Sequence-specific Oligonucleotide Probes Research Articles

Usefulness of human leucocyte antigen‐B27 subtypes in predicting ankylosing spondylitis: Taiwan experience

Genetic factors are clearly attributed to the susceptibility of ankylosing spondylitis (AS). The human leucocyte antigen (HLA)-B27 proved to be the very useful marker for diagnosing AS. The aim of this study was to determine the prevalence of HLA-B27 subtypes in Taiwan and to investigate whether these subtypes may be of help in predicting the diagnosis of AS. A total of 314 patients with AS and a control group of 71 subjects positive for HLA-B27 detected by flow cytometry analysis were recruited for the study. HLA-B27 subtypes were confirmed by the polymerase chain reaction-sequence-specific primers and sequence-specific oligonucleotide probing. Four B27 alleles were identified: B*2704, B*2705, B*2706 and B*2707. HLA-B*2704 was the predominant allele. There were significant differences in the distribution of HLA-B27 subtypes between patients with AS and controls. Five of them who were homozygous for the B*2704 allele were solely found in AS group but not in controls. Statistical analysis showed that B*2704 was positively associated with AS, which suggested an increased possibility of having AS. Other HLA-B27 subtypes showed no strong correlation with AS. In the Taiwanese population, susceptibility to AS was determined by the presence of HLA-B*2704. Although B*2706 was reported to have a negative association with AS in Taiwanese, Thai and Chinese Singaporean populations, we report, in our study, two AS patients with B*2706 (0.6%). Disease heterogeneity suggests that other than genetic background, many pathogenic factors could be associated with AS. This may need to be investigated with a larger group of patients with AS and controls.

Association of HLA DRB1-DQA1-DQB1 haplotypes with rheumatic heart disease in Taiwan

This case–control study was carried out to investigate the possible relationship between the gene frequencies of HLA-DRB1, -DQA1 and -DQB1 alleles/haplotypes and rheumatic heart disease (RHD) among the Chinese population in Taiwan. A group of 115 patients with RHD documented by echocardiography, and a group of 115 normal controls were studied. The HLA-DRB1, -DQA1 and -DQB1 allele frequencies were determined by polymerase chain reaction and sequence-specific oligonucleotide probe. As compared with controls, patients with RHD had an increased frequency of DR11-05-DQ7 haplotype and a decreased frequency of DR4-03-DQ4 haplotype. The frequencies of DRB1, DQA1 or DQB1 alleles were not significantly different between RHD patients and controls. Further categorization of RHD patients into mitral valve disease and combined valve disease subgroups revealed no statistical difference in these alleles when compared with the two subgroups. Patients with RHD have a higher frequency of DR11-05-DQ7 haplotype and a lower frequency of DR4-03-DQ4 haplotype , which indicates that certain HLA DRB1-DQA1-DQB1 haplotypes in determining the risk/protection of RHD in Taiwan Chinese.

HLA-B51 gene and its expression in association with Behçet’s Disease in Denizli Province of Turkey

Behçet's Disease (BD) is a multisystemic inflammatory disorder as a triad of symptoms including recurrent oral and genital aphthous ulceration, and uveitis with unknown pathogenesis. Many researchers have tried to investigate the association of HLA-B51 gene with the BD. We aimed to investigate the association of the HLA-B51 gene and its expression, also polymorphic structure by PCR, RT-PCR and sequence specific oligonucleotide primers and probes in BD patients (n: 35) and control group (n: 50). According to our results, we did not observe any association in between HLA-B51 gene, its polymorphism, expression and BD patients.

