Strong Positive Linkage Disequilibrium Research Articles

Association study of dopamine receptor genes polymorphisms with the risk of schizophrenia in the Han Chinese population.

Schizophrenia is a highly heritable psychiatric disorder often associated with dopamine-related genetic variations. Thus, we performed a case-control study in 1504 Han Chinese population to evaluate the association of DRD1, DRD2 and DRD3 polymorphisms with schizophrenia. No statistically significant difference in allelic or genotypic frequency was found between schizophrenia and control subjects. Strong positive linkage disequilibrium was detected among the SNPs within DRD1 and DRD2. However, no positive haplotype distribution was found to be associated with schizophrenia. Our results indicated that DRD1, DRD2 and DRD3 may not be the susceptibility genes for schizophrenia in the Chinese Han population.

Study of the structure and impact of human leukocyte antigen (HLA)-G-A, HLA-G-B, and HLA-G-DRB1 haplotypes in families with recurrent miscarriage

A 14-base pair (bp) long insertion (ins) /deletion (del) polymorphism in exon 8 in the 3′-untranslated region of the human leukocyte antigen (HLA)-G gene is suggested to affect transcription of the gene. Carriage of the G14bp ins is associated with low levels of soluble HLA-G and increases the risk of recurrent miscarriage (RM). Due to existence of strong linkage disequilibrium (LD) in the HLA region, the primary susceptibility genes for RM in the HLA-G region have not yet been identified. HLA-A, -B, -DRB1, and -G14bp polymorphisms were investigated in 29 Caucasian families with two or more siblings suffering unexplained RM. Strong positive LD was detected between the G14bp ins and HLA-A*01, -A*11, -A*31, -B*08, and DRB1*03, whereas strong negative LD was found between G14bp ins and HLA-A*02, -A*03, and -A*24. The frequency of haplotypes with HLA-G14bp ins inherited from the mother was significantly increased in probands with RM ( p = 0.05). The increased compatibility between probands and their mothers for maternal G14 ins positive haplotypes suggests that maternal-fetal compatibility for chromosomal segments adjacent to HLA-G locus is a risk factor for female offspring to experience RM in their later reproductive life.

A study of HLA-G polymorphism and linkage disequilibrium in renal transplant patients and their donors

The role of the Major Histocompatibility Complex (MHC) in transplantation immunology is widely known. Incompatibilities associated with Human Leukocyte Antigens (HLA) between donors and recipients are related to poorer prognosis in allograft acceptance and survival, often resulting in rejection episodes. HLA-A, HLA-B, HLA-DR and HLA-DQ compatibility are widely studied in clinical transplants but few studies investigated the influence of non-classical HLA loci, such as HLA-G, a non-classical class I HLA gene located at 6p21.31 in the MHC region, i.e. 300 kb telomeric to HLA-A. MHC region genes are characterized by extreme polymorphism as well as strong positive linkage disequilibrium (LD) between HLA loci (alleles). LD studies related to MHC region provide investigators with a tool to assess candidate genes with an at-risk HLA haplotype, with implications for allograft transplants, human reproduction and disease susceptibility. Many studies reported striking LD between HLA-G and HLAA alleles and also between HLA-G and HLA Class II alleles, but the biologicalimplications for these findings are not clear yet. DNA sequencing methodology was used to determine HLA-G (exons 2 and 3) polymorphisms from 52 patients who underwent kidney transplantation and their donors. It is the purpose of this study to investigate the influence of HLA-G polymorphism in a set of kidney transplants and the occurrence of rejection episodes. It was observed that pairs with 2 HLA-G matches presented a lower risk of rejection occurrence than those pairs with 0 or 1 match. It was also observed that subjects whose genotype presented one synonymous substitution (S) in one HLA-G allele in the HLA-G⁎0101 group of alleles and another allele with a non-synonymous substitution (N/S) on HLA-G⁎0103, HLA-G⁎010401, HLA-G⁎010403 or HLA-G⁎0105N alleles, apparently had a greater chance of rejection episodes. Additionally, HLA-G, as well as HLA-A, -B e -DR, compatibility may also be important for allograft acceptance (rejection probability lower than 0.09%). Besides, heterozygous S/NS patients had a five times greater chance of rejection than S/S and NS/NS patients. Some haplotypes found in the present study were already described in literature: A⁎01-G⁎01B (⁎010102 or ⁎0106), A⁎03-G⁎0101A, A⁎23-G⁎010401, A⁎26-G⁎01B, A⁎31-G⁎0103, A⁎02-G⁎0101A, A⁎24-G⁎0101A, A⁎33-G⁎0103, A⁎68-G⁎01B. We have also described LD between HLA-G alleles and HLA class II DRB1⁎ allelic groups and found significant LD between DRB1⁎04-G⁎01B, DRB1⁎13-G⁎010401, DRB1⁎14-G⁎010108, DRB1⁎15-G⁎0103, DRB1⁎03-G⁎0101A and DRB1⁎03-G⁎01B.

