Logistic Procedures Research Articles

Simulation study of instrumental variable approaches with an application to a study of the antidiabetic effect of bezafibrate

We studied the application of the generalized structural mean model (GSMM) of instrumental variable (IV) methods in estimating treatment odds ratios (ORs) for binary outcomes in pharmacoepidemiologic studies and evaluated the bias of GSMM compared to other IV methods. Because of the bias of standard IV methods, including two-stage predictor substitution (2SPS) and two-stage residual inclusion (2SRI) with binary outcomes, we implemented another IV approach based on the GSMM of Vansteelandt and Goetghebeur. We performed simulations under the principal stratification setting and evaluated whether GSMM provides approximately unbiased estimates of the causal OR and compared its bias and mean squared error to that of 2SPS and 2SRI. We then applied different IV methods to a study comparing bezafibrate versus other fibrates on the risk of diabetes. Our simulations showed that unlike the standard logistic, 2SPS, and 2SRI procedures, our implementation of GSMM provides an approximately unbiased estimate of the causal OR even under unmeasured confounding. However, for the effect of bezafibrate versus other fibrates on the risk of diabetes, the GSMM and two-stage approaches yielded similarly attenuated and statistically non-significant OR estimates. The attenuation of the OR by the two-stage and GSMM IV approaches suggests unmeasured confounding, although violations of the IV assumptions or differences in the parameters estimated could be playing a role. The GSMM IV approach provides approximately unbiased adjustment for unmeasured confounding on binary outcomes when a valid IV is available.

79 THE TRUE RISK OF BLOOD TRANSFUSION AFTER NEPHRECTOMY FOR RENAL MASSES

You have accessJournal of UrologyGeneral & Epidemiological Trends & Socioeconomics: Evidence-based Medicine & Outcomes II1 Apr 201279 THE TRUE RISK OF BLOOD TRANSFUSION AFTER NEPHRECTOMY FOR RENAL MASSES Gino Vricella, Antonio Finelli, Shabbir Alibhai, Lee Ponsky, Rabii Madi, and Robert Abouassaly Gino VricellaGino Vricella Cleveland, OH More articles by this author , Antonio FinelliAntonio Finelli Toronto, Canada More articles by this author , Shabbir AlibhaiShabbir Alibhai Toronto, Canada More articles by this author , Lee PonskyLee Ponsky Cleveland, OH More articles by this author , Rabii MadiRabii Madi Cleveland, OH More articles by this author , and Robert AbouassalyRobert Abouassaly Cleveland, OH More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2012.02.125AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Perioperative blood transfusions are costly and have attendant risks and safety concerns. Reported blood transfusion rates after nephrectomy (radical and partial) demonstrate considerable variability, likely due to the referral patterns and selection biases that influence reports from tertiary academic centers. To our knowledge, the transfusion rate in general practice has not been previously reported. The aim of our study was to examine the actual transfusion rate and risk factors for blood transfusion after nephrectomy for renal masses on a population-level. METHODS We performed a population-based, retrospective observational study using a national discharge abstract database. Our cohort consisted of 10,902 patients treated by radical (RN) or partial nephrectomy (PN) for a renal mass between April 1, 2003 and March 31, 2008. Patient demographics and treatment approach (i.e. open vs. laparoscopic) were available for all patients. Surgeon and institution volume quartiles for kidney surgery were created. Adjustment for comorbidity was performed using the Charlson-Deyo Index. The association between blood transfusion and various explanatory variables was examined using the Chi-square test, as well as with multivariable logistic regression. RESULTS The overall blood transfusion rate for patients in our study was 18.1%. Transfusions occurred after 28.2%, 12.7%, 9.2% and 8.6% of open RN, open PN, laparoscopic RN and laparoscopic PN, respectively (p<.0001). Transfusion rate was found to be strongly associated with age and comorbidity, such that patients <50 years old and having Charlson scores of 0 were transfused 11.2% and 14.5% of the time, compared with 28.2% and 40.7% in patients ≥80 years old and with Charlson scores of ≥3, respectively (p<.0001). On multivariable logistic regression, age (p<.0001), Charlson score (p<.0001), procedure type (p<.0001), surgeon (p<.0001) and hospital volume quartile (p<.0001) were found to be associated with the rate of blood transfusions, whereas year of surgery, gender and income quintile were not. CONCLUSIONS The transfusion rate after nephrectomy in general clinical practice is higher than that reported in the urologic literature. Patient and provider factors appear to contribute to the considerable variability that exists in the observed transfusion rate. A more detailed understanding of these factors may help in preoperative patient counseling and informed consent. © 2012 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 187Issue 4SApril 2012Page: e33-e34 Peer Review Report Advertisement Copyright & Permissions© 2012 by American Urological Association Education and Research, Inc.MetricsAuthor Information Gino Vricella Cleveland, OH More articles by this author Antonio Finelli Toronto, Canada More articles by this author Shabbir Alibhai Toronto, Canada More articles by this author Lee Ponsky Cleveland, OH More articles by this author Rabii Madi Cleveland, OH More articles by this author Robert Abouassaly Cleveland, OH More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

