Prakash Gorroochurn - Academia.edu (original) (raw)

Papers by Prakash Gorroochurn

Research paper thumbnail of Androgen and c-Kit receptors in desmoplastic small round cell tumors resistant to chemotherapy: novel targets for therapy

Cancer Chemotherapy and Pharmacology, 2007

Purpose Desmoplastic small round cell tumor (DSRCT) is a highly fatal, mainly peritoneal cell ori... more Purpose Desmoplastic small round cell tumor (DSRCT) is a highly fatal, mainly peritoneal cell origin cancer which predominantly affects young adult males. This predilection in young males led us to examine the role of androgen receptors (AR), testosterone, and growth factors in the biology of DSRCT. Methods Slides were prepared from 27 multi-institutional patients all with end-stage DSRCT. Slides were stained for AR, c-Kit, various growth factors, and drug resistance-associated proteins. Immunohistochemical (IHC) expression was scored semi-quantitatively. Western blot and MTT studies were performed to validate the IHC findings of over-expression of the AR and its functional status by stimulation of growth by dihydrotestosterone, respectively. Six patients with positive AR status were treated solely with combined androgen blockade (CAB) as used for prostate cancer. Results Twenty-two patients were male (81%) and five were female (19%) with a median age at diagnosis of 23. All patients had failed at least two prior multi-agent chemotherapy regimens and 44% had progressed after autologous stem cell transplant. DSRCT samples from 10 of 27 patients were ≥2+ IHC positive for AR (37%,P = 0.0045) and 7 of 20 patients were ≥2+ IHC positive for c-Kit (35%, P = 0.018). We found elevated IHC expression of GST-pi, MRP and thymidylate synthase in smaller subsets of patients. In vitro studies for AR by Western blot and stimulation of growth by dihydrotestosterone in MTT assays suggest that the AR in DSRCT cells is functional. Six patients with positive AR status were treated with CAB alone and three of six attained clinical benefit (1-PR, 1-MR, 1-SD) in a range of 3–4 months. The three patients who responded to CAB had normal testosterone levels before CAB, while the three who did not respond to CAB had baseline castrate levels of testosterone. Conclusions DSRCT has significant IHC expression of AR and c-Kit in heavily pre-treated patients. The presence of significant AR expression in 37% suggests that these patients could possibly respond to CAB. The significance of c-Kit expression in 35% of DSRCT patients is unknown and warrants further investigation.

Research paper thumbnail of Relationship Between Medication Adherence and Treatment Outcomes: The COMBINE Study

Alcoholism-clinical and Experimental Research, 2008

Background: Within the alcoholism field, there is mounting evidence supporting an important rela... more Background: Within the alcoholism field, there is mounting evidence supporting an important relationship between medication adherence and drinking outcomes. Little is known however, about the complex relationships between medication and treatment variables and drinking outcomes. The present paper reports on the differential impact of medication adherence and treatment factors on drinking outcomes. Data derived from the COMBINE Study was used to investigate the interrelationships between medication adherence, combination treatments and drinking outcomes.Methods: Twelve hundred and twenty-six patients were randomized to 1 of 8 different combination treatments involving 2 medications—naltrexone and acamprosate and placebo, and 2 behavioral treatments—medical management (MM) and combined behavioral intervention (CBI). Two primary drinking outcomes were percent days abstinent (PDA) and time to first heavy drinking day. Medication adherence was defined as a proportion that reflects the number of pills taken by the maximum number of pills expected to be taken over the course of the trial. A generalized linear mixed model was used to estimate the effects of adherence on PDA while proportional hazards model was used to examine similar co-variate effects on time to first heavy drinking day.Results: Concerning time to first heavy drinking day, a significant three-way interaction was found between medication adherence, CBI and naltrexone (p = 0.0160). Within the MM only plus placebo group (no CBI), significant differences were found in “recovery” (i.e., no heavy drinking days) rates between adherers and nonadherers (40% vs. 10%, p < 0.0001). Such differences became nonsignificant (p = 0.12) when CBI was introduced into the relationship. CBI did not add any such advantage to naltrexone-treated patients.Conclusions: CBI might serve a protective function for nonadherers in the placebo group; the median relapse time was reduced when these nonadherers were exposed to the alcohol specialty intervention. CBI offered little additional benefit to nonadherers in the naltrexone group. Among nonadherers in the naltrexone group, relapse rates appear to be more a function of inadequate exposure to the active medication and less influenced by CBI.

