Mikiko Soejima

Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2

The two genes SLC24A5 and SLC45A2 were recently identified as major determinants of pigmentation in humans and in other vertebrates. The allele p.A111T in the former gene and the allele p.L374F in the latter gene are both nearly fixed in light-skinned Europeans, and can therefore be considered ancestry informative marker (AIMs). AIMs are becoming useful for forensic identification of the phenotype from a DNA profile sampled, for example, from a crime scene. Here, we generate new allelic data for these two genes from samples of Chinese, Uygurs, Ghanaians, South African Xhosa, South African Europeans, and Sri Lankans (Tamils and Sinhalese). Our data confirm the earlier results and furthermore demonstrate that the SLC45A2 allele is a more specific AIM than the SLC24A5 allele because the former clearly distinguishes the Sri Lankans from the Europeans.

Population differences in DNA sequence variation and linkage disequilibrium at the PON1 gene

Polymorphisms of the promoter region (−108C/T) and the coding region (192Q/R) of the paraoxonase 1 gene (PON1) showed differences in association with cardiovascular disease risk in various populations. To characterize the genetic variation underlying these important polymorphisms, we examined DNA sequence variation both in a 1.3‐kb promoter region 16.5 kb from codon 192, and in a 1.7‐kb region centered on the 192Q/R polymorphic site of the coding region of PON1, in 30 Africans, 30 Europeans and 64 Japanese. We found 10 polymorphic sites and 11 haplotypes in the 1.3‐kb promoter region and 10 biallelic polymorphic sites and 10 haplotypes in the 1.7‐kb region. From the PON1 sequences of chimpanzees and an orangutan, the ancestral type of codon 192 was found to be R. The number of pairs of polymorphic sites between the promoter and 1.7‐kb regions that were in significant linkage disequilibrium was much higher in a Japanese population than in African and European populations. In addition, the pairs of polymorphic sites in linkage disequilibrium differed among the three populations. These results suggest that some of the population differences in association with risk for coronary heart disease can be explained by population differences in haplotype frequency of PON1 haplotypes.

A biochemical and genetic study on all non-synonymous single nucleotide polymorphisms of the gene encoding human deoxyribonuclease I potentially relevant to autoimmunity

A reduction of deoxyribonuclease I (DNase I) activity levels in the serum of patients with autoimmune diseases has been reported. The objectives of this study were to clarify genetic and biochemical aspects of 12 non-synonymous SNPs in the human gene (DNASE1), potentially giving rise to an alteration in the in vivo DNase I activity levels. Genotyping of all the non-synonymous SNPs was performed in healthy subjects of three ethnic groups including 15 populations using newly developed methods. Among them, only four SNPs, R-21S, Y95S, G105R, and Q222R were polymorphic in all or some populations; Asian group showed a relatively low genetic diversity of these SNPs. Furthermore, the distribution pattern of the common SNP Q222R was classified into three ethnic groups. The activity levels of the amino acid-substituted DNase I forms derived from SNPs R-21S, G105R, P132A, and P197S were significantly high compared with that of the wild-type; the polymorphic SNPs R-21S and G105R gave rise to a high activity-harboring DNase I isoform. On the other hand, activity levels from Q35H, R85G, V89M, C209Y, Q222R, and A224P were significantly low, but these SNPs, except Q222R, were not distributed in any of the populations. However, since these SNPs may produce potentially low levels of in vivo DNase I activity, a minor allele in each SNP will be served as a genetic risk factor for autoimmune diseases. These findings on non-synonymous SNPs in DNASE1 may provide a biochemical-genetic basis for the clarification of a possible relationship between DNase I and the diseases.

Global analysis of genetic variation in human arsenic ( + 3 oxidation state) methyltransferase (AS3MT)

Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene at the global level. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was performed in 827 individuals from 10 populations (Japanese, Korean, Chinese, Mongolian, Tibetans, Sri Lankan Tamils, Sri Lankan Sinhalese, Nepal Tamangs, Ovambo, and Ghanaian). In the African populations, the A allele in A6144T was not observed; the allele frequencies of C35587 were much lower than those in other populations; the allele frequencies of A37616 and C37950 were relatively higher than those in other populations. Among Asian populations, Mongolians showed a different genotype distribution pattern. A lower C3963 and T6144 frequencies were observed, and, in the C37616A and T37950C polymorphism, the Mongolian population showed higher A37616 and C37950 allele frequencies than other Asian populations, similarly to the African populations. A total of 66 haplotypes were observed in the Ovambo, 48, in the Ghanaian, 99, in the Japanese, 103, in the Korean, 103, in the South Chinese, 20, in the Sri Lankan Tamil, 12, in the Sri Lankan Sinhalese, 21, in the Nepal Tamang, 50, in the Tibetan, and 45, in the Mongolian populations. The D values between the SNP pairs were extremely high in the Sri Lankan Sinhalese population. Relatively higher D values were observed in Mongolian and Sri Lankan Tamil populations. Network analysis showed two clusters that may have different origins, African and Asians (Chinese and/or Japanese). The present study is the first to demonstrate the existence of genetic heterogeneity in a world wide distribution of 18 SNPs in AS3MT.