IT enabled logistics procedure redesign for high value pharmaceutical shipments

PurposeThe purpose of this paper is to introduce a method for (re)designing complex logistics networks, which interact with various governmental bodies (e.g. in FDA and USDA) for regulatory clearance and control purpose. The method (the e3‐control methodology) is demonstrated to be a useful approach to analyzing and redesigning international logistics procedures in reaction to a technological innovation in a government‐business (G2B) network.Design/methodology/approachAn action research method relying on Living Lab study was used in this research. To illustrate and better understand the application of the e3‐control methodology, the authors place the development of e3‐control as a design tool for deploying the pharmaceutical case. The authors collected data with multiple methods including workshops, semi‐structured interviews and document analysis.FindingsThe e3‐control methodology has been successfully applied in this paper to carry out a step‐by‐step redesign for an international pharmaceutical logistics network. It was found that a win‐win situation can be achieved if business and government see each other as partners and share the responsibility of carrying out government regulatory and Customs controls. In this situation, Customs administrations can be relieved from redundant control tasks, and businesses will be rewarded with simplified procedures.Originality/valueThe authors' e3‐control methodology is an innovative redesign methodology for analyzing and redesigning business logistic networks including government agencies. With this approach, one can achieve a clear overview on critical problems within the logistics chains; disclose unclear procedures and in the meanwhile take into consideration the different concerns of the partners within the network.

Relationship between cognition disorders and Claassen scale in patients with aneurysmal subarachnoid hemorrhage after endovascular treatment

Objective To study the relationship between Claassen scale,age of patients,anatomical location of aneurysms and the cognitive disorders in patients with aneurysmal subarachnoid hemorrhage (aSAH) after endovascular treatment.Methods 40 patients underwent endovascular coiling for aSAH were studied.The preoperative and postoperative course in all patients was uneventful.CT,cerebral angiography (CAG),neuropsychological examination (Wechsler adult intelligence scale,WAIS - R) were used for examination.Results After logistic procedure analysis,it was found that Claassen Scale was a risk factor for cognition disorders ( P ＜0.01 ).The level of Claassen Scale was negatively correlated with the score of total intelligence quotient ( r =- 0.398,P ＜ 0.01 ).According to anatomical location of aneurysms,there was no significantly statistical difference between the anterior communicating aneurysm (Acoa) group and non- Acoa group in total intelligence quotient,verbal intelligence quotient and performance intelligence quotient( P ＞0.05 ).Conclusions Despite good outcomes after aSAH,cognition disorders in patients are still common,suggesting that the common impairments of brain after treatment of ruptured aneurysms may be due to SAH itself.Claassen Scale may account for predictive value for cognition disorders. Key words: Endovascular procedures; Subarachnoid hemorrhage; Intracranial aneurysm; Cognition disorders; Claassen scale

Immediate List Recall as a Measure of Short-Term Episodic Memory: Insights from the Serial Position Effect and Item Response Theory

