Replication and extension of association of choline acetyltransferase with nicotine dependence in European and African American smokers

Choline acetyltransferase is critical in the synthesis of acetylcholine and regulation of cholinergic neuron functions. We recently reported association of the encoding gene ChAT with both smoking cessation and nicotine dependence (ND) in two independent European American (EA) samples; however, in the replication sample, only limited SNPs partially covering the gene were examined. In this study, we examined the association of 14 SNPs, which cover the entire gene, with ND, assessed by smoking quantity (SQ), heaviness of smoking index (HSI), and Fagerström Test for ND (FTND), in 2,037 subjects from 602 families of African American (AA) or EA origin. Individual SNP-based association analysis revealed that five SNPs showed nominal association with at least one ND measure in one of the samples (P = 0.022–0.042); none remained significant after correction for multiple testing. Haplotype-based association analysis revealed that haplotypes G–G–A–C, formed by rs1880676–rs3810950–rs10082479–rs8178990 (P = 0.005–0.0178), and G–G–T–C–G–C, formed by rs1880676–rs3810950–rs10082479–rs8178990–rs3793790–rs12266458 (P = 0.00247–0.00468), displayed significant association with all three ND measures in the AA sample, as did haplotype T–C–G–A–T, formed by rs12266458–rs11101191–rs8178991–rs4838544–rs4838547 (P = 0.00741–0.0103), in the EA sample. All these detected haplotype-based associations remained significant after correction for all major haplotypes for a given SNP combination. Together, our findings, in conjunction with the previous report of the association, warrant further investigation of ChAT in ND.     

Significant association of DRD1 with nicotine dependence

Epidemiologic studies have strongly implicated genetics in smoking behavior. Genes in the dopaminergic system, which mediates the reinforcing and dependence-producing properties of nicotine, are plausible candidates for roles in nicotine dependence (ND). In this study, we examined five single-nucleotide polymorphisms (SNPs) within or near the dopamine D₁ receptor gene (DRD1) for their association with ND, which was assessed by smoking quantity (SQ), the Heaviness of Smoking Index (HSI), and the Fagerström Test for ND (FTND). The samples were obtained from 2,037 participants representing 200 European American (EA) and 402 African American (AA) families. Although we found significant associations of SNPs rs265973, rs686, and rs4532 in the AA sample; of rs4532 in the EA sample; and of rs265975, rs686, and rs4532 in the pooled sample with various ND measures, only the association of rs686 in the AA sample and of rs686 and rs4532 in the pooled sample remained significant after correction for multiple testing. Haplotype-based association analysis revealed that haplotype C-T-A, formed by rs265973, rs265975, and rs686, was significantly associated with all three ND measures in both the AA and the pooled sample. Another haplotype, T-A-T, formed by rs265975, rs686, and rs4532, showed a significant association with FTND in the pooled sample. Furthermore, in a luciferase reporter assay, rs686, located in the 3′ untranslated region, caused differential luciferase activities, indicating that rs686 is a functional polymorphism affecting expression of DRD1.     

Association of amyloid precursor protein-binding protein,family B,member 1 with nicotine dependence in African and European American smokers

Although epidemiological studies reveal that cigarette smoking is inversely associated with Alzheimer’s disease (AD) and Parkinson’s disease (PD), the underlying mechanism remains largely unknown. Considering the facts that amyloid precursor protein-binding protein, family B, member 1 (APBB1) is mapped to a suggestive linkage region on chromosome 11 for nicotine dependence (ND), and has been implicated in the pathogenesis of AD and PD, it represents a plausible candidate for genetic study of ND. Five single nucleotide polymorphisms (SNPs) within APBB1 were genotyped in a sample consisting of 2,037 participants of either African-American (AA) or European-American (EA) origin, and examined their associations with ND assessed by three commonly used measures: Smoking Quantity (SQ), the Heaviness of Smoking Index (HSI), and the Fagerström Test for ND (FTND). Individual SNP-based association analysis showed that all five SNPs are associated with at least one ND measure in one of the three samples; however, only the association of SNP rs4758416 with SQ and HSI remained significant after correction for multiple testing in the pooled sample. Haplotype analysis demonstrated three major haplotypes significantly associated with ND after Bonferroni correction. Formed by rs4758416-rs10839562-rs1079199, haplotype C-C-T showed positive association with FTND in the AA and pooled samples, and conversely, haplotype G-C-T showed negative association with SQ and HSI in AA and EA samples. Another haplotype, C-T-G, formed by rs10839562-rs1079199-rs8164, was significantly associated with HSI in the EA sample. Based on these findings, we conclude that APBB1 represents an important candidate gene in the genetic study on ND and neurodegenerative diseases and warrants further investigation in future.     

