Exact P-value Research Articles

Association of ADAMTS13 polymorphism with cerebral malaria

BackgroundCerebral malaria is one of the most severe manifestations of Plasmodium falciparum malaria. The sequestration of parasitized red blood cells (PRBCs) to brain microvascular endothelium has been shown to contribute to the pathophysiology of cerebral malaria. Recent studies reported increased levels of von Willebrand factor (VWF) and reduced activity of VWF-cleaving protease, ADAMTS13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13), in patients with cerebral malaria.MethodsAssociation of six single nucleotide polymorphisms (SNPs) of the ADAMTS13 gene with cerebral malaria was examined in 708 Thai patients with P. falciparum malaria.ResultsAmong six SNPs, the derived allele of a SNP located in intron 28, rs4962153-A, was significantly associated with protection against cerebral malaria when 115 cerebral malaria patients were compared with 367 mild malaria patients (Fisher's exact P-value = 0.0057; OR = 0.27; 95% CI = 0.096-0.76). Significant association was also detected between 115 cerebral malaria and 593 non-cerebral malaria (226 non-cerebral severe malaria and 367 mild malaria) patients (Fisher's exact P-value = 0.012; OR = 0.30; 95% CI = 0.11-0.83).ConclusionsExcessive adhesion of PRBCs to the platelet-decorated ultra-large VWF (ULVWF) appears to enhance the sequestration of PRBCs to cerebral microvascular endothelium. The genetic association observed in the present study implies that the regulation of platelet-decorated ULVWF strings by ADAMTS13 may play a role in the development of cerebral malaria.

The Role of Ret Genomic Variants in Infantile Hypertrophic Pyloric Stenosis

Infantile hypertrophic pyloric stenosis (IHPS) is a common childhood pathology affecting approximately 1-5 children pro 1000 newborns, with a genetic background as suggested by the familial occurrence. RET is a candidate gene for IHPS due to its role in the development of the intrinsic innervation and ganglia of the smooth musculature and the association of RET variants with another motility disorder (Hirschsprung's disease). Accordingly, we investigated RET-IHPS associations through sequencing of the complete RET coding region in 32 IHPS patients. Genotype frequencies were compared between patients and 48 controls using the Cochran-Armitage trend test or Fischer's test for exact p-values. We found 19 RET variants in IHPS, including polymorphisms in the promoter region (c.-200 G>A and c.-196 C>A). There was no statistically significant difference between the frequencies of the variants in both groups. There was no deviation from the Hardy-Weinberg equilibrium, yet a significant correlation (linkage disequilibrium) for variants in the promoter region, in exons 11, 13, 14 and 19 and in the 3' UTR. We conclude that RET variants are present in IHPS patients yet show no significant statistical association with the IHPS phenotype, suggesting at best an adjuvant role for RET in IHPS.

Hydroxyurea Dose and Toxicity in African American Patients with Sickle Cell Disease and Renal Impairment

Abstract 4844 Background:Hydroxyurea (HU) use in patients with sickle cell anemia is associated with a well established laboratory and clinical benefits by inducing fetal hemoglobin. The principal toxicity observed with HU is hematologic and it includes reversible and transient depression of white blood cells, platelets, and hemoglobin concentration. An initial HU dose of 15mg/kg/day is indicated in patients with normal renal function. Approximately 37% of an orally administered dose of HU is excreted by the kidneys in patients with normal renal function. This can be altered in patients with renal insufficiency and, based on recent pharmacokinetic data, a 50% dose reduction was proposed in patients with creatinine clearance (CrCl) less than 60 mL/min. The safety and the proper dosage of this agent in sickle cell patients with impaired renal function have not been well studied in the clinical setting. The purpose of our study was to evaluate HU dose and hematological toxicity in adult African American patients with sickle cell disease and impaired renal function. Methods:A retrospective study, approved by the institutional review board, was conducted in a tertiary care academic institution by reviewing the medical records of 250 adult African American patients with sickle cell disease. Patients who were on HU for at least one year were included in the study. The average HU dose (assumed to be the most effective and the least toxic) and the mean CrCl (calculated by using Cockcroft and Gault equation) over the last year were used in the analysis. Patients were considered to have renal insufficiency if their CrCl <60 mL/min. Patients on hemodialysis were excluded from the study. Hematological toxicity was defined by the presence of any of the following: absolute neutrophil count less than 2000/mm3, platelets count less than 80,000/mm3 or absolute reticulocyte count less than 80,000/mm3 (when the hemoglobin concentration is below 9 g/dL). Results:Among the 250 patients with sickle cell disease, we found 60 patients on HU for at least one year. Eight patients (13%) were found to have renal insufficiency (CrCl < 60 mL/min). The mean age in the renal insufficiency group was 51 years compared to 36 years in the normal renal function group. Table-1 shows different CrCl groups with their correspondence HU dose. The average HU dose in the renal insufficiency group was 10.9 mg/kg/day (656 mg/day) as compared to 20 mg/kg/day (1433mg/day) in the normal renal function group (table-2). Eleven patients (18%) developed hematological toxicity while on HU. The most common toxicity was neutropenia (7 patients) followed by reticulocytopenia (5 patients including one patient developed both toxicities). In patients with CrCl<60 mL/min only one patient (14%) developed hematological toxicity compared to 10 (19%) in patients with CrCl ≥ 60 mL/min (Fisher’s exact test P-value = 1) (table-2).Table-1CrCl (mL/min)Patients (No.)Average HU (mg/day)HU/Kg (mg/kg/day)Toxicity15-29175011.3030-59764310.9160-899119419.43≥9043148320.27Table-2CrCl (mL/min)Patients (No.)Average HU (mg/day)HU/Kg (mg/kg/day)Toxicity<60865610.91≥605214332010 Conclusion:Our data shows that around 55 % dose reduction in HU dose was needed and it was associated with a comparable hematological toxicity profile in adult African American patients with sickle cell disease and renal insufficiency compared to patients with normal kidney function. Patients with CrCl < 60 mL/min needed around 55% lower HU dose than patients with CrCl ≥ 60 mL/min. In addition to that, there was no statistically significant difference in HU hematological toxicity (P-value = 1) between the two groups. The above data correlates well with the pharmacokinetic data reported in the literature. Disclosures:No relevant conflicts of interest to declare.

