Duplex dual-labeled fluorescence probe-based melting curve and endpoint genotyping assays for genotyping of rs2000999 and haptoglobin gene deletion.

Haptoglobin (Hp) is a hemoglobin-binding serum glycoprotein. Some variations in the Hp gene (HP) or Hp-related gene (HPR), including a single-nucleotide polymorphism in intron 2 of HRP, rs2000999, and a complete deletion of the HP gene (HPde l ), one of the rare variants of HP, have been reported to correlate with the serum cholesterol concentration as well as the serum Hp concentration. In this study, we developed a duplex dual-labeled fluorescence probe-based method to simultaneously determine the rs2000999 G > A polymorphism by melting curve genotyping and the zygosity of HPde l by endpoint genotyping. This method was then validated by using the genomic DNA from 94 Japanese subjects for whom genotypes of rs2000999 and HPdel zygosity had already been determined. The results obtained with this method were in perfect agreement with the previous ones. Thus, the present method enables us to estimate these two polymorphisms in relatively large-scale groups of subjects, especially in Asian populations where the HPdel is distributed.

Detection of five common variants of ABO gene by a triplex probe-based fluorescence-melting-curve-analysis.

Current studies have suggested that the ABO blood group system is associated with several clinical conditions. For large-scale genotyping of ABO alleles, we developed a triplex fluorescence melting curve analysis (FMCA) to determine five single nucleotide variants (SNVs), c.261delG, c.796C>A, c.802G>A and c.803G>C and c.1061delC, responsible for common ABO phenotypes using dual-labeled self-quenched (TaqMan) probes in a single tube. We accurately determined c.796C>A, c.802G>A, and c.803G>C genotypes using a FAM-labeled probe, c.261delG using a CAL Fluor Orange 560- labeled probe, and c.1061delC using a Cy5-labeled probe. The present genotyping results of five SNVs in 214 subjects of the 1000 Genomes Project were in full agreement with those of the database sequence. The predicted ABO phenotypes using combinations of these five SNVs by this method in 288 Japanese subjects were in complete agreement with those by hemagglutination assay, although we did not find any A2 (alleles containing c.1061delC) or O.02 (alleles containing c.802G>A) alleles. The present triplex probe-based FMCA is a valid and credible method for a considerably accurate large-scale determination of ABO allele genotypes and estimation of phenotypes.

Rapid genotyping of 508G>A (rs3745635) and 1067T>A (rs3894326) of FUT3 by a duplex Eprobe-mediated melting curve analysis.

BACKGROUND AND OBJECTIVES: Lewis histo-blood group phenotypes are regulated by the action of FUT3-encoded α(1,3/1,4)fucosyltransferase and FUT2-encoded α(1,2)fucosyltransferase. Since Lewis phenotypes are suggested to be associated with various clinical conditions, a method for large-scale FUT3 genotyping is desirable. In worldwide populations, 508G>A and 1067T>A of FUT3 are two of three common causal single nucleotide polymorphisms for Lewis-negative alleles. MATERIALS AND METHODS: We developed a duplex Eprobe-mediated melting curve analysis for genotyping 508G>A and 1067T>A simultaneously and applied this method to 106 Ghanaian and 140 Japanese subjects. RESULTS: The results of both 508G>A and 1067T>A genotyping by duplex Eprobe-mediated melting curve analysis were completely in agreement with the results of a DNA sequence analysis in 106 Ghanaians and polymerase chain reaction-restriction fragment length polymorphism analysis in 140 Japanese subjects. CONCLUSION: The present duplex Eprobe-mediated melting curve analysis is valid and credible for large-scale estimation of Lewis-negative alleles.

Estimation of Lewis-negative alleles by high-resolution melting analysis of three tag SNPs of FUT3.