Genetic factors for lone atrial fibrillation

Atrial fibrillation (AF) may result from an electric conduction disturbance, increased hemodynamic stress, ischemia, inflammation, or remodeling in atria. Although genetic epidemiological studies have identified several genetic variants as risk factors for AF, the genetic determinants of this condition remain largely unknown. The purpose of the present study was to identify gene polymorphisms that confer susceptibility to lone AF. The study population comprised 1069 unrelated Japanese individuals, including 196 subjects with chronic lone AF and 873 controls. The genotypes for 40 polymorphisms of 32 candidate genes were determined by a method that combines the polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. Multivariable logistic regression analysis with adjustment for age, sex, body mass index, and the prevalence of smoking, hypertension, diabetes mellitus, and hyperchole-sterolemia as well as a stepwise forward selection procedure revealed that the -1306C-->T polymorphism of the matrix metalloproteinase 2 gene (MMP2) and the -592A-->C polymorphism of the interleukin 10 gene (IL10) were significantly (false discovery rate of <0.05) associated with the prevalence of AF. The T allele of the MMP2 polymorphism and the C allele of the IL10 polymorphism were a risk factor for and protective factor against AF, respectively. Determination of the genotypes for these polymorphisms may thus prove informative for assessment of the genetic component of AF.

Indiscernible benefit of high-resolution HLA typing in improving long-term clinical outcome of unrelated umbilical cord blood transplant

The success of allogeneic hematopoietic stem cell transplantation depends in part on the accuracy of human leukocyte antigen (HLA) matching between the donor-recipient pair. The higher the number of matching HLA alleles, the smaller the chance that the transplant recipient will develop complications. Umbilical cord blood (UCB) transplantation was noted to result in a remarkably low frequency and severity of graft-versus-host disease (GvHD) and graft rejection compared to that in unrelated bone marrow transplant recipients. At present most banks match UCB donors for respective recipients by HLA-A, -B low-resolution typing and -DRB1 high-resolution typing. We retrospectively conducted high-resolution sequence-based HLA typing on DNA samples available from 65 Chinese UCB-recipient pairs typed previously by using low-resolution sequence-specific oligonucleotide probes and sequence-specific primers, and evaluated the clinical outcome. High-resolution typing revealed imperceptible HLA alleles that were hardly identified in low-resolution typing. Univariate analyses demonstrated no significant correlation between the extents of high-resolution HLA disparity with engraftment, graft failure, acute GvHD, transplant-related mortality and long-term 6-year overall survival. Data from the study suggest that high-resolution typing for HLA-A, -B and -DRB1 contributed no substantial improvement to UCB transplant outcome. Low-resolution typing appears to be amenable to matching UCB-recipient pairs without compromising the quality of transplant.

High-throughput killer cell immunoglobulin-like receptor genotyping by MALDI-TOF mass spectrometry with discovery of novel alleles

The killer cell immunoglobulin-like receptors (KIR) interact with major histocompatibility complex (MHC) class I ligands to regulate the functions of natural killer cells and T cells. Like human leukocyte antigens class I, human KIR are highly variable and correlated with infection, autoimmunity, pregnancy syndromes, and transplantation outcome. Limiting the scope of KIR analysis is the low resolution, sensitivity, and speed of the established methods of KIR typing. In this study, we describe a first-generation single nucleotide polymorphism (SNP)-based method for typing the 17 human KIR genes and pseudogenes that uses analysis by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. It is a high-throughput method that requires minute amounts of genomic DNA for discrimination of KIR genes with some allelic resolution. A study of 233 individuals shows that the results obtained by the SNP-based KIR/MALDI-TOF method are consistent with those obtained with the established sequence-specific oligonucleotide probe or sequence-specific polymerase chain reaction methods. The added sensitivity of the KIR/MALDI-TOF method allowed putative novel alleles of the KIR2DL1, KIR3DL1, KIR2DS5, and KIR2DL5 genes to be identified. Sequencing the KIR2DL5 variant proved it was a newly discovered allele, one that appears associated with Hispanic and Native American populations. This KIR/MALDI-TOF method of KIR typing should facilitate population and disease-association studies that improve knowledge of the immunological functions of KIR-MHC class I interactions.