HLA class-I and HLA class-II phenotypic, gene and haplotypic frequencies in Tunisians by using molecular typing data.

The aim of this study is to define a reliable reckoning of gene frequencies and six-locus haplotypic frequencies of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1 and HLA-DPB1 in the Tunisian population. One hundred unrelated random, healthy people originating from various parts of Tunisia were typed for the alleles of the loci mentioned above by using the molecular techniques polymerase chain reaction--hybridization with oligonucleotide probe (PCR-SSO) and sequence specific primers (SSP). The population studied appeared to be in Hardy-Weinberg equilibrium. Allelic frequency distributions were observed at each locus. The most frequent HLA-A alleles were HLA-A*02 (39%) HLA-A*0101 (25%), HLA-A*30 (21%) and HLA-A*2301 (18%). Moreover, HLA-3A*3601, HLA-1A*6601, HLA-1A*3402 and HLA-2A*8001 were found; however, no HLA-A*4301 was detected. For the HLA-B locus, the most common in descending order were HLA-B*44 (22%), HLA-B*5001 (19%), HLA-B*51 (16%) and HLA-B*18 (15%). Among the 28 alleles HLA-Cw detected, HLA-Cw*6 and HLA-Cw*7 were highly predominant with the frequencies of 33 and 30%, respectively. For the HLA class-II loci, HLA-DRB1*0701, HLA-DRB1*11, HLA-DRB1*13 and HLA-DRB1*03 were the most frequent DR alleles. For the HLA-DPB1, HLA-DPB1*0401, HLA-DPB1*0301 and HLA-DPB1*0201 were the most frequent DP alleles. Many haplotypes were in a strong positive-linkage disequilibrium. The most frequent haplotypes for HLA-A, HLA-B, HLA-C and HLA-DRDQ were HLA-A*3301, HLA-B*1402, HLA-Cw*0802, HLA-DRB1*0102, HLA-DQA1*0101 and HLA-DQB1*0501; HLA-A*2402, HLA-B*0801, HLA-Cw*0702, HLA-DRB1*0301, HLA-DQA1*0501 and HLA-DQB1*0201; HLA-A*2902, HLA-B*4403.1, HLA-Cw*1601, HLA-DRB1*0701, HLA-DQA1*0201 and HLA-DQB1*0202; HLA-A*3002, HLA-B*1801, HLA-Cw*0501, HLA-DRB1*0301, HLA-DQA1*0501 and HLA-DQB1*0201, with frequencies between 0.025 and 0.015. These data can be used as control data for HLA disease associations and paternity studies, but they are also important for the evaluation of the probability rate of success in determining the optimal matched donor in unrelated stem transplantation for Tunisian patients or patients of Tunisian origin.

