Positive Haplotypes Research Articles

No Association of Catechol-O-Methyltransferase Polymorphisms with Schizophrenia in the Han Chinese Population

Genetics play a major role in the etiology of schizophrenia (SZ). Catechol-O-methyltransferase (COMT) is one of the promising candidate genes for SZ. A nonsynonymous single-nucleotide polymorphism (SNP), rs4680, causing a Valine (Val) to Methionine (Met) substitution, has been widely studied in relation to psychiatric phenotypes, including SZ, but with conflicting results. We conducted a two-stage study to examine the association of COMT polymorphisms with SZ in the Han Chinese population. Association analysis of nine SNPs in 768 patients and 1348 controls failed to detect any positive markers or haplotypes. Then, we tested rs4680 in a validation sample of 963 patients and 992 controls, and no significant association was observed, but the cases significantly deviated from Hardy-Weinberg equilibrium (p=5.7e-4). There was no association of rs4680 with SZ in the combined sample (n=4071, p=0.110, odds ratio=1.08). Our results do not support the association of COMT with SZ in the Han Chinese population.

Major histocompatibility complex class I chain related gene‐A microsatellite polymorphism shows secondary association with type 1 diabetes and celiac disease in North Indians

Microsatellite polymorphism in exon 5 of major histocompatibility complex class I chain related gene-A (MIC-A) has been implicated in the etiology of autoimmune diseases including type 1 diabetes (T1D) and celiac disease (CD). In this study on North Indian population, the MIC-A5.1 allele, carrying a premature termination codon in transmembrane region, was observed with increased frequency in T1D (29.6%, odds ratio OR = 2.1, P = 0.00017) and CD patients (40.3%, OR = 3.37, P = 1.67E-05) than in controls (16.7%). When the MIC-A5.1 association was adjusted for linkage with human leukocyte antigen (HLA)-DR3, the statistical significance of the association was abolished. This implies that the observed association of MIC-A5.1 is due to its linkage disequilibrium (D' = 0.94) with HLA-B8-DR3-DQ2 haplotype and is secondary to the overall association with DR3 positive MHC haplotypes.

Decreased humoral antibody episodes of acute renal allograft rejection in recipients expressing the HLA-DQβ1*0202 allele

The present investigation was designed to show the effect of human leukocyte antigen (HLA) class II molecular allelic specificities in the recipient on the induction of humoral antibody rejection, identified by C4d peritubular capillary staining, as well as specific antibody identified by Luminex technology. Major histocompatibility complex (MHC) class II molecules are expressed on dendritic cells, macrophages, and B lymphocytes and they present antigenic peptides to CD4 positive T lymphocytes. Human renal peritubular and glomerular capillaries express class II MHC molecules upon activation. Expression of class II molecules on renal microvascular endothelial cells exposes them to possible interaction with specific circulating antibodies. We hypothesize that HLA-DQβ1*0202 expression in recipients decreases the likelihood of antibody-mediated renal allograft rejection. We found that 80% (=25) of DQ2 positive haplotype recipients failed to induce humoral antibody renal allograft rejection and 20% (n=25) of DQ2 positive haplotype recipients induced humoral antibody renal allograft rejection (p=0.008). By contrast, 48% (n=46) of DQ2 negative haplotype recipients failed to induce a humoral antibody component of renal allograft rejection and 52% (n=46) of DQ2 negative haplotype recipients induced humoral antibody-mediated renal allograft rejection. Our results suggest that recipients who express the DQβ1*0202 allele are less likely to induce a humoral antibody component of acute renal allograft rejection than are those expressing DQ1, DQ3, or DQ4 alleles. DQβ1*0202 allele expression in recipients could possibly be protective against acute humoral allograft rejection and might serve as a future criterion in recipient selection and in appropriate therapy for acute renal rejection episodes.

