Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation.

Mitochondrial DNA copy number (mtDNA-CN) measured from blood specimens is a minimally invasive marker of mitochondrial function that exhibits both inter-individual and intercellular variation. To identify genes involved in regulating mitochondrial function, we performed a genome-wide association study (GWAS) in 465,809 White individuals from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank (UKB). We identified 133 SNPs with statistically significant, independent effects associated with mtDNA-CN across 100 loci. A combination of fine-mapping, variant annotation, and co-localization analyses was used to prioritize genes within each of the 133 independent sites. Putative causal genes were enriched for known mitochondrial DNA depletion syndromes (p = 3.09 × 10-15) and the gene ontology (GO) terms for mtDNA metabolism (p = 1.43 × 10-8) and mtDNA replication (p = 1.2 × 10-7). A clustering approach leveraged pleiotropy between mtDNA-CN associated SNPs and 41 mtDNA-CN associated phenotypes to identify functional domains, revealing three distinct groups, including platelet activation, megakaryocyte proliferation, and mtDNA metabolism. Finally, using mitochondrial SNPs, we establish causal relationships between mitochondrial function and a variety of blood cell-related traits, kidney function, liver function and overall (p = 0.044) and non-cancer mortality (p = 6.56 × 10-4).

Rare, low frequency and common coding variants in CHRNA5 and their contribution to nicotine dependence in European and African Americans.

The common nonsynonymous variant rs16969968 in the α5 nicotinic receptor subunit gene (CHRNA5) is the strongest genetic risk factor for nicotine dependence in European Americans and contributes to risk in African Americans. To comprehensively examine whether other CHRNA5 coding variation influences nicotine dependence risk, we performed targeted sequencing on 1582 nicotine-dependent cases (Fagerström Test for Nicotine Dependence score⩾4) and 1238 non-dependent controls, with independent replication of common and low frequency variants using 12 studies with exome chip data. Nicotine dependence was examined using logistic regression with individual common variants (minor allele frequency (MAF)⩾0.05), aggregate low frequency variants (0.05>MAF⩾0.005) and aggregate rare variants (MAF<0.005). Meta-analysis of primary results was performed with replication studies containing 12 174 heavy and 11 290 light smokers. Next-generation sequencing with 180 × coverage identified 24 nonsynonymous variants and 2 frameshift deletions in CHRNA5, including 9 novel variants in the 2820 subjects. Meta-analysis confirmed the risk effect of the only common variant (rs16969968, European ancestry: odds ratio (OR)=1.3, P=3.5 × 10(-11); African ancestry: OR=1.3, P=0.01) and demonstrated that three low frequency variants contributed an independent risk (aggregate term, European ancestry: OR=1.3, P=0.005; African ancestry: OR=1.4, P=0.0006). The remaining 22 rare coding variants were associated with increased risk of nicotine dependence in the European American primary sample (OR=12.9, P=0.01) and in the same risk direction in African Americans (OR=1.5, P=0.37). Our results indicate that common, low frequency and rare CHRNA5 coding variants are independently associated with nicotine dependence risk. These newly identified variants likely influence the risk for smoking-related diseases such as lung cancer.

Lack of evidence of a major gene acting on postaxial polydactyly in South America.

Data on polydactyly were obtained from two large samples: the Latin American Collaborative Study of Congenital Malformations (ECLAMC), and from a migrant Northeastern Brazilian population of rural origin (Hospedaria). ECLAMC is a case-control clinical epidemiological program comprising 10,035 individuals distributed among 2,030 segregating nuclear families. Hospedaria data consisted of 6,586 examined individuals belonging to 1,040 nuclear families. Using complex segregation analysis methodology we found no evidence of two loci (a major gene and a modifier locus) acting on postaxial polydactyly in the present study. Very high heritability values (in a classical multifactorial model) of postaxial polydactyly were detected, for several sets of analyses in ECLAMC and in Hospedaria. For the whole ECLAMC sample there is a peculiar suggestion of a major recessive gene effect responsible for the trait; however, no comparison with a model involving transmission probabilities (tau) was possible in this highly heterogeneous sample. If the whole ECLAMC sample is divided in subsamples, according to Black admixture proportions, the same multifactorial picture emerges. Two different inheritance patterns were verified for hand (HP) and foot (FP) postaxial polydactyly: For HP there is evidence of a non-Mendelian transmission mechanism, while for FP the parental/sib transmission appears to be due only to multifactorial causes.