Molecular diversity of HLA‐A, ‐B and ‐C alleles in a North Indian population as determined by PCR‐SSOP

We have used molecular methods to determine the frequencies of human leukocyte antigen (HLA)-A, -B and -C alleles in normal, healthy, unrelated individuals from North India using polymerase chain reaction and hybridization with sequence-specific oligonucleotide probes as there is no comprehensive report showing molecular diversity of all the class-I alleles present in North Indians. A*0101, A*0206, A*0301, A*1101, A*6801, A*2401 and A*3101 were the most prevalent alleles of the A locus with 91.11% of the samples showing heterozygosity. At the HLA-B locus a total of 47 B locus alleles were observed and the only allele found with an allele frequency of 15% was B*5801. Other frequent B-locus alleles observed were B*5101, B*3503 and B*4006 with relatively less frequent alleles like B*5201, B*3501, B*0702, B*4403, B*5701, B*1801 and B*5501. Of the samples studied 92.31% were heterozygous for B-locus alleles. Cw*0602 and Cw*0401 were the most frequent C-locus alleles. Other frequent C-locus alleles were Cw*0102, Cw*0302, Cw*0701, Cw*0702, Cw*1202, Cw*1203, Cw*1502 and Cw*1503. HLA alleles common in Africans like B*5801, A*68012, B*5301, B*44032, B*4006 and Cw*1701 were observed in the North Indians besides oriental alleles like B*1301, B*1502 and B*4001 confirming that the genetic make-up of North Indians is Caucasoid with elements of Mongoloid and Negrito races. Some new/rare alleles like B*1802, described as a new allele from Thailand and B*8101, described earlier in a Bubi population were also observed although with low frequencies, showing the diversity of HLA class-I alleles present in the North Indians.

The association of HLA-DRB1 alleles with rheumatoid arthritis in the Chinese Shantou population: a follow-up studyThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process.

We investigated the distribution of HLA-DRB1 alleles in a sample of the Chinese Shantou population, and explored the relationship between HLA-DRB1 alleles and the susceptibility and clinical features of rheumatoid arthritis (RA). We studied 117 consecutive patients with RA and control groups, including 38 cases of systemic lupus erythematosus and 100 healthy individuals. HLA-DRB1 genotyping was performed using PCR with sequence-specific primers. HLA-DRB1*04 subtypes were detected using spot hybridization of PCR products with sequence-specific oligonucleotide probes. We compared the frequency of HLA-DRB1 alleles in healthy control patients with that in patients with RA. Patients with RA were evaluated for sex, age at disease onset, disease duration, extra-articular involvement, presence of autoantibodies, global functional status, and radiographic damage. The frequency of HLA-DRB1*04 was found to be significantly higher in RA patients than in healthy individuals (49.6% vs 18.0%, odds ratio = 4.478, P < 0.001). HLA-DRB1*0405 was the most prominently associated subtype in RA patients (62.1% vs 27.8%, odds ratio = 4.255, P = 0.011). Compared with the HLA-DRB1*04-negative RA group, the mean duration of RA in the HLA-DRB1*04-positive RA group was longer, and the mean age at disease onset was lower. A 2-9 year follow-up study was performed, and the risk factors associated with the radiographic progression of RA were determined. Logistic regression analysis revealed that only HLA-DRB1*04 alleles were significantly associated with the radiographic progression of RA (B = 2.652, P = 0.018, Exp(B) = 14.182). Our observations indicated that the HLA-DRB1*04 alleles, especially the subtype HLA-DRB1*0405, were significantly associated with RA susceptibility in the Chinese Shantou population. The HLA-DRB1*04 alleles may be associated with the severity of RA.

Gender differences in the association of gene polymorphisms with type 2 diabetes mellitus

Type 2 diabetes mellitus is a complex metabolic disorder in which endogenous sex hormones may contribute to sex-dependent etiologies. We hypothesized that genetic variants related to type 2 diabetes mellitus might differ between men and women. We thus performed a large-scale association study to identify gene polymorphisms associated with type 2 diabetes mellitus in men and women separately. The study population comprised 4854 unrelated Japanese individuals (2688 men, 2166 women), including 1490 subjects with type 2 diabetes mellitus (969 men, 521 women). The genotypes for 16 gene polymorphisms were determined with a method that combines the polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. Multivariable logistic regression analysis with adjustment for age, body mass index, and smoking status revealed that the T-->G (3' UTR) polymorphism of the thrombospondin 2 gene (THBS2), the -603A-->G polymorphism of the coagulation factor III gene (F3), and the G-->T (intron 2) polymorphism of the adipocyte, C1Q, and collagen domain containing (adiponectin) gene (ADIPOQ) were significantly associated with the prevalence of type 2 diabetes mellitus in men, and that the A-->G (Arg160Gly) polymorphism of the paraoxonase 1 gene (PON1) was significantly associated with this condition in women. A stepwise forward selection procedure demonstrated that genotypes of THBS2, F3, and ADIPOQ were significant determinants of type 2 diabetes mellitus in men, and that genotype of PON1 significantly affected this condition in women. Genotyping of these polymorphisms may prove informative for assessment of the genetic component of type 2 diabetes mellitus for men and women separately.