Research paper thumbnail of Comments on: Review and Evaluation of Methods Correcting for Population Stratification with a Focus on Underlying Statistical Principles

Research paper thumbnail of The Effect of Inbreeding on the Distribution of Compound Heterozygotes: A Lesson from Lipase H Mutations in Autosomal Recessive Woolly Hair/Hypotrichosis

Human Heredity, 2009

phenotype in each of these families. DNA sequencing identified two distinct LIPH mutations (280_3... more phenotype in each of these families. DNA sequencing identified two distinct LIPH mutations (280_369dup90 and 659_ 660delTA). Each affected individual (n = 38) was either homozygous for one mutation (n = 7 and 16 respectively), or compound heterozygous (n = 15). A review of the literature identified several reports of compound heterozygotes in consanguineous families. Prompted by this finding, we derived the probability that a patient affected with a recessive disease is carrying two mutations at the disease locus. We suggest that the validity of the IBD assumption may be challenged in large consanguineous families.

Research paper thumbnail of An Improved Delta-Centralization Method for Population Stratification

Human Heredity, 2011

recently criticized our delta-centralization (DC) method of controlling for population stratifica... more recently criticized our delta-centralization (DC) method of controlling for population stratification (PS) and concluded that DC does not work. To explore our method, the authors simulated data under the Balding-Nichols (BN) model, which is more general than the model we had used in our simulations. They determined that the DC method underestimated the PS parameter ( ␦ ) and inflated the type I error rates when applied to BNsimulated data, and from this they concluded that the DC method is invalid. However, we argue that this conclusion is premature. In this paper, we (1) show why ␦ is underestimated and type I error rates are inflated when BN-simulated data are used, and (2) present a simple adjustment to DC that works reasonably well for data from both kinds of simulations. We also show that the adjusted DC method has appropriate power under a range of scenarios.

Research paper thumbnail of Estimating Allele Frequencies and Inbreeding Coefficients in K-Allele Models

Mathematical Population Studies, 2006

Research paper thumbnail of Effect of Population Stratification on Case-Control Association Studies

Human Heredity, 2004

There has been considerable debate in the literature concerning bias in case-control association ... more There has been considerable debate in the literature concerning bias in case-control association mapping studies due to population stratification. In this paper, we perform a theoretical analysis of the effects of population stratification by measuring the inflation in the test&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s type I error (or false-positive rate). Using a model of stratified sampling, we derive an exact expression for the type I error as a function of population parameters and sample size. We give necessary and sufficient conditions for the bias to vanish when there is no statistical association between disease and marker genotype in each of the subpopulations making up the total population. We also investigate the variation of bias with increasing subpopulations and show, both theoretically and by using simulations, that the bias can sometimes be quite substantial even with a very large number of subpopulations. In a companion simulation-based paper (Heiman et al., Part I, this issue), we have focused on the CRR (confounding risk ratio) and its relationship to the type I error in the case of two subpopulations, and have also quantified the magnitude of the type I error that can occur with relatively low CRR values.

Research paper thumbnail of NON-REPLICATION IN ASSOCIATION STUDIES: 'PSEUDO-FAILURES' TO REPLICATE

Research paper thumbnail of Evidence for a two-stage model of dependence using the NESARC and its implications for genetic association studies