The serial position effect shows that two interrelated cognitive processes underlie immediate recall of a supraspan word list. The current study used item response theory (IRT) methods to determine whether the serial position effect poses a threat to the construct validity of immediate list recall as a measure of verbal episodic memory. Archival data were obtained from a national sample of 4,212 volunteers aged 28-84 in the Midlife Development in the United States study. Telephone assessment yielded item-level data for a single immediate recall trial of the Rey Auditory Verbal Learning Test (RAVLT). Two parameter logistic IRT procedures were used to estimate item parameters and the Q(1) statistic was used to evaluate item fit. A two-dimensional model better fit the data than a unidimensional model, supporting the notion that list recall is influenced by two underlying cognitive processes. IRT analyses revealed that 4 of the 15 RAVLT items (1, 12, 14, and 15) were misfit (p < .05). Item characteristic curves for items 14 and 15 decreased monotonically, implying an inverse relationship between the ability level and the probability of recall. Elimination of the four misfit items provided better fit to the data and met necessary IRT assumptions. Performance on a supraspan list learning test is influenced by multiple cognitive abilities; failure to account for the serial position of words decreases the construct validity of the test as a measure of episodic memory and may provide misleading results. IRT methods can ameliorate these problems and improve construct validity.

Sample size estimation for alternating logistic regressions analysis of multilevel randomized community trials of under-age drinking.

Under-age drinking is an enormous public health issue in the USA. Evidence that community level structures may impact on under-age drinking has led to a proliferation of efforts to change the environment surrounding the use of alcohol. Although the focus of these efforts is to reduce drinking by individual youths, environmental interventions are typically implemented at the community level with entire communities randomized to the same intervention condition. A distinct feature of these trials is the tendency of the behaviours of individuals residing in the same community to be more alike than that of others residing in different communities, which is herein called 'clustering'. Statistical analyses and sample size calculations must account for this clustering to avoid type I errors and to ensure an appropriately powered trial. Clustering itself may also be of scientific interest. We consider the alternating logistic regressions procedure within the population-averaged modelling framework to estimate the effect of a law enforcement intervention on the prevalence of under-age drinking behaviours while modelling the clustering at multiple levels, e.g. within communities and within neighbourhoods nested within communities, by using pairwise odds ratios. We then derive sample size formulae for estimating intervention effects when planning a post-test-only or repeated cross-sectional community-randomized trial using the alternating logistic regressions procedure.

Inflammatory Polymorphisms Link the Risk of Acute Chest Syndrome with Asthma in Adults with Sickle Cell Disease