BACKGROUND AND OBJECTIVES: The expression of type 1 chain Lewis blood group antigens is regulated by secretor-type α(1,2)fucosyltransferase, encoded by FUT2, and Lewis α(1,3/1,4)fucosyltransferase, encoded by FUT3. Accumulating evidence has linked Lewis phenotypes or genotypes to various clinical conditions. Thus, in addition to FUT2, large-scale FUT3 genotyping is important. Because FUT3 has two paralogous genes (FUT5 and FUT6) with high DNA sequence similarity, we should select the polymerase chain reaction (PCR) primers carefully for FUT3 genotyping. Previously, we suggested that 13G>A (rs28362458), 59T>G (rs28362459) and 202T>C (rs812936) could be selected as tag single nucleotide polymorphisms (SNPs) for detection of Lewis-negative alleles (le). MATERIALS AND METHODS: In this study, three high-resolution melting (HRM) analyses for genotyping these SNPs were developed and applied for 140 Japanese, eight Ghanaians and four Sinhalese subjects. RESULTS: Each of three genotypes of 13G>A (G/G, G/A, A/A), 59T>G (T/T, T/G, G/G) and 202T>C (T/T, T/C, C/C) was discriminated clearly. Although we need to be careful in interpretation of results due to SNPs other than the 59T>G in the amplicon, the results of 59T>G genotyping were in full agreement with the results by a previous PCR-restriction fragment length polymorphism analysis in 140 Japanese. In addition, three heterozygotes of 202C substitution were identified, and no one having a 13A substitution was found in 140 Japanese. CONCLUSION: The present HRM analyses are useful and reliable methods for large-scale estimation of le alleles.

Detection of the weak-secretor rs1047781 (385A>T) single nucleotide polymorphism using an unlabeled probe high-resolution melting-based method.

FUT2 encodes galactoside 2-α-l-fucosyltransferase 2 which determines the secretor status of ABO(H) blood group antigens. Secretors have at least one functional FUT2 allele (Se), while nonsecretors or weak secretors are homozygous for nonfunctional (non- or weak secretor) FUT2 alleles (se or Sew ). The Sew having the 385A>T missense SNP (rs1047781) is the prevalent nonfunctional allele in East and Southeast Asians. In this study, we developed an unlabeled-probe high-resolution melting (HRM) analysis for genotyping of 385A>T and validated the method by analyzing 72 Japanese whose 385A>T genotypes were confirmed by DNA sequencing. The unlabeled-probe HRM analysis clearly discriminated three genotypes of 385A>T. In addition, the results obtained for the 72 Japanese by this method were fully concordant with previous ones. Estimation of secretor status using this cost-effective method may be useful in East and Southeast Asian populations.

High-resolution melting analysis for detection of fusion allele of FUT2.

The secretor status of ABH antigens, determined by FUT2 polymorphisms, affects susceptibility to various infectious diseases. In addition to many SNPs responsible for the nonsecretor phenotype, five nonfunctional alleles (se) resulting from copy number variations have been reported. One of the five alleles generated by an unequal crossover between FUT2 and a pseudogene (SEC1), is sefus . This allele may be misidentified as a functional allele if only common inactivating SNPs are genotyped because it contains the 3' region of the functional FUT2. Therefore, accurate detection of sefus is desirable. For this purpose, a high-resolution melting (HRM) analysis is developed for detection of sefus in which a 284bp fragment of SEC1 and sefus but not FUT2, are amplified. This HRM analysis detected sefus reliably. Thus, an initial screening or prescreening for sefus using HRM analysis seems to be useful for association studies of FUT2.

Effect of tolvaptan on renal involvement in patients with autosomal dominant polycystic kidney disease according to different gene mutations.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is an inherited disorder caused by mutations in the polycystic kidney disease (PKD) gene. Although tolvaptan has benefits for renal involvement, the different effects depending on the gene mutation type are unknown. Thus, we explore the different effects of tolvaptan on the annual changes in total kidney volume (%TKV) and estimated glomerular filtration rate (eGFR) according to the gene mutation type in ADPKD patients. METHODS: In total, 135 ADPKD patients were screened, and 22 patients taking tolvaptan for at least a year were retrospectively studied at the Kurume University Hospital. We examined the decline in renal function and %TKV by computed tomography and analyzed the gene mutation. Patients were classified into the following four groups according to gene mutation type: PKD1-truncated, PKD1-non-truncated, PKD2, and mutation not found. Patients were treated with tolvaptan, and the effects of tolvaptan were analyzed according to the gene mutation type. RESULTS: Patients (age: 52.3 ± 11.2 years) were administered tolvaptan at a dose of 45 or 60 mg. No variation was observed in the annual changes in eGFR (%eGFR) (before: - 10.5% ± 13.9%, after: - 14.4% ± 8.1%, P = 0.139), whereas %TKV was significantly improved after the tolvaptan treatment (before: 14.9% ± 8.0%, after: - 5.4% ± 7.6%, P < 0.001). Unlike %eGFR, tolvaptan treatment significantly improved %TKV, regardless of the type of gene mutation. CONCLUSIONS: A year treatment with tolvaptan significantly improved %TKV in patients with ADPKD, regardless of the gene mutation type.

Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR-mediated deletion and characterization of 4 nonsynonymous single-nucleotide polymorphisms.

BACKGROUND: The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population-specific single-nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans. STUDY DESIGN AND METHODS: To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay. RESULTS: We identified three novel nonfunctional alleles (se178,357 , se841 , and sedel4 ) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat-mediated recombination with a 4.3-kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians. CONCLUSION: We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat-mediated gene recombination event at the FUT2 locus has been detected.

Haptoglobin promoter polymorphism rs5472 as a prognostic biomarker for peptide vaccine efficacy in castration-resistant prostate cancer patients.

Personalized peptide vaccination (PPV) is an attractive approach to cancer immunotherapy with strong immune-boosting effects conferring significant clinical benefit. However, as with most therapeutic agents, there is a difference in clinical efficacy among patients receiving PPV. Therefore, a useful biomarker is urgently needed for prognosticating clinical outcomes to preselect patients who would benefit the most from PPV. In this retrospective study, to detect a molecular prognosticator of clinical outcomes for PPV, we analyzed whole-genome gene expression profiles of peripheral blood mononuclear cells (PBMCs) in castration-resistant prostate cancer (CRPC) patients before administration of PPV. Cox regression analysis revealed that mRNA expression of myeloperoxidase, haptoglobin, and neutrophil elastase was significantly associated with overall survival (OS) among vaccinated CRPC patients (adjusted P < 0.01). By promoter sequence analysis of these three genes, we found that rs5472 of haptoglobin (HP), an acute-phase plasma glycoprotein, was strongly correlated to OS of vaccinated CRPC patients (P = 0.0047, hazard ratio 0.47; 95 % confidence interval 0.28-0.80). Furthermore, both HP mRNA expression in PBMCs and protein level in plasma of CRPC patients before administration of PPV exhibited rs5472 dependence (P < 0.001 for mRNA expression and P < 0.05 for protein level). Our findings suggest that rs5472 may play an important role in the immune response to PPV via regulation of HP. Thus, we concluded that rs5472 is a potential prognostic biomarker for PPV.

Identification and Diagnosis of Complete Haptoglobin Gene Deletion, One of the Genes Responsible for Adverse Posttransfusion Reactions.

Allergic reactions are the most frequent adverse events in blood transfusion, and anaphylactic shock, although less frequent, is systemic and serious. The cause of allergic reactions to blood transfusions are largely unknown, but deficiencies in serum proteins such as haptoglobin (Hp) can lead to anaphylactic shock. A complete deletion of the haptoglobin gene (HPdel) was first identified in families with anomalous inheritance and then verified as a genetic variant that can cause anaphylactic shock because homozygotes for HPdel have complete Hp deficiency. Thereby, they may produce antibodies against Hp from blood transfusions. HPdel is found in East and Southeast Asian populations, with a frequency of approximately 0.9% to 4%, but not in other populations. Diagnosis of Hp deficiency due to HPdel prior to transfusion is advisable because severe adverse reactions can be prevented by washing the red blood cells and/or platelets with saline or by administering plasma products obtained from an Hp-deficient donor pool. This review outlines the background of the identification of HPdel and several genetic and immunological methods developed for diagnosing Hp deficiency caused by HPdel.

Detection of c.375A>G, c.385A>T, c.571C>T, and sedel2 of FUT2 via Real-Time PCR in a Single Tube.

