Haplotype tagging for the identification of common disease genes.

Genome-wide linkage disequilibrium (LD) mapping of common disease genes could be more powerful than linkage analysis if the appropriate density of polymorphic markers were known and if the genotyping effort and cost of producing such an LD map could be reduced. Although different metrics that measure the extent of LD have been evaluated, even the most recent studies have not placed significant emphasis on the most informative and cost-effective method of LD mapping-that based on haplotypes. We have scanned 135 kb of DNA from nine genes, genotyped 122 single-nucleotide polymorphisms (SNPs; approximately 184,000 genotypes) and determined the common haplotypes in a minimum of 384 European individuals for each gene. Here we show how knowledge of the common haplotypes and the SNPs that tag them can be used to (i) explain the often complex patterns of LD between adjacent markers, (ii) reduce genotyping significantly (in this case from 122 to 34 SNPs), (iii) scan the common variation of a gene sensitively and comprehensively and (iv) provide key fine-mapping data within regions of strong LD. Our results also indicate that, at least for the genes studied here, the current version of dbSNP would have been of limited utility for LD mapping because many common haplotypes could not be defined. A directed re-sequencing effort of the approximately 10% of the genome in or near genes in the major ethnic groups would aid the systematic evaluation of the common variant model of common disease.

Analysis of HLA class II genes in Hashimoto's thyroiditis reveals differences compared to Graves' disease.

Graves' disease (GD) and Hashimoto's thyroiditis (HT) represent the commonest forms of autoimmune thyroid disease (AITD) each presenting with distinct clinical features. Progress has been made in determining association of HLA class II DRB1, DQB1 and DQA1 loci with GD demonstrating a predisposing effect for DR3 (DRB1(*)03-DQB1(*)02-DQA1(*)05) and a protective effect for DR7 (DRB1(*)07-DQB1(*)02-DQA1(*)02). Small data sets have hindered progress in determining HLA class II associations with HT. The aim of this study was to investigate DRB1-DQB1-DQA1 in the largest UK Caucasian HT case control cohort to date comprising 640 HT patients and 621 controls. A strong association between HT and DR4 (DRB1(*)04-DQB1(*)03-DQA1(*)03) was detected (P=6.79 x 10(-7), OR=1.98 (95% CI=1.51-2.59)); however, only borderline association of DR3 was found (P=0.050). Protective effects were also detected for DR13 (DRB1(*)13-DQB1(*)06-DQA1(*)01) (P=0.001, OR=0.61 (95% CI=0.45-0.83)) and DR7 (P=0.013, OR=0.70 (95% CI=0.53-0.93)). Analysis of our unique cohort of subjects with well characterized AITD has demonstrated clear differences in association within the HLA class II region between HT and GD. Although HT and GD share a number of common genetic markers this study supports the suggestion that differences in HLA class II genotype may, in part, contribute to the different immunopathological processes and clinical presentation of these related diseases.

Contribution of single nucleotide polymorphisms within FCRL3 and MAP3K7IP2 to the pathogenesis of Graves' disease.

CONTEXT: Recently six DNA variants, two of which (M55V and 001Msp) are present in nuclear factor-kappaB inhibitors SUMO-4 and MAP3K7IP2 and four of which (fcrl3_3, fcrl3_4, fcrl3_5, and fcrl3_6) modulate nuclear factor-kappaB binding and production of the B cell surface molecule FCRL3, have been reported to be associated with a number of autoimmune diseases. OBJECTIVE: The aim of this study was to investigate the association of these polymorphisms with disease in a large UK Caucasian Graves' disease (GD) data set. DESIGN: The study was a case-control association study of six polymorphisms. SETTING: The study was conducted at a UK academic department of medicine. PATIENTS OR PARTICIPANTS: Study population included 1056 GD patients and 864 controls. INTERVENTIONS: There were no interventions. MAIN OUTCOME MEASURES: Tests for association with disease were measured. RESULTS: No association with disease was found for the M55V single-nucleotide polymorphism (SNP). Association was, however, found between GD and the 001Msp SNP [odds ratio (OR) 1.19 (95% confidence interval [CI]) 1.03-1.37], fcrl3_3 SNP [OR 1.17 (95% CI 1.02-1.34)], fcrl3_5 SNP [OR 1.18 (95% CI 1.04-1.35)], and fcrl3_6 SNP [OR 1.20 (95% CI 1.05-1.36)]. The 001Msp SNP was found to be associated with the presence of TSH receptor autoantibodies [OR 1.75 (95% CI 1.09-2.79)]. CONCLUSION: Functional evidence suggests that the 001Msp, fcrl3_3, fcrl3_5, and fcrl3_6 SNPs could cause changes in B cell signaling and activation pathways that could account for their association with GD. Further replication in independent data sets and fine mapping of the surrounding gene regions are needed to confirm the magnitude of the effect and location of the etiological variant(s) present within these gene regions.