Exact score distribution computation for ontological similarity searches.

BackgroundSemantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., finding functionally related proteins with the Gene Ontology or phenotypically similar diseases with the Human Phenotype Ontology (HPO). We have recently shown that the performance of semantic similarity searches can be improved by ranking results according to the probability of obtaining a given score at random rather than by the scores themselves. However, to date, there are no algorithms for computing the exact distribution of semantic similarity scores, which is necessary for computing the exact P-value of a given score.ResultsIn this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik's definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the HPO. It is shown that exact P-value calculation improves clinical diagnosis using the HPO compared to approaches based on sampling.ConclusionsThe new algorithm enables for the first time exact P-value calculation via exact score distribution computation for ontology similarity searches. The approach is applicable to any ontology for which the annotation-propagation rule holds and can improve any bioinformatic method that makes only use of the raw similarity scores. The algorithm was implemented in Java, supports any ontology in OBO format, and is available for non-commercial and academic usage under: https://compbio.charite.de/svn/hpo/trunk/src/tools/significance/

P-Value Precision and Reproducibility

P-values are useful statistical measures of evidence against a null hypothesis. In contrast to other statistical estimates, however, their sample-to-sample variability is usually not considered or estimated, and therefore not fully appreciated. Via a systematic study of log-scale p-value standard errors, bootstrap prediction bounds, and reproducibility probabilities for future replicate p-values, we show that p-values exhibit surprisingly large variability in typical data situations. In addition to providing context to discussions about the failure of statistical results to replicate, our findings shed light on the relative value of exact p-values vis-a-vis approximate p-values, and indicate that the use of *, **, and *** to denote levels 0.05, 0.01, and 0.001 of statistical significance in subject-matter journals is about the right level of precision for reporting p-values when judged by widely accepted rules for rounding statistical estimates.

Higher incidence of perineal community acquired MRSA infections among toddlers

BackgroundA six-fold increase in pediatric MRSA infections, prompted us to examine the clinical profile of children with MRSA infections seen at Mercy Children's Hospital, Toledo, Ohio and to characterize the responsible strains.MethodsRecords were reviewed of pediatric patients who cultured positive for MRSA from June 1 to December 31, 2007. Strain typing by pulsed field gel electrophoresis (PFT) and DiversiLab, SCCmec typing, and PCR-based lukSF-PV gene (encodes Panton-Valentine leukocidin), arginine catabolic mobile element (ACME) and cap5 gene detection was performed.ResultsChart review of 63 patients with MRSA infections revealed that 58(92%) were community acquired MRSA (CAMRSA). All CAMRSA were skin and soft tissue infections (SSTI). Twenty five (43%) patients were aged < 3 yrs, 19(33%) aged 4-12 and 14(24%) aged 13-18. Nineteen (76%) of those aged < 3 yrs had higher incidence of perineal infections compared to only 2(11%) of the 4-12 yrs and none of the 13-18 yrs of age. Infections in the extremities were more common in the older youth compared to the youngest children. Overall, there was a significant association between site of the infection and age group (Fisher's Exact p-value < 0.001). All CAMRSA were USA300 PFT, clindamycin susceptible, SCCmec type IVa and lukSF-PV gene positive. Nearly all contained ACME and about 80% were cap5 positive. Of the 58 USA300 strains by PFT, 55(95%) were also identified as USA300 via the automated repetitive sequence-based PCR method from DiversiLab.ConclusionsCAMRSA SSTI of the perineum was significantly more common among toddlers and that of the extremities in older children. The infecting strains were all USA300 PFT. Further studies are needed to identify the unique virulence and colonization characteristics of USA300 strains in these infections.

