Comparison of linkage disequilibrium patterns and haplotype structure of eight single nucleotide polymorphisms across the CYP1A2 gene between the Korean, and other populations registered in the International HapMap database

Background and objective: The aim of this study was to determine the frequencies of CYP1A2 gene polymorphisms, analyze Linkage disequilibrium (LD) blocks and haplotypes in a Korean population, and compare them with those in African, European, Japanese and Chinese populations. Methods: We searched across diverse studies conducted in Korea and the Knowledge Base for Korean Pharmacogenomics Research Network operated by Seoul National University to determine the frequency of single nucleotide polymorphisms (SNPs) of the CYP1A2 gene and to choose frequently occurring SNPs in a Korean population. We analyzed and confirmed the frequencies of CYP1A2 SNPs that are inferred as MAF >0·05 in 400 healthy Korean subjects, using direct sequencing and a TaqMan assay. The LD block and haplotypes were constructed from the SNP databases in the other races registered in the International HapMap (Europeans, Chinese, Japanese and Africans) and the haplotype frequencies in each race were compared with those in the Korean population. Results and discussion: We found 12 SNPs with minor allele frequency (MAF) values above 5% in the 5′ regulatory regions, the exon, and surrounding introns of CYP1A2 gene based on previous reports in Koreans. In this study, two of twelve SNPs were lower than 5% in frequency (n = 400). The CYP1A2 haplotypes were analyzed based on 10 SNPs, confirmed to have MAF >0·05 in this study. Four haplotypes (H1, H2, H3 and H4) represented most of the Korean population (>94%). Conclusions: The haplotype frequencies among the five ethnic groups revealed that haplotype distributions in Koreans were similar to those of the Japanese and Chinese, but were quite different to those of the Africans and Europeans. These LD and haplotype data should be useful in drug development and in understanding genetic associations of CYP1A2 with adverse drug effects. These inter‐ethnic differences in frequencies of SNPs and haplotypes may help to explain inconsistencies that have been reported in association studies and could contribute to predict the pharmacokinetics and pharmacodynamics of drugs that are metabolized by CYP1A2.     

Platelet glycoprotein I(b)alpha and integrin alpha2 beta1 polymorphisms: gene frequencies and linkage disequilibrium in a population diversity panel.

Genetic variants in the GP1BA and ITGA2 genes have been proposed as potential modifiers for arterial vascular disease and bleeding disorders. Since ancestry may play an important role in the prevalence of these variants, we sought to determine their allele frequency and linkage disequilibrium in a collection of 1064 DNA samples from 51 ethnic groups. We studied haplotypes of ITGA2 defined by single nucleotide substitutions at positions -52, 807, and 1648, and GP1BA variants defined by sequence changes in positions -5 (Kozak), 1018 (T145M, HPA-2) and 1285 (VNTR A, B, C and D). Frequency of haplotypes of ITGA2 showed considerable variation across the different groups, with a higher prevalence of the haplotype -52C or T/807C/1648A observed in African compared with caucasian and Asian populations. The haplotypes 52C/807T/1648A and -52T/807T/1648A were not observed in caucasians or South Americans. While relative frequencies of the GP1BA Kozak alleles were comparable across groups, the methionine allele (HPA-2b) showed a higher frequency in Africa (0.26) than in the other groups. We also observed a high prevalence of the VNTR B allele in the African and Israeli populations. Haplotype analysis revealed incomplete linkage disequilibrium between the HPA-2 and VNTR alleles. Incorporation of GP1BA variants into the set of SNPs already genotyped by the HapMap project disrupted the pre-existing haplotype block. These data provide a valuable resource for optimal selection of variants best tailored for association studies of vascular disease or bleeding disorders when examining individuals of different ancestral origins.     

The Genetic and Clinical Significance of Fetal Hemoglobin Expression in Sickle Cell Disease