A new human T-cell lymphoma cell line (Karpas 384) of the T-cell receptor gamma/delta lineage with translocation t(7:14) (p13;q11.2).

A new human T-cell non-Hodgkin lymphoma cell line of the T-cell receptor (TCR) gamma/delta lineage has been derived from the peripheral blood of a patient with a subcutaneous T-cell lymphoma in leukemic phase. The cell line (Karpas 384) initially had the same characteristics as malignant cells from the patient. Both the original tumor and the cell line failed to express any T-cell differentiation antigens other than very weak cell-surface expression of CD3 and cytoplasmic CD7; with continued growth in vitro, surface CD3 became undetectable in the presence of maintained strong cytoplasmic expression. The cell line has a complex karyotype with six abnormal chromosomes exhibiting not only t(7;14) (p13;q11.2) but also inv7(p13;q22.1), t(1;2)(q11;q35), t(2;1;14) (q35;q11-q32.1;q22.1), interstitial deletion 12(q24.1q24.3), and an unidentified marker chromosome. DNA blot analysis showed that TCR C beta and TCR J alpha-C alpha DNA sequences were in germline configuration in all restriction endonuclease digests. TCR gamma sequences showed biallelic V gamma 9-J gamma P-C gamma 1 rearrangements, the TCR gamma rearrangement detected in the majority of normal TCR gamma/delta bearing cells. Use of a range of TCR delta probes showed biallelic deletion of both J delta 1 and J delta 2, but three rearranged fragments when probed with a 3' C delta genomic probe. Similar breakpoints at 7p13 have been reported in a wide range of hematologic malignancies. Molecular cloning of the t(7;14)(p13;q11.2) translocation breakpoint in this cell line may define new DNA sequences of oncogenic potential at the 7p13 locus.

Concurrent activation of MYC and BCL2 in B cell non-Hodgkin lymphoma cell lines by translocation of both oncogenes to the same immunoglobulin heavy chain locus.

Concurrent activation of BCL2 and MYC usually occurs in B cell non-Hodgkin lymphoma (B-NHL) by translocation of both oncogenes to both immunoglobulin heavy chain (IGH) alleles: this abrogates immunoglobulin synthesis. We have studied three B-NHL cell lines (DoHH2, VAL and ROS 50) and show that concurrent activation of BCL2 and MYC may follow translocation of both oncogenes to the same IGH allele. Conventional cytogenetics of DoHH2 suggested the presence of a t(14;18)(q32;q21) translocation. However, fluorescent in situ hybridization (FISH) studies using whole chromosome paints, alpha satellite probes and flow-sorted chromosomes as probes revealed an unexpected complexity of rearrangements involving chromosomes 8, 14 and 18, namely t(8;14;18)(q24;q32;q21). DNA blot and previous PCR analysis confirmed the juxtaposition of BCL2 major breakpoint region (mbr) with IGJH6, but also demonstrated a rearrangement within the first exon of MYC. The centromeric (5') MYC rearranged fragment comigrated with the BCL2-JH6 rearranged fragment in BamHI, EcoRI and Bg/II restriction digests. The der(8)t(8;14;18) therefore comprised 5' MYC (exon I)-Sgamma4-JH6-BCL2 mbr. Similar rearrangements were observed in both ROS 50 and VAL cell lines which contained two and three copies of the der(8)t(8;14;18) respectively. Quantitative flow cytometry for BCL2 and MYC expression showed abundant expression of both proteins in all three lines. These data indicate the der(14)t(14;18)(q32;q21) may itself be the target for any second translocation. The presence of the intact BCL2-JH fusion gene on the der(8)t(8;14;18) allowed concurrent activation of both BCL2 and MYC with no loss of immunoglobulin expression.