α(1,2)fucosyltransferase (Se enzyme) encoded by FUT2 is involved in the secretor status of ABH(O) blood group antigens. The sedel2 allele is one of the non-functional FUT2 (se) alleles in which 9.3 kb, containing the entire coding region of FUT2, is deleted by Alu-mediated nonhomologous recombination. In addition to this allele, three SNPs of FUT2, c.375A>G, c.385A>T, and c.571C>T, appear to be prevalent in certain Oceanian populations such as Polynesians. Recently, we developed an endpoint genotyping assay to determine sedel2 zygosity, using a FAM-labeled probe for detection of the sedel2 allele and a VIC-labeled probe for the detection of FUT2. In this study, instead of the VIC probe, a HEX-labeled probe covering both c.375A>G and c.385A>T and a Cy5-labeled probe covering c.571C>T were added to the sedel2 allele assay mixture to allow for the simultaneous detection of these four variations via endpoint genotyping for sedel2 zygosity and fluorescence melting curve analysis for c.375A>G, c.385A>T, and c.571C>T genotyping. The results obtained from 24 Samoan subjects using this method were identical to those obtained using previous methods. Therefore, it appears that the present method can accurately determine these four variations simultaneously.

FUT1 variants responsible for Bombay or para-Bombay phenotypes in a database.

Rare individuals with Bombay and para-Bombay phenotypes lack or have weak expression of the ABO(H) antigens on surface of red blood cells due to no or very weak H-type α(1,2)fucosyltransferase activity encoded by FUT1. These phenotypes are clinically important because subjects with these phenotypes can only accept transfusions of autologous blood or blood from subjects with the same phenotypes due to the anti-H antibody. To survey FUT1 alleles involved in Bombay and para-Bombay phenotypes, the effect of 22 uncharacterized nonsynonymous SNPs in the Erythrogene database on the α(1,2)fucosyltransferase activity were examined by transient expression studies and in silico analysis using four different online software tools. Two nonfunctional alleles (FUT1 with c.503C>G and c.749G>C) and one weakly functional allele (with c.799T>C) were identified in transient expression studies, while the software predicted that the proteins encoded by more alleles including these would be impaired. Because both nonfunctional FUT1 alleles appear to link to the nonsecretor alleles, homozygotes of these alleles would be of the Bombay phenotype. The present results suggest that functional assays are useful for characterization of nonsynonymous SNPs of FUT1 when their phenotypes are not available.

Estimation of Lewis Blood Group Status by Fluorescence Melting Curve Analysis in Simultaneous Genotyping of c.385A>T and Fusion Gene in FUT2 and c.59T>G and c.314C>T in FUT3.

Lewis blood group status is determined by two fucosyltransferase activities: those of FUT2-encoded fucosyltransferase (Se enzyme) and FUT3-encoded fucosyltransferase (Le enzyme). In Japanese populations, c.385A>T in FUT2 and a fusion gene between FUT2 and its pseudogene SEC1P are the cause of most Se enzyme-deficient alleles (Sew and sefus), and c.59T>G and c.314C>T in FUT3 are tag SNPs for almost all nonfunctional FUT3 alleles (le59, le59,508, le59,1067, and le202,314). In this study, we first conducted a single-probe fluorescence melting curve analysis (FMCA) to determine c.385A>T and sefus using a pair of primers that collectively amplify FUT2, sefus, and SEC1P. Then, to estimate Lewis blood group status, a triplex FMCA was performed with a c.385A>T and sefus assay system by adding primers and probes to detect c.59T>G and c.314C>T in FUT3. We also validated these methods by analyzing the genotypes of 96 selected Japanese people whose FUT2 and FUT3 genotypes were already determined. The single-probe FMCA was able to identify six genotype combinations: 385A/A, 385T/T, sefus/sefus, 385A/T, 385A/sefus, and 385T/sefus. In addition, the triplex FMCA successfully identified both FUT2 and FUT3 genotypes, although the resolutions of the analysis of c.385A>T and sefus were somewhat reduced compared to that of the analysis of FUT2 alone. The estimation of the secretor status and Lewis blood group status using the form of FMCA used in this study may be useful for large-scale association studies in Japanese populations.

Genetic variation of FUT2 in a Vietnamese population: identification of two novel Se enzyme-inactivating mutations.