Genetic variation of FUT2 in a Ghanaian population: identification of four novel mutations and inference of balancing selection

The FUT2 is rich in polymorphisms that show population-specific patterns in its coding sequence. In this study, we found four novel substitutions in 121 Ghanaian samples. In addition, statistical tests considering population expansion scenarios suggested that balancing selection might be responsible for the genetic diversity of FUT2 in this population.

Genetic factors associated with serum haptoglobin level in a Japanese population

BACKGROUNDnHaptoglobin (HP) is an acute-phase protein induced by inflammatory stimuli. Its serum level varies in several clinical conditions and among individuals. The common HP alleles (HP(1) and HP(2)), HP complete deletion allele (HP(del)), and two SNPs (rs5472 and rs2000999) have been reported to be possible genetic determinants of serum HP levels so far. However, no studies have explored the relationship among the polymorphisms using the same samples. For this purpose, the impact of these polymorphisms was examined using Japanese heterozygote samples of the HP(del) allele because all of the polymorphisms were found in Japanese samples.nnnMETHODSnWe collected 194 HP(del) heterozygotes and 385 randomly selected samples without HP(del) from 5679 Japanese samples. Genotyping of all polymorphisms was performed by PCR using hydrolysis probes. Phenotyping of the common HP alleles was determined by polyacrylamide gel electrophoresis. Serum HP level was measured by a sandwich ELISA.nnnRESULTSnWe observed a significant association between each of the polymorphisms and serum HP level. Two SNPs, rs5472 and rs2000999, were found to be in almost absolute linkage disequilibrium.nnnCONCLUSIONSnWe suggest that rs5472 is a strong genetic determinant of HP levels in Japanese samples, in addition to rs2000999, the common HP alleles, and HP(del). Further, the haplotypes of these polymorphisms were determined automatically and the effects of the polymorphisms were clearer in HP(del) heterozygotes than samples without HP(del).

Genetic variation of FUT3 in Ghanaians, Caucasians, and Mongolians

BACKGROUND: The FUT3 gene regulates the expression of Lewis blood group antigens. Several lines of evidence suggest association between expression of these antigens and Helicobacter pylori infection or susceptibility to cardiovascular diseases. Single‐nucleotide polymorphisms (SNPs) responsible for the Lewis‐negative phenotype have been reported, but systematic sequence analyses have not yet been performed.

The distribution of haptoglobin-gene deletion (Hpdel) is restricted to East Asians

cally valid. The intention-to-treat analysis is a decidedly inferior method when bias or imputed data are introduced into the analysis or by including large numbers of untreated or improperly treated patients. These caveats have not been considered in most previously published meta-analyses. In general, the treatment that leads to the best outcomes for individual patients, based on scientifically valid observations and clinical trials, should guide public policy. If a policy leads to individual benefit, it benefits the public health. In our view, a policy that allows many patients to receive inferior, more dangerous, nonleukoreduced transfusions, as selective leukoreduction does, is not in the public interest. Although not mentioned in our meta-analysis, we believe that the findings from randomized trials of leukoreduction in surgical patients, as well as multiple other proven benefits of leukoreduction, mandate universal leukoreduction as a cost and sometimes life-saving advance in transfusion medicine. In the United States, unlike the Netherlands, universal leukoreduction has not yet been implemented. We hope that our study provides a rationale and impetus for moving forward this improvement in patient care. Neil Blumberg, MD Transfusion Medicine Unit Department of Pathology and Laboratory Medicine e-mail: neil_blumberg@urmc.rochester.edu Joanna M. Heal, MBBS, MRCP Hematology-Oncology Unit Department of Medicine University of Rochester Medical Center Rochester, NY

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.

Sec1-FUT2-Sec1 hybrid allele generated by interlocus gene conversion.

BACKGROUND: Many single‐nucleotide polymorphisms have been identified in the coding region of the FUT2 locus, which encodes secretor type α(1,2)fucosyltransferase. In addition, three recombination alleles have been reported. Of these recombination alleles, a fusion gene generated by an unequal crossing over between Sec1, a pseudogene that locates 23u2003kb upstream to and has high sequence homology with FUT2 and FUT2, was identified as a Japanese‐specific nonsecretor allele (sefus).