A heterozygous deletion of the autoimmune regulator (AIRE1) gene, autoimmune thyroid disease, and type 1 diabetes: no evidence for association.

Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a rare monogenic autoimmune disease with endocrine components including type 1 diabetes, adrenal failure, and thyroid dysfunction, with major autoantibodies directed against adrenal, pancreas, and thyroid tissue. A 13-bp deletion in exon 8 of the autoimmune regulator (AIRE1) gene on chromosome 21q22.3 accounts for more than 70% of mutant alleles in United Kingdom subjects with APECED. To determine whether this polymorphism contributes to disease susceptibility in subjects with autoimmune disease in general, we screened 302 patients with Graves' disease, 154 patients with autoimmune hypothyroidism, 235 patients with type 1 diabetes, and 318 control subjects for the 13-bp deletion of the AIRE1 gene. The mutation was present in only 1 (0.33%) patient with Graves' disease, 1 patient with autoimmune hypothyroidism (0.6%), and 1 (0.315) of the control subjects. No patients with type 1 diabetes were found to carry the mutation. We conclude, therefore, that the 13-bp deletion of the AIRE1 gene is not a susceptibility locus for the more common autoimmune endocrinopathies in the United Kingdom.

No association of an interleukin 4 gene promoter polymorphism with Graves' disease in the United Kingdom.

Graves' disease (GD) is an autoimmune thyroid disease of unknown etiology, although predisposition to the development of this disease is thought to be caused by both genetic and environmental factors. Recently, an association between a promoter polymorphism of the interleukin 4 gene and GD has been reported. A C-T base change at position -590 showed modest protection against the development of GD in a United Kingdom data set of 135 patients with GD and 101 controls. This polymorphism was, therefore, investigated in a much larger case-control cohort of 384 patients with GD and 288 control subjects using PCR, followed by restriction fragment length polymorphism analysis. No protective effect of the T allele of this polymorphism was observed in our data set, and indeed no significant difference in either allelic or genotypic distribution was seen between the patient and control groups. Moreover, calculation of probabilities indicate that the original study lacked sufficient power to support the conclusions drawn. Our data support the hypothesis that the C-T promoter polymorphism of the interleukin 4 gene does not confer protection against the development of GD in Caucasians in the United Kingdom.

Association of a rare thyroglobulin gene microsatellite variant with autoimmune thyroid disease.

Genetic and environmental factors contribute to the development of Graves' disease and Hashimoto's thyroiditis. These diseases, although clinically distinct, share many immunological and histological features. Susceptibility genes for autoimmune thyroid disease (AITD) have been investigated, although only the human leukocyte antigen and cytotoxic T lymphocyte-associated antigen-4 gene regions have been consistently associated with disease. Recent data, however, have shown linkage and association of chromosome 8q24 (containing the thyroglobulin gene) to AITD. Therefore, we performed a case-control association study on patients with AITD and controls using previously associated markers (D8S284 and Tgms2). No differences in allele frequencies were observed between AITD cases and controls for D8S284. Compared with the three common alleles (frequencies >10%), the rare alleles of Tgms2 were increased (chi(2)= 10.6; P = 0.001) at Tgms2. This group included the 336-bp allele (increased in cases vs. controls: chi(2)= 24.97; P < 0.001), which has previously been reported to be associated with AITD. The rarity of this allele in the United Kingdom, however, precluded analysis in our family dataset. Although these findings may represent a random chance event, in view of previous reports of linkage and association of this gene region to AITD, this may be an example of a rare causal variant of a complex disease.

Common allelic variants of exons 10, 12, and 33 of the thyroglobulin gene are not associated with autoimmune thyroid disease in the United Kingdom.