A model for intra-familial distribution of an infectious disease (Chagas' disease).

A probabilistic model for intra-familial distribution of infectious disease is proposed and applied to the prevalence of positive serology for Trypanosoma cruzi infection in a Northeastern Brazilian sample. This double binomial with one tail excess model fits satisfactorily to the data and its interpretation says that around 51% of these 982 families are free of infection risk; among those that are at risk, 3% have a high risk (0.66), probably due to high domestic infestation of the vector bug; while 97% show a small risk (0.11), probably due to accidental, non-domestic transmission.

Some factors affecting the secondary sex ratio in a Latin American sample.

A sample based on hospital birth records from the Latin American Collaborative Study on Congenital Malformations (ECLAMC) was used in this study. ECLAMC, which covers 11 countries (Uruguay, Chile, Argentina, Brazil, Bolivia, Peru, Paraguay, Ecuador, Venezuela, Colombia, and Costa Rica), registered 1,037,272 live births in the period 1982-1986. We applied several multivariate analysis models to the data and found that the sex ratio was significantly affected by secular, spatial (countries), biological (maternal age, birth order, and ethnic group), and socioeconomic (evaluated by hospital payment) variables. The black ethnic component carried sufficient weight to remove the spatial effect (Brazil and Venezuela) in certain cases. The Amerindian admixture effect on the sex ratio was negative and significant.

PIP: A sample based on hospital birth records from the Latin American Collaborative Study on Congenital Malformations (ECLAMC) was used. ECLAMC, which covers Uruguay, Chile, Argentina, Brazil, Bolivia, Peru, Paraguay, Ecuador, Venezuela, Colombia, and Costa Rica, registered 1,037,272 live births in the period 1982-1986. Weighted stepwise multiple regression analyses were used, and in all models the sex ration was the dependent variable. Maternal ages were grouped in categories of 5-year intervals, from mothers up to 19 years of age to mothers over 45 years of age. The 1st analysis of the sex ratio used biological (maternal age, birth order), temporal (year), and spatial (country) factors as independent variables. The sex ratio was significantly affected by secular, spatial, biological (maternal age, birth order, and ethnic group), and socioeconomic (evaluated by hospital payment) variables. The black ethnic component removed the spatial effect (Brazil and Venezuela) in certain cases. The Amerindian admixture effect on the sex ratio was negative and significant. Sex ratios were highest in mothers under 17 years old, gradually declined with age up to about 27 years, and thereafter increased slightly. Sex ratios decreased as birth order increased. In addition, a positive secular trend was observed (regression coefficient = 0.00082/yr). Other analyses included black and Amerindian components to verify whether the observed spatial effects were caused by different ethnic compositions. A final model with all the variables together with ethnic group indicated that ethnic stratification and form of payment had a negative correlation to sex ratio without any dramatic change compared to the previous analysis. Both the black and the Amerindian components are capable of removing the spatial effects of Brazil and Venezuela on the sex ratio.

Demography of the human sex ratio in some Latin American countries, 1967-1986.

A sample based on hospital births recorded for the Latin American Collaborative Study on Congenital Malformations (ECLAMC) program was used in the present study to determine sex ratios for live births and for stillbirths. Sixty-four cities and 147 hospitals in 11 countries (Uruguay, Chile, Argentina, Brazil, Bolivia, Peru, Paraguay, Ecuador, Venezuela, Colombia, and Costa Rica) were included in the present analyses. The number of live births was 1,886,653 in the period 1967-1986, and the number of stillbirths was 24,818 in the period 1978-1986. The sex ratio for the total sample was 0.5112 for live births and 0.5477 for stillbirths. The sex ratio as a whole is decreasing with time in a parabolic fashion. Each country in our study behaved differently. Except for Peru and Uruguay, the countries experienced a significant decrease in the sex ratio after 1978 for live births; only Brazil did not show a temporal trend for the sex ratio for stillbirths.