WDR36andP53Gene Variants and Susceptibility to Primary Open-Angle Glaucoma: Analysis of Gene-Gene Interactions

To investigate the role of WDR36 and P53 sequence variations in POAG susceptibility. The authors performed a case-control genetic association study in 268 unrelated Spanish patients (POAG1) and 380 control subjects matched for sex, age, and ethnicity. WDR36 sequence variations were screened by either direct DNA sequencing or denaturing high-performance liquid chromatography. P53 polymorphisms p.R72P and c.97-147ins16bp were analyzed by single-nucleotide polymorphism (SNP) genotyping and PCR, respectively. Positive SNP and haplotype associations were reanalyzed in a second sample of 211 patients and in combined cases (n = 479). The authors identified almost 50 WDR36 sequence variations, of which approximately two-thirds were rare and one-third were polymorphisms. Approximately half the variants were novel. Eight patients (2.9%) carried rare mutations that were not identified in the control group (P = 0.001). Six Tag SNPs were expected to be structured in three common haplotypes. Haplotype H2 was consistently associated with the disease (P = 0.0024 in combined cases). According to a dominant model, genotypes containing allele P of the P53 p.R72P SNP slightly increased glaucoma risk. Glaucoma susceptibility associated with different WDR36 genotypes also increased significantly in combination with the P53 RP risk genotype, indicating the existence of a genetic interaction. For instance, the OR of the H2 diplotype estimated for POAG1 and combined cases rose approximately 1.6 times in the two-locus genotype H2/RP. Rare WDR36 variants and the P53 p.R72P polymorphism behaved as moderate glaucoma risk factors in Spanish patients. The authors provide evidence for a genetic interaction between WDR36 and P53 variants in POAG susceptibility, although this finding must be confirmed in other populations.

HLA class II DPB1 and DRB1 polymorphisms associated with genetic susceptibility to beryllium toxicity

ObjectivesChronic beryllium disease (CBD) is a hypersensitivity granulomatous pulmonary disease caused by exposure to the metal beryllium (Be2+). Our objective was to extend current knowledge of the genetics of beryllium...

An assessment of the association between childhood asthma and HLA DRB1*03 using extended haplotype analysis

Ancestral haplotypes between human leukocyte antigen (HLA) class I and class II alleles are well-recognized in the literature. We previously published a positive association between the class II HLA allele DRB1*03 and the subsequent development of asthma in a retrospective cohort of 383 children. To refine this association, we investigated whether DRB1*03-specific haplotypes extending across the HLA are associated with asthma incidence. We found evidence of strong HLA DRB1*03-dependent linkage disequilibrium across the region, but no association between DRB1*03 ancestral haplotypes and childhood asthma. We did, however, observe a trend toward a positive association between HLA DRB1*03 and asthma by adding non-ancestral DRB1*03 positive haplotypes. Our results suggest that the role of the HLA DRB1*03 in asthma susceptibility is independent of ancestral-haplotype-mediated linkage disequilibrium.

HLA DPA1, DPB1 Alleles and Haplotypes Contribute to the Risk Associated With Type 1 Diabetes

OBJECTIVETo determine the relative risk associated with DPA1 and DPB1 alleles and haplotypes in type 1 diabetes.RESEARCH DESIGN AND METHODSThe frequency of DPA1 and DPB1 alleles and haplotypes in type 1 diabetic patients was compared to the family based control frequency in 1,771 families directly and conditional on HLA (B)-DRB1-DQA1-DQB1 linkage disequilibrium. A relative predispositional analysis (RPA) was performed in the presence or absence of the primary HLA DR-DQ associations and the contribution of DP haplotype to individual DR-DQ haplotype risks examined.RESULTSEight DPA1 and thirty-eight DPB1 alleles forming seventy-four DPA1-DPB1 haplotypes were observed; nineteen DPB1 alleles were associated with multiple DPA1 alleles. Following both analyses, type 1 diabetes susceptibility was significantly associated with DPB1*0301 (DPA1*0103-DPB1*0301) and protection with DPB1*0402 (DPA1*0103-DPB1*0402) and DPA1*0103-DPB1*0101 but not DPA1*0201-DPB1*0101. In addition, DPB1*0202 (DPA1*0103-DPB1*0202) and DPB1*0201 (DPA1*0103-DPB1*0201) were significantly associated with susceptibility in the presence of the high risk and protective DR-DQ haplotypes. Three associations (DPB1*0301, *0402, and *0202) remained statistically significant when only the extended HLA-A1-B8-DR3 haplotype was considered, suggesting that DPB1 alone may delineate the risk associated with this otherwise conserved haplotype.CONCLUSIONSHLA DP allelic and haplotypic diversity contributes significantly to the risk for type 1 diabetes; DPB1*0301 (DPA1*0103-DPB1*0301) is associated with susceptibility and DPB1*0402 (DPA1*0103-DPB1*0402) and DPA1*0103-DPB1*0101 with protection. Additional evidence is presented for the susceptibility association of DPB1*0202 (DPA1*0103-DPB1*0202) and for a contributory role of individual amino acids and DPA1 or a gene in linkage disequilibrium in DR3-DPB1*0101 positive haplotypes.