Sickle cell disease (SCD) is phenotypically heterogeneous. One major genetic modifying factor is the patient''s fetal hemoglobin (HbF) level. The latter is determined by the patient''s β-globin gene cluster haplotype and cis- and trans-acting single nucleotide polymorphisms (SNPs) at other distant quantitative trait loci (QTL). The Arab/India haplotype is associated with persistently high HbF levels and also a relatively mild phenotype. This haplotype carries the Xmn1 (C/T) SNP, rs7482144, in the HBG2 locus. The major identified trans-acting QTL contain SNPs residing in the BCL11A on chromosome 2 and the HMIP locus on chromosome 6. These collectively account for 15–30% of HbF expression in different world populations and in patients with SCD or β-thalassemia. Patients with SCD in Kuwait and Eastern Saudi Arabia uniformly carry the Arab/India haplotype, but despite this, the HbF and clinical phenotypes show considerable heterogeneity. Pain episodes and avascular necrosis of the femoral head are particularly common, but severe bacterial infections, stroke, priapism, and leg ulcers are uncommon. Moreover, the HbF modifiers appear to be different; the reported BCL11A and HMIP SNPs appear to play insignificant roles. There are probably novel modifiers to be discovered in this population. This review examines the common clinical phenotypes in Kuwaiti patients with elevated HbF and the available information on HbF modifiers. The response of the patients to hydroxyurea is discussed. The presentation of patients with other sickle compound heterozygotes (Sβthal and HbSD), vis-à-vis their HbF levels, is also addressed critically.     

Fibrinogen gene variation and ischemic stroke

Summary.  Background : Plasma fibrinogen level and fibrin clot structure are heritable traits that may be of importance in the pathogenesis of ischemic stroke. Objectives : To investigate associations between variation in the fibrinogen gamma (FGG), alpha (FGA) and beta (FGB) genes, fibrinogen level, and ischemic stroke. Methods : The Sahlgrenska Academy Study on Ischemic Stroke comprises 600 cases and 600 matched population controls. Stroke subtypes were defined according to TOAST criteria. Plasma fibrinogen level was measured by an automated clot-rate assay. Eight tagging single nucleotide polymorphisms (SNPs) were selected to capture genetic variation in the FGA, FGG, and FGB genes. Results:  Plasma fibrinogen was independently associated with overall ischemic stroke and all subtypes, both in the acute stage ( P  < 0.001) and at three-month follow-up ( P  < 0.05). SNPs belonged to two haplotype blocks, one containing the FGB gene and the other the FGG and FGA genes. FGB haplotypes were associated with fibrinogen level ( P  < 0.01), but not with ischemic stroke. In contrast, FGG/FGA haplotypes showed independent association to ischemic stroke but not to fibrinogen level. In an additive model with the most common FGG/FGA haplotype (A1) as reference, the adjusted odds ratios of ischemic stroke were 1.4 [95% confidence interval (95% CI) 1.1–1.8], P  < 0.01, 1.4 (95% CI 1.0–1.8), P  < 0.05, and 1.5 (95% CI 1.0–2.1), P  < 0.05 for the A2, A3, and A4 FGG/FGA haplotypes, respectively. Conclusion:  FGG/FGA haplotypes show association to ischemic stroke. This association is independent of fibrinogen level, thus suggesting that the association between ischemic stroke and variation at the FGG/FGA genes is mediated by qualitative rather than quantitative effects on fibrin(ogen).     

成都汉族群体MMPs和TIMPs基因单核苷酸多态性及单体型分析

目的研究MMPs和TIMPs基因单核苷酸多态性(SNPs)在中国成都汉族人群中的分布特点。方法采用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)方法检测132名中国成都汉族个体MMPs基因6个SNPs(MMP1-1607 1G/2G、MMP2-1306C/T、MMP2-735C/T、MMP3-1612 5A/6A、MMP9-1562C/T、MMP21 572C/T)和TIMPs基因2个SNPs(TIMP2 303C/T、TIMP3-1296C/T)的多态性,并与中国北方汉族及日本、欧洲群体的MMPs和TIMPs基因SNPs等位基因频率的分布进行比较。结果获得了成都汉族人群的MMPs和TIMPs基因8个SNPs的群体遗传学资料。除MMP21 572C/T位点外,其余MMPs和TIMPs的SNPs基因型及等位基因频率及单体型的频率分布与中国北方汉族人群、日本及欧洲等人群之间的比较具有统计学意义(P<0.05)。结论成都地区汉族人群MMPs和TIMPs基因8个SNPs的等位基因频率同其他地区人群的存在较明显的不同。     

Definition of novel GP6 polymorphisms and major difference in haplotype frequencies between populations by a combination of in-depth exon resequencing and genotyping with tag single nucleotide polymorphisms

