinal tract. By calculation, ∼57.2% of ingested esterified butyrate was released in the colon. Microbial analysis showed that this release was probably facilitated mainly by Parabacteroides distasonis, which increased in abundance with HAMSB40 (days 12-13) (P < 0.001). CONCLUSIONS: This study shows that cooked butyrylated starch delivers esterified butyrate to the human colon effectively and has the potential to improve human bowel health. This trial is registered in the Australian Clinical Trials Registry as ACTRN012606000398505.

The role of hippocampal subregions in memory for stimulus associations.

The hippocampus is hypothesised to be critical for episodic memory in humans and episodic-like memory in animals. Human data regarding the roles of the various subregional networks within the hippocampus is difficult to obtain. In this article we examine the current rodent literature on episodic-like memory and associative recognition and review the roles of the hippocampal subregions in these behavioural tasks. We focus on the large amount of recent data reporting roles for CA3 and CA1 in allocentric spatial and temporal associative memory respectively. Our own recent data are then presented detailing critical roles for CA3 and CA1 in an associative recognition task which does not require allocentric spatial or temporal processing. These data support more generic roles for CA3 and CA1 in episodic-like memory, based on anatomical and theoretical literature on hippocampal function. We also present a novel analysis of our data in which we suggest that the encoding of object, place and context information is unaffected by lesions of the hippocampus and therefore infer that it may be the storage or retrieval phase of this associative memory which is critically dependent on hippocampal function. In conclusion however, more specific anatomically and temporally controlled methods are needed to fully define the role of hippocampal subregions in episodic-like memory.

Regulation of epithelial apical junctions and barrier function by Galpha13.

The epithelial tight junction forms a barrier to paracellular solute movement. In this study we show that the heterotrimeric G-protein Galpha13 regulates the epithelial tight junction barrier. We generated MDCKII kidney epithelial cell lines in which the expression of an active Galpha13 mutant (Galpha13Q226L) could be induced. We demonstrated that Galpha13Q226L expression increased paracellular permeability and caused the disruption and redistribution of proteins comprising the tight junction and the adherens junction away from sites of cell contact and the appearance of basal stress fibers. The effects on the junctional proteins and the actin cytoskeleton were abrogated by the Rho kinase inhibitor Y27632 but not by the Src kinase inhibitor PP2. The Galpha13 mediated increase in permeability was also Src kinase independent but was partly dependent on Rho kinase signalling. Our data establish a link between Galpha13, Rho kinase signaling and epithelial barrier function and not only demonstrate that Galpha13 regulates epithelial apical junction properties but that it does so via signaling pathways that are distinct from the closely related protein Galpha12.

Assessing the potential usefulness of IGF-related peptides and adiponectin for predicting disease risk.

OBJECTIVE: Insulin-like growth factors (IGF), their binding proteins and adiponectin have been investigated as potential blood-based biomarkers for a variety of diseases. Before these circulating proteins can be considered as biomarkers, their variation within and between individuals and between published studies must be critically assessed. The purpose of this study was to use the D-value to predict the potential usefulness of IGF-related peptides and adiponectin as biomarkers for the diagnosis of colorectal cancer (CRC). DESIGN: Intra- and inter-individual variation of total IGF-I and -II, IGF binding protein 1 (IGFBP-1), -2 and -3 and adiponectin, was examined in 10 healthy subjects over a 5 week period. This data was analysed in conjunction with previous publications to provide a D-value, which is a theoretical value that identifies the usefulness of the analyte individually and as a panel, as a biomarker for CRC. RESULTS: A single measurement of total IGF-I and -II, and adiponectin provided a reproducible representation of their circulating concentrations. The D-value for total IGF-II and IGFBP-3 were 0.5 and 0.47, respectively, which corresponded to area under the curve (AUC) values of 64 and 63%. Combining these analytes into a panel only slightly improved the D-value to 0.63 (AUC was 67%). CONCLUSIONS: Although serum levels of total IGF-I, total IGF-II and IGFBP-3 are stable and reproducible, the D-value calculations indicate that they have limited importance when used as biomarkers of CRC.

Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference.

A simple method of inferring the genotyping error rate of SNP arrays and similar high-throughput genotyping methods from Mendelian errors is described. Application to genotypes from small families using the Affymetrix GeneChip Human Mapping 50 k Array indicates an error rate of about 0.1%, and this rate can be reduced by increasing the quality criterion for calls, though at the cost of a reduced genotype call rate, which limits the benefit available. Simulated data are used to show that the number of SNPs on this array is sufficient for such a low error rate to have little impact on identical by descent-based inference for disease linkage in sib-pair studies.

A range of simple summary genome-wide statistics for detecting genetic linkage using high density marker data.

A simple approach to design and analysis of genome-wide linkage scans is described, based on an approximation to the joint distribution of likelihood ratio statistics at a large number of single nucleotide polymorphism (SNP) loci. The approximation is readily calculated and makes it feasible to study the test properties of a range of summary statistics for the entire sequence of point-wise test values. Both the null distribution in the absence of genetic effects and the alternative distribution under various models of single or multi-gene inheritance can readily be simulated. This allows the power of a variety of statistics to be evaluated. The most powerful statistics proved to be the "quantile statistics" defined as quantiles of the set of pointwise test statistics. As a proof of principle study, the method was applied to a small dataset of 40 individuals from 8 families known to be segregating mutations in one or other of the DNA mismatch repair genes, MLH1 and MSH2. These included seven affected sib pairs and 11 discordant sib pairs, who were genotyped at 57,429 autosomal SNPs using the Affymetrix GeneChip Human Mapping 50 k Xba 240 Array. While the sample size was not sufficient to detect the linkage, there was a clear signal at the MLH1 location indicating that relatively small sample sizes would have been adequate to detect linkage to this gene.

A measure of the performance of biomarkers for disease.

The statistical properties required for effective biomarkers for disease are examined. It is shown that an "effectiveness parameter" D can be calculated that summarises the performance of a given biomarker and can distinguish between effective and ineffective biomarkers. D can be readily calculated from published summaries of biomarker levels and provides a simpler alternative to the commonly used "Area under the Curve" statistic. The impact of within-individual and between-individual variation in biomarker levels is also evaluated. An approach to the choice of sample size for experiments to estimate D is described.