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Mendelian randomization analysis using mixture models for robust and efficient estimation of causal effects

Mendelian randomization (MR) has emerged as a major tool for the investigation of causal relationship among traits, utilizing results from large-scale genome-wide association studies. Bias due to horizontal pleiotropy, however, remains a major concern. We propose a novel approach for robust and efficient MR analysis using large number of genetic instruments, based on a novel...

Author Correction: Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration

Nilanjan Chatterjee Anand Swaroop In the version of this article initially published, in Supplementary Data 5, the logFC, FC, P value and adjusted P value for advanced AMD versus control (DE 4/1) without

Association of Genome-Wide Association Study (GWAS) Identified SNPs and Risk of Breast Cancer in an Indian Population

To date, no studies have investigated the association of the GWAS-identified SNPs with BC risk in Indian population. We investigated the association of 30 previously reported and replicated BC susceptibility SNPs in 1,204 cases and 1,212 controls from a hospital based case-control study conducted at the Tata Memorial Hospital, Mumbai. As a measure of total susceptibility burden...

Combined Associations of Genetic and Environmental Risk Factors: Implications for Prevention of Breast Cancer

 Chatterjee 0 0 Grove , Rm 7E146, Rockville, MD 20852 ( Genome-wide association studies (GWAS) have identified hundreds of genetic susceptibility loci for cancers and other complex diseases. However, the

Controlling the local false discovery rate in the adaptive Lasso

The Lasso shrinkage procedure achieved its popularity, in part, by its tendency to shrink estimated coefficients to zero, and its ability to serve as a variable selection procedure. Using data-adaptive weights, the adaptive Lasso modified the original procedure to increase the penalty terms for those variables estimated to be less important by ordinary least squares. Although...

Testing Gene-Environment Interaction in Large-Scale Case-Control Association Studies: Possible Choices and Comparisons

Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (Nilanjan Chatterjee). This research was partially supported by National ... Chatterjee 0 0 National Institutes of Health, Department of Health and Human Services , 6120 Executive Boulevard, Rockville, MD 20852 ( Several methods for screening gene-environment interaction have recently

Mukherjee et al. Respond to “GE-Whiz! Ratcheting Up Gene-Environment Studies”

, Rockville, MD 20852 ( 1 Institutes of Health, Department of Health and Human Services , Rockville, Maryland (Nilanjan Chatterjee). Conflict of interest: none declared 2 Author affiliations: Department of

Alcohol and Risk of Breast Cancer in Postmenopausal Women: An Analysis of Etiological Heterogeneity by Multiple Tumor Characteristics

Catherine Schairer Nilanjan Chatterjee Jerome E. Mabie Christopher Cunningham Saundra S. Buys Claudine Isaacs Regina G. Ziegler Initially submitted December 19, 2013; accepted for publication June 24, 2014 ... emerge. ACKNOWLEDGMENTS Author affiliations: National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, Maryland (Roni T. Falk, Paige Maas, Catherine Schairer, Nilanjan Chatterjee

Efficient p-value evaluation for resampling-based tests

FAMING LIANG JULIA CIAMPA, NILANJAN CHATTERJEE 1. INTRODUCTION To whom correspondence should be addressed. Equal contribution. 2. REVIEW OF THE SAMC ALGORITHM for a prespecified positive value of t0

Invited Commentary: Efficient Testing of Gene-Environment Interaction

Nilanjan Chatterjee Sholom Wacholder Gene-environment-wide interaction studies of disease occurrence in human populations may be able to exploit the same agnostic approach to interrogating the human ... . association; environment; genes; genetic markers; genetics; genome Abbreviations: E, environmental factor; G, genetic factor. Correspondence to Dr. Nilanjan Chatterjee, 6120 Executive Boulevard, EPS 8020

Likelihood Ratio Test for Detecting Gene (G)-Environment (E) Interactions Under an Additive Risk Model Exploiting G-E Independence for Case-Control Data

Genetics, National Cancer Institute, Bethesda, Maryland (Summer S. Han, Philip S. Rosenberg, Jonine D. Figueroa, Debra Silverman, Stephen J. Chanock, Nathaniel Rothman, Nilanjan Chatterjee); and Section of