Effects of Acute Alkalosis and Acidosis on Performance

Ingestion of agents that modify blood buffering action may affect high-intensity performance. Here we present a meta-analysis of the effects of acute ingestion of three such agents - sodium bicarbonate, sodium citrate and ammonium chloride - on performance and related physiological variables (blood bicarbonate, pH and lactate). A literature search yielded 59 useable studies with 188 observations of performance effects. To perform the mixed-model meta-analysis, all performance effects were converted into a percentage change in mean power and were weighted using standard errors derived from exact p-values, confidence limits (CLs) or estimated errors of measurement. The fixed effects in the meta-analytic model included the number of performance-test bouts (linear), test duration (log linear), blinding (yes/no), competitive status (athlete/nonathlete) and sex (male/female). Dose expressed as buffering mmoL/kg/body mass (BM) was included as a strictly proportional linear effect interacted with all effects except blinding. Probabilistic inferences were derived with reference to thresholds for small and moderate effects on performance of 0.5% and 1.5%, respectively. Publication bias was reduced by excluding study estimates with a standard error >2.7%. The remaining 38 studies and 137 estimates for sodium bicarbonate produced a possibly moderate performance enhancement of 1.7% (90% CL ± 2.0%) with a typical dose of 3.5 mmoL/kg/BM (∼0.3 g/kg/BM) in a single 1-minute sprint, following blinded consumption by male athletes. In the 16 studies and 45 estimates for sodium citrate, a typical dose of 1.5 mmoL/kg/BM (∼0.5 g/kg/BM) had an unclear effect on performance of 0.0% (±1.3%), while the five studies and six estimates for ammonium chloride produced a possibly moderate impairment of 1.6% (±1.9%) with a typical dose of 5.5 mmoL/kg/BM (∼0.3 g/kg/BM). Study and subject characteristics had the following modifying small effects on the enhancement of performance with sodium bicarbonate: an increase of 0.5% (±0.6%) with a 1 mmoL/kg/BM increase in dose; an increase of 0.6% (±0.4%) with five extra sprint bouts; a reduction of 0.6% (±0.9%) for each 10-fold increase in test duration (e.g. 1-10 minutes); reductions of 1.1% (±1.1%) with nonathletes and 0.7% (±1.4%) with females. Unexplained variation in effects between research settings was typically ±1.2%. The only noteworthy effects involving physiological variables were a small correlation between performance and pre-exercise increase in blood bicarbonate with sodium bicarbonate ingestion, and a very large correlation between the increase in blood bicarbonate and time between sodium citrate ingestion and exercise. The approximate equal and opposite effects of sodium bicarbonate and ammonium chloride are consistent with direct performance effects of pH, but sodium citrate appears to have some additional metabolic inhibitory effect. Important future research includes studies of sodium citrate ingestion several hours before exercise and quantification of gastrointestinal symptoms with sodium bicarbonate and citrate. Although individual responses may vary, we recommend ingestion of 0.3-0.5 g/kg/BM sodium bicarbonate to improve mean power by 1.7% (±2.0%) in high-intensity races of short duration.

Effects of Acute Carbohydrate Supplementation on Endurance Performance

Research on the performance effects of acute carbohydrate supplementation is comprehensive. Here we present the first meta-analytic review of this research. Eighty-eight randomized crossover studies in which carbohydrate supplements were consumed with or without protein before and/or during exercise provided 155 estimates for performance effects in time-to-exhaustion tests or in time trials with or without a preload. For the mixed-model meta-analysis, all effects were converted into percentage changes in mean power in a non-preloaded time trial and weighted using percentage standard errors derived from exact p-values (in a minority of studies) or from estimated errors of measurement (in all other studies). Publication bias was assessed with a plot of t-values for the random-effect solutions versus standard errors. Probabilistic inferences were derived with reference to thresholds for small, moderate and large effects on performance of 0.5, 1.5 and 2.7%. Publication bias was reduced by excluding studies with a standard error >1.25%. In the remaining 73 studies and 122 estimates, the meta-analysed performance effects of carbohydrate supplements ranged from clear large improvements of ∼6% to clear moderate impairments of ∼2%. The best supplement inferred from the analysis consisted of a ∼3-10% carbohydrate-plus-protein drink providing ∼0.7 g/kg/h glucose polymers, ∼0.2 g/kg/h fructose and ∼0.2 g/kg/h protein. Substantial increases in the benefit of a supplement were probably small with an additional 9-hour fast and with the inclusion of ∼0.2 g/kg/h of protein, probably small to moderate with ingesting the first bolus not at the start of exercise but 1-4 hours before exercise, and possibly small with increasing the frequency of ingestion by three boluses per hour. Substantial reductions in the benefit of a supplement were possibly moderate with a supplement providing >0.25 g/kg/h fructose, and possibly small with an increase in ambient temperature of 10°C. The effect in subjects with maximal oxygen consumption higher by 10 mL/kg/min was probably trivial, and the effects of exercise duration were dependent on the concentration of carbohydrate plus protein in the supplement. The effect of including salt was unexpectedly trivial, and the effect of gender was unclear. Carbohydrate supplements with an appropriate composition and administration regimen can have large benefits on endurance performance. More research and better reporting are required to investigate the moderating effects of gender and salt.