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.

Genetic susceptibility to type 1 diabetes: clinical and molecular heterogeneity of IDDM1 and IDDM12 in a german population.

Type 1 Diabetes mellitus (IDDM) results from an immune-mediated destruction of the pancreatic b-cells. The genetic predisposition is mainly confered by variations within MHC class II region on chromosome 6p as well as the CTLA4 gene located on chromosome 2q33. We analysed the transmission of HLA DQA1, DQB1, DRB1*04 alleles as well as an endogenous retroviral element (DQLTR3) in 130 families with a type 1 diabetic offspring in order to evaluate their role in genetic susceptibility to IDDM. Also the combined transmission of HLA and CTLA4 haplotypes was investigated. MHC class II alleles were typed using sequence-specific primer analysis. The presence or absence of DQLTR3 was defined by a nested PCR approach and CTLA4 microsatellite polymorphisms were detected with fluorescence-labeled primer on an automated sequencing system. By transmission distortion test we confirm the linkage of HLA DQA1*0501 DQB1*0201 (DR3 DQ2) as well as DQA1*0301 DQB1*0302 (DR4 DQ8) with IDDM. Whereas the combination with CTLA4 risk markers leads to the highest transmission rate on DR3 positive haplotypes, the predisposing CTLA4 variant does not modulate the risk on DR4 haplotypes. However, the absence of DQLTR3 on DR3, but its presence on DR4 haplotypes significantly increases the genetic risk for type 1 diabetes. Therefore predisposing MHC class II haplotypes are defined by distinct loci which differentially control genetic susceptibility. The combined transmission of protective CTLA4 and HLA DR3 as well as DR4 haplotypes confirms the dominant role of HLA class II polymorphisms in defining disease susceptibility to type 1 diabetes mellitus.

Association of the dopamine D2 receptor gene with alcohol dependence: haplotypes and subgroups of alcoholics as key factors for understanding receptor function

The dopamine D2 receptor (DRD2) plays an important role in the reinforcing and motivating effects of ethanol. Several polymorphisms have been reported to affect receptor expression. The amount of DRD2, expressed in a given individual, is the result of the expression of both alleles, each representing a distinct haplotype. We examined the hypothesis that haplotypes composed of polymorphisms, associated with reduced receptor expression, are more frequent in alcoholics compared with healthy individuals. The polymorphisms -141ins/del, C957T, A1385G, and TaqlA were genotyped in a case-control sample comprising 360 alcoholics and 368 controls, and in a family-based sample of 65 trios. To investigate more homogenous groups, we constructed two subgroups with respect to age at onset and antisocial personality disorder. In addition, a subgroup with positive family history of alcoholism was investigated. The haplotypes I-C-G-A2 and I-C-A-A1 occurred with a higher frequency in alcoholics [P=0.026, odds ratio (OR): 1.340; P=0.010, OR: 1.521, respectively]. The rare haplotype I-C-A-A2 occurred less often in alcoholics (P=0.010, OR: 0.507), and was also less often transmitted from parents to their affected offspring (1 vs.7). Among the subgroups, I-C-G-A2 and I-C-A-A1 had a higher frequency in Cloninger 1 alcoholics (P=0.083 and 0.001, OR: 1.917, respectively) and in alcoholics with a positive family history (P=0.031, OR: 1.478; P=0.073, respectively). Cloninger 2 alcoholics had a higher frequency of the rare haplotype D-T-A-A2 (P<0.001, OR: 4.614) always compared with controls. In patients with positive family history haplotype I-C-A-A2 (P=0.004, OR: 0.209), and in Cloninger 1 alcoholics haplotype I-T-A-A1 (P=0.045 OR: 0.460) were less often present. We confirmed the hypothesis that haplotypes, which are supposed to induce a low DRD2 expression, are associated with alcohol dependence. Furthermore, supposedly high-expressing haplotypes weakened or neutralized the action of low-expressing haplotypes.