Drug and Alcohol Dependence, 2008

Some twin studies suggest that substance initiation and dependence are part of a complex, two-sta... more Some twin studies suggest that substance initiation and dependence are part of a complex, two-stage process and that some genetic influences are stage-specific, acting on either the transition from abstinence to initiation, or on the transition from use to dependence. However, questions remain about the two-stage model, especially for illicit drugs. Using a familial aggregation design, we tested the hypothesized two-stage model of dependence on illicit substances and alcohol in a large, nationally representative sample. Family history of drug or alcohol problems is significantly associated with initiation that does not progress to dependence (i.e., conditional initiation). Furthermore, family history of drug or alcohol problems is significantly associated with dependence even after conditioning on factors influencing initiation (i.e., conditional dependence). These results suggest that substance initiation and dependence involve at least partially distinct familial factors. The possibility that different genetic factors affect initiation and dependence has important implications for control group selection in case-control genetic association studies, and may explain some inconsistent results for drug dependence. If some genetic factors are stage-specific (i.e., not common across initiation and dependence), inclusion of abstainers in the control group may mix the genetic effects for initiation with those for transition to dependence, providing unclear results. Depending on the specific question about the nature of the genetic effect (whether on initiation, on dependence, or both), investigators designing case-control genetic association studies should carefully consider inclusion and exclusion criteria of the control group.

Research paper thumbnail of Effect of Population Stratification on Case-Control Association Studies

Human Heredity, 2004

There has been considerable debate in the literature concerning bias in case-control association ... more There has been considerable debate in the literature concerning bias in case-control association mapping studies due to population stratification. In this paper, we perform a theoretical analysis of the effects of population stratification by measuring the inflation in the test&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s type I error (or false-positive rate). Using a model of stratified sampling, we derive an exact expression for the type I error as a function of population parameters and sample size. We give necessary and sufficient conditions for the bias to vanish when there is no statistical association between disease and marker genotype in each of the subpopulations making up the total population. We also investigate the variation of bias with increasing subpopulations and show, both theoretically and by using simulations, that the bias can sometimes be quite substantial even with a very large number of subpopulations. In a companion simulation-based paper (Heiman et al., Part I, this issue), we have focused on the CRR (confounding risk ratio) and its relationship to the type I error in the case of two subpopulations, and have also quantified the magnitude of the type I error that can occur with relatively low CRR values.

Research paper thumbnail of Comments on ‘Delta-Centralization Fails to Control for Population Stratification in Genetic Association Studies

Human Heredity, 2010

ABSTRACT No abstract available.

Research paper thumbnail of Can We Increase the Likelihood of Success for Future Association Studies in Epilepsy

Research paper thumbnail of Non-replication of association studies: ???pseudo-failures??? to replicate

Genetics in Medicine, 2007

Recently, serious doubts have been cast on the usefulness of association studies as a means to ge... more Recently, serious doubts have been cast on the usefulness of association studies as a means to genetically 'dissect' complex diseases, because most initial findings fail to replicate in subsequent studies. The reasons usually invoked are population stratification, genetic heterogeneity and inflated Type I errors. In this article, we argue that, even when these problems are addressed, the scientific community usually has unreasonably high expectations on replication success, based on initial low p-values -a phenomenon known as the 'replication fallacy.' We present a modified formula which gives the replication power of a second association study based on the p-value of an initial study. When both studies have similar sample sizes, this formula shows that: (i) A p-value only slightly less than the nominal α results in only about 50% replication power, (ii) very low p-values are required in order to achieve a replication power of least 80% (e.g., at α = .05, a p-value of less than .005 is required). Because many initially significant findings have low replication power, replication failure should not be surprising or be interpreted as necessarily refuting the initial findings. We refer to replication failures for which the replication power is low as 'pseudo-failures.'

Research paper thumbnail of Centralizing the non-central chi-square: a new method to correct for population stratification in genetic case-control association studies