Gametic non-random associations in North-West African populations ofDrosophila melanogaster

Three North-west African populations ofDrosophila melanogaster were analyzed for chromosomal and enzyme polymorphism as well as for gametic associations between non allelic elements mapped on the same chromosome arm. Strong geographic heterogeneity was found between populations, both for enzyme and chromosomal polymorphism. Out of the 43 possible comparisons for gametic association, 14 (32.5%) were statistically significant.     

Genetic differentiation between American and European Drosophila melanogaster populations could be attributed to admixture of African alleles

A total of 48 polymorphic microsatellite loci were characterized in 13 Drosophila melanogaster populations originating from Europe, America, and Africa. Consistent with previous results, the African D. melanogaster populations were the most differentiated populations and harbored most variation. Despite an overall similarity, American and European populations were significantly differentiated. Interestingly, genetic distances based on the proportion of shared alleles as well as FST values suggested that the American D. melanogaster populations are more closely related to the African populations than European ones are. We also detected a higher proportion of putative African alleles in the American populations, indicating recent admixture of African alleles on the American continent.     

Comparison and confirmation of SNP-bud burst associations in European beech populations in Germany

European beech (Fagus sylvatica L.) is one of the most important forest tree species in Central Europe. Climate change scenarios predict an increase in annual mean temperatures that may cause earlier bud burst in spring, potentially leading to an increased late frost-risk. Despite the ecologic and economic importance of beech, knowledge about the molecular basis of bud burst is still scarce in this species. Here, an association analysis was used to detect SNPs that are significantly associated with beech bud burst. A translocation experiment was established with progenies of six different beech populations from three widely separated regions in Northeast, Central, and Southwest Germany. In total, 600 individuals of the translocation experiment were genotyped using a set of 46 SNPs located in bud burst candidate genes. The association analysis revealed seven SNPs significantly associated with bud burst, each SNP explaining only a few percent of the observed phenotypic variation. Since the same SNP set was used in a previous association analysis with European beech, we were able to compare and confirm significant associations between SNPs and bud burst in distinct beech populations growing in different environments.     

African and European mitochondrial haplotypes in South American Creole cattle

South American Creole cattle are direct descendants of the animals brought to the New World by the Spanish and Portuguese during the 16th century. A portion of the mitochondrial D-loop was sequenced in 36 animals from five Creole cattle populations in Argentina and four in Bolivia. Individuals belonging to the potentially ancestral Spanish breed Retinta were also analysed. Sequence comparisons revealed three main groups: two with the characteristics of European breeds and a third showing the transitions representative of the African taurine breeds. The African sequences were found in two populations from Argentina and three populations from Bolivia, whose only connections go back to colonial times. The most probable explanation for the finding is that animals could have been moved from Africa to Spain during the long-lasting Arabian occupation that started in the seventh century, and from the Iberian Peninsula to America eight centuries later. However, since African haplotypes were not found in the Spanish sample, the possibility of cattle transported directly from Africa cannot be disregarded.     

Mitochondrial genetic variation in European, African and Indian cattle populations

Mitochondrial DNA from representative animals of 13 different cattle breeds was assayed for restriction fragment length polymorphisms (RFLP) to determine phylogenetic relationships and levels of variation among breeds; 16 different mitotypes were found, described by 20 polymorphisms. Within these 16 mitotypes two major lineages were apparent: an Afro-European and an Asian type. These were found to differ at over 2.3% of sites surveyed. None of the mitotypes found in the Asian lineage was detectable in the Afro-European lineage and vice versa. Within each of the major mitotypes there were no further significant differences within or among breeds. Using rates of mitochondrial evolution estimated from other species, the two lineages were estimated to have diverged between 575000 and 1150000 years ago; well outside the 10000 years bp timeframe postulated by a single domestication hypothesis. The results presented are concordant with those generated in other studies and provide strong evidence for an independent domestication of Asian Bos indicus. Furthermore, the grouping of all African indicine populations within the clade containing all Bos taurus lineages points to the hybrid origins of the humped cattle of that continent.     