Association of canine anal furunculosis with TNFA is secondary to linkage disequilibrium with DLA‐DRB1*

Anal furunculosis (AF) is a chronic inflammatory disease of perianal tissues that particularly affects German Shepherd dogs (GSD). An immune-mediated aetiopathogenesis is suggested by T-cell infiltration, upregulated cytokine gene expression, clinical response to ciclosporin therapy and a strong genetic association with the DLA-DRB1*00101 allele. Given the close proximity of TNFA and DLA-DRB1 in the canine major histocompatibility complex (MHC), together with the strong linkage disequilibrium (LD) observed across this region, the primary disease association could be with either locus. We have investigated whether there may be an association of AF with TNFA gene polymorphism in GSDs. Cohorts of AF-affected and AF-unaffected GSDs of known dog leucocyte antigen (DLA) class II profile were genotyped for 10 single nucleotide polymorphisms (SNPs) in the canine TNFA locus using Sequenom iPLEX technology. Seven discrete TNFA haplotypes were identified in GSDs for combinations of these SNPs. TNFA haplotype frequencies were compared in cases and controls. The TNFA haplotype 3 (ATCGTTACGG), was at significantly increased frequency in cases (29% vs 15%, OR 2.5, 95% CI 1.4-4.8; P = 0.003). All seven discrete TNFA SNP haplotypes were examined for their association with DLA-DRB1/DQA1/DQB1 established haplotypes. TNFA haplotype 3 was preferentially associated with both DLA-DRB1*00101(3A)- and DLA-DRB1*00102(3B)-positive haplotypes. The DLA-DRB1* 00101/TNFA-3A haplotype was significantly associated with AF (19.3% vs 5.8%; OR 3.7, 95% CI: 1.5-8.9; P = 0.003), whereas the DLA-DRB1*00102/TNFA-3B haplotype was not (P = NS). These findings suggest that susceptibility to AF in GSDs is primarily associated with DLA-DRB1*00101 and any association with the TNFA locus is secondary and is likely to be because of LD.

Analysis of HLA haplotype frequency and linkage disequilibrium in patients with acute lymphoblastic leukemia from Northern Chinese Han

To analyze the difference between the frequencies of HLA-A-B, B-DRB1 and A-B-DRB1 haplotype, as well as their linkage disequilibrium pattern in patients with acute lymphoblastic leukemia(ALL) and healthy controls from Northern Chinese Han. The frequencies of HLA-A-B, B-DRB1, A-B-DR haplotypes and linkage disequilibrium were estimated by Expectation Maximization method based on the genotypes of 643 patients with ALL and 2 0359 unrelated healthy donors, and the statistical significance between the two groups were estimated by chi-square test. Linkage disequilibrium was analyzed with population genetic methods. The most common HLA-A-B, B-DRB1, and A-B-DR haplotypes were A30-B13, A2-B46, A33-B58, B13-DR7, B46-DR9, B52-DR15, B58-DR17, A30-B13-DR7, A33-B58-DR17 and A1-B37-DR10 in both groups. The frequencies of A30-B13, A2-B46, A33-B44, B13-DR7, A30-B13-DR7 and A2-B46-DR9 haplotypes and linkage disequilibrium value were significantly decreased (P<0.05) in the patient group than that in the control group. On the other hand, the frequencies of A2-B52, A31-B61, A24- B8, B60-DR9, B27-DR4, B52-DR14, B44-DR17, B27-DR12 and A11-B27-DR12 haplotypes and linkage disequilibrium value were significantly increased (P<0.05) in the patient group than that in the control group. There are some common and positive linkage disequilibrium haplotypes in both the ALL patients and the healthy donors in Northern Chinese Han. Interestingly, some haplotypes and their linkage disequilibrium patterns had significantly different distributions between the two groups. The study provided basic data for the relationship of ALL and HLA haplotype and for finding the HLA-A, B, DR matching donors.

Genetic Disparities in Killer Cell Immunoglobulin-Like Receptors (KIR) and MHC Class I in Bone Marrow Failure Syndromes