Genetic Epidemiology, 2006

We present a new method, the δ-centralization (DC) method, to correct for population stratificati... more We present a new method, the δ-centralization (DC) method, to correct for population stratification (PS) in case-control association studies. DC works well even when there is a lot of confounding due to PS. The latter causes overdispersion in the usual chi-square statistics which then have non-central chi-square distributions. Other methods approach the non-centrality indirectly, but we deal with it directly, by estimating the non-centrality parameter τ itself. Specifically: (1) We define a quantity δ, a function of the relevant subpopulation parameters. We show that, for relatively large samples, δ exactly predicts the elevation of the false positive rate due to PS, when there is no true association between marker genotype and disease. (This quantity δ is quite different from Wright's FST and can be large even when FST is small.) (2) We show how to estimate δ, using a panel of unlinked “neutral” loci. (3) We then show that δ2 corresponds to τ the non-centrality parameter of the chi-square distribution. Thus, we can centralize the chi-square using our estimate of δ; this is the DC method. (4) We demonstrate, via computer simulations, that DC works well with as few as 25–30 unlinked markers, where the markers are chosen to have allele frequencies reasonably close (within ±.1) to those at the test locus. (5) We compare DC with genomic control and show that where as the latter becomes overconservative when there is considerable confounding due to PS (i.e. when δ is large), DC performs well for all values of δ. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc.

Research paper thumbnail of A Unified Approach for Quantifying, Testing and Correcting Population Stratification in Case-Control Association Studies

Human Heredity, 2007

The HapMap project has given case-control association studies a unique opportunity to uncover the... more The HapMap project has given case-control association studies a unique opportunity to uncover the genetic basis of complex diseases. However, persistent issues in such studies remain the proper quantification of, testing for, and correction for population stratification (PS). In this paper, we present the first unified paradigm that addresses all three fundamental issues within one statistical framework. Our unified approach makes use of an omnibus quantity ( ␦ ), which can be estimated in a case-control study from suitable null loci. We show how this estimated value can be used to quantify PS, to statistically test for PS, and to correct for PS, all in the context of case-control studies. Moreover, we provide guidelines for interpreting values of ␦ in association studies (e.g., at ␣ = 0.05, a ␦ of size 0.416 is small, a ␦ of size 0.653 is medium, and a ␦ of size 1.115 is large). A novel feature of our testing procedure is its ability to test for either strictly any PS or only 'practically important' PS. We also performed simulations to compare our correction procedure with Genomic Control (GC). Our results show that, unlike GC, it maintains good Type I error rates and power across all levels of PS.

Research paper thumbnail of Antiprostate cancer activity of a ß-carboline alkaloid enriched extract from Rauwolfia vomitoria

The tropical shrub, Rauwolfia vomitoria, is a medicinal plant used traditionally to treat a varie... more The tropical shrub, Rauwolfia vomitoria, is a medicinal plant used traditionally to treat a variety of ailments. A bioactive ß-carboline alkaloid, alstonine, present in this extract was previously shown to have anti-cancer activity against cancer cell lines. This study considers the potential anti-prostate cancer activity of this extract in vitro and in vivo. Rauwolfia vomitoria extract standardized for ß-carboline alkaloids was tested for ability to influence the growth and survival of the human LNCaP prostate cancer cell line. A WST-1 assay was used to measure cell growth, and cell cycle analyses were conducted with flow cytometry. Western blot detection of PARP cleavage and accumulation of cells containing sub-genomic DNA indicated induction of apoptosis. Pathway specific microarray analyses were utilized to identify the effect of Rauwolfia extract on the expression of 225 genes. Mice xenografted with LNCaP cells were treated with the extract or placebo control, and tumor growth was measured for 5 weeks. The effects of the extract on xenografted tumor cell proliferation and apoptosis were measured by in situ BrdU incorporation and TUNEL staining. Rauwolfia extract decreased in vitro cell growth in a dose-dependent manner (p<0.001) and induced the accumulation of G1 phase cells. PARP cleavage demonstrated that apoptosis was induced only at the highest concentration tested (500 μg/ml) which was confirmed by detection of cells containing sub-genomic DNA. The expression of genes associated with DNA damage signaling pathway was up-regulated by Rauwolfia treatment, including that of GADD153 and MDG. The expression of a few cell cycle genes (p21, cyclin D1 and E2F1) was also modulated. These alterations were confirmed by RT-PCR. Tumor volumes were decreased by 60%, 70% and 58% in the groups fed the 75, 37.5 or 7.5 mg/kg Rauwolfia, respectively (Kruskal-Wallis test, p<0.001). The Rauwolfia vomitoria extract significantly suppressed the growth and cell cycle progression of LNCaP cells, in vitro and in vivo.