Differential gene expression between African American and European American colorectal cancer patients

The incidence and mortality of colorectal cancer (CRC) is higher in African Americans (AAs) than other ethnic groups in the U. S., but reasons for the disparities are unknown. We performed gene expression profiling of sporadic CRCs from AAs vs. European Americans (EAs) to assess the contribution to CRC disparities. We evaluated the gene expression of 43 AA and 43 EA CRC tumors matched by stage and 40 matching normal colorectal tissues using the Agilent human whole genome 4x44K cDNA arrays. Gene and pathway analyses were performed using Significance Analysis of Microarrays (SAM), Ten-fold cross validation, and Ingenuity Pathway Analysis (IPA). SAM revealed that 95 genes were differentially expressed between AA and EA patients at a false discovery rate of ≤5%. Using IPA we determined that most prominent disease and pathway associations of differentially expressed genes were related to inflammation and immune response. Ten-fold cross validation demonstrated that following 10 genes can predict ethnicity with an accuracy of 94%: CRYBB2, PSPH, ADAL, VSIG10L, C17orf81, ANKRD36B, ZNF835, ARHGAP6, TRNT1 and WDR8. Expression of these 10 genes was validated by qRT-PCR in an independent test set of 28 patients (10 AA, 18 EA). Our results are the first to implicate differential gene expression in CRC racial disparities and indicate prominent difference in CRC inflammation between AA and EA patients. Differences in susceptibility to inflammation support the existence of distinct tumor microenvironments in these two patient populations.     

GSTT1 and GSTM1 gene polymorphisms in European and African populations

Glutathione S-transferases (GSTs) are a superfamily of detoxificant enzymes. Pharmacogenomic studies have revealed interethnic differences in GST allelic frequencies. This study is focused on GSTT1 (gene deletion, rs17850155, rs2234953, and rs11550605) and GSTM1 (gene deletion) gene frequency distributions in two population samples of Europe origin (Italy, n = 120; Spain, n = 94) and two population samples of Africa origin (Cameroon, n = 126; Ethiopia, n = 153). Detection of GSTT1 and GSTM1 null genotypes was performed by multiplex PCR analysis, while the other GSTT1 gene polymorphisms were detected using allele specific PCR and sequencing. GSTT1 and GSTM1 null frequencies in the samples analyzed fit with the variability range observed in European and African populations, respectively. The SNP analysis in GSTT1 gene did not highlight any nucleotide substitution in 493 individuals analyzed. The comparisons among GSTM1 and GSTT1 null phenotype frequencies in worldwide populations show different patterns between Asians, Africans, and Europeans. Important insights into the effects of GSTM1 and GSTT1 gene deletions on the pathogenesis of human diseases have been hypothesized. Detailed studies on the geography of GST variants could therefore increase knowledge about the relationship between ethnicity and the prevalence of certain diseases.     

Elevated male European and female African contributions to the genomes of African American individuals

The differential relative contribution of males and females from Africa and Europe to individual African American genomes is relevant to mapping genes utilizing admixture analysis. The assessment of ancestral population contributions to the four types of genomic DNA (autosomes, X and Y chromosomes, and mitochondrial) with their differing modes of inheritance is most easily addressed in males. A thorough evaluation of 93 African American males for 2,018 autosomal single nucleotide polymorphic (SNP) markers, 121 X chromosome SNPs, 10 Y chromosome haplogroups specified by SNPs, and six haplogroup defining mtDNA SNPs is presented. A distinct lack of correlation observed between the X chromosome and the autosomal admixture fractions supports separate treatment of these chromosomes in admixture-based gene mapping applications. The European genetic contributions were highest (and African lowest) for the Y chromosome (28.46%), followed by the autosomes (19.99%), then the X chromosome (12.11%), and the mtDNA (8.51%). The relative order of admixture fractions in the genomic compartments validates previous studies that suggested sex-biased gene flow with elevated European male and African female contributions. There is a threefold higher European male contribution compared with European females (Y chromosome vs. mtDNA) to the genomes of African American individuals meaning that admixture-based gene discovery will have the most power for the autosomes and will be more limited for X chromosome analysis. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Comparison of Primatological Literature in Latin American, European and African Countries