BACKGROUND: Activating (KIRDS) natural killer cell receptors (NKR) containing an intracellular ITAM activation domain are expressed on NK and some T-cells to invoke effector responses against MHC class I-deficient tumor cells and virus-infected cells. Effector cell activation is abrogated by inhibitory forms (KIRDL) of killer cell immunoglobulin-like receptors (KIR) that bind specific epitopes of MHC class I and prevent reaction against normal cells. Since HLA class I and KIR genes are not linked, KIR gene inheritance may occur in the absence of self HLA-class I alleles (i.e., KIR/HLA-class I mismatch) and thus increase the potential for generation of autoreactive T-cells in autoimmune-mediated bone marrow failure (BMF) syndromes such as LGL leukemia, aplastic anemia (AA), and myelodysplastic syndromes (MDS).METHODS: Genotypic KIR analysis and HLA typing was performed on peripheral blood from 157 cases recruited by the Bone Marrow Failure Rare Disease Clinical Research Network and compared to 93 healthy controls. T-LGL leukemia was defined as increased numbers of CD3+, CD8+, or CD57+ lymphocytes with T-cell receptor clonality (N=35). The diagnosis of AA (N=47) and MDS (N=53) was established by bone marrow biopsy and 22 patients displayed BMF syndromes with overlapping characteristics or presence of paroxysmal nocturnal hemaglobuinuria (PNH).RESULTS: Individual KIR gene content was similar in BMF cases and healthy controls although patients with 2–3 activating KIR genes were more common among cases compared to controls (33% in cases vs. 23% in controls, p=0.1). Antigens at the HLA-C locus were divided into two groups, HLA C1 Group with alleles encoding Ser-77-Asn80 (consisting of Cw01, 03, 07, 08, 12, 14 and 16) and HLA C2 alleles encoding Asn-77-Lys-80 (Cw02, 04, 05, 06, 15, 17, and 18). The frequency of a KIR2DL2 or KIR2DL3 positive haplotype in the absence of the corresponding C1 allele in BMF patients (C1 inhibitory mismatch) in marrow failure cases was 20% compared to 8% in controls (p=0.05). There was no difference in the frequency of KIR-C1 mismatch by disease diagnosis (20% BMF vs 21% AA, 16% MDS, and 19% LGL) but all were greater than controls. The presence of KIR2DL1 and the absence of the C2 allele was not statistically different between cases and controls. The activating counterparts of these inhibitory KIRs bind their putative HLA ligands but may also bind alternative activating ligands with similar structural determinants and/or immunoglobulin domains. We compared the frequencies of mismatches in the activating KIR genes and their ligands and found that the combined the presence of KIR2DS2 or KIR2DS3 and absence of the appropriate HLA C1 allele (KIR-C1 mismatch) was more frequent in BMF patients (12%) compared to that of healthy controls (0%) (p=0.007). The disease types of AA, MDS, and LGL leukemia displayed similar frequencies in KIR-C1 activating mismatches with 16%, 13%, and 6%, respectively (p=0.005 AA, p=0.01 MDS, and p=0.14 LGL leukemia). BMF syndromes have been linked to a T-cell dominant autoimmune process. KIR expression and other NKR expression in T-cells occurs after rearrangement of the TCR and thymic education suggesting that the KIR repertoire develops in memory T-cells. Since we have identified that clonal T-cells in LGL leukemia express a unique memory phenotype characterized by expression of CD45RA in the absence of the lymphoid homing receptor L-selectin (CD62L), we examined the phenotype of T-cells that express NK proteins including NKG2A, KIR2DL2/2DS2 (CD158b), KIR2DL1/DS1 (CD158a), and KIR3DL1 (NKB1). For all NKRs, only 0.5% ± .5 of naïve CD4+ T-cells expressed NKRs compared to 3% (p=0.01) and 6% (p=0.0003) of CD4+ effector and terminal effector memory cells, respectively. CD8+ T-cells with a naïve phenotype displayed higher NKR expression (2.6%±2.8) compared to CD4+ T-cells (0.006). The highest overall NKR expression compared to all other T cell types was present in CD8+ terminal effector memory cells (15.5%±15, p=0.006). Terminal effector memory cells (CD8+) are dramatically overrepresented in BMF syndromes particularly in association with bone marrow infiltration.CONCLUSIONS: KIR expression in the absence of HLA interactions may skew the memory T-cell compartment favoring autoreactivity and impaired peripheral self-tolerance due to expansion of NKR positive T-cells in patients with BMF syndromes. Infiltration of KIR+ T-cells in tissues has been linked to organ dysfunction in several autoimmune diseases including rheumatoid arthritis and diabetes.