Research paper thumbnail of Androgen and c-Kit receptors in desmoplastic small round cell tumors resistant to chemotherapy: novel targets for therapy

Cancer Chemotherapy and Pharmacology, 2007

Purpose Desmoplastic small round cell tumor (DSRCT) is a highly fatal, mainly peritoneal cell ori... more Purpose Desmoplastic small round cell tumor (DSRCT) is a highly fatal, mainly peritoneal cell origin cancer which predominantly affects young adult males. This predilection in young males led us to examine the role of androgen receptors (AR), testosterone, and growth factors in the biology of DSRCT. Methods Slides were prepared from 27 multi-institutional patients all with end-stage DSRCT. Slides were stained for AR, c-Kit, various growth factors, and drug resistance-associated proteins. Immunohistochemical (IHC) expression was scored semi-quantitatively. Western blot and MTT studies were performed to validate the IHC findings of over-expression of the AR and its functional status by stimulation of growth by dihydrotestosterone, respectively. Six patients with positive AR status were treated solely with combined androgen blockade (CAB) as used for prostate cancer. Results Twenty-two patients were male (81%) and five were female (19%) with a median age at diagnosis of 23. All patients had failed at least two prior multi-agent chemotherapy regimens and 44% had progressed after autologous stem cell transplant. DSRCT samples from 10 of 27 patients were ≥2+ IHC positive for AR (37%,P = 0.0045) and 7 of 20 patients were ≥2+ IHC positive for c-Kit (35%, P = 0.018). We found elevated IHC expression of GST-pi, MRP and thymidylate synthase in smaller subsets of patients. In vitro studies for AR by Western blot and stimulation of growth by dihydrotestosterone in MTT assays suggest that the AR in DSRCT cells is functional. Six patients with positive AR status were treated with CAB alone and three of six attained clinical benefit (1-PR, 1-MR, 1-SD) in a range of 3–4 months. The three patients who responded to CAB had normal testosterone levels before CAB, while the three who did not respond to CAB had baseline castrate levels of testosterone. Conclusions DSRCT has significant IHC expression of AR and c-Kit in heavily pre-treated patients. The presence of significant AR expression in 37% suggests that these patients could possibly respond to CAB. The significance of c-Kit expression in 35% of DSRCT patients is unknown and warrants further investigation.

Research paper thumbnail of Relationship Between Medication Adherence and Treatment Outcomes: The COMBINE Study

Alcoholism-clinical and Experimental Research, 2008

Background: Within the alcoholism field, there is mounting evidence supporting an important rela... more Background: Within the alcoholism field, there is mounting evidence supporting an important relationship between medication adherence and drinking outcomes. Little is known however, about the complex relationships between medication and treatment variables and drinking outcomes. The present paper reports on the differential impact of medication adherence and treatment factors on drinking outcomes. Data derived from the COMBINE Study was used to investigate the interrelationships between medication adherence, combination treatments and drinking outcomes.Methods: Twelve hundred and twenty-six patients were randomized to 1 of 8 different combination treatments involving 2 medications—naltrexone and acamprosate and placebo, and 2 behavioral treatments—medical management (MM) and combined behavioral intervention (CBI). Two primary drinking outcomes were percent days abstinent (PDA) and time to first heavy drinking day. Medication adherence was defined as a proportion that reflects the number of pills taken by the maximum number of pills expected to be taken over the course of the trial. A generalized linear mixed model was used to estimate the effects of adherence on PDA while proportional hazards model was used to examine similar co-variate effects on time to first heavy drinking day.Results: Concerning time to first heavy drinking day, a significant three-way interaction was found between medication adherence, CBI and naltrexone (p = 0.0160). Within the MM only plus placebo group (no CBI), significant differences were found in “recovery” (i.e., no heavy drinking days) rates between adherers and nonadherers (40% vs. 10%, p < 0.0001). Such differences became nonsignificant (p = 0.12) when CBI was introduced into the relationship. CBI did not add any such advantage to naltrexone-treated patients.Conclusions: CBI might serve a protective function for nonadherers in the placebo group; the median relapse time was reduced when these nonadherers were exposed to the alcohol specialty intervention. CBI offered little additional benefit to nonadherers in the naltrexone group. Among nonadherers in the naltrexone group, relapse rates appear to be more a function of inadequate exposure to the active medication and less influenced by CBI.