BACKGROUND: The human FUT2 gene encodes a secretor-type α(1,2)fucosyltransferase, and many population-specific polymorphisms have been reported in the coding region. STUDY DESIGN AND METHODS: Direct sequencing, real-time polymerase chain reaction, and high-resolution melt (HRM) analysis were done to detect single-nucleotide polymorphism (SNPs) and copy number variations (CNVs) in a Vietnamese population. The impacts of two novel mutations on the encoded enzyme were examined by a transient expression study. RESULTS: The major nonfunctional allele in the 294 Vietnamese was se(357,385), whereas no CNV was detected. Two novel SNPs, 818C>A (Thr273Asn) and 853G>A (Ala285Thr), distributed at low frequency, were shown to remarkably affect the enzyme activity. CONCLUSION: The allelic polymorphism of FUT2 in Vietnamese is similar to that of other East and Southeast Asian populations. This result may reflect the history and gene flow of this population. In addition, HRM analysis seems to be a simple and effective method for screening rare SNPs of FUT2 in a large number of samples. [Correction statement added after online publication 21-Dec-2011: Thr273Ala has been updated to Thr273Asn throughout.]

Simultaneous genotyping of three major Se enzyme inactivating SNPs of FUT2 based on a triplex probe-based fluorescence melting-curve analysis.

BACKGROUND: The ABO(H) secretor status is controlled by FUT2-encoded α(1,2)fucosyltransferase (Se enzyme) activity. Three SNPs of FUT2, 302C>T (rs200157007), 385A>T (rs1047781), and 428G>A (rs601338), cause three major variants of nonsecretor (se) or weak-secretor (Sew) alleles. Evidence has been accumulating that suggests the secretor status is associated with various conditions including infectious diseases but a robust multiplex method for assaying relatively large-scale samples to determine the genotype of these three SNPs simultaneously has not been developed yet. METHODS: By combined usage of two Eprobes and a dual-labeled fluorescence probe, we developed a real-time PCR, followed by triplex probe-based fluorescent melting-curve analysis (FMCA) for genotyping of 302C>T, 385A>T, and 428G>A of FUT2 in a single tube. RESULTS: Three genotypes of each of three variants of FUT2 were accurately determined by the triplex probe-based FMCA. We then validated this method using genomic DNA samples of 47 Bangladeshis, and the results obtained by using this method were fully concordant with those by previous Sanger sequencing. CONCLUSIONS: Since the present single triplex probe-based FMCA is robust, fast, and cost-effective, we are able to effectively estimate the secretor status of subjects on a large scale in many populations around the world.

Real-time PCR-based detection of the Alu-mediated deletion of FUT2 (sedel2).

Secretor status of the ABH(O) histoblood group antigens is regulated by secretor type α(1,2)fucosyltransferase encoded by FUT2. The sedel2 allele is a complete deletion of the FUT2 coding region generated by Alu-mediated homologous recombination. This deletion seems to be exclusively encountered in certain Oceanian populations. From the perspective of forensic science, sedel2 is considered to be one of ancestry informative markers for these populations. Real-time PCR followed by melting curve analysis was employed to find primer set to specifically amplify sedel2. We designed primers which produced a 231-bp amplicon specific to sedel2. The specificity of these primers was also confirmed by gel electrophoresis and sequencing of the PCR product. Then, two real-time PCR methods based on melting curve analysis and a hydrolysis probe were designed to determine sedel2 zygosity by adding FUT2-specific primers. These two methods were validated by analyzing 24 Samoan subjects. The results obtained from 24 Samoan subjects by the two methods were fully in accordance with those obtained by a previous conventional PCR method that amplified a 2.7-kb fragment of sedel2. Therefore, these two methods seemed to accurately determine the zygosity of sedel2 and were useful for investigation of the distribution and origin of this deletion.

Fluorescence Melting Curve Analysis for Concurrent Genotyping of Three Tag SNPs in FUT3.

The synthesis of Lewis blood group antigens is governed by two fucosyltransferase genes, FUT2 and FUT3. Evidence is accumulating to suggest that functional polymorphisms of FUT2 and FUT3 are associated with a variety of clinical conditions. Fluorescence melting curve analysis (FMCA), using three different dual-labeled probes for concurrent genotyping of three single nucleotide polymorphisms (SNPs) of FUT3, c.59T>G, c.314C>T, and c.484G>A for Lewis-negative allele inference, was developed and validated using Ghanaian and Caucasian subjects. Although two other SNPs, c.55G>A, and c.61C>T, are located in the probe sequence for c.59T>G, it seems feasible to detect these two SNPs along with c.59T>G. The results obtained by probe-based FMCA were in perfect accordance with those obtained by Sanger sequencing for 106 Ghanaians and 100 Caucasians. The present method is useful and reliable for estimating Lewis-negative alleles on a relatively large scale.