Effect of gel‐instillation sonography on Doppler ultrasound findings in endometrial polyps

Saline infusion sonohysterography has been reported to suppress the color signal within the endometrium at color or power Doppler evaluation. The aim of this study was to evaluate if gel-instillation sonography (GIS) affects the power Doppler signal in patients with endometrial polyps. Ultrasound volumes of the uterus, obtained by three-dimensional ultrasound imaging of 25 women with histologically confirmed endometrial polyps, were assessed offline by six gynecologists with a special interest in gynecological ultrasound. Each woman contributed four volumes: one gray-scale volume and one power Doppler volume before GIS, and one gray-scale volume and one power Doppler volume at GIS. Power Doppler features before and after gel infusion were compared. At unenhanced ultrasound a pedicle artery was seen in 27-46% of cases, whereas, after gel infusion the examiners reported a pedicle artery in 30-46% of cases (Exact McNemar's test P-values ranged from 0.50 to 1.00). The level of agreement between unenhanced ultrasound and GIS ranged from 59 to 91% (Cohen's kappa values ranged from 0.17 to 0.79). There was no tendency for a pedicle artery to be identified less often at GIS than before gel instillation. Gel infusion does not affect the power Doppler signal in patients with endometrial polyps.

ANOTHER NUMERICAL METHOD OF FINDING CRITICAL VALUES FOR THE ANDREWS STABILITY TEST

We propose a method, alternative to that of Estrella (2003, Econometric Theory 19, 1128–1143), of obtaining exact asymptotic p-values and critical values for the popular Andrews (1993, Econometrica 61, 821–856) test for structural stability. The method is based on inverting an integral equation that determines the intensity of crossing a boundary by the asymptotic process underlying the test statistic. Further integration of the crossing intensity yields a p-value. The proposed method can potentially be applied to other stability tests that employ the supremum functional.

Evaluating the value of continuing docetaxel and prednisone (DP) beyond 10 cycles in men with metastatic castration-resistant prostate cancer (mCRPC).

4582 Background: The optimal number of cycles of 3-weekly DP therapy for mCRPC has not been ascertained. An exploratory analysis was conducted comparing results of 335 men on the DP arm of the TAX-327 study, which limited chemotherapy to 10 cycles, and a recently completed randomized clinical trial of 221 men allocated to either DP+AT-101 (bcl-2 inhibitor) versus DP+placebo, which allowed up to 17 cycles of DP. Methods: Patients who initiated cycle 10 of therapy without progression in both studies were included. Per protocol, men on the TAX-327 study received 1 additional cycle, while men on the AT-101 study received up to cycle 17. Men in both arms of the AT-101 study were combined for analysis, as no significant differences in outcomes were observed. Overall survival (OS) was estimated from the cycle 10 D infusion date, using the Kaplan-Meier method. Results: The number of men receiving cycle 10 cycle was similar (Fisher's exact test p-value=0.60) between the two studies (166 or 49.6% in the TAX-327 study versus 99 or 44.8% in the AT-101 study), though of these men, death date information was more complete due to longer follow-up in TAX-327 (79.5% versus 34.4%). Six- and 12-month estimated survival from cycle 10 was 92.2% (95% CI: 86.9-95.4%) and 74.6% (CI: 67.2-80.5%) for TAX-327 patients, compared with 92.8% (CI: 85.5-96.5) and 63.4% (CI: 51.8-72.9%) for those on AT-101. Survival statistics were similar beyond cycle 10 within good, intermediate and poor risk groups. 38 (38.4%) men on the AT-101 study completed all 17 cycles. Of men on the AT-101 study, 24 and 13 had consistently declining PSA through cycles 13 and 17. Conclusions: A survival benefit was not detected with more than 10 cycles of DP chemotherapy in men with mCRPC in this hypothesis-generating exploratory analysis. A subset of men with mCRPC continue to have declines in PSA up to cycle 17 and thus may have ongoing benefit to continued chemotherapy administration. However, a randomized clinical trial is necessary to establish the optimal duration of therapy.