Research paper thumbnail of Comments on: Review and Evaluation of Methods Correcting for Population Stratification with a Focus on Underlying Statistical Principles

Research paper thumbnail of The Effect of Inbreeding on the Distribution of Compound Heterozygotes: A Lesson from Lipase H Mutations in Autosomal Recessive Woolly Hair/Hypotrichosis

Human Heredity, 2009

phenotype in each of these families. DNA sequencing identified two distinct LIPH mutations (280_3... more phenotype in each of these families. DNA sequencing identified two distinct LIPH mutations (280_369dup90 and 659_ 660delTA). Each affected individual (n = 38) was either homozygous for one mutation (n = 7 and 16 respectively), or compound heterozygous (n = 15). A review of the literature identified several reports of compound heterozygotes in consanguineous families. Prompted by this finding, we derived the probability that a patient affected with a recessive disease is carrying two mutations at the disease locus. We suggest that the validity of the IBD assumption may be challenged in large consanguineous families.

Research paper thumbnail of An Improved Delta-Centralization Method for Population Stratification

Human Heredity, 2011

recently criticized our delta-centralization (DC) method of controlling for population stratifica... more recently criticized our delta-centralization (DC) method of controlling for population stratification (PS) and concluded that DC does not work. To explore our method, the authors simulated data under the Balding-Nichols (BN) model, which is more general than the model we had used in our simulations. They determined that the DC method underestimated the PS parameter ( ␦ ) and inflated the type I error rates when applied to BNsimulated data, and from this they concluded that the DC method is invalid. However, we argue that this conclusion is premature. In this paper, we (1) show why ␦ is underestimated and type I error rates are inflated when BN-simulated data are used, and (2) present a simple adjustment to DC that works reasonably well for data from both kinds of simulations. We also show that the adjusted DC method has appropriate power under a range of scenarios.

Research paper thumbnail of Estimating Allele Frequencies and Inbreeding Coefficients in K-Allele Models

Mathematical Population Studies, 2006

Research paper thumbnail of Effect of Population Stratification on Case-Control Association Studies

Human Heredity, 2004

There has been considerable debate in the literature concerning bias in case-control association ... more There has been considerable debate in the literature concerning bias in case-control association mapping studies due to population stratification. In this paper, we perform a theoretical analysis of the effects of population stratification by measuring the inflation in the test&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s type I error (or false-positive rate). Using a model of stratified sampling, we derive an exact expression for the type I error as a function of population parameters and sample size. We give necessary and sufficient conditions for the bias to vanish when there is no statistical association between disease and marker genotype in each of the subpopulations making up the total population. We also investigate the variation of bias with increasing subpopulations and show, both theoretically and by using simulations, that the bias can sometimes be quite substantial even with a very large number of subpopulations. In a companion simulation-based paper (Heiman et al., Part I, this issue), we have focused on the CRR (confounding risk ratio) and its relationship to the type I error in the case of two subpopulations, and have also quantified the magnitude of the type I error that can occur with relatively low CRR values.

Research paper thumbnail of NON-REPLICATION IN ASSOCIATION STUDIES: 'PSEUDO-FAILURES' TO REPLICATE

Research paper thumbnail of Evidence for a two-stage model of dependence using the NESARC and its implications for genetic association studies

