Association between polymorphisms at N-acetyltransferase 1 (NAT1) & risk of oral leukoplakia & cancer.

Background & objectives: N-acetyltransferases 1 and 2 (NAT1 and NAT2) are important enzymes for metabolism of tobacco carcinogens. Due to polymorphisms, improper activities of these enzymes might lead to the formation of DNA adducts that may modulate risk of tobacco related oral precancer and cancer. Previously, it was shown that NAT2 polymorphisms did not modulate the risk of oral precancer and cancer. We undertook this study to check whether polymorphisms at NAT1 can modulate the risk of oral leukoplakia and cancer either alone or in combination with NAT2. Methods: Genotypes at four SNPs on NAT1 were determined by TaqMan method in 389 controls, 224 leukoplakia and 310 cancer patients. Genotype data were analyzed to know haplotypes and acetylation status of individuals and, then to estimate the risk of diseases. Using our previously published NAT2 data, combination of NAT1 and NAT2 acetylation genotypes of patients and controls were also analyzed to estimate the risk of diseases. Results: Analysis of NAT1 genotype data revealed that 1088T and 1095C alleles exist in strong linkage disequilibrium (r2=0.97, P<0.0001) and SNPs are in Hardy-Weinberg Equilibrium (P=0.1). Wild type or normal acetylating and variant or rapid acetylating alleles were two major alleles (frequencies 0.62 and 0.36, respectively) present in the control population. NAT1 rapid acetylation could not modulate the risk of leukoplakia and cancer (OR=0.9, 95% CI: 0.6-1.3; OR=1.0, 95% CI: 0.7-1.4, respectively). Analysis of combined NAT1 and NAT2 acetylating data also showed no significant enhancement of the risk of diseases. Interpretation & conclusions: NAT1 rapid acetylation alone as well as combination of NAT1 rapid-NAT2 slow acetylation did not modulate the risk of oral precancer and cancer in our patient population. So, NAT1/NAT2 metabolized carcinogen products may not be involved in tobacco related oral precancer and cancer. It may be interpreted that large sample size as well as combination of polymorphisms at other candidate loci may be important to estimate the risk of a complex disease like oral cancer.

Power comparison between population-based case–control studies and family-based transmission–disequilibrium tests: An empirical study.

BACKGROUND: There are two major classes of genetic association analyses: population based and family based. Population-based case–control studies have been the method of choice due to the ease of data collection. However, population stratification is one of the major limitations of case–control studies, while family-based studies are protected against stratification. In this study, we carry out extensive simulations under different disease models (both Mendelian as well as complex) to evaluate the relative powers of the two approaches in detecting association. MATERIALS AND METHODS: The power comparisons are based on a case–control design comprising 200 cases and 200 controls versus a Transmission Disequilibrium Test (TDT) or Pedigree Disequilibrium Test (PDT) design with 200 informative trios. We perform the allele-level test for case–control studies, which is based on the difference of allele frequencies at a single nucleotide polymorphism (SNP) between unrelated cases and controls. The TDT and the PDT are based on preferential allelic transmissions at a SNP from heterozygous parents to the affected offspring. We considered five disease modes of inheritance: (i) recessive with complete penetrance (ii) dominant with complete penetrance and (iii), (iv) and (v) complex diseases with varying levels of penetrances and phenocopies. RESULTS: We find that while the TDT/PDT design with 200 informative trios is in general more powerful than a case–control design with 200 cases and 200 controls (except when the heterozygosity at the marker locus is high), it may be necessary to sample a very large number of trios to obtain the requisite number of informative families. CONCLUSION: The current study provides insights into power comparisons between population-based and family-based association studies.

Associação entre marcadores inflamatórios e fatores de risco cardiovascular em mulheres de Kolkata, W.B, Índia / Association between inflammatory markers and cardiovascular risk factors in women from Kolkata, W.B, India / Asociación entre marcadores inflamatorios y factores de riesgo cardiovascular en mujeres de Kolkata, W.B, India

FUNDAMENTO: Recentes pesquisas tem se concentrado no uso de biomarcadores inflamatórios na previsão de risco cardiovascular. Entretanto, a informação é escassa em relação à associação entre esses marcadores inflamatórios com outros fatores de risco cardiovasculares em indianos asiáticos, particularmente em mulheres. OBJETIVO: Explorar a associação entre marcadores inflamatórios tais como proteína C-reativa de alta sensibilidade (PCR-as) e contagem de leucócitos (LEU) e fatores de risco cardiovascular tais como adiposidade geral e central, pressão arterial, variáveis lipídicas e lipoproteicas e glicemia de jejum. MÉTODOS: Conduzimos uma análise transversal de 100 mulheres com idade entre 35-80 anos. As participantes foram selecionadas através da metodologia de amostragem por cluster, de 12 distritos urbanos selecionadas ao acaso na Corporação Municipal de Kolkata, Índia. RESULTADOS: A PCR-as apresentou uma associação significante com o índice de massa corporal (IMC) (p < 0,001) e circunferência da cintura (CC) (p = 0,002). Associações significantes inversas foram observadas entre a lipoproteína de alta densidade colesterol (HDL-c) e ambos marcadores inflamatórios PCR-as (p = 0,031) e LEU (p = 0,014). A apo-lipoproteína A1 (Apo A1) também estava negativamente associada com a PCR-as. A contagem de leucócitos apresentou uma correlação significante com a glicemia de jejum e a razão colesterol total (CT) /HDL-C. Usando regressão logística ajustada para idade, IMC (odds ratio/OR, 1,186; intervalo de confiança/IC, 1,046-1,345; p=0,008) e LEU (OR, 1,045; IC, 1,005-1,087; p=0,027) foram as covariantes significantemente associadas com a PCR-as. CONCLUSÃO: No presente estudo, os fatores de risco tais como IMC, CC e HDL-c e Apo-A1 mostraram uma associação significante com PCR-as. A contagem de leucócitos estava significantemente associada com os níveis de HDL-c, glicemia de jejum, razão CT/HDL-c em mulheres.