BACKGROUND: Common genetic variants of cell surface receptors contribute to differences in functional responses and disease susceptibility. We have previously shown that single nucleotide polymorphisms (SNPs) in platelet glycoprotein VI (GP6) determine the extent of response to agonist. In addition, SNPs in the GP6 gene have been proposed as risk factors for coronary artery disease. METHODS: To completely characterize genetic variation in the GP6 gene we generated a high-resolution SNP map by sequencing the promoter, exons and consensus splice sequences in 94 non-related Caucasoids. In addition, we sequenced DNA encoding the ligand-binding domains of GP6 from non-human primates to determine the level of evolutionary conservation. RESULTS: Eighteen SNPs were identified, six of which encoded amino acid substitutions in the mature form of the protein. The single non-synonymous SNP identified in the exons encoding the ligand-binding domains, encoding for a 103Leu > Val substitution, resulted in reduced ligand binding. Two common protein isoforms were confirmed in Caucasoid with frequencies of 0.82 and 0.15. Variation at the GP6 locus was characterized further by determining SNP frequency in over 2000 individuals from different ethnic backgrounds. CONCLUSIONS: The SNPs were polymorphic in all populations studied although significant differences in allele frequencies were observed. Twelve additional GP6 protein isoforms were identified from the genotyping results and, despite extensive variation in GP6, the sequence of the ligand-binding domains is conserved. Sequences from non-human primates confirmed this observation. These data provide valuable information for the optimal selection of genetic variants for use in future association studies.     

Phase I Metabolic Genes and Risk of Lung Cancer: Multiple Polymorphisms and mRNA Expression

Polymorphisms in genes coding for enzymes that activate tobacco lung carcinogens may generate inter-individual differences in lung cancer risk. Previous studies had limited sample sizes, poor exposure characterization, and a few single nucleotide polymorphisms (SNPs) tested in candidate genes. We analyzed 25 SNPs (some previously untested) in 2101 primary lung cancer cases and 2120 population controls from the Environment And Genetics in Lung cancer Etiology (EAGLE) study from six phase I metabolic genes, including cytochrome P450s, microsomal epoxide hydrolase, and myeloperoxidase. We evaluated the main genotype effects and genotype-smoking interactions in lung cancer risk overall and in the major histology subtypes. We tested the combined effect of multiple SNPs on lung cancer risk and on gene expression. Findings were prioritized based on significance thresholds and consistency across different analyses, and accounted for multiple testing and prior knowledge. Two haplotypes in EPHX1 were significantly associated with lung cancer risk in the overall population. In addition, CYP1B1 and CYP2A6 polymorphisms were inversely associated with adenocarcinoma and squamous cell carcinoma risk, respectively. Moreover, the association between CYP1A1 rs2606345 genotype and lung cancer was significantly modified by intensity of cigarette smoking, suggesting an underling dose-response mechanism. Finally, increasing number of variants at CYP1A1/A2 genes revealed significant protection in never smokers and risk in ever smokers. Results were supported by differential gene expression in non-tumor lung tissue samples with down-regulation of CYP1A1 in never smokers and up-regulation in smokers from CYP1A1/A2 SNPs. The significant haplotype associations emphasize that the effect of multiple SNPs may be important despite null single SNP-associations, and warrants consideration in genome-wide association studies (GWAS). Our findings emphasize the necessity of post-GWAS fine mapping and SNP functional assessment to further elucidate cancer risk associations.     

SIRT1 gene polymorphisms are associated with growth traits in Nanyang cattle

Growth is under complex genetic control and uncovering the molecular mechanisms how the genes and polymorphisms affect economic growth traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle populations. SIRT1 is a NAD⁺-dependent deacetylase that belongs to the class III histone deacetylases. It plays an important role in numerous fundamental cellular processes including gene silencing, DNA repair, and metabolic regulation. In addition, SIRT1 acts as an inhibitor of adipogenesis and has been associated with body weight regulation. The objective of the present study was to identify single nucleotide polymorphisms (SNPs) of bovine SIRT1 using 1255 animals representing the five main Chinese breeds and to determine if these SNPs are associated with economically important traits in Nanyang cattle. The approach consisted of resequencing SIRT1 using a panel of DNA from unrelated animals of five different breeds and the process revealed five novel SNPs. SNPs g.17324T>C and g.17491G>A exhibited a high degree of linkage disequilibrium in all tested breeds. Seven major haplotypes accounting for 91.2% of the alleles were observed and the haplotype ‘GCCGA’ was the most common haplotype in NY, QC, LX and JX breeds. An association analysis was performed between the five SNPs and six performance traits. SNP g.-274C>G was demonstrated to have a strong effect on 24-months-old body weight and g.17379A>G polymorphism was related to 6 and 12-months-old body weight in NY population, although these effects did not remained significant after the Bonferroni correction. Our results provide evidence that polymorphisms in SIRT1 are associated with growth efficiency traits, and may be used for marker-assisted selection and management in feedlot cattle.     