Study on association of single nucleotide polymorphism of CAPN1 gene with muscle fibre and carcass traits in quality chicken populations

This study was aimed at investigating the effect of the calpain 1 (CAPN1) gene on carcass and meat quality traits in eight meat-type chicken populations, including five pure lines (developed from Chinese local breeds) and three cross-breeds. Primer pairs for the Coding Sequence (CDS) region in CAPN1 were designed from the chicken genomic sequence database. Polymorphisms were detected by polymerase chain reaction (PCR)-Single Strand Conformation Polymorphism (SSCP) and DNA sequencing. Three single nucleotide polymorphisms (SNP; C2546T, G3535A and C7198A) were detected among individuals in each population. The associations of their haplotypes (H1 = CGA, H2 = CGC, H3 = CAA, H4 = CAC, H5 = TGA and H7 = TAA) with chicken breast muscle fibre and carcass traits were analysed. Results showed that the haplotypes were associated with live weight (LW), carcass weight (CW), breast muscle weight (BMW) and leg muscle weight (LMW) (p < 0.05), and were also related to eviscerated percentage (%EP) and breast muscle fibre density (p < 0.01). H1H3 haplotype was dominant for LW, CW and BMW; H1H5 haplotype was dominant for EP; H3H4 haplotype was dominant for LMW and H1H1 haplotype was dominant for BFD. It was concluded that the CAPN1 gene may be a major gene affecting meat quality traits of chicken or it is linked with the major gene. H1H3, H1H5 and H3H4 were the most advantageous haplotypes for carcass traits whereas H1H1 was the positive haplotype for breast muscle fibre trait.

HLA-B27-Associated Uveitis With a Chorioretinitis Manifestation

A 29-year-old man who had been treated for acute anterior uveitis in a local medical office and observed for 1 month presented complaining of distorted vision in his left eye for 1 week. On ophthalmic examination, the anterior segment was relatively quiet with few cells. A posterior segment examination revealed cystoid macular edema and multiple splinter retinal hemorrhages. Results of all laboratory and imaging studies were negative, except for a positive HLA-B27 haplotype. Fluorescein angiography revealed massive leakage in the mid and late phase, consistent with chorioretinitis. Periocular corticosteroid injections and oral prednisolone were administered. The patient responded to the treatment well with subsequent resolution of chorioretinitis 2 months later. Although rare, chorioretinitis can occur in the setting of uveitis associated with HLA-B27 and seems to respond well to corticosteroid treatment.

HLA Antigens in Nadars a Native Dravidian Caste Group of Tamil Nadu, South India

One hundred and thirty seven unrelated Nadar individuals residing in Tamil Nadu, (South India) were studied for HLA A, B, C and DR locus antigen profiles. The allele frequencies of HLA A9, B5, Cw4, Cw7, DR2 and DR6 were increased while frequencies of HLA A10, B8, B16, B46, B78, Cw5, Cw9 and DR9 were decreased in the Nadars. The gene frequencies of HLA A1, A3, A28, B5, B17, B37, Cw4, Cw5, DR1, DR6 and DR10 were increased while that of A2, A19, B16, B46, Cw3, DR5 and DR9 were decreased when compared with gene frequencies of other Asian populations reported. Two Locus haplotype analyses revealed that A11-B5, A1-B17, A3-B44, A24-B51, B5- Cw9, B44-Cw1, DR4-DQ2 and DR6-DQ1 were significant haplotypes among the positive linkage disequilibrium haplotypes. Where as A1-B5, B5-Cw1 and DR1-DQ2 were significant haplotypes among the negative linkage disequilibrium haplotypes. The haplotypes A3-B44, A24-B51, B44-Cw1 and DR6-DQ1 observed in Nadars were unique when compared to other Indian populations reported in literature. The observed antigen frequencies and linkage disequilibrium in Nadars suggest the influence of genetic drift caused by selection, geography and culture with a lesser degree of admixture. Further the study reveals that the Nadar population of India cannot be considered as a single panmictic population with reference to genetic characteristics, which may have a clinical relevance in unrelated donor selection for allogenic Bone marrow transplantation in India.

Nucleotide variability at the acetyl coenzyme A carboxylase gene and the signature of herbicide selection in the grass weed Alopecurus myosuroides (Huds.).

Acetyl coenzyme A carboxylase (ACCase) is the target of highly effective herbicides. We investigated the nucleotide variability of the ACCase gene in a sample of 18 black-grass (Alopecurus myosuroides [Huds.]) populations to search for the signature of herbicide selection. Sequencing 3,396 bp encompassing ACCase herbicide-binding domain in 86 individuals revealed 92 polymorphisms, which formed 72 haplotypes. The ratio of nonsynonymous versus synonymous substitutions was very low, in agreement with ACCase being a vital metabolic enzyme. Within black grass, most nonsynonymous substitutions were related to resistance to ACCase-inhibiting herbicides. Differentiation between populations was strong, in contrast to expectations for an allogamous, annual plant. Significant H tests revealed recent hitchhiking events within populations. These results were consistent with recent and local positive selection. We propose that, although they have only been used since at most 15 black-grass generations, ACCase-inhibiting herbicides have exerted a positive selection targeting resistant haplotypes that has been strong enough to have a marked effect upon ACCase nucleotide diversity. A minimum-spanning network of nonrecombinant haplotypes revealed multiple, independent apparitions of resistance-associated mutations. This study provides the first evidence for the signature of ongoing, recent, pesticide selection upon variation at the gene encoding the targeted enzyme in natural plant populations.