Can air pollution affect tear film stability? a cross-sectional study in the aftermath of an explosion accident

BackgroundAfter an explosion and fire in two tanks containing contaminated oil and sulphur products in a Norwegian industrial harbour in 2007, the surrounding area was polluted. This caused an intense smell, lasting until the waste was removed two years later. The present study reports examinations of tear film break up time among the population. The examinations were carried out because many of the people in the area complained of sore eyes. The purpose of the study was to assess the relationship between living or working close to the polluted area and tear film stability one and a half years after the explosion.MethodsAll persons working or living in an area less than six kilometres from the explosion site were invited to take part in the study together with a similar number of persons matched for age and gender living more than 20 kilometres away. Three groups were established: workers in the explosion area and inhabitants near the explosion area (but not working there) were considered to have been exposed, and inhabitants far away (who did not work in the explosion area) were considered to be unexposed. A total of 734 people were examined, and the response rate was 76 percent. Tear film stability was studied by assessing non-invasive break-up time (NIBUT) using ocular microscopy. In addition Self-reported Break Up Time (SBUT) was assessed by recording the time the subject could keep his or hers eyes open without blinking when watching a fixed point on a wall. Background information was obtained using a questionnaire. Non-parametric Wilcoxon-Mann-Whitney-tests with exact p-values and multiple logistic regression analyses were performed.ResultsBoth NIBUT and SBUT were shorter among the male exposed workers than among the inhabitants both near and far away from the explosion area. This was also found for SBUT among males in a multiple logistic regression analysis, adjusting for age and smoking.ConclusionsReduced tear film stability was found among workers in an area where an explosion accident had occurred.

The 11-13+6 Weeks Scan: Where do We Stand? A 5-year Review at Fernandez Hospital

ABSTRACT Objective To examine the clinical utility of 11-13+6 weeks scan for screening for chromosomal abnormalities and to assess the potential value of the same ultrasound examination in the early diagnosis of fetal structural anomalies. Design A prospective interventional study at Fetal Medicine Unit, Fernandez Hospital Pvt Ltd, a tertiary care perinatal center, Hyderabad, India, between September 2005 and March 2010. Methods All pregnant women &lt; 13+6 weeks at booking are offered a routine obstetric scan between 11 and 13+6 weeks. All scans are done by obstetricians who are accredited by Fetal Medicine Foundation. All expectant mothers undergoing 11-13+6 weeks scan were included; all expectant mothers with antenatal booking after 14 weeks were excluded from the study. Results Between September 2005 and March 2010, a total of 11,012 scans were done between 11 and 13+6 weeks. Complete follow-up was available for 7,916 cases; 1,460 are ongoing pregnancies and 1,636 expectant mothers were lost to follow-up. The median maternal age in our population is 27 years and 340 (4.30%) mothers had advanced (&gt; 35 years) maternal age. The median NT in our population is 1.58 mm. Increased nuchal translucency (NT &gt; 95th percentile) was found in 362 (4.59%) scans. Miscarriages/abortions and termination of pregnancy were significantly higher in women whose fetus had an increased nuchal translucency thickness. Nuchal translucency thickness was significantly higher in women with advanced maternal age (ANOVA F = 0.002, Fishers exact test p-value for equality of medians = 0.04). Absent fetal nasal bones were present in 20 (5.57%) of women with increased NT compared to five (0.07%) women with normal NT. Among 7,916 women, 367 (4.64%) women were screen positive for chromosomal abnormalities. After counseling, only 40 screen-positive women accepted prenatal diagnostic procedures. Skull/brain abnormalities were found in 25 fetal images, abdominal abnormalities in 17, spinal abnormalities in eight, bladder abnormalities in five and cardiac abnormalities in five fetal images. Conclusion The 11-13+6 weeks ultrasound scan is an important diagnostic tool that should be offered to all pregnant women as a routine standard of antenatal care in the first trimester of pregnancy in India. However, as a screening tool, it mandates addition of cost-effective biochemical tests. To make the combined screening cost-effective, this study calls for making a national policy for Down's syndrome screening for India.

A Phase III Randomized Trial of Thalidomide (THAL) Plus Zoledronic Acid (ZLD) Versus Zoledronic Acid Alone In Patients with Early Stage Multiple Myeloma (MC0289)