I compare the primatological literature in 4 Latin American (Brazil, Perú, Mexico and Argentina) 2 European (Great Britain and France) and one African (Kenya) countries with regard to: (1) total number of publications; (2) productivity of scientists; (3) quality of the publications; and (4) the range of subjects studied. Data are from Current Primate References (CPR; 1985–1994). Publications included in the sample show an address from the countries considered. The results showed that GB and France had a far larger number of publications than the other countries. They have respectively >7 and 4 times more authors than Brazil, the country with the highest number of authors among Latin American and African countries. But the mean number of publications per author shows little difference among the 7 countries. The quality of publications as measured by the percentage indexed by ISI shows that, GB and France fare much better than the Latin American countries. Kenya did not follow the pattern of the other underdeveloped countries and showed a high percentage of indexed publications. Not all subjects reviewed in CPR were studied by scientists from the 7 countries. GB and France presented the widest range of subjects. Scientists in countries with greater primate diversity concentrated their publications in behavior, ecology and conservation, colony management and general primatology with the exception of Kenya. These results suggest that scientific production in Latin American countries can be increased by increasing the number of scientists, either through educational programs or via incentives for the career. However, more specific action is needed to improve the quality of publications and the range of subjects studied.     

Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations

Population linkage disequilibrium occurs as a consequence of mutation, selection, genetic drift, and population substructure produced by admixture of genetically distinct ethnic populations. African American and Hispanic ethnic groups have a history of significant gene flow among parent groups, which can be of value in affecting genome scans for disease-gene discovery in the case-control and transmission/disequilibrium test designs. Disease-gene discovery using mapping by admixture linkage disequilibrium (MALD) requires a map of polymorphic markers that differentiate between the founding populations, along with differences in disease-gene allele frequencies. We describe markers appropriate for MALD mapping by assessing allele frequencies of 744 short tandem repeats (STRs) in African Americans, Hispanics, European Americans, and Asians, by choosing STR markers that have large differences in composite delta, log-likelihood ratios, and/or I*(2) for MALD. Additional markers can be added to this MALD map by utilization of the rapidly growing single-nucleotide-polymorphism databases and the literature, to achieve a 3-10-cM scanning scale. The map will be useful for studies of diseases, including prostate and breast cancer, diabetes, hypertension, and end-stage renal disease, that have large differences in incidence between the founding populations of either Hispanics or African Americans.     

Odontometric variation among American black, European, and Mongoloid populations

Quantified dental parameters (including root and pulp areas and shape variables) derived from periapical radiographs were used to make comparisons among a sample of American Black (8 males--124 teeth, 9 females--138 teeth), European derivative (31 males--304 teeth, 43 females--497 teeth) and Mongoloid populations (12 males--166 teeth, 19 females--252 teeth). The magnitude of sexual dimorphism within each ethnic stock was also examined. Teeth from American Black males were robust. Sexual dimorphism was unambiguous in all groups although a hierarchical order existed from the highly dichotomous American Black sample to the more homogeneous European sample. The female dental phenotype was down-scaled from their male counterparts, but not gracile in form. Easily obtained area and shape parameters derived from dental radiographs proved useful as discriminators among racial groups and the sexes. The relationships among these data lend further support to the hypothesis of an African origin of modern humans.     

Significant association of glutamate receptor, ionotropic N-methyl-d-aspartate 3A (GRIN3A), with nicotine dependence in European- and African-American smokers

The glutamate receptor gene, ionotropic N-methyl-d-aspartate 3A (GRIN3A), is one of the seven that code for subunits of N-methyl-d-aspartate receptors, which play an essential role at many synapses in the brain, regulating ion flow across membranes in response to glutamate signaling. In this study, we analyzed 25 single nucleotide polymorphisms (SNPs) within GRIN3A for association with nicotine dependence (ND), which was assessed by smoking quantity, heaviness of smoking index, and the Fagerström test for ND. Both individual SNP and haplotype association tests were performed in African-American (AA) and European-American (EA) samples as well as in the pooled sample consisting of 2,037 individuals from 602 nuclear families. Individual SNP analysis revealed significant associations of 5, 5, and 4 SNPs with at least one ND measure in the pooled, EA, and AA samples, respectively. Of them, SNPs rs17189632 and rs10121600 in the pooled sample and rs11788456 in the EA sample remained significant after correction for multiple testing. On the basis of the blocks determined with Haploview, we performed haplotype-based association analysis and found 2, 4, and 1 haplotype(s) that are significantly associated with at least one ND measure in the pooled, EA, and AA samples, respectively. Some of them remained significant after correction for multiple testing. We concluded that GRIN3A represents a strong candidate for involvement in the etiology of ND and warrants further investigation in independent samples.