PIP: Hospital birth records of the Latin American Collaborative Study on Congenital Malformations (ECLAMC) program were utilized for a sample to determine sex ratios (proportion of males to total births) for live births and for stillbirths from 147 hospitals in 64 cities in Uruguay, Chile, Argentina, Brazil, Bolivia, Peru, Paraguay, Ecuador, Venezuela, Colombia, and Costa Rica. The ECLAMC program recorded 1,886,653 live births during the period 1967-1987, and 24,818 stillbirths in the period 1978-1987. Weighted stepwise multiple regression analyses were used to estimate the parameters of linear and parabolic regression models. Year, Year 2, and country were the independent variables; the sex ratio was the dependent variable. The sex ratio for the total sample was .5112 for live births and .5477 for stillbirths. The regression analysis showed a secular trend in the stillbirth rates: the rates increased until 1984 and became stable afterward. The countries underwent a significant decrease in the sex ratio after 1978 for live births except for Peru and Uruguay; only Brazil did not show a temporal trend for the sex ratio for stillbirths. There was a sharp decline in the stillbirth rate in the sample, possible as a result of socioeconomic and sanitary conditions, and the live-birth sex ratio might begin to increase. In Japan the decrease in the stillbirth rate was negatively correlated with the live-birth sex ratio. Similar demographic changes may be occurring in Latin America, although the pace of change may differ from the rates observed in Japan and among American whites. Nonetheless, the inferences are similar to those for American blacks indicating that in populations with slow health improvements and access to modern health care the secular trends show a slow decrease in the secondary sex ratio.

An appraisal of the epidemiology of Trypanosoma cruzi serology in Brazil.

A large bibliographic survey provided data on Trypanosoma cruzi serology covering the period 1948-1984. Epidemiological-demographic methods provided an estimate of 11% for the prevalence of positive serology in Brazil, by 1984. Significant temporal trends were observed for most of the Brazilian geographical regions as well as for Brazil, as a whole. The parabolic curve that fit best for the entire country, indicates that by 1991, the incidence of new positive serology would be close to zero. This conclusion needs further fine-adjustment, since the forecast point is somewhat distant from the measured period.

Major gene effect on body mass index: the role of energy intake and energy expenditure.

The evidence for a major gene for body mass index (BMI) was investigated using complex segregation analysis (POINTER) in 1691 individuals belonging to 432 nuclear families residing in the Chittoor district of Andhra Pradesh, India. Since the BMI is significantly correlated with energy intake (EI) and energy expenditure of activity (EEA), the effects of each were removed from the BMI using regression analysis, and the segregation analysis was repeated on the energy-adjusted BMI. For BMI, a putative major locus could not be ruled out, and the effect (q = 0.25, accounting for 37% of the phenotypic variance) was remarkably similar to that reported in Western populations. After adjusting the BMI for EI and EEA, however, no evidence in support of a major gene could be observed, suggesting either that EI and EEA mediate the expression of the major gene effect on BMI, or that the same major gene may influence both traits. The pleiotropy hypothesis was further explored using a simple bivariate familial correlation model, in which the significance of familial cross-trait correlations (e.g., BMI in parents with BMI as predicted from the energy variables in the offspring) was examined. The cross-trait resemblance between the two measures was significant for all biological relatives, verifying the presence of shared heritable determinants (i.e., the same gene[s] and/or familial environments) accounting for 58% of the covariation. The significant cross-trait spouse correlations further suggested that at least part of the cross-trait resemblance may be due to shared environmental factors. Therefore, we conclude that there is strong evidence for shared genetic effects between BMI and the energy variables.

The genetic epidemiology of leprosy in a Brazilian population.