AbstractAbstract 3053 Background:Patients with smoldering multiple myeloma (SMM) have a higher chance of progression to active MM than patients with monoclonal gammopathy of undetermined significance (MGUS). Since active MM remains incurable and since patients with SMM can have a long time to requiring treatment, observation remains an option for these patients. Bisphosphonates can prevent the bone complications of myeloma. The immunomodulatory (IMiD) drugs are well-tolerated and have documented anti-tumor activity in active MM. We hypothesized that treatment with the IMiD THAL and a bisphosphonate (ZLD) would prolong the time to progression (TTP) over the control arm of ZLD alone. This is the first report of this phase III trial of THAL/ZLD vs ZLD alone for patients with untreated SMM. Goals:The primary goal of this trial was to compare the TTP between patients treated with THAL/ZLD versus ZLD alone in asymptomatic MM. Secondary goals were progression rate at one year, response rate, duration of response, time to next therapy, and toxicity. Methods:Patients were required to have measurable disease as defined by either a serum monoclonal protein >1.0 g by protein electrophoresis or nephelometry or >200 mg of monoclonal protein in the urine on 24 hour electrophoresis or a measurable soft tissue plasmacytoma; >10% plasma cells as measured on the bone marrow aspirate, bone marrow biopsy, or labeling index; absolute neutrophil count >1500/μL; platelet count >100,000/μL; creatinine <2.0 mg/dL, and a performance status of 0, 1, or 2. Patients could not have symptomatic MM that required chemotherapy. The statistical plan was to accrue 120 eligible patients (60 per arm) over 4 years and after a minimum follow-up of 12 months the study would provide >90% power at a type I error rate of 0.05 to detect an increase in the median TTP from 12 months (ZLD) to 24 months (THAL/ZLD), and >80% power to detect an increase in median TTP from 12 to 21 months). Results:The study was activated in July 2003 and closed March 2009 due to slow accrual. Sixty-eight patients (35 Thal/ZLD; 33 ZLD) with a median age 63 years (range, 47–84) were randomized. The median TTP for Thal/ZLD versus ZLD was 2.4 years versus 1.2 years, respectively, P=0.02 one-sided log-rank. After adjusting for pre-specified stratification factors, the hazard ratio for TTP was 2.2 (one-sided p value = 0.01, univariate stratified Cox PH model) for ZLD compared to Thal/ZLD. 89% of patients on the Thal/ZLD arm were progression-free survival (PFS) at one year compared to 55% on ZLD alone (one-sided p<0.001, chi-square). Similar results were obtained (Table and Figures) when the CRAB (calcium, renal, anemia, bone) criteria were applied. Confirmed response was evaluated using the first 12 months of treatment. In the Thal/ZLD arm the response rate was 31% with a median duration of response of 5.1 years (95% CI: 1.9 - NA). There were no confirmed responses in the ZLD alone arm. The median overall survival has not been reached for either arm. In regards to toxicity, no grade 5 adverse events (AEs) have been reported. Thirty patients have reported grade 3+ AEs (17 Thal/ZLD; 13 ZLD, Fisher's exact p-value 0.47). Eight patients have reported grade 4 adverse events (5 Thal/ZLD; 3 ZLD, Fisher's exact p-value 0.71). Overall, only one grade 4 event was felt to be at least possibly related to study treatment – grade 4 neutropenia in Thal/ZLD. Conclusions:While the trial did not meet its planned accrual goals, there was a significant improvement in improved in outcomes in the Thal/ZLD arm compared to control (ZLD). Thal/ZLD produces anti-tumor responses that are quite durable with the median response duration of over 5 years. ZLD alone did not produce any anti-tumor responses. This study indicates that a non-chemotherapy approach can be effective in SMM and may be a useful strategy to test in future studies.Table:TTP & PFS Estimates for Protocol and CRAB Progression CriteriaCriteriaThal/ZLD (n=35)ZLD (n=33)p-value (unadjusted, log-rank, one-sided)p-value (adjusted for stratification factors using a univariate Cox model, one-sided)TTP Protocol2.4 years1.2 years0.020.01# of Events2124TTP CRAB4.1 years3.1 years0.030.02# of Events1520PFS Protocol2.4 years1.2 years0.020.005# of Events2325PFS CRAB3.8 years2.3 years0.030.008# of Events1822 [Display omitted] [Display omitted] Disclosures:Off Label Use: Thalidomide for smoldering myeloma. Lacy:Celgene: Research Funding. Dispenzieri:Celgene: Honoraria, Research Funding; Binding Site: Honoraria. Kumar:Celgene: Consultancy, Research Funding; Millennium: Research Funding; Merck: Consultancy, Research Funding; Novartis: Research Funding; Genzyme: Consultancy, Research Funding; Cephalon: Research Funding. Gertz:Celgene: Honoraria; Millennium: Honoraria.

Identification of A Pharmacogenomic Profile Associated with High Sensitivity and Low Toxicity to a Combination of Gemtuzumab Ozogamicin Plus Fludarabine, Cytarabine, Idarubicin Regimen In CD33-Positive Acute Myeloid Leukemia (AML) Patients