Drug and Alcohol Dependence, 2008

Some twin studies suggest that substance initiation and dependence are part of a complex, two-sta... more Some twin studies suggest that substance initiation and dependence are part of a complex, two-stage process and that some genetic influences are stage-specific, acting on either the transition from abstinence to initiation, or on the transition from use to dependence. However, questions remain about the two-stage model, especially for illicit drugs. Using a familial aggregation design, we tested the hypothesized two-stage model of dependence on illicit substances and alcohol in a large, nationally representative sample. Family history of drug or alcohol problems is significantly associated with initiation that does not progress to dependence (i.e., conditional initiation). Furthermore, family history of drug or alcohol problems is significantly associated with dependence even after conditioning on factors influencing initiation (i.e., conditional dependence). These results suggest that substance initiation and dependence involve at least partially distinct familial factors. The possibility that different genetic factors affect initiation and dependence has important implications for control group selection in case-control genetic association studies, and may explain some inconsistent results for drug dependence. If some genetic factors are stage-specific (i.e., not common across initiation and dependence), inclusion of abstainers in the control group may mix the genetic effects for initiation with those for transition to dependence, providing unclear results. Depending on the specific question about the nature of the genetic effect (whether on initiation, on dependence, or both), investigators designing case-control genetic association studies should carefully consider inclusion and exclusion criteria of the control group.

Research paper thumbnail of Effect of Population Stratification on Case-Control Association Studies

Human Heredity, 2004

There has been considerable debate in the literature concerning bias in case-control association ... more There has been considerable debate in the literature concerning bias in case-control association mapping studies due to population stratification. In this paper, we perform a theoretical analysis of the effects of population stratification by measuring the inflation in the test&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s type I error (or false-positive rate). Using a model of stratified sampling, we derive an exact expression for the type I error as a function of population parameters and sample size. We give necessary and sufficient conditions for the bias to vanish when there is no statistical association between disease and marker genotype in each of the subpopulations making up the total population. We also investigate the variation of bias with increasing subpopulations and show, both theoretically and by using simulations, that the bias can sometimes be quite substantial even with a very large number of subpopulations. In a companion simulation-based paper (Heiman et al., Part I, this issue), we have focused on the CRR (confounding risk ratio) and its relationship to the type I error in the case of two subpopulations, and have also quantified the magnitude of the type I error that can occur with relatively low CRR values.

Research paper thumbnail of Comments on ‘Delta-Centralization Fails to Control for Population Stratification in Genetic Association Studies

Human Heredity, 2010

ABSTRACT No abstract available.

Research paper thumbnail of Can We Increase the Likelihood of Success for Future Association Studies in Epilepsy

Research paper thumbnail of Non-replication of association studies: ???pseudo-failures??? to replicate

Genetics in Medicine, 2007

Recently, serious doubts have been cast on the usefulness of association studies as a means to ge... more Recently, serious doubts have been cast on the usefulness of association studies as a means to genetically 'dissect' complex diseases, because most initial findings fail to replicate in subsequent studies. The reasons usually invoked are population stratification, genetic heterogeneity and inflated Type I errors. In this article, we argue that, even when these problems are addressed, the scientific community usually has unreasonably high expectations on replication success, based on initial low p-values -a phenomenon known as the 'replication fallacy.' We present a modified formula which gives the replication power of a second association study based on the p-value of an initial study. When both studies have similar sample sizes, this formula shows that: (i) A p-value only slightly less than the nominal α results in only about 50% replication power, (ii) very low p-values are required in order to achieve a replication power of least 80% (e.g., at α = .05, a p-value of less than .005 is required). Because many initially significant findings have low replication power, replication failure should not be surprising or be interpreted as necessarily refuting the initial findings. We refer to replication failures for which the replication power is low as 'pseudo-failures.'

Research paper thumbnail of Centralizing the non-central chi-square: a new method to correct for population stratification in genetic case-control association studies