High prevalence of an anti-hypertriglyceridemic variant of the MLXIPL gene in Central Asia.

MLXIPL is a transcription factor integral to the regulation of glycolysis and lipogenesis in the liver. Common variants of the MLXIPL gene (MLXIPL) are known to influence plasma triglyceride levels in people of European descent. As MLXIPL has a key role in energy storage, genetic variations of the MLXIPL may be relevant to physiological adaptations to nutritional stresses that have occurred during the evolution of modern humans. In the present study, we assessed the phenotypic consequences of the Q241H variant of MLXIPL in populations of Asian and Oceanian origin and also surveyed the prevalence of Q241H variant in populations worldwide. Multiple linear regression models based on 2373 individuals of Asian origin showed that the H allele was significantly associated with decreased concentrations of plasma triglycerides (P=0.0003). Direct genotyping of 1455 individuals from Africa, Asia and Oceania showed that the triglyceride-lowering H allele was found at quite low frequencies (0.00-0.16) in most of the populations examined. The exceptions were some Central Asian populations, including Mongolians, Tibetans and Uyghurs, which exhibited much higher frequencies of the H allele (0.21-0.26). The high prevalence of the H allele in Central Asia implies that the Q241H variant of MLXIPL might have been significant for utilization of carbohydrates and fats in the common ancestors of these populations, who successfully adapted to the environment of Central Asia by relying on nomadic livestock herding.

Confirmation that SNPs in the high mobility group-A2 gene (HMGA2) are associated with adult height in the Japanese population; wide-ranging population survey of height-related SNPs in HMGA2.

Adult height is a highly heritable trait in that multiple genes are involved. Recent genome-wide association studies have identified a novel single-nucleotide polymorphism (SNP) rs1042725 in the high mobility group-A2 gene (HMGA2) and shown it to be associated with human height in Caucasian populations. We performed a replication study to examine the associations between SNPs in HMGA2 and adult height in the Japanese population based on autopsy cases. Although we could not confirm a significant association between rs1042725 in HMGA2 and adult height, another SNP, rs7968902, in the gene achieved significance for its association in the same populations, and the effect was the same as that documented previously. These findings permit us to conclude that the SNPs in HMGA2 are common variants influencing human height across different populations. Moreover, a worldwide population study of these SNPs using 14 different populations including Asians, Africans and Caucasians demonstrated that both haplotypes and genotypes for three height-related SNPs (rs1042725, rs7968682 and rs7968902) in HMGA2 were distributed in an ethnicity-dependent manner. This information will be useful for clarifying the genetic basis of human height.

Polymorphic trial in oxidative damage of arsenic exposed Vietnamese.

Arsenic causes DNA damage and changes the cellular capacity for DNA repair. Genes in the base excision repair (BER) pathway influence the generation and repair of oxidative lesions. Single nucleotide polymorphisms (SNPs) in human 8-oxoguanine DNA glycosylase (hOGG1) Ser326Cys; apurinic/apyrimidinic endonuclease (APE1) Asp148Glu; X-ray and repair and cross-complementing group 1 (XRCC1) Arg280His and Arg399Gln in the BER genes were analyzed, and the relationship between these 4 SNPs and the urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) concentrations of 100 Vietnamese population exposed to arsenic was investigated. Individuals with hOGG1 326Cys/Cys showed significantly higher urinary 8-OHdG concentrations than did those with 326 Ser/Cys and Ser/Ser. As for APE1 Asp148Glu, heterozygous subjects showed significantly higher urinary 8-OHdG concentrations than did those homozygous for Asp/Asp. Moreover, global ethnic comparison of the allelic frequencies of the 4SNPs was performed in 10 population and previous reported data. The mutant allele frequencies of hOGG1 Ser326Cys in the Asian populations were higher than those in the African and Caucasian populations. As for APE1 Asp148Glu, Caucasians showed higher mutant frequencies than those shown by African and Asian populations. Among Asian populations, the Bangladeshi population showed relatively higher mutant allele frequencies of the APE1 Asp148Glu polymorphism. This study is the first to demonstrate the existence of genetic heterogeneity in a worldwide distribution of SNPs (hOGG1 Ser326Cys, APE1 Asp148Glu, XRCC1 Arg280His, and XRCC1 Arg399Gln) in the BER genes.