Haplotypic QTL mapping in an outbred pedigree.

An offspring genome can be viewed as a mosaic of chromosomal segments or haplotypes contributed by multiple founders in any quantitative trait locus (QTL) detection study but tracing these is especially complex to achieve for outbred pedigrees. QTL haplotypes can be traced from offspring back to individual founders in outbred pedigrees by combining founder-origin probabilities with fully informative flanking markers. This haplotypic method was illustrated for QTL detection using a three-generation pedigree for a woody perennial plant, Pinus taeda L. Growth rate was estimated using height measurements from ages 2 to 10 years. Using simulated and actual datasets, power of the experimental design was shown to be efficient for detecting QTLs of large effect. Using interval mapping and fully informative markers, a large QTL accounting for 11.3% of the phenotypic variance in the growth rate was detected. This same QTL was expressed at all ages for height, accounting for 7.9-12.2% of the phenotypic variance. A mixed-model inheritance was more appropriate for describing genetic architecture of growth curves in P. taeda than a strictly polygenic model. The positive QTL haplotype was traced from the offspring to its contributing founder, GP3, then the haplotypic phase for GP3 was determined by assaying haploid megagametophytes. The positive QTL haplotype was a recombinant haplotype contributed by GP3. This study illustrates the combined power of fully informative flanking markers and founder origin probabilities for (1) estimating QTL haplotype magnitude, (2) tracing founder origin and (3) determining haplotypic transmission frequency.

RHD positive haplotypes in D negative Europeans

BackgroundBlood group genotyping is increasingly utilized for prenatal diagnosis and after recent transfusions, but still lacks the specificity of serology. In whites, the presence of antigen D is predicted, if two or more properly selected RHD-specific polymorphism are detected. This prediction must fail, if an antigen D negative RHD positive allele is encountered. Excluding RHDψ and CdeS frequent only in individuals of African descent, most of these alleles are unknown and the population frequency of any such allele has not been determined.MethodsWe screened 8,442 antigen D negative blood donations by RHD PCR-SSP. RHD PCR positive samples were further characterized by RHD exon specific PCR-SSP or sequencing. The phenotype of the identified alleles was checked and their frequencies in Germans were determined.ResultsWe detected 50 RHD positive samples. Fifteen samples harbored one of three new Del alleles. Thirty samples were due to 14 different D negative alleles, only 5 of which were previously known. Nine of the 14 alleles may have been generated by gene conversion in cis, for which we proposed a mechanism triggered by hairpin formation of chromosomal DNA. The cumulative population frequency of the 14 D negative alleles was 1:1,500. Five samples represented a D+/- chimera, a weak D and three partial D, which had been missed by routine serology; two recipients transfused with blood of the D+/- chimera donor became anti-D immunized.ConclusionThe results of this study allowed to devise an improved RHD genotyping strategy, the false-positive rate of which was lower than 1:10,000. The number of characterized RHD positive antigen D negative and Del alleles was more than doubled and their population frequencies in Europe were defined.

DQB1*0602 confers genetic susceptibility to multiple sclerosis in Afro-Brazilians.

We studied the distribution of the HLA-DRB1, -DQA1 and -DQB1 alleles in 44 Afro-Brazilian patients with multiple sclerosis and 88 controls. Although no significant differences were found between the patients and controls for the DRB1 and DQA1 alleles, the HLA-DQB1*0602 allele was positively associated with multiple sclerosis (45.0% vs. 17.0%, Pc=0.024, RR=3.31). The positive extended haplotypes for DQB1*0602 were more frequent in patients than controls, although the differences were not statistically significant in any of them. These results in Afro-Brazilians are in line with other studies which have found DQB1*0602 to be associated with the disease in the absence of the DRB1*1501 allele. We therefore think that the association with the disease in this ethnic group is more allelic than haplotypic.