Gene-Environment Interactions in Genome-Wide Association Studies: A Comparative Study of Tests Applied to Empirical Studies of Type 2 Diabetes

Marilyn C. Cornelis Eric J. Tchetgen Tchetgen Liming Liang Lu Qi Nilanjan Chatterjee Frank B. Hu Peter Kraft American Journal of Epidemiology The Author 2011. Published by Oxford University Press ... School, Boston, Massachusetts (Lu Qi, Frank B. Hu); and Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (Nilanjan Chatterjee

Retrospective analysis of haplotype-based case–control studies under a flexible model for gene–environment association

, Taiwan , People's Republic of China NILANJAN CHATTERJEE∗ RAYMOND J. CARROLL Case-control studies; EM algorithm; Gene-environment interactions; Haplotype; Semiparametric methods 1. INTRODUCTION 2

Potential Excess Mortality in BRCA1/2 Mutation Carriers beyond Breast, Ovarian, Prostate, and Pancreatic Cancers, and Melanoma

Background Although the increase in risk of developing breast, ovarian, and prostate cancer in BRCA1 and BRCA2 mutation carriers has been studied extensively, its impact on mortality is not well quantified. Further, possible effect of BRCA mutations on non-cancer mortality risk has not been examined. Methodology/Principal Findings Using mortality data from the relatives of 5,287...

Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers

The chromosome 9p21 region has been implicated in the pathogenesis of multiple cancers. We analyzed 9p21 single nucleotide polymorphisms (SNPs) from eight genome-wide association studies (GWAS) with data deposited in dbGaP, including studies of esophageal squamous cell carcinoma (ESCC), gastric cancer (GC), pancreatic cancer, renal cell carcinoma (RCC), lung cancer (LC), breast...

Nitric oxide synthase gene polymorphisms and prostate cancer risk

Nitric oxide (NO) induces cytotoxicity and angiogenesis, and may play a role in prostate carcinogenesis, potentially modulated by environmental exposures. We evaluated the association of prostate cancer with genetic polymorphisms in two genes related to intracellular NO: NOS2A [inducible nitric oxide synthase (NOS); −2892T>C, Ex16 + 14C>T (S608L), IVS16 + 88T>G and IVS20 + 524G>A...

Increased Hepatitis C Virus Load among Injection Drug Users Infected with Human Immunodeficiency Virus and Human T Lymphotropic Virus Type II

Coinfection of hepatitis C virus (HCV) and human immunodeficiency virus (HIV) and/or human T-lymphotropic virus type II (HTLV-II) is common among drug users. We compared HCV RNA detection and load in a cohort of 6570 injection drug users from 9 US cities during 1987-1991. Of 385 subjects selected from 16 strata by sex, race (black or nonblack), and HIV/HTLV-II group (HIV positive...

SLC6A3 and body mass index in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial

Background To investigate the contribution of the dopamine transporter to dopaminergic reward-related behaviors and anthropometry, we evaluated associations between polymorphisms at the dopamine transporter gene(SLC6A3) and body mass index (BMI), among participants in the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. Methods Four polymorphisms (rs6350...

A cross-sectional investigation of regional patterns of diet and cardio-metabolic risk in India

Devasenapathy Lakshmy Ramakrishnan Preethi S George Hemali Shetty Leah M Ferrucci 0 Susan Yurgalevitch Nilanjan Chatterjee 0 KS Reddy Tanuja Rastogi Prakash C Gupta Aleyamma Mathew Rashmi Sinha 0 0 Division of

Transforming growth factor beta 1 (TGFB1) gene polymorphisms and risk of advanced colorectal adenoma

Transforming growth factor beta 1 (TGFB1) is a multifunctional cytokine that has been implicated in the pathogenesis of colorectal neoplasia. To investigate the association between genetic variants in TGFB1 and the risk of colorectal adenoma, we conducted a case–control study of 754 advanced adenoma cases and 769 controls from the baseline screening exam of the Prostate, Lung...