The Impact of Apolipoprotein A-I Polymorphisms on the Lipid Profiles in Middle Aged Healthy Men and Women

Background and Objectives:Apolipoprotein A-I is the major lipoprotein constituent of high density lipoprotein in plasma. In this study, the role of two polymorphisms in the apo A-I gene was investigated on the serum lipid profiles and apo A-I levels in healthy men and women. Subjects and Methods:Blood samples were ob- tained from 417 subjects (M:F=169:248, mean age 47.2 years). The apo A-I genotypes were determined by SNP-IT assays using the SNPstream 25K TM system. Results:The frequencies of the A allele at the XmnI restriction site and position -75 bp were 0.25/0.23 and 0.19/0.17 in men and women, respectively. A strong positive linkage disequilibrium (D' =0.990) between two polymorphisms was detected. In men, the A allele at the XmnI restriction site was associated with significantly lower levels of triglyceride (p=0.028) compared to the G/G subjects, but no significant associations were detected between the G-75A polymorphism and any of the lipid traits examined. In women, each A allele for the XmnI restriction site and -75 bp polymorphisms were significantly associated with higher levels of apo A-I (p=0.032 and p=0.012). In the multiple regression analysis, the HDL, being a current drinker and the A allele of the XmnI restriction site polymorphism were major determinants of the serum apo A-I levels in women (R 2 =0.272, p<0.05). Conclusion:Our study showed that the A allele at XmnI restriction site in the apo A-I gene was associated with decreased triglyceride levels in men. Each A allele of two polymorphisms was associated with an elevated apo A-I level in women.

Genetic variation in the 5-HT3 receptor gene: No association with schizophrenia or drug response

Schizophrenia is a highly heritable psychiatric disorder often associated with dopamine-related genetic variations. Thus, we performed a case-control study in 1504 Han Chinese population to evaluate the association of DRD1, DRD2 and DRD3 polymorphisms with schizophrenia. No statistically significant difference in allelic or genotypic frequency was found between schizophrenia and control subjects. Strong positive linkage disequilibrium was detected among the SNPs within DRD1 and DRD2. However, no positive haplotype distribution was found to be associated with schizophrenia. Our results indicated that DRD1, DRD2 and DRD3 may not be the susceptibility genes for schizophrenia in the Chinese Han population.

Five frequent polymorphisms of the PAI-1 gene: lack of association between genotypes, PAI activity, and triglyceride levels in a healthy population.

The main function of plasminogen activator inhibitor type 1 (PAI-1) is to decrease fibrinolysis, which leads to fibrin accumulation. An elevated plasma PAI-1 concentration has been identified as a risk factor for the development of myocardial infarction, and an association between 1 polymorphism of the PAI-1 promoter and plasma PAI-1 levels has been described. Our aim was to identify new polymorphisms in the PAI-1 gene and to further examine the relationship between PAI-1 genotypes and circulating PAI-1 levels. We report the presence of 4 new polymorphisms that were identified by non-isotopic single-strand conformational polymorphism analysis followed by sequencing. These polymorphisms were investigated in relation to PAI-1 levels in a sample of 256 healthy men, aged 50-59 years, from France and Northern Ireland. Two G/A substitutions were detected at positions -844 and +9785. The former is in strong positive linkage disequilibrium with the previously described 4G/5G polymorphism at position -675. Two polymorphisms in the 3' untranslated region were identified. One corresponds to a T/G substitution at position +11,053 and is in negative linkage disequilibrium with the G/A substitution (+9785). The other is a 9-nucleotide insertion/deletion located between nucleotides +11,320 and +11,345 in a threefold-repeated sequence. This polymorphism is in strong positive linkage disequilibrium with the G/A substitution (+9785). The overall heterozygosity provided by the 5 PAI-1 polymorphisms (including the 4 new variants and the 4G/5G polymorphism) was .77. No significant association was found between PAI activity and genotypes; furthermore, the well known associations between PAI activity and body mass index, serum triglycerides, or insulin were homogeneous according to PAI-1 genotypes.

Nucleotide variation and conservation at the dpp locus, a gene controlling early development in Drosophila.