Identification of genetic polymorphisms of human OAT1 and OAT2 genes and their relationship to hOAT2 expression in human liver

BackgroundOrganic anion transporters (OATs) play an essential role in the disposition of numerous organic anions. To clarify the interindividual variation in the function of OATs, genetic polymorphisms of the SLC22A6 and SLC22A7 in Korean subjects were investigated and associated with hepatic hOAT2 expression and the SLC22A7 genotype.MethodsThe genetic variants and their frequencies for the SLC22A6 and SLC22A7 genes in 50 Korean subjects were investigated by direct sequencing. The expression of hOAT2 protein from 34 human liver samples was examined by western blot analysis.ResultsEight SNPs including 2 novel SNPs were identified in the SLC22A6 gene and eight SNPs including 4 novel SNPs were identified in the SLC22A7 gene. No amino acid alteration was found. Linkage disequilibrium (LD) analysis revealed that the SLC22A6 and SLC22A7 genes have separated single LD blocks and consist of a limited number of haplotypes (14 haplotypes for SLC22A6 and 5 haplotypes for SLC22A7). The expression of the hOAT2 protein varied 10-fold among 34 human livers but was not associated with the SLC22A7 genotype (p = 0.16).ConclusionsThe SLC22A7 genomic sequences showed low variability. A 10-fold variation in hOAT2 protein expression in the liver specimens was not correlated with SLC22A7 genotypes. These results suggest that genetic polymorphisms may not be a significant contributing factor to variations in the hOAT2 expression or hOAT2 transport activity.     

Spontaneous mutations in the Plasmodium falciparum sarcoplasmic/ endoplasmic reticulum Ca2+-ATPase (PfATP6) gene among geographically widespread parasite populations unexposed to artemisinin-based combination therapies

Recent reports on the decline of the efficacy of artemisinin-based combination therapies (ACTs) indicate a serious threat to malaria control. The endoplasmic/sarcoplasmic reticulum Ca(2+)-ATPase ortholog of Plasmodium falciparum (PfSERCA) has been suggested to be the target of artemisinin and its derivatives. It is assumed that continuous artemisinin pressure will affect polymorphism of the PfSERCA gene (serca) if the protein is the target. Here, we investigated the polymorphism of serca in parasite populations unexposed to ACTs to obtain baseline information for the study of potential artemisinin-driven selection of resistant parasites. Analysis of 656 full-length sequences from 13 parasite populations in Africa, Asia, Oceania, and South America revealed 64 single nucleotide polymorphisms (SNPs), of which 43 were newly identified and 38 resulted in amino acid substitutions. No isolates showed L263E and S769N substitutions, which were reportedly associated with artemisinin resistance. Among the four continents, the number of SNPs was highest in Africa. In Africa, Asia, and Oceania, common SNPs, or those with a minor allele frequency of ≥0.05, were less prevalent, with most SNPs noted to be continent specific, whereas in South America, common SNPs were highly prevalent and often shared with those in Africa. Of 50 amino acid haplotypes observed, only one haplotype (3D7 sequence) was seen in all four continents (64%). Forty-eight haplotypes had frequencies of less than 5%, and 40 haplotypes were continent specific. The geographical difference in the diversity and distribution of serca SNPs and haplotypes lays the groundwork for assessing whether some artemisinin resistance-associated mutations and haplotypes are selected by ACTs.     

Associations Between Cytokine Gene Variations and Severe Persistent Breast Pain in Women Following Breast Cancer Surgery

Persistent pain following breast cancer surgery is a significant clinical problem. Although immune mechanisms may play a role in the development and maintenance of persistent pain, few studies have evaluated for associations between persistent breast pain following breast cancer surgery and variations in cytokine genes. In this study, associations between previously identified extreme persistent breast pain phenotypes (ie, no pain vs severe pain) and single nucleotide polymorphisms (SNPs) spanning 15 cytokine genes were evaluated. In unadjusted analyses, the frequency of 13 SNPs and 3 haplotypes in 7 genes differed significantly between the no pain and severe pain classes. After adjustment for preoperative breast pain and the severity of average postoperative pain, 1 SNP (ie, interleukin [IL] 1 receptor 2 rs11674595) and 1 haplotype (ie, IL10 haplotype A8) were associated with pain group membership. These findings suggest a role for cytokine gene polymorphisms in the development of persistent breast pain following breast cancer surgery.PerspectiveThis study evaluated for associations between cytokine gene variations and the severity of persistent breast pain in women following breast cancer surgery. Variations in 2 cytokine genes were associated with severe breast pain. The results suggest that cytokines play a role in the development of persistent postsurgical pain.     