Distribution of the killer cell immunoglobulin‐like receptors in Mexican Mestizos

Understanding the complex interaction between human leukocyte antigen (HLA) and killer immunoglobulin-like receptor (KIR) requires study of both HLA and KIR diversity in the same population. The presence of KIR genes 2DL1, 2, 3, 4, 5, KIR3DL1, 3DL2, 3DL3, KIR2DS1, 2DS2, 2DS3, 2DS4, 2DS5, KIR3DS1, KIR3DP1, KIR2DP1 was determined in 54 unrelated Mexican Mestizo donors. The PCR sequence-specific oligonucleotide probe One Lambda kit (Luminex) kindly given by J. Lee was used for typing. The software analyses the combination obtained for each of the five exons. Five controls (UCLA DNA exchange) were run as quality control. The gene frequency (GF) was calculated for the 16 KIR loci; the GF of individual genes was 100% for 2DL4, 3DL1, 3DL2, 3DL3, 3DP1. KIR2DL1 (76.43%), KIR2DL2 (37.64%), KIR2DL3 (76.43%), KIR2DL5 (29.29%), KIR3DS1 (23.02%), KIR2DS1 (21.83%), KIR2DS2 (37.64%), KIR2DS3 (50.93%), KIR2DS4 (86.93%), KIR2DS5 (29.29%), KIR2DP1 (86.39%). We observed similar frequencies with Caucasians and Mediterraneans, with exceptions: KIR3DL1 which was present in 100% Mexicans, ranged from 62% to 75% in Caucasians; 2DS3 (50.9%) vs 14-20% 2DS4 (86.39%) vs 65-79% and 2DS5 (29.29%) vs 11-18% in Caucasians. The finding of 23 phenotypes in 54 individuals accounting for both chromosomes, demonstrates the enormous diversity. We found 14 different combinations of stimulatory KIRs in the phenotypes; every subject had at least one stimulatory KIR; in all of them, 2DS4 existed except for one person who may have some new combination: 2DS2 2DS3. Extended family data will offer accurate and precise haplotypes to provide an insight on the significance of ethnic distribution and KIR repertoire.

Island-wide diversity in single nucleotide polymorphisms of the Plasmodium vivax dihydrofolate reductase and dihydropteroate synthetase genes in Sri Lanka

BackgroundSingle nucleotide polymorphisms (SNPs) in the Plasmodium vivax dihydrofolate reductase (Pfdhfr) and dihydropteroate synthetase (Pvdhps) genes cause parasite resistance to the antifolate drug combination, sulphadoxine/pyrimethamine (SP). Monitoring these SNPs provide insights into the level of drug pressure caused by SP use and presumably other antifolate drugs. In Sri Lanka, chloroquine (CQ) with primaquine (PQ) and SP with PQ is used as first and second line treatment, respectively, against uncomplicated Plasmodium falciparum and/or P. vivax infections. CQ/PQ is still efficacious against P. vivax infections, thus SP is rarely used and it is assumed that the prevalence of SNPs related to P. vivax SP resistance is low. However, this has not been assessed in Sri Lanka as in most other parts of Asia. This study describes the prevalence and distribution of SNPs related to P. vivax SP resistance across Sri Lanka.Subjects and methodsP. vivax-positive samples were collected from subjects presenting at government health facilities across nine of the major malaria endemic districts on the island. The samples were analysed for SNPs/haplotypes at codon 57, 58, 61 and 117 of the Pvdhfr gene and 383, 553 and 585 of the Pvdhps gene by applying PCR followed by a hybridization step using sequence specific oligonucleotide probes (SSOPs) in an ELISA format.ResultsIn the study period, the government of Sri Lanka recorded 2,149 P. vivax cases from the nine districts out of which, 454 (21.1%) blood samples were obtained. Pvdhfr haplotypes could be constructed for 373 of these. The FSTS wild-haplotype was represented in 257 samples (68.9%), the double mutant LRTS haplotype was the most frequently observed mutant (24.4%) while the triple mutation (LRTN) was only identified once. Except for two samples of the single mutated Pvdhps GAV haplotype, the remaining samples were wildtype. Geographical differences were apparent, notably a significantly higher frequency of mutant Pvdhfr haplotypes was observed in the Northern districts.ConclusionSince SP is rarely used in Sri Lanka, the high frequency and diversity of Pvdhfr mutations was unexpected indicating the emergence of drug resistant parasites despite a low level of SP drug pressure.