Thyroglobulin (Tg) is a major autoantigen for autoimmune thyroid disease (AITD). The Tg gene (Tg) has been mapped to chromosome 8q24, which has recently been linked in two independent studies to AITD. Association of specific alleles of microsatellite markers within Tg itself supports a role for Tg as a good candidate susceptibility locus for AITD. Resequencing of the Tg exons has led to the identification of a number of novel single nucleotide polymorphisms, four of which have been reported to be associated with AITD. Resequencing of Tg in Caucasian subjects in the United Kingdom (UK) has confirmed the presence of four single nucleotide polymorphisms in exons 10, 12, and 33. However, in the largest case-control association study to date with adequate power to detect the reported effect if present, we found no evidence for association of the Tg DNA variants with AITD in the UK. These data suggest that the recently identified single nucleotide polymorphisms do not have a causal role for AITD in the UK. At this stage, we cannot exclude the Tg region as harboring a susceptibility locus for AITD, and only large scale sequencing and fine mapping of the region, including neighboring genes, will allow us to identify any potential causal variants within this region.

Linkage disequilibrium between the human leukocyte antigen class II region of the major histocompatibility complex and Graves' disease: replication using a population case control and family-based study.

Early case control studies found association of the DRB1 allele, DR3, with Graves' disease (GD). Recent reports, claim the DQA1 allele, DQA1*0501, to be the primary susceptibility determinant within the human leukocyte antigen (HLA) class II region. We typed 228 GD patients, 364 controls, and 98 families (parents, GD, and unaffected sibling) at the DRB1, DQB1, and DQA1 loci. The case control study showed an increased frequency in GD, compared to controls, of DRB1*0304 (47% vs. 24%; pc < 1.4 x 10(-5)), DQB1*02 (58% vs. 46%; pc < 0.035), DQB1*0301/4 (42% vs. 28%; pc < 3.5 x 10(-3)) and DQA1*0501 (67%, vs. 39%; pc < 7 x 10(-6)). The DRB1*0304-DQB1*02-DQA1*0501 haplotype was increased in GD (47%) vs. controls (24%; pc < 1.8 x 10(-5); odds ratio = 2.72). No independent association of these alleles was observed. Preferential transmission of DRB1*0304-DQB1*02-DQA1*0501 from parents heterozygous for the haplotype to GD siblings (72%) was seen in the families (chi2 = 11.95; 1 d.f.; P = 0.0005). Lack of preferential transmission to unaffected siblings (53%; chi2 = 0.19; 1 d.f.; P = NS) excluded segregation distortion. These results show that linkage disequilibrium between GD and the HLA class II region is due to the extended haplotype DRB1*0304-DQB1*02-DQA1*0501.

The development of Graves' disease and the CTLA-4 gene on chromosome 2q33.

Case-control studies suggest that the CTLA-4 gene may be a susceptibility locus for Graves' disease. The previously reported A/G polymorphism at position 49 in exon 1 of the CTLA-4 gene was, therefore, investigated in a case-control (n = 743) and family-based (n = 179) dataset of white Caucasian subjects with Graves' disease. The relationship between CTLA-4 genotype and severity of thyroid dysfunction at diagnosis was also investigated. An increase in frequency of the G (alanine) allele was seen in Graves' patients compared with control subjects (42% vs. 31.5%, respectively; corrected P<0.0002; odds ratio = 1.58), and a significant difference in the distribution of GG, GA, and AA genotypes was observed between the groups (chi2 = 21.7; corrected P<0.00003). Increased transmission of the G allele was seen from heterozygous parents to affected offspring compared to unaffected offspring (chi2 = 5.7; P = 0.025). Circulating free T4 concentrations at diagnosis were significantly associated with CTLA-4 genotype (F = 3.26; P = 0.04). These results support the hypothesis that CTLA-4 may play a role in regulating self-tolerance by the immune system and in the pathogenesis of autoimmune disorders such as Graves' disease.

The insulin gene region and susceptibility to insulin-dependent diabetes mellitus in four races; new insights from Afro-Caribbean race-specific haplotypes.