CYP2C9 haplotype structure in European American warfarin patients and association with clinical outcomes

OBJECTIVE: The goal of this study was to define the haplotype structure of the cytochrome P450 (CYP) 2C9 gene in a European American population and evaluate associations between CYP2C9 haplotypes and anticoagulation-related outcomes. METHODS: Genomic deoxyribonucleic acid from 192 European American patients stabilized on warfarin therapy was resequenced across 60 kilobases of the CYP2C9 genomic region, including all exons, dense sampling of introns, approximately 10 kilobases of the 5'-flanking region, and approximately 1.7 kilobases of the 3'-untranslated region. RESULTS: A total of 132 single nucleotide polymorphisms (SNPs) were detected, of which 47 were present in the 5'-flanking promoter region, 11 in the exonic coding region, and 74 in the intron regions. Nine nonsynonymous SNPs in the coding region consisted of CYP2C9*2 , *3 , *9 , *11 , and *12 ; R125H; and 3 new structural variants. Sixty SNPs were present at a minor allele frequency of greater than 5%, and from this subpopulation, 23 haplotypes were inferred. Clustering analysis identified 6 major groups of related haplotypes that were further designated 1A, 1B, 1C, 1D, 2, or 3. The *2 and *3 SNPs appeared exclusively in groups 2 and 3, and these groups combined were associated with significantly reduced warfarin maintenance doses, longer time to stable dosing, and increased risk of bleeding. In contrast, combinations of haplotypes 1A, 1B, 1C, and 1D were not associated with differences in any of these outcomes. CONCLUSION: These data establish a whole-gene, high-resolution haplotype structure for CYP2C9 in a European American patient population and suggest that genetic variation in exons, rather than the promoter or other regulatory regions, is largely responsible for warfarin sensitivity associated with CYP2C9 variants in this population.     

Haplotype analysis and identification of genes for a complex trait: examples from schizophrenia

For more than a decade there has been intensive research into the genetic etiology of schizophrenia, yet it is only recently that the first findings of promising genes associating with the disorder have been reported. Linkage analyses in families collected from different populations have provided relatively well defined genomic loci. These have been typically followed by fine mapping studies using single nucleotide polymorphisms (SNPs). A number of analysis programs have been produced to test SNPs and their haplotypes for association. Typically association has been established to specific haplotypes representing an allelic variant of the corresponding gene. The inherent problem of multiple testing in the analysis of haplotypes needs to be addressed fully, to determine if any of these recent findings can be considered as confirmed susceptibility genes for schizophrenia. However, informative haplotypes have provided a way to define allelic variants of genes associated with schizophrenia in numerous study samples, and are a useful tool in characterizing the extent of allelic diversity of putative schizophrenia susceptibility genes within different populations.     

Evolution of Alternative Splicing Regulation: Changes in Predicted Exonic Splicing Regulators Are Not Associated with Changes in Alternative Splicing Levels in Primates

Alternative splicing is tightly regulated in a spatio-temporal and quantitative manner. This regulation is achieved by a complex interplay between spliceosomal (trans) factors that bind to different sequence (cis) elements. cis-elements reside in both introns and exons and may either enhance or silence splicing. Differential combinations of cis-elements allows for a huge diversity of overall splicing signals, together comprising a complex ‘splicing code’. Many cis-elements have been identified, and their effects on exon inclusion levels demonstrated in reporter systems. However, the impact of interspecific differences in these elements on the evolution of alternative splicing levels has not yet been investigated at genomic level. Here we study the effect of interspecific differences in predicted exonic splicing regulators (ESRs) on exon inclusion levels in human and chimpanzee. For this purpose, we compiled and studied comprehensive datasets of predicted ESRs, identified by several computational and experimental approaches, as well as microarray data for changes in alternative splicing levels between human and chimpanzee. Surprisingly, we found no association between changes in predicted ESRs and changes in alternative splicing levels. This observation holds across different ESR exon positions, exon lengths, and 5′ splice site strengths. We suggest that this lack of association is mainly due to the great importance of context for ESR functionality: many ESR-like motifs in primates may have little or no effect on splicing, and thus interspecific changes at short-time scales may primarily occur in these effectively neutral ESRs. These results underscore the difficulties of using current computational ESR prediction algorithms to identify truly functionally important motifs, and provide a cautionary tale for studies of the effect of SNPs on splicing in human disease.     