The role of human leukocyte antigen genes in the formation of abdominal aortic aneurysms

Increasing evidence suggests an autoimmune component to abdominal aortic aneurysm (AAA) formation. This study was conducted to determine if a difference exists in human leukocyte antigen (HLA) allele distribution between patients with AAA and population controls, and between patients with small and large AAA. Patients with known AAA attending the vascular unit were consented for recruitment. HLA-A, HLA-B and HLA-DR was determined by polymerase chain reaction and sequence-specific oligonucleotide probes. The distribution of these alleles in the Northern Ireland general population was obtained from the histocompatibility and immunogenetics database. The chi(2) test was used for statistical analysis with Bonferroni correction. A total of 241 AAA patients were recruited, with a wide range of aneurysm size. In class I, the most frequent allele families were HLA-A*02 and *01 and HLA-B*07, *08, and *44. In class II, HLA-DRB1*03, *04, *07, and *15 were the most frequent. HLA-A*11 was lower in AAA cases (10.4% vs 15.0%; P = .08), whereas HLA-B*08 was lower in the controls (29.8% vs 36.5%; P = .05) and HLA-DRB1*11 was lower in cases (4.2% vs 8.1%; P = .05). After Bonferroni correction, however, the proportion of allele families was not significantly different in AAA patients compared with the proportion seen in controls. HLA-DRB1*11 and *14 had a lower prevalence in large AAAs (0.9% vs 6.7% [P = .05]; 0.0% vs 5.9% [P = .03]). HLA-A*68 was also lower in large AAA (1.9% vs 11.9%; P = .0075). After Bonferroni correction, however, no difference was demonstrated between small and large aneurysms. This study provides more definitive results on this important subject and has failed to demonstrate the risk association between AAA and these alleles as reported by others. Therefore, the role of these particular genes and the autoimmune component in AAA etiology does not appear to be as crucial as previously proposed.

Identification of a New HLA-B Allele (B*1576) by Haplotype Specific Extraction

Routine typing of a potential bone marrow donor by sequence-specific oligonucleotide probes (SSOP) and sequence based typing (SBT) produced inconclusive subtyping results, suggesting a new allele. A magnetic bead-based method, haplotype specific extraction (HSE), was used to separate the diploid sample into its haploid components. The sample was then re-typed using standard SBT, revealing a new human leukocyte antigen (HLA) allele, since named B*1576. HSE used in conjunction with standard SBT is a convenient and simple tool for resolving ambiguous and novel allele combinations without the need for amplification or subcloning.

Genetic risk for restenosis after coronary stenting

Objectives The purpose of the present study was to identify gene polymorphisms that confer susceptibility to restenosis after bare-metal stenting of coronary arteries, and thereby to predict the genetic risk for this condition. Methods and results The study population comprised 461 unrelated Japanese individuals (350 men, 111 women) who underwent stent implantation, including 107 subjects who developed in-stent restenosis and 354 subjects without this condition. The genotypes for 142 polymorphisms of 121 candidate genes were determined with a method that combines the polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. Multivariate logistic regression analysis with adjustment for the prevalence of diabetes mellitus revealed that the 1615G → A polymorphism of BCHE, the 7,067,365C → A polymorphism of INSR, the C → T polymorphism of GPX1, the G → A polymorphism of ROS1, and the G → A polymorphism of MMP9 were associated ( P < 0.05) with in-stent restenosis. Further analysis with adjustment both for the prevalence of diabetes mellitus and for quantitative coronary angiographic measurements revealed that the BCHE, GPX1, and ROS1 genotypes were independently associated ( P < 0.05) with in-stent restenosis. Conclusions Determination of the genotypes for BCHE, GPX1, and ROS1 may prove informative for assessment of the genetic risk for in-stent restenosis.