AbstractAbstract 967Human genome sequence variation, in the form of single nucleotide polymorphisms (SNPs) as well as more complex structural variation (such as insertions, duplications and deletions) in drug-metabolizing enzyme and transporter genes (DMETs), affects each individual's response to anticancer agents and thus the likelihood of experiencing an adverse drug reaction. Therefore, understanding relationships between genetic variation and differential drug responses is a challenge to improve both the safety and efficacy of drugs. Accordingly, in order to investigate a potential association between SNPs and clinical response and toxicity, we comprehensively assessed the allele frequencies of 1931 genetic variations of 225 absorption, distribution, metabolism and excretion genes in 59 AML patients younger than 65 years, using the new Affymetrix drug-metabolizing enzyme and transport (DMET Plus) genotyping platform (Affymetrix, Inc. Santa Clara, CA, USA). All patients were enrolled in a phase III multicenter clinical trial combining low dose of Gemtuzumab-ozogamicin (GO) with FLAI regimen (Fludarabine, Cytarabine, Idarubicin) as Induction chemotherapy i (eudract: 2007–005248-26; ClinicalTrials.gov NCT00909168). The induction regimen (GO-FLAI) included fludarabine (25 mg/sqm) and Ara-C (2 g/sqm) on days 1–5, idarubicin (10 mg/sqm) on days 1, 3, and 5 and GO (3 mg/sqm) on day 6. Hematopoietic stem cell transplant was planned for all high risk AML patients in first complete remission (CR) after consolidation with intermediate doses of Ara-C and idarubicin (ID-AC and IDA). Cytogenetic, multidrug-resistance phenotype, FLT3 and NPM mutation status, WT1 quantitative expression analyses, were performed at diagnosis in all patients. Furthermore, high-resolution SNP array analysis by GeneChip® Human Mapping 250K NspI and Genome-Wide Human SNP 6.0 (Affymetrix) was also performed. DNA processing and genotype identifications were performed according to the Affymetrix DMET platform's instructions. All statistical analyses were performed using the R package 2.11.1. Allele frequencies estimation and principal component analyses (PCAs) were performed using the adegenet library, whereas an ad hoc R function was developed to compute two-side Fisher's exact test p-values for each SNP in order to test their association with clinical response and toxicity.Results of potential interest were limited to those in which the p-value was <0.01. The median SNP call rate was 99.48% (range, from 98.05 – 100%). Two samples were run in duplicate and results with “passed call rate” were compared across all the 1931 polymorphic sites, showing a repeatability of 99.99%. In an initial screening procedure, we tested the association among SNPs and response to the induction cycle (FLAI + Gemtuzumab-Ozogamicin). We compared the genotyping profiling of 50 patients in complete (81%) and partial (5%) remission versus that of patients (14%) with no response finding out that 2 SNPs in the alcohol dehydrogenase enzyme (ADH1A) were highly associated with response to therapy. Since genetic polymorphisms may influence the toxicity of chemotherapy drugs, we stratified SNPs according to liver toxicity and 2 genes (SLC22A5 and ABCC4) were found to be associated with a grade I/II liver toxicity. Moreover, SNPs in SLC7A8 and SULT2B1 genes were found to be strongly associated (p <0.001) with fever to gemtuzumab-ozogamicin and finally SNPs in UGT2B15, CYP2B6 and PPARD (peroxisome proliferator-activated receptor delta) were found to be associated with a higher level of expression of P-glycoprotein (defined as a mean fluorescence index > 6). In conclusion, we performed an exploratory pharmacogenomic study that related SNPs in multidrug enzymes and transporters genes with the efficacy and toxicity of a combination of Gemtuzumab-ozogamicin (GO) with FLAI regimen used in a clinical trial of AML patients younger than 65 years. We identified for the first time a pharmacogenomic panel made up of 1 gene (ADH1A) associated with clinical outcome and 4 genes associated with toxicity. Findings obtained from this exploratory study are being tested in a larger clinical sample sets to confirm the predictive value of the SNP panel. Supported by European LeukemiaNet, AIL, AIRC, FIRB 2006, PRIN 2008, Ateneo RFO grants, Project of integreted program (PIO), Programma di Ricerca Regione – Università 2007 – 2009. Disclosures:Martinelli:Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Pfizer: Consultancy.

Evaluation of six CTLA-4 polymorphisms in high-risk melanoma patients receiving adjuvant interferon therapy in the He13A/98 multicenter trial

PurposeInterferon is approved for adjuvant treatment of patients with stage IIb/III melanoma. The toxicity and uncertainty regarding survival benefits of interferon have qualified its acceptance, despite significant durable relapse prevention in a fraction of patients. Predictive biomarkers that would enable selection of patients for therapy would have a large impact upon clinical practice. Specific CTLA-4 polymorphisms have previously shown an association with response to CTLA-4 blockade in patients with metastatic melanoma and the development of autoimmunity.Experimental design286 melanoma patients and 288 healthy controls were genotyped for six CTLA-4 polymorphisms previously suggested to be important (AG 49, CT 318, CT 60, JO 27, JO30 and JO 31). Specific allele frequencies were compared between the healthy and patient populations, as well as presence or absence of these in relation to recurrence. Alleles related to autoimmune disease were also investigated.ResultsNo significant differences were found between the distributions of CTLA-4 polymorphisms in the melanoma population compared with healthy controls. Relapse free survival (RFS) and overall survival (OS) did not differ significantly between patients with the alleles represented by these polymorphisms. No correlation between autoimmunity and specific alleles was shown. The six polymorphisms evaluated where strongly associated (Fisher's exact p-values < 0.001 for all associations) and significant linkage disequilibrium among these was indicated.ConclusionNo polymorphisms of CTLA-4 defined by the SNPs studied were correlated with improved RFS, OS, or autoimmunity in this high-risk group of melanoma patients.