The IDDM2 component of the genetic susceptibility to insulin-dependent diabetes mellitus (IDDM) has been mapped to chromosome 11p15.5. The exact identity of IDDM2 remains uncertain. It has been suggested that IDDM2 maps within the 5' VNTR (variable number tandem repeat) polymorphism upstream of the insulin gene (INS). This has not been confirmed and a contribution from other INS gene region polymorphisms cannot be excluded. We present INS region genotype data from four racial groups: the Japanese, Hong Kong Chinese, North Indian Asians and Afro-Caribbeans (two groups; one born and resident in the UK, one in Jamaica). These races have not been previously studied with the range of INS region polymorphisms included here. No INS polymorphism was associated with IDDM across all races. These data from this study thus do not identify any INS polymorphism as IDDM2. The Afro-Caribbean race showed a very different distribution of INS genotypes from the other races and novel race-specific INS haplotypes were identified. Analysis of these excluded a contribution to susceptibility to IDDM from the- 23HphI INS polymorphism. An Afro-Caribbean INS haplotype which differed only at the VNTR from the very protective INS haplotype (VPH) identified in white Caucasians was detected. Population analysis of this haplotype will allow direct assessment of the role of the VNTR in susceptibility to IDDM. In conclusion, the diverse Afro-Caribbean TH/INS/IGF2 haplotypes identified in this study will be valuable in mapping IDDM2 more precisely.

Lack of association between polymorphism of the thyrotropin receptor gene and Graves' disease in United Kingdom and Hong Kong Chinese patients: case control and family-based studies.

The thyrotropin receptor (TSH-R) gene is a candidate for genetic susceptibility to Graves' disease (GD). Previous case control studies investigating allelic association of a polymorphism at position 253 (C253 to A253) of the TSH-R gene have shown conflicting results. We genotyped two independent case control datasets (UK Caucasian and Hong Kong Chinese), for the A253 polymorphism. The Transmission Disequilibrium Test was also used in a third family-based dataset that included 89 UK Caucasian families (both parents, a GD sibling and an unaffected sibling). Genotyping was performed by polymerase chain reaction (PCR)-amplification of genomic DNA and Tth111 I restriction enzyme digestion. No difference in frequencies of the A253 polymorphism between GD (21/204, 10.3%) and controls (34/358, 9.5%) was found in the UK Caucasians (chi2 = 0.093; p = NS). A similar finding was observed in GD (0/96, 0%) and controls (2/71, 2.8%) in Hong Kong Chinese subjects (chi2 = 2.73; p = NS). Results from the 89 UK families showed no deviation from the expected transmission frequency of 0.5, from parents heterozygous for the A253 allele to either Graves' or unaffected offspring (Fisher's exact test p = 0.22) and, therefore, confirmed a lack of evidence of linkage disequilibrium between the A253 allele and GD.

Preliminary evidence for interaction of PTPN12 polymorphism with TSHR genotype and association with Graves' ophthalmopathy.

OBJECTIVE: Protein tyrosine phosphatases (PTPs), such as PTPN22, are important regulators of signal transduction from the T cell receptor and have been associated with autoimmunity. PTPN12 interacts with the same T cell activation accessory molecules, Grb2 and Csk kinase, as the Graves' disease (GD) associated PTPN22 encoded lymphoid tyrosine phosphatase (LYP) molecule and also plays a key role in T cell receptor signalling, leading to the hypothesis that it too may be involved in GD susceptibility. DESIGN: PTPN12 was tested for association in a large well-characterized UK Caucasian case control cohort using seven tagging single nucleotide polymorphisms (SNPs). Patients A total of 1058 GD patients and 864 controls. Measurements Tests for association with the disease. RESULTS: Despite adequate statistical power to detect an effect if present, none of the seven tag SNPs were associated with GD (P = 0.925-0.089). Three SNPs (rs1468682, rs4729535 and rs17467232), however, demonstrated association with the presence of ophthalmopathy NOSPECS classes 2-4 (P = 0.039-0.004). Four SNPs (rs1468682, rs4729535, rs17155601 and rs17467232) revealed evidence of interaction with the previously associated thyrotropin hormone receptor (TSHR) rs2268458 SNP (P = 0.035-0.002). CONCLUSIONS: No association was detected between individual PTPN12 tag SNPs and GD but preliminary evidence suggests PTPN12 confers an increased risk of mild/moderate ophthalmopathy (NOSPECS classes 2-4) and that PTPN12 interacts with the TSHR. Replication of these preliminary results is now required in larger independent datasets to validate these findings.