Genetic Epidemiology, 2006

We present a new method, the δ-centralization (DC) method, to correct for population stratificati... more We present a new method, the δ-centralization (DC) method, to correct for population stratification (PS) in case-control association studies. DC works well even when there is a lot of confounding due to PS. The latter causes overdispersion in the usual chi-square statistics which then have non-central chi-square distributions. Other methods approach the non-centrality indirectly, but we deal with it directly, by estimating the non-centrality parameter τ itself. Specifically: (1) We define a quantity δ, a function of the relevant subpopulation parameters. We show that, for relatively large samples, δ exactly predicts the elevation of the false positive rate due to PS, when there is no true association between marker genotype and disease. (This quantity δ is quite different from Wright's FST and can be large even when FST is small.) (2) We show how to estimate δ, using a panel of unlinked “neutral” loci. (3) We then show that δ2 corresponds to τ the non-centrality parameter of the chi-square distribution. Thus, we can centralize the chi-square using our estimate of δ; this is the DC method. (4) We demonstrate, via computer simulations, that DC works well with as few as 25–30 unlinked markers, where the markers are chosen to have allele frequencies reasonably close (within ±.1) to those at the test locus. (5) We compare DC with genomic control and show that where as the latter becomes overconservative when there is considerable confounding due to PS (i.e. when δ is large), DC performs well for all values of δ. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc.

Research paper thumbnail of A Unified Approach for Quantifying, Testing and Correcting Population Stratification in Case-Control Association Studies

Human Heredity, 2007

The HapMap project has given case-control association studies a unique opportunity to uncover the... more The HapMap project has given case-control association studies a unique opportunity to uncover the genetic basis of complex diseases. However, persistent issues in such studies remain the proper quantification of, testing for, and correction for population stratification (PS). In this paper, we present the first unified paradigm that addresses all three fundamental issues within one statistical framework. Our unified approach makes use of an omnibus quantity ( ␦ ), which can be estimated in a case-control study from suitable null loci. We show how this estimated value can be used to quantify PS, to statistically test for PS, and to correct for PS, all in the context of case-control studies. Moreover, we provide guidelines for interpreting values of ␦ in association studies (e.g., at ␣ = 0.05, a ␦ of size 0.416 is small, a ␦ of size 0.653 is medium, and a ␦ of size 1.115 is large). A novel feature of our testing procedure is its ability to test for either strictly any PS or only 'practically important' PS. We also performed simulations to compare our correction procedure with Genomic Control (GC). Our results show that, unlike GC, it maintains good Type I error rates and power across all levels of PS.

Research paper thumbnail of Antiprostate cancer activity of a ß-carboline alkaloid enriched extract from Rauwolfia vomitoria

The tropical shrub, Rauwolfia vomitoria, is a medicinal plant used traditionally to treat a varie... more The tropical shrub, Rauwolfia vomitoria, is a medicinal plant used traditionally to treat a variety of ailments. A bioactive ß-carboline alkaloid, alstonine, present in this extract was previously shown to have anti-cancer activity against cancer cell lines. This study considers the potential anti-prostate cancer activity of this extract in vitro and in vivo. Rauwolfia vomitoria extract standardized for ß-carboline alkaloids was tested for ability to influence the growth and survival of the human LNCaP prostate cancer cell line. A WST-1 assay was used to measure cell growth, and cell cycle analyses were conducted with flow cytometry. Western blot detection of PARP cleavage and accumulation of cells containing sub-genomic DNA indicated induction of apoptosis. Pathway specific microarray analyses were utilized to identify the effect of Rauwolfia extract on the expression of 225 genes. Mice xenografted with LNCaP cells were treated with the extract or placebo control, and tumor growth was measured for 5 weeks. The effects of the extract on xenografted tumor cell proliferation and apoptosis were measured by in situ BrdU incorporation and TUNEL staining. Rauwolfia extract decreased in vitro cell growth in a dose-dependent manner (p<0.001) and induced the accumulation of G1 phase cells. PARP cleavage demonstrated that apoptosis was induced only at the highest concentration tested (500 μg/ml) which was confirmed by detection of cells containing sub-genomic DNA. The expression of genes associated with DNA damage signaling pathway was up-regulated by Rauwolfia treatment, including that of GADD153 and MDG. The expression of a few cell cycle genes (p21, cyclin D1 and E2F1) was also modulated. These alterations were confirmed by RT-PCR. Tumor volumes were decreased by 60%, 70% and 58% in the groups fed the 75, 37.5 or 7.5 mg/kg Rauwolfia, respectively (Kruskal-Wallis test, p<0.001). The Rauwolfia vomitoria extract significantly suppressed the growth and cell cycle progression of LNCaP cells, in vitro and in vivo.