Data on leprosy patients have been obtained from the Dispensary of Leprosy of Campinas, São Paulo, where records on practically all cases of leprosy in the Campinas area during the period 1960-70 are filed. The whole sample comprises 10,886 individuals, distributed among 1,568 families. Complex segregation analysis was utilized to determine the nature of the genetic factors that may operate on leprosy and its subtypes. The results suggest the presence of a recessive major gene controlling susceptibility to leprosy per se, with frequency of approximately .05, although there are deviations from the expected Mendelian segregation proportions. Possible etiologic heterogeneity was examined by considering two subtypes separately: for lepromatous leprosy and tuberculoid leprosy there are suggestions for a segregating major effect; however, Mendelian transmission could not be demonstrated in either case. Therefore, there is no evidence to suggest unique genetic determinants for leprosy subtypes.

The inheritance of factors associated with joint mobility.

From a sample of 1,500 individuals belonging to 442 migrant nuclear families from northeastern Brazil, information on the interphalangial mobility was obtained: (a) the grades of extension of both the right and left thumbs and (b) the angle (in degrees) formed by the distant and proximal phalanx of the thumb. The first principal component of these variables was estimated and called "extensibility." A negative association of extensibility and age, as well as with inbreeding, was detected. Complex segregation analysis was applied to extensibility and both a multigenic mechanism and an extra transmissible component were detected. Mendelian inheritance was rejected, while a model with multifactorial inheritance, together with a factor that is inherited with a transmission probability different from 1/2 (tau = 0.63), was not rejected. These findings were supported by path analysis, which showed an important biologic inheritance (h2 = 0.675) and the existence of a small but significant cultural component (c2 = 0.003). The observed "inbreeding" effect, therefore, could not be attributed to a genetic mechanism and probably is the effect of concomitant environmental variability.

Segregation analysis of regional fat distribution in families from Andhra Pradesh, India.

OBJECTIVE: Segregation analysis was used to examine the major gene evidence for regional fat distribution and whether the effects of covariates such as energy variables (intake and expenditure) or total subcutaneous fat, impact on the major gene inference. SUBJECTS: The data consist of measurements made on 1691 individuals in 432 pedigrees residing in the Chittor district of Andhra Pradesh, India, during the period from January 1989 to February 1990. MEASUREMENTS: Fat distribution was computed as the ratio of trunk skinfold sum (subscapular + suprailiac + abdominal) to extremity skinfold sum (biceps + triceps + medial calf). The trunk/extremity skinfold ratio (TER) was also analyzed after adjusting for the amount of energy expended in various activities and energy intake (TER-E), as well as after adjusting for overall level of fatness as measured by the sum of six skinfolds (TER-SF6). METHODS: Segregation analysis was applied using the unified model (POINTER). RESULTS: For the TER all of the conditions needed to satisfy a major gene hypothesis were met, and a putative recessive locus in the presence of a multifactorial component was inferred. Adjusting the TER for energy intake (EI) and energy expenditure (EE) did not change these results. However, adjusting for total subcutaneous fat did alter the results. Specifically, after removing the effects due to total fat, there was a major non-Mendelian effect (free tau s) with additional multifactorial influences, and with generation heterogeneity in both components. CONCLUSIONS: A putative major locus for fat distribution as indexed by the TER was found. However, further analyses suggested the hypothesis that this major gene may be primarily for total fat with secondary effects on fat distribution (that is, major gene pleiotropy). The possibility that there is a second locus that is modified by interactions with gender and age, and that impacts on the preferential accumulation of fat in the trunk vs extremity depots could be inferred.

No evidence of linkage between Mitsuda reaction and the NRAMP1 locus.

Thirty sib-pairs were ascertained through unrelated lepromatous probands. They consisted of 22 healthy individuals and 8 leprosy patients. The Mitsuda reactions of all sibs were evaluated both macroscopically and histologically, and high molecular weight genomic DNA was extracted from the white blood cells of all sib-pairs. Three DNA polymorphisms identified by polymerase chain reaction (274C/T, D543N, 1729 + 55del4) were used as chromosome markers at the NRAMP1 locus. Sib-pair comparisons did not disclose any sign of close linkage between the Mitsuda reaction and the genetic markers.