Mannose-binding lectin gene polymorphisms in a cohort study of ANCA-associated small vessel vasculitis.

OBJECTIVE: To investigate whether single nucleotide polymorphisms (SNPs) within the mannose-binding lectin (MBL) gene are associated with small vessel vasculitis (SVV) and are a risk factor for intercurrent infection, as described previously in other autoimmune diseases. METHODS: Six SNPs in the MBL promoter and coding region were genotyped by sequence-specific polymerase chain reaction or restriction fragment length polymorphism assay in 170 white Caucasians with SVV and 372 ethnically matched controls in a case-control association study. Serum MBL levels were measured by ELISA. The genotype and protein concentrations were correlated to clinical details retrieved from hospital records. RESULTS: No differences in allelic and genotypic frequencies were detected between patients with SVV and control subjects. MBL deficiency did not increase the susceptibility to infection (P = 0.6, Fisher's exact test) or the duration of hospital stay. CONCLUSION: Our data suggest that MBL polymorphisms are not associated with SVV and do not influence the incidence of concomitant infections. These results raise doubts about the usefulness of MBL polymorphisms as a predictive marker for infection in SVV.

Tag SNP screening of the PDCD1 gene for association with Graves' disease.

OBJECTIVE: The Programmed Cell Death 1 gene (PDCD1) on chromosome 2q37.3 encodes PD-1 which is involved in providing a negative signal to activated T cells. Large case-control studies have shown association of PDCD1 with several autoimmune diseases although, to date, no such studies have been performed for Graves' disease (GD). The objective of our study was to investigate eight tag SNPs representing the majority of common variation in PDCD1 within a well-characterized large UK Caucasian GD dataset. DESIGN: A case control association study of eight polymorphisms. PATIENTS: 2671 Graves' disease patients and 864 controls. MEASUREMENTS: Tests for association with disease. RESULTS: No association with disease was seen for any of the +4163, +5049, +5318, +5640, +5678 and +7078 SNPs genotyped in this study. Association was detected between the +2375 SNP (P = 0.021, OR = 1.14 [95% CI = 1.01-1.29]) and GD and a small protective effect was seen with the +6799 SNP genotypes (P = 0.028, OR = 0.77 [95% CI = 0.58-1.03]). CONCLUSIONS: This study has, for the first time, shown that small effects within PDCD1 may contribute towards the development of GD, supporting the hypothesis that much of the currently unknown genetic contribution to GD could be due to several small genetic effects with ORs 1.2. Replication of this result is now needed to confirm our findings and justify more detailed fine mapping of a primary aetiological variant in this gene region.

Association of the BTNL2 rs2076530 single nucleotide polymorphism with Graves' disease appears to be secondary to DRB1 exon 2 position beta74.

OBJECTIVE: The HLA region encodes numerous immune response genes, with the DR/DQ molecules consistently associated with autoimmune disease (AID). Recent studies in sarcoidosis have identified association of a single nucleotide polymorphism (SNP) rs2076530 within BTNL2, a potential T-cell inhibitor, independent of the known DRB1 association. The aim of this study was to investigate the association rs2076530 with disease in a large UK Caucasian Graves' disease (GD) dataset. DESIGN: A case control association study of the rs2076530 polymorphism. PATIENTS: Eight hundred sixty-four Graves' disease patients and 864 controls. MEASUREMENTS: Tests for association with disease. RESULTS: We detected association of rs2076530 within a large GD dataset [OR = 1.32 (95% CI = 1.14-1.52)], however, linkage disequilibrium (LD) analysis revealed association of rs2076530 to be secondary to the previously established DRB1 exon 2 encoded position beta74 effect although a rare haplotype effect, including both loci, cannot be excluded. CONCLUSIONS: BTNL2 may be a sarcoidosis-specific susceptibility loci, although only extensive examination of the whole HLA region in different inflammatory/AIDs will enable DR/DQ independent HLA effects to be determined.