Association between patterns of nucleotide variation across the three fibrinogen genes and plasma fibrinogen levels: the Coronary Artery Risk Development in Young Adults (CARDIA) study

BACKGROUND: Previous genotype-phenotype association studies of fibrinogen have been limited by incomplete knowledge of genomic sequence variation within and between major ethnic groups in FGB, FGA, and FGG. METHODS: We characterized the linkage disequilibrium patterns and haplotype structure across the human fibrinogen gene locus in European- and African-American populations. We analyzed the association between common polymorphisms in the fibrinogen genes and circulating levels of both 'functional' fibrinogen (measured by the Clauss clotting rate method) and total fibrinogen (measured by immunonephelometry) in a large, multi-center, bi-racial cohort of young US adults. RESULTS: A common haplotype tagged by the A minor allele of the well-studied FGB-455 G/A promoter polymorphism (FGB 1437) was confirmed to be strongly associated with increased plasma fibrinogen levels. Two non-coding variants specific to African-American chromosomes, FGA 3845 A and FGG 5729 G, were each associated with lower plasma fibrinogen levels. In European-Americans, a common haplotype tagged by FGA Thr312Ala and several other variant alleles across the fibrinogen gene locus was strongly associated with decreased fibrinogen levels as measured by functional assay, but not by immunoassay. Overall, common polymorphisms within the three fibrinogen genes explain < 2% of the variability in plasma fibrinogen concentration. CONCLUSIONS: In young adults, fibrinogen multi-locus genotypes are associated with plasma fibrinogen levels. The specific single nucleotide polymorphism and haplotype patterns for these associations differ according to population and also according to phenotypic assay. It is likely that a substantial proportion of the heritable component of plasma fibrinogen concentration is due to genetic variation outside the three fibrinogen genes.     

Haplotype analysis and identification of genes for a complex trait: examples from schizophrenia

For more than a decade there has been intensive research into the genetic etiology of schizophrenia, yet it is only recently that the first findings of promising genes associating with the disorder have been reported. Linkage analyses in families collected from different populations have provided relatively well defined genomic loci. These have been typically followed by fine mapping studies using single nucleotide polymorphisms (SNPs). A number of analysis programs have been produced to test SNPs and their haplotypes for association. Typically association has been established to specific haplotypes representing an allelic variant of the corresponding gene. The inherent problem of multiple testing in the analysis of haplotypes needs to be addressed fully, to determine if any of these recent findings can be considered as confirmed susceptibility genes for schizophrenia. However, informative haplotypes have provided a way to define allelic variants of genes associated with schizophrenia in numerous study samples, and are a useful tool in characterizing the extent of allelic diversity of putative schizophrenia susceptibility genes within different populations.     

Mitochondrial diversity evaluated by the single strand conformation polymorphism method in African and North American house flies (Musca domestica L.)

Single strand conformation polymorphisms (SSCPs) provide a convenient and inexpensive method of surveying mitochondrial genetic variation in large samples. We investigated how much variation should be incorporated into such surveys by scoring SSCP variation at eight mitochondrial loci in each of four sub-Saharan African and four North American house fly (Diptera: Muscidae.) populations. Hierarchical analysis of diversity was performed on haplotype frequencies at each locus and on haplotype frequencies formed by combining haplotypes from two, three, four, five and eight loci. Composite haplotypes at two loci were as informative about population structure as those composed of a greater number of loci. Increasing the number of loci increased diversity estimates within, but not between, populations. Mean composite haplotype diversities (16S2 and COII) were 0.49 +/- 0.09 among the African populations and 0.32 +/- 0.08 among the North American populations. Only two of 16 haplotypes were shared between continents. Nei's genetic differentiation statistic between populations in continents GPC was 0.30 +/- 0.06 and mean genetic differentiation between continents GCT was 0.39 +/- 0.06. We conclude that there has been little detectable gene flow between North America and sub-Saharan Africa.