Abstract 1072Acute chest syndrome (ACS) is a common cause of death among patients with sickle cell disease (SCD). There is increasing evidence that asthma may represent a significant risk factor for the development of ACS in children with SCD and it is associated with increased mortality (Newaskar, et al. 2010; Poulter, et al. 2011).The incidence of ACS in adolescent SCD patients is associated with the occurrence of asthma and genetic polymorphisms in NOS1 and NOS3 (Duckworth, et al. 2007). Polymorphisms in inflammatory genes, including IL-12A, IL-12B, and IL-4 receptor have been previously associated with the incidence and severity of asthma in non-SCD cohorts (Chen, et al. 2011; Mannino, et al. 2002; Caggana, et al. 1999). These data imply that the association of asthma with increased risk for ACS in adolescent SCD patients has a genetic component. However, the clinical and genetic associations among ACS, asthma, and inflammation have not been evaluated in adults with SCD. Our goals were (1) to identify clinical risk factors for ACS and (2) to identify single nucleotide polymorphisms (SNPs) in inflammatory genes associated with asthma and ACS in our population of adult SCD patients. All clinical data were collected using standardized report forms. Use of bronchodilators served as a surrogate for the occurrence of asthma. We analyzed 94 SNPs within 14 inflammatory genes in 675 DNA samples from SCD patients ascertained from Duke University, University of North Carolina-Chapel Hill, and Emory University. In order to achieve greater coverage in our genes of interest, SNP genotyping data was derived from two methods, Taqman genotyping assays from Applied Biosystems and genome-wide association studies (GWAS) using the Illumina-610 SNP array. Clinical and genetic associations with ACS and use of bronchodilators were examined using regression analysis (PROC LOGISTIC or GLM in SAS version 9.2, Cary, NC). The incidence of ACS in our population was 73%. Six percent of our population used bronchodilators, similar to the overall incidence of asthma in the US population (Newaskar et al., 2011). We observed a significant association between the use of bronchodilators and the incidence of ACS in our dataset, such that the percentage of patients with a history of ACS among bronchodilator users was 90% versus 73% in non-users (p=0.028). ACS was also associated with an increase in pain episodes (OR=1.6, p<0.0001), narcotics use (OR=1.5, p=0.0002), WBC counts (p=0.04), platelet counts (p=0.007), and higher mean hemoglobin (Hb) levels (p=0.003). ACS was also associated with decreased Hb F levels (p=0.05). After controlling for age, gender, and use of hydroxyurea, SNPs in IL-12A (rs568408; p=0.007), IL-12B (rs2195940; p=0.022), and IL-4R (rs3024537; p=0.049) were significantly associated with ACS. In addition, IL-12A (rs568408; p=0.037), IL-12B (rs2853694; p=0.009), and IL-4R (rs2283563; p=0.031) were significantly associated with the use of bronchodilators in our adult SCD cohort. None of the SNPs in IL=12B or IL-4R were found to be in linkage disequilibrium (LD) with each other. After multiple regression analysis, SNPs in IL-12A (rs568408; p=0.013), IL-12B (rs2195940; p=0.01), and IL-4R (rs3024537; p=0.02) remained significantly associated with ACS, and SNPs in IL-12A (rs568408; p=0.048), IL-12B (rs2853694; p=0.005), and IL-4R (rs2283563; p=0.01) remained significantly associated with use of bronchodilators. The functional significance of these SNPs is presently unknown. All of the polymorphisms are intronic except for rs568408, located in the 3’untranslated region of IL-12A. In summary, our findings in adult SCD patients support previous data in children demonstrating associations among inflammatory markers and asthma with the occurrence of ACS. Our data also support the association between asthma and increased risk of ACS. Finally, we have identified potential genetic risk factors for both asthma and ACS in adults with SCD. Our findings suggest that further investigation into the role of these inflammatory mediators in pulmonary dysfunction in SCD is warranted. Disclosures:No relevant conflicts of interest to declare.

Radical Relocation: Adapting Print Collections to an E-Centric World

With the advent of e-journal preservation projects and publisher digitization of journal backfiles, academic libraries have begun to move their corresponding print volumes of these titles to storage to avoid duplication and save space. This article examines the supporting justifications, outreach mechanisms, and logistical procedures undertaken at American University Library to relocate the entire bound journal collection to offsite storage in order to address severe physical space constraints and to support patron use of and preference for electronic journal content. In addition, the article presents preliminary data regarding the use of bound volumes sent to storage and an overall analysis of this transformational project.

Five-Year Trajectories of Long-Term Benzodiazepine Use by Adolescents: Patient, Provider, and Medication Factors

Five-Year Trajectories of Long-Term Benzodiazepine Use by Adolescents: Patient, Provider, and Medication Factors

Timed artificial insemination and early diagnosis of pregnancy to reduce breeding season in Nelore beef cows

The purpose of this study was conducted to evaluate the use of a system of timed artificial insemination (TAI) and early diagnosis of pregnancy in Nelore beef cows in order to reduce the breeding season (BS) from 150 to 90days and analyze the factors affecting the conception rate of cows selected for TAI. The study included 110 Nelore cows belonging to the Experimental Farm Capim Branco, Brazil. The body condition scores (BCS) were evaluated, and those above 2.50 were included in the TAI protocol. Five groups of cows were formed at intervals of 21days postpartum and then commenced a 9-day progesterone protocol. Progesterone devices were used three times. Statistical analysis of binary variables was performed by logistic regression in the program Proc Logistic of Sas. A 5% of significance (P < 0.05) was used to determine the presence of statistical differences and the effect of independent variables on conception rate. The TAI and early diagnosis of pregnancy reduces the BS from 150 to 90days without changing the pregnancy rate. The conception rate was not affected by the presence of the calf (P > 0.05), the corpus luteum (P > 0.05), the BCS (P > 0.05), or the number of reuses of the intravaginal progesterone device (P > 0.05). Therefore, this technique is beneficial for breeding Nelore beef cattle and can be used in anestrous cows with a BCS above 2.50. Additionally, the progesterone devices can be reused to reduce the cost of the protocol without compromising the results.