Inheritance of the waist-to-hip ratio in the National Heart, Lung, and Blood Institute Family Heart Study.

OBJECTIVE: Considering that waist-to-hip ratio (WHR) is a simple anthropometric measure of obesity and is a better predictor of coronary heart disease than body mass index (BMI), the genetic underpinnings of WHR are of interest. The inheritance pattern of WHR, before and after adjustment for BMI (WHR-BMI), was investigated in 2713 individuals from 1038 nuclear families in the National Heart, Lung, and Blood Institute Family Heart Study (NHLBI-FHS). RESEARCH METHODS AND PROCEDURES: Waist and hip measurements were taken twice, and the means of the measurements were used to calculate the WHR. Adjustments for age were carried out separately by sex, using stepwise multiple regression procedures for WHR and WHR-BMI phenotypes. Segregation analysis was applied using the unified model as implemented in the computer program POINTER. RESULTS: For age-adjusted WHR, the segregation results suggested an additive major gene that accounts for 35% of the phenotypic variance, and approximately 30% of the sample are homozygous for the "high" genotype. The results for age- and BMI-adjusted WHR were also compatible with a major gene; however, the multifactorial model provided the most parsimonious fit to the data. DISCUSSION: Although the genetic mechanisms for several obesity traits have been studied, tests of Mendelian segregation on this simple anthropometric measure (WHR) have not been reported previously. This study provides evidence for the presence of a major gene for age-adjusted WHR, suggesting that it is an appropriate trait for further genetic analysis, especially because it has strong predictive value and probably relates biologically to cardiovascular risk.

Mannan-binding lectin enhances susceptibility to visceral leishmaniasis.

Levels of the serum opsonin mannan-binding lectin (MBL) were directly correlated with the probability of developing visceral leishmaniasis. Monocytes infected with MBL-opsonized Leishmania chagasi promastigotes secreted higher levels of tumor necrosis factor alpha and interleukin-6 than cells infected with nonopsonized parasites. Our findings indicate that MBL can modulate the clinical outcome of infection with L. chagasi and the function of infected macrophages.

A model for intra-familial distribution of an infectious disease (Chaga's disease)

A probabilistic model for intra-familial distribution of infectous disease is proposed and applied to the prevalence of positive serology for Trypanosoma cruzi infection in Northeastern Brazilian sample. This double with one tail excess model fits satisfactorily to the data and its interpretation says that around 51% of these 982 families are free of infection risk; among those that are at risk, 3% have a high risk (0.66), probably due to high domestic infestation of the vector bug; while 97% show a small risk (0.11), probably due to accidental, non-domestic transmission

An appraisal of the epidemiology of Trypanosoma cruzi serology in Brazil

A large bibliographic survey provided data on Trypanosoma cruzi serology covering the period l948-l984. Epidemiological-demographic methods provided an estimate of 11% for the prevalenceof positive serology in Brazil, by 1984. Significant temporal trends were observed for most of the Brazilian geographical regions as well as for Brazil, as a whole. The parabolic curve that fit best for the entire country, indicates that by 1991, the incidence of new positive serology would be close to zero. This conclusion needs further fine-adjustment, since the forecast point is somewhat distant from the measured period

ABO segregation analysis of sib-pairs in two Brazilian samples

Com o objetivo de testar as discrepâncias observadas na segregaçäo dos grupos sanguineos ABO entre pares consecutivos de irmäos, como foi sugerido por Cifuentes and Valenzuela (1986) em uma populaçäo chilena, foram analisadas duas amostras brasileiras, cada uma com cerca de 1000 pares de irmäos. Os resultados mostram claramente a inexistência de diferenças significativas tanto nas amostras totais como nas subdividas de acordo com os fenótipos maternos, näo permitindo, portanto, a generalizaçäo dos resultados chilenos. As observaçöes agrupadas, das amostras brasileiras e a chilena näo apoiam a hipótese da existência de um mecanismo de "tolerância", postulada por Cirfuentes e Valenzuela. A necessidade de informaçöes completas de famílias nucleares é enfatizada, no sentido de evitar achados inconsistentes