Contribution of MHC class I region to genetic susceptibility for giant cell arteritis

The aim of this study was to assess the potential contribution of HLA-class I MICA and HLA-B gene polymorphisms towards the pathogenesis of giant cell arteritis (GCA). Ninety-eight biopsy-proven GCA patients and 225 ethnically matched controls from Lugo, Northwest Spain, were genotyped for the MICA-TM microsatellite polymorphism using a polymerase chain reaction (PCR)-based method. Genotyping of HLA-B was performed using PCR and detection with a reverse sequence-specific oligonucleotide (SSO) probes system. A significant difference in the distribution of the alleles of MICA between patient and control groups (P = 0.005) was found. This was due to an increased frequency of the MICA A5 allele in GCA patients compared with controls (26 vs 13.6%; P = 0.0001; P(C) = 0.0005; OR 2.2, 95% CI 1.4-3.4). In addition, the HLA-B*15 allele showed a higher frequency in GCA patients compared with controls (P = 0.004; P(C) = 0.04; OR 2.7, 95% CI 1.3-5.7). Interestingly, the association observed with the MICA A5 allele seems to be independent of linkage disequilibrium with HLA-B, as well as independent of that previously described with HLA-DRB1*04. Remarkably, simultaneous presence of MICA A5 and HLA-B*15 or HLA-DRB1*04 genetic markers leads to an increase in the OR obtained for each individual genetic marker (MICA A5 + B*15 OR 3.2; MICA A5 + DRB1*04 OR 5.8). Our results provide the first evidence that the MICA and HLA-B genes are independently associated with the genetic susceptibility to GCA, and suggest that several genes within the MHC might have independent effects in the susceptibility to this systemic vasculitis.

HLA-B Bw4 alleles and HIV-1 transmission in heterosexual couples

Genetic factors may play a role in the transmission of HIV-1. Because HLA-B alleles influence HIV-1 disease progression and viral levels, they might also influence HIV-1 transmission. To investigate if the presence of HLA-B alleles with the Bw4 epitope in HIV-1-infected men decreased the risk of transmission to their female sex partners. The study comprised 304 HIV-1-infected men with hemophilia and 325 female sex partners. HLA class I genes were amplified using sequence-specific primers. Products of the polymerase chain reaction were blotted on nylon membranes and hybridized with sequence-specific oligonucleotide probes. Logistic regression models were used to calculate odds ratios (OR) and 95% confidence intervals (CI) for HIV-1 infection among the women. Among the 325 women, 44 (13.5%) were infected with HIV-1. HIV-1 infection in the women was associated with the HLA-B genotype of their male partner [Bw6/Bw6, 22/118 (18.6%); Bw4/Bw6, 18/154 (11.7%); Bw4/Bw4, 4/53 (7.6%)]. Compared with men who were homozygous for Bw6, men who carried Bw4 were about half as likely to have transmitted HIV-1 to their female partner (OR, 0.52; 95% CI, 0.27-0.98; P = 0.04). Transmission was higher among couples in which the man's ethnicity was other than White (OR, 2.60; 95% CI, 1.25-5.40; P = 0.01), but the association between HIV-1 transmission and HLA-B genotype was not confounded by race. The presence of HLA-Bw4 in HIV-1-infected men was associated with a decreased risk of male-to-female HIV-1 transmission, which suggests that these alleles reduce infectivity for HIV-1.