Characteristics and Factors Associated with the Risk of a Nicotine Exposed Pregnancy: Expanding the CHOICES Preconception Counseling Model to Tobacco

The preconception counseling model tested in the CDC funded Project CHOICES efficacy trial to reduce the risk of an alcohol-exposed pregnancy (AEP) could be extended to smokers to prevent a nicotine-exposed pregnancy (NEP), when pharmacotherapy can be provided safely and disclosure of these risk behaviors is more likely. The CHOICES model, which incorporates motivational interviewing, encourages reduction of AEP risk by decreasing risky drinking or using effective contraception; in the efficacy trial, most women chose both options. We conducted a secondary analysis of the CHOICES epidemiologic survey data (N = 2,672) (Project CHOICES Research Group in Am J Prev Med 23(3), 166-173, 2002) to identify the prevalence of risk of NEP and the factors associated with this risk using logistic regression modeling procedures. Conducted in six settings with women at risk for AEP, the percentage of AEP was 12.5% (333/2,672) among women of childbearing age (18-44). A total of 464 of the 2,672 (17.4%) were at risk for NEP. Among women at-risk of an unplanned pregnancy (n = 1,532), the co-occurrence of AEP and NEP risk was more prevalent (16.3%) than AEP risk alone (5.5%) or NEP risk alone (14.0%). In the multivariable model, statistically significant correlates for NEP risk included lifetime drug use, prior alcohol/drug treatment, drug use in the last 6 months, being married or living with a partner, having multiple sexual partners in the last 6 months, physical abuse in the last year, and lower levels of education. These findings suggest that preconception counseling for NEP could be combined with a program targeting AEP.

P2-S7.07 Adherence and difficulties with antiretroviral medication in an Australian sample of people living with HIV

BackgroundWhile combination antiretroviral therapy (cART) has revolutionised the course of HIV infection, a high level of adherence to cART is required to achieve the full mortality benefit. While a number...

Information supply issues in tourist transport in Nigeria: Role for logistics and information technology

This paper examines the role of logistics and information technology in tourists systems in Nigeria. Data used were collected through questionnaire. A structured questionnaire was administered to 30 randomly selected respondents at the Port Harcourt International Airport. Data were analysed using descriptive statistics. The findings reveal the various roles of information technology and logistics in tourists transport as being very vital to increasing customers’ satisfaction, patronage and also having good competitive advantage over others. It important that for any tourist transport organization to be in the business, there should be good information technology, adequate logistic procedure and other important condition that would improve the tourist satisfaction.

Significance of sleep problems in the diagnosis of depressive and anxiety disorders

To explore the significance of sleep problems in the diagnosis of depressive and anxiety disorders. A cross-sectional study was conducted through stratified convenient sampling in outpatients at our hospital from November 19, 2009 to January 19, 2010. A total of 203 outpatients (≥ 16 years old) were recruited from Department of Internal Medicine, Department of Surgery, Department of Obstetrics & Gynecology and other departments. Sleep Questionnaire was used as a screening tool for depressive and anxiety disorders. Composite international diagnostic interview (CIDI) was conducted by trained interviewers. According to diagnostic and statistical manual of mental disorders, Fourth Edition (DSM-IV) using the outcome from the logistic diagnostic procedure of CIDI as a golden standard for depressive and anxiety disorders, the validities of Sleep Questionnaire were calculated. According to the Sleep Questionnaire, the 12-month prevalence of any sleep problem was 31.0% (63/203). The Cronbach's α coefficient of the questionnaire was 0.764 and the area under the ROC (receiver operating characteristic) curve 0.741. With a cut-off point of 1, the sensitivity was 68.0% and the specificity 74.2% respectively. And it achieved the best composite diagnostic capacity. The positive predictive values were at least 27.0%. Sleep problem is a common complaint at a general hospital. When the duration and severity of sleep problem meet the standards of Sleep Questionnaire, a physician should be aware of possible depressive and anxiety disorders and more detailed information should be collected.