Exact tests based on pre-estimation and second order pivotals: non-inferiority trials

Pre-estimation is a technique for adjusting a standard approximate P-value to be close to exact. While conceptually simple, it can become computationally intensive. Second order pivotals [N. Reid, Asymptotics and the theory of inference, Ann. Statist. 31 (2003), pp. 1695–1731] are constructed to be closer to exact than standard approximate pivotals. The theory behind these pivotals is complex, and their properties are unclear for discrete models. However, since they are typically given in closed form they are easy to compute. For the special case of non-inferiority trials, we investigate Wald, Score, likelihood ratio and second order pivotals. Each of the basic pivotals are used to generate an exact test by maximising with respect to the nuisance parameter. We also study the effect of pre-estimating the nuisance parameter, as described in Lloyd [C.J. Lloyd, Exact P-values for discrete models obtained by estimation and maximisation, Aust. N. Z. J. Statist. 50 (2008), pp. 329–346]. It appears that second order methods are not as close to exact as might have been hoped. On the other hand, P-values, based on pre-estimation are very close to exact, are more powerful than competitors and are hardly affected by the basic generating statistic chosen.

How to link call rate and p‐values for Hardy–Weinberg equilibrium as measures of genome‐wide SNP data quality

We study the link between two quality measures of SNP (single nucleotide polymorphism) data in genome-wide association (GWA) studies, that is, per SNP call rates (CR) and p-values for testing Hardy-Weinberg equilibrium (HWE). The aim is to improve these measures by applying methods based on realized randomized p-values, the false discovery rate and estimates for the proportion of false hypotheses. While exact non-randomized conditional p-values for testing HWE cannot be recommended for estimating the proportion of false hypotheses, their realized randomized counterparts should be used. P-values corresponding to the asymptotic unconditional chi-square test lead to reasonable estimates only if SNPs with low minor allele frequency are excluded. We provide an algorithm to compute the probability that SNPs violate HWE given the observed CR, which yields an improved measure of data quality. The proposed methods are applied to SNP data from the KORA (Cooperative Health Research in the Region of Augsburg, Southern Germany) 500 K project, a GWA study in a population-based sample genotyped by Affymetrix GeneChip 500 K arrays using the calling algorithm BRLMM 1.4.0. We show that all SNPs with CR = 100 per cent are nearly in perfect HWE which militates in favor of the population to meet the conditions required for HWE at least for these SNPs. Moreover, we show that the proportion of SNPs not being in HWE increases with decreasing CR. We conclude that using a single threshold for judging HWE p-values without taking the CR into account is problematic. Instead we recommend a stratified analysis with respect to CR.

The use and abuse of hypothesis tests: how to present P values

This overview highlights some of the key issues involved in performing and interpreting hypothesis tests. We describe the general approach taken in performing a hypothesis test with a focus on how to state the null and alternative hypothesis, and why two-sided tests are usually more appropriate than one-sided tests. We describe best practice techniques in performing and presenting the results of hypothesis tests. We recommend that, alongside any p-values, authors should also present estimates of the size of any treatment effects and their confidence intervals. Furthermore, they should specify the exact p-value rather than using terms such as 'NS' or the commonly used asterix notation. We discuss other pitfalls that are encountered at the analysis stage such as the use of repeated observations on individuals, the use of multiple tests on the data and the erroneous use of parametric tests when data are not normally distributed and vice versa. We highlight these points using two different examples: one looking at the use of compression stockings for preventing the occurrence of DVT on long-haul flights and a second hypothetical study comparing laser versus surgery techniques for the removal of varicose veins.

Soil arsenic surveys of New Orleans: localized hazards in children’s play areas

Arsenic (As) ranks first on the 2005 and 2007 hazardous substances priority lists compiled for the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). This study describes two New Orleans soil As surveys: (1) a survey of composite soil samples from 286 census tracts and (2) a field survey of soil As at 38 play areas associated with the presence of chromated-copper-arsenate (CCA)-treated wood on residential and public properties. The survey of metropolitan New Orleans soils revealed a median As content of 1.5mg/kg (range <0.2-16.4) and no distinctive differences between the soils of the city core and outlying areas. Play area accessible soils associated with CCA-treated wood (N=32) had a median As of 57mg/kg and 78% of the samples were ≥12mg/kg, the Louisiana soil As standard. The field survey of play areas for CCA-treated wood (N=132 samples at 38 sites) was conducted with a portable energy-dispersive X-ray fluorescence (XRF) analyzer. Seventy-five of 132 wood samples (56.8%) were deemed CCA-treated wood. Of the 38 play areas surveyed, 14 (36.8%) had CCA-treated wood. A significant association (Fisher's exact p-value=0.348×10(-6)) was found between CCA-treated wood and soil As (N=75). At one elementary school CCA-treated woodchips (As range 813-1,654mgAs/kg) covered the playgrounds. The situation in New Orleans probably exists in play areas across the nation. These findings support a precautionary program for testing soils and wood for hazardous substances at all play areas intended for children.