Studies on the Expression of the Deleted KIR2DS4*003 Gene Product and Distribution of KIR2DS4 Deleted and Nondeleted Versions in Different Populations

A KIR2DS4 deletion variant allele, previously identified through killer immunoglobulinlike receptor (KIR) polymerase chain reaction–sequence-specific oligonucleotide probe (PCR-SSOP) typing, was functionally investigated using an in vitro cell line model system and in vivo protein expression studies. The KIR2DS4 deletion variant has previously been found in 80% of individuals from Northern Ireland, indicating that it is present at a high incidence in this population. It differs from the normal KIR2DS4 sequence by a 22 bp deletion in exon 5, which causes a frame shift, yielding a truncated KIR2DS4 protein with loss of the transmembrane and cytoplasmic domains of the full-length KIR2DS4 protein. This study has determined that the deleted variant of KIR2DS4 is not anchored to the cell membrane but encodes a soluble form of the protein that is potentially secreted. The frequencies of the deleted and nondeleted versions were also determined in several world-wide populations. A trend was observed towards decreased frequencies of KIR2DS4 deleted variant occurrence in populations having KIR2DS4 as the only activating KIR gene.

Association of gene polymorphisms with myocardial infarction in individuals with or without conventional coronary risk factors

The purpose of the present study was to assess the genetic risk for myocardial infarction (MI) in individuals with or without conventional coronary risk factors and thereby to contribute to the personalized prevention of MI in such individuals. The study population comprised 3483 unrelated Japanese individuals (1913 men, 1570 women). The 1192 subjects with MI (926 men, 266 women) and 2291 controls (987 men, 1304 women) either had or did not have conventional coronary risk factors, including hypertension, hypercholesterolemia, and diabetes mellitus. The genotypes for 164 polymorphisms of 137 candidate genes were determined by a method that combines the polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. Multivariable logistic regression analysis and a stepwise forward selection procedure revealed that nine different polymorphisms were significantly (P<0.005) associated with MI among individuals with or without hypertension, hypercholesterolemia, or diabetes mellitus: 1018Cright curved arrow T of GP1BA, -108/3Gright curved arrow 4G of IPF1, 677Cright curved arrow T of MTHFR, and Gright curved arrow A of UTS2 in hypertensive individuals; 2445Gright curved arrow A of FABP2, -108/3Gright curved arrow 4G of IPF1, 677Cright curved arrow T of MTHFR, -11,377Cright curved arrow G of ACDC, Aright curved arrow G of AKAP10, 11,496Gright curved arrow A of F7, and 46Cright curved arrow T of F12 in individuals without hypercholesterolemia; 2445Gright curved arrow A of FABP2 in diabetic individuals; and -108/3Gright curved arrow 4G of IPF1 in nondiabetic individuals. Polymorphisms associated with MI may thus differ among individuals with different conventional coronary risk factors. Stratification of subjects on the basis of such risk factors may thus be important in order to achieve personalized prevention of MI with the use of genetic information.

The preparation of oligonucleotide chips for detecting BMPR-IB gene polymorphism in sheep

BMPR-IB gene increases ovulation rate and litter size as a major gene in Chinese Merino, because of 746 A to G mutation. The aim of this study was to make oligonucleotide chips to determine single nucleotide polymorphism (SNP) in BMPR-IB gene. The oligonucleotide chips were manufactured by using six sequence-specific oligonucleotide probes derived from polymorphic regions in the mutation and spotting the probes by microarrayer onto the aldehyde modified glass slides. The 746 A to G mutation was detected with ovine blood in reaction cells of chips. The results were identified by designed the Arraydoctor 2.0 software, in accordance with those of restriction fragment length polymorphisms (RFLP). The results showed the oligonucleotide chips are a parallel, accurate and effective way for screening prolificacy in molecular-assisted selection(MAS)of sheep.

Complete Sequencing of the HLA-A*68020102 Novel Allele Identified in Two Caucasoid Families

We describe here the isolation and the full-length sequence of the coding region of the HLA new variant at the HLA-A locus officially named A*68020102. This variant shows an 11 base pairs deletion within the 5′ UTR region. The exon sequence is identical to that of A*6802 and the commercially available anti-A68 typing sera react with the antigen coded by the allele A*68020102. This variant was originally identified in two unrelated Caucasoid families because of discrepant HLA typing results between serology, Sequence Specific Oligonucleotide Probe (SSOP), and SBT. In fact, the A68 assigned by serology was undetectable with the molecular techniques. This has occurred because the deletion present in A*68020102 prevents specific amplification of HLA-A locus by some commercially available typing kits.