A study of polymorphism and species divergence of the dpp gene of Drosophila has been made. Eighteen lines from a population of D. melanogaster were sequenced for 5200 bp of the Hin region of the gene, coding for the dpp polypeptide. A comparison was made with sequence from D. simulans. Ninety-six silent polymorphisms and three amino acid replacement polymorphisms were found. The overall silent polymorphism (0.0247) is low, but haplotype diversity (0.0066 for effectively silent sites and 0.0054 for all sites) is in the range found for enzyme loci. Amino acid variation is absent in the N-terminal signal peptide, the C-terminal TGF-beta peptide and in the N-terminal half of the pro-protein region. At the nucleotide level there is strong conservation in the middle half of the large-intron and in the 3' untranslated sequence of the last exon. The 3' untranslated conservation, which is perfect for 110 bp among all the divergent species, is unexplained. There is strong positive linkage disequilibrium among polymorphic sites, with stretches of apparent gene conversion among originally divergent sequences. The population apparently is a migration mixture of divergent clades.

Nco I Restriction Fragment Length Polymorphism (RFLP) of the Tumor Necrosis Factor (TNFα) region in four autoimmune diseases

The two-allele NcoI Restriction Fragment Length Polymorphism (RFLP) of the TNF alpha region yielding bands of 5.5 and 10.5 kb was investigated in patients with systemic lupus erythematosus (SLE), pauciarticular juvenile rheumatoid arthritis (P-JRA), rheumatoid arthritis (RA) and primary Sjögren's syndrome (pSS). In all four disease, we found a decreased frequency of the 10.5 kb allele which, however, was significant only in the SLE group. In all conditions except RA, the frequency of the 5.5 kb fragment was increased. In pSS and SLE, the frequency of HLA-B8 was increased in 5.5 kb fragment positive patients compared with corresponding controls and thus, the increase of this band and the decrease of the 10.5 kb band may be secondary to HLA-B8 associations owing to strong positive linkage disequilibrium between HLA-B8 and the 5.5 kb band.

Mapping of a restriction fragment length polymorphism associated with defective DR β chain expression to the HLA-DRB1 gene

The HLA-DR β4 chaine, encoded by the DRB4 gene, carries two DRw53 determinants normally expressed by DR4, DR7, and DR9 individuals. However, some DR7 individuals (DR7,Dw11) fail to express the DR β4 chain. At the genomic level, a HindIII restriction fragment length polymorphism can be detected in these individuals with a DRβ cDNA probe. The association of this altered HindIII fragment with defective β4 chain expression suggested the possibility that the polymorphic fragment was derived from the DRB4 gene and might, therefore, be related to the defect in expression. However, detailed Southern blot analysis has now mapped the polymorpbic fragment to the 3′ end of the DRB1 gene, approximately 100 kb away from the defective DRB4 gene. Although the alteration in the DRB1 gene might involve sequences important in regulating the expression of the DRB4 gene, it is more likely that the association results from strong positive linkage disequilibrium between these DR β chain genes.

Association of systemic lupus erythematosus and sle-like syndromes with hereditary and acquired complement deficiency states

The most prominent association of rheumatic diseases with hereditary complement deficiency is systemic lupus erythematosus (SLE) and discoid lupus erythematosus with homozygous C2 deficiency in females. The lupus disease in these patients differ from classic lupus in 1) the increased incidence of discoid lesions, 2) the low incidence of renal disease, 3) the low or absent titers of antibodies to native DNA, and 4) the infrequent finding of immunoglobulin and complement in skin lesions. The strong positive linkage disequilibrium between C2 deficiency and HLA genes raises the possibility that genes other than those determining C2 levels may have the primary role in determining predisposition to disease in these patients. However, the finding of similar diseases in certain patients with hereditary angioedema and SLE-related syndrome who have acquired deficiency of the early components of complement supports a primary role of the C2 deficiency gene in predisposing to lupus disease in these patients.