Multiclass Functional Discriminant Analysis and Its Application to Gesture Recognition

We consider applying a functional logistic discriminant procedure to the analysis of handwritten character data. Time-course trajectories corresponding to the X and Y coordinate values of handwritten characters written in the air with one finger are converted into a functional data set via regularized basis expansion. We then apply functional logistic modeling to classify the functions into several classes. In order to select the values of adjusted parameters involved in the functional logistic model, we derive a model selection criterion for evaluating models estimated by the method of regularization. Results indicate the effectiveness of our modeling strategy in terms of prediction accuracy.

Salmonella Control Measures with Special Focus on Vaccination and Logistic Slaughter Procedures

This study focussed on the effectiveness of Salmonella control measures to decrease Salmonella prevalence at slaughter. Considered measures were the control of hygiene and husbandry management as well as vaccination and logistic slaughter procedures. Results emphasized the capabilities of the farrowing stage to influence slaughter pig prevalence. Limited Salmonella entry by the implementation of hygiene control measures at farrowing farms obtained a significant decrease in prevalence after lairage at slaughterhouse. In contrast, hygiene control measures at finishing stage were less effective. Husbandry control measures, preventing physical contacts between pigs, were proved to decrease slaughter pig prevalence whether they were implemented at farrowing or finishing stage. Furthermore, the vaccination of sows and piglets was an appropriate control measure to decrease slaughter pig prevalence, if a large part of farms established this control measure. Simultaneous implementation of control measures showed that vaccination and especially hygiene measures are mutually supportive. Concerning logistic slaughter procedures it became obvious that with decreasing prevalence, infections at transport and lairage become more and more important. The herd status separation significantly decreased the percentage of infected pigs that became infected at lairage.

(A143) European Project SICMA (Simulation of Crisis Management Activities) for Medical Management of Maxi Emergency Trauma Patients

IntroductionModern emergencies and disasters are progressively changing from relatively simple, predictable events controllable with standard management solutions to complex critical situations for which managers and first responders require innovative and affordable tools.MethodsThe European Project SICMA (Simulation of Crisis Management Activities) provides a modeling of the behavior of the entire Health Service System during field emergency operations, as well as the rules it operates by. Use of simulation technologies offers a significant improvement on current management activities allowing decision makers to confront several organizational alternatives not only with static situations but with evolving scenarios.ResultsSICMA simulates main structural and behavioral elements of maxi emergency and mass casualties, from individual casualties and evolution of their health status, activity of the police force and fire brigade on the accident site, crowd dynamics, sanitary personnel expertise, to ambulance and helicopter transportation depending on traffic and weather conditions. The system also simulates rescue doctrines (i.e. “Casualty Clearing Station” or “Scoop and run”), transportation priorities according to color codes, doctrines for assignment of new casualty to neighboring hospitals, hospital resources and involvement, final clinical outcome of individual casualties. Patient health status and physiological reserve of single casualty is based on the ABCD ATLS system, considering with a simple algorithm both level of damage and rate of worsening in time.ConclusionUtilizing this simulation system, managers who predispose organizational and logistic procedures may modify the main elements in order to identify the optimal resource allocation and the best procedures to save the most human lives.

Gravelly soils that liquefied during 2008 Wenchuan, China earthquake, Ms=8.0

Field investigations following the 2008 Wenchuan earthquake ( M s =8.0) identified 118 liquefaction sites nearly all of which are underlain by gravelly sediment in the Chengdu Plain and adjacent Mianyang area. Field studies, including core drilling, dynamic penetration tests (DPT), and multiple channel analysis of surface wave velocity tests (MASW) for measurement of shear wave velocities, reveal the following: (1) Sand boils and ground fissures, indicative of liquefaction, occurred across hundreds of square kilometers affecting 120 villages, 8 schools and 5 factories. (2) The Chengdu plain is underlain by sandy gravels ranging in thickness up to 540 m; loose upper layers within the gravels beds liquefied. (3) Mean grain sizes for gravelly layers that liquefied range from 1 mm to more than 30 mm. (4) Shear wave velocities in gravels that liquefied range up to 250 m/s. (5) A 50% probability curve, developed from logistic procedures, correctly bounds all but four data points for the 47 compiled V s data.