BACKGROUND: Recent research has focused on the use of inflammatory biomarkers in the prediction of cardiovascular risk. However, information is scant regarding the association between these inflammatory markers with other cardiovascular risk factors in Asian Indians, particularly in women. OBJECTIVE: To explore the association between inflammatory markers such as high-sensitivity C-reactive protein (hs-CRP) and white blood cell (WBC) count and cardiovascular risk factors such as overall and central adiposity, blood pressure, lipid and lipoprotein variables and fasting glucose. METHODS: We conducted a cross-sectional analysis on 100 women aged 35-80 years. Participants were selected following cluster sampling methodology from 12 different randomly selected urban wards of Kolkata Municipal Corporation. RESULTS: Hs-CRP has a significant association with body mass index (BMI) ( p < 0.001) and waist circumference (WC) (p = 0.002). Significant inverse associations were observed between high-density lipoprotein cholesterol (HDL-C) and both inflammatory markers, hs-CRP (p = 0.031) and WBC count, (p = 0.014). Apolipoprotein A1 (Apo A1) was also negatively associated with hs-CRP. WBC count has significant correlation with fasting glucose and total cholesterol (TC) /HDL-C ratio. Using logistic regression, adjusting for age, BMI (odds ratio/OR, 1.186; confidence interval/CI, 1.046-1.345; p=0.008) and WC (OR, 1.045; CI, 1.005-1.087; p=0.027) were the covariates significantly associated with hs-CRP. CONCLUSION: In the present study, risk factors like BMI, WC, and HDL-C and apo A1 show significant association with hs-CRP. WBC count was significantly correlated with HDL-C, fasting glucose, TC/HDL-C ratio in women.

FUNDAMENTO: Recientes investigaciones se han concentrado en el uso de biomarcadores inflamatorios en la previsión de riesgo cardiovascular. Entre tanto, la información es escasa en relación a la asociación entre esos marcadores inflamatorios con otros factores de riesgo cardiovasculares en indios asiáticos, particularmente en mujeres. OBJETIVO: Explorar la asociación entre marcadores inflamatorios tales como proteína C-reactiva de alta sensibilidad (PCR-as) y recuento de leucocitos (LEU) y factores de riesgo cardiovascular tales como adiposidad general y central, presión arterial, variables lipídicas y lipoproteicas y glucemia de ayuno. MÉTODOS: Condujimos un análisis transversal de 100 mujeres con edad entre 35-80 años. Las participantes fueron seleccionadas a través de la metodología de muestreo por cluster, de 12 distritos urbanos seleccionadas al azar en la Corporación Municipal de Kolkata, India. RESULTADOS: La PCR-as presentó una asociación significativa con el índice de masa corporal (IMC) (r=0,373, p<0,001) y circunferencia de la cintura (CCI) (r=0,301, p=0,002). Asociaciones significativas inversas fueron observadas entre la lipoproteína de alta densidad colesterol (HDL-c) y ambos marcadores inflamatorios (r= -0,220, p=0,031 y r= -0,247, p=0,014 para PCR-as y LEU, respectivamente). La apo-lipoproteína A1 (Apo A1) también estaba negativamente asociada con la PCR-as (r= -0,237, p=0,031). El recuento de leucocitos presentó una correlación significativa con la glucemia de ayuno (r=0,253, p=0,011) y la razón colesterol total (CT) /HDL-C (r=0,284, p=0,004). Usando regresión logística ajustada para edad, IMC (odds ratio/OR, 1,186; intervalo de confianza/IC, 1,046-1,345; p=0,008) y LEU (OR, 1,045; IC, 1,005-1,087; p=0,027) fueron las covariantes significativamente asociadas con la PCR-as. CONCLUSIÓN: En el presente estudio, los factores de riesgo tales como IMC, CCI y HDL-c y Apo-A1 mostraron una asociación significativa con PCR-as. El recuento de leucocitos estaba significativamente asociado a los niveles de HDL-c, glucemia de ayuno, razón CT/HDL-c en mujeres.

Interpreting a genetic case-control finding: What can be said, what cannot be said and implications in Indian populations.

Identification of genetic variants responsible for complex disorders using association mapping is an active area of research. There are two broad classes of association methodologies: population-based case-control studies and family-based transmission analyses. While case-control analyses are more popular and in general, more powerful than family-based analyses, they suffer from some inherent limitations. Thus, it is of importance, to understand the implications of an association finding obtained from a case-control study design. This article discusses the relative advantages and disadvantages of the two classes of association analyses, particularly in the context of genetic diversity in Indian populations.

Dissecting the correlation structure of a bivariate phenotype: common genes or shared environment?

High correlations between two quantitative traits may be either due to common genetic factors or common environmental factors or a combination of both. In this study, we develop statistical methods to extract the genetic contribution to the total correlation between the components of a bivariate phenotype. Using data on bivariate phenotypes and marker genotypes for sib-pairs, we propose a test for linkage between a common QTL and a marker locus based on the conditional cross-sib trait correlations (trait 1 of sib 1 - trait 2 of sib 2 and conversely) given the identity-by-descent (i.b.d.) sharing at the marker locus. We use Monte-Carlo simulations to evaluate the performance of the proposed test under different trait parameters and quantitative trait distributions. An application of the method is illustrated using data on two alcohol-related phenotypes from a project on the collaborative study on the genetics of alcoholism.