Abstract 5607: Fine-mapping of GWAS loci in African American breast cancer cases and controls from the Black Women's Health Study

Abstract Genome-wide association studies in European and Asian ancestry populations have identified more than 10 SNPs associated with breast cancer, but to date there have been no reports from GWAS in African ancestry (AA) populations. We carried out fine-mapping of the associated loci in an AA population by genotyping a dense set of tagSNPs in each of 12 regions among 906 breast cancer cases and 1,111 controls from the Black Women's Health Study (BWHS). The BWHS is a prospective cohort study of 59,000 U.S. black women who have been followed since 1995; 50% of participants gave a saliva sample by the mouthwash-swish method. Controls were selected from among participants who had never reported breast cancer and were matched to cases on geographic region (Northeast, South, Midwest, West), and year of birth (plus or minus one year). Genotyping was carried out at the Broad Institute on the Sequenom iPLEX genotyping system. For each GWAS locus, we selected all tagSNPs with a minor allele frequency ≥ 5% and r2 ≥ 0.9 in the linkage disequilibrium (LD) block that contained the index SNP or, if a LD block was not evident, +/- 100 kb around the index SNP. We downloaded SNPs from the Hapmap Yoruba database (public release #26) and then selected tagSNPs using Tagger software implemented in the Haploview program version 4.1. We also selected the top 30 ancestral informative markers (AIMs) from a list of validated SNPs with allele frequency differences of at least 0.75 for Africans versus Europeans so that we could estimate and control for individual European admixture proportions An average reproducibility of 99.4% was obtained from 98 blinded duplicates and all SNPs showed concordance of &amp;gt;95%. Mean calling rate in the final data set for both SNPs and samples was 99.0%. We used PLINK software version 1.06 to calculate summary statistics and to perform Cochran-Armitage trend tests of association with breast cancer. Odds ratios and 95% confidence intervals were estimated with logistic regression implemented in the PROC LOGISTIC in SAS. ORs were adjusted for age, region of residence, birthplace (US, foreign country), and % European admixture. Only one of the 12 index GWAS SNPs was replicated in our sample and it has been reported separately. For six of the loci (including chr 8q24 and chr 2q35), other SNPs in the same LD block as the index SNP were significantly associated with breast cancer (empirical p for trend &amp;lt;0.05). Haplotypes of the index SNP and “best” SNP from these data were constructed. Results will be presented for breast cancer overall and by estrogen receptor status. The results indicate that many of the regions first identified in agnostic scans of European or Asian ancestry populations are also important for AA populations. In some instances, fine-scale mapping has helped to narrow the likely causal regions, as would be expected given the smaller LD blocks in AA persons. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5607. doi:10.1158/1538-7445.AM2011-5607

Diagnostics for matched case control studies : SAS macro for Proc Logistic

Conditional logistic regression models have been extensively used in the field of medicine and mainly applied in matched case control studies. However, none of the major statistical packages, i.e. SAS, MINITAB, SPSS provide diagnostics to assess the goodness-of-fit of these models. In addition the freely downloadable package R provides no functions for this purpose. The objectives of this study are to review the available diagnostics for software for testing goodness-of-fit of conditional logistic regression models by the development of a computer programme and to test this programme which implements some of the reviewed methods on real data. The computer programme is implemented using Visual Basic for Applications (VBA) for Microsoft Excel and connected to the Statistical Analysis Software (SAS) version 9.1 using the Object Linking and Embedding (OLE) automation. The software thus developed is tested on a matched case control study on endometrial cancer. A conditional logistic regression model is fitted to these data and the risk factors for endometrial cancer are identified. MINITAB and SPSS are incapable of doing conditional logistic regression. For testing goodness of the fitted model Proc Logistic in SAS is only capable of giving delta-beta plots which explain the influence of each observation on the parameters of the model. Besides, plots obtained from the developed computer programme, in addition provide information on stratum specific lack-of-fit statistics. These plots were very successful in identifying 3 outlying strata which were quite different from the other strata. In these 3 strata the case had not received estrogen whereas one or more control had received estrogen. Keywords: Conditional logistic regression, dynamic data exchange (DDE), goodness-of-fit, matched case control studies, Object Linking and Embedding (OLE) automation. Doi: 10.4038/jnsfsr.v39i1.2919 J.Natn.Sci.Foundation Sri Lanka 2011 39 (1): 13-23