Strong Genetic Association Research Articles

Kernel weight per spike: what contributes to it at the individual QTL level?

Spike length (SL), spikelet number (SPN) per spike, kernel number per spike (KNPS), and thousand-kernel weight (TKW) have strong genetic associations with kernel weight per spike (KWPS) in wheat. To investigate their genetic relationships at the individual quantitative trait locus (QTL) level, both unconditional and conditional QTL mapping for KWPS with respect to SL, SPN, KNPS, and TKW were conducted. Two related F8:9 recombinant inbred line populations, comprising 485 and 229 lines, respectively, were used. The trait phenotypic performances of each population were evaluated in four different environments. Unconditional QTL mapping analysis identified 22 putative additive QTL for KWPS, five of which were stable QTL, and only QKwps-WJ-1B.2 showed significant additive-by-environment interaction effects. In comparison with unconditional QTL mapping analysis, conditional QTL mapping analysis indicated that, at the QTL level, KNPS and TKW contributed more to KWPS than did SL and SPN. Any unconditional QTL for KWPS detected in this study was associated with at least one of its four related traits. The present study will provide assistance in the understanding of the genetic relationships between KWPS and its related traits.

SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

BackgroundSingle nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice.ResultsOf the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species.ConclusionsSNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.

PNPLA3 Polymorphisms and Liver Aminotransferase Levels in a Mexican American Population

This study examined genetic associations of patatin-like phospholipase domain containing 3 gene (PNPLA3) polymorphisms and liver aminotransferases in an extensively documented, randomly recruited Mexican American population at high risk of liver disease. Two single nucleotide polymorphisms (SNP) in the PNPLA3 gene (i.e., rs738409 and rs2281135) were genotyped in 1532 individuals. Population stratification was corrected by the genotyping of 103 ancestry informative markers (AIMs) for Mexican Americans. Both PNPLA3 SNPs showed highly significant association with alanine aminotransferase (ALT) levels, but was also, in males, associated with aspartate aminotransferase (AST) levels. Haplotypic association test of the two SNPs suggested stronger genetic association with rs738409 than rs2281135. Obvious sex effects were observed: rs738409-sex interaction in ALT levels P = 8.37 x 10(-4); rs738409-sex interaction in AST levels P = 5.03 x 10(-3). This population study highlights a sex-specific association of PNPLA3 polymorphisms and elevated liver enzymes in a population-based study, independent of common pathological factors of the metabolic syndrome. The strong genetic association found in women ≤ 50 years old, but not in women > 50 years old, suggests that sex hormones may mediate the sex effect.

The role of MAPT sequence variation in mechanisms of disease susceptibility

The microtubule-associated protein tau (MAPT or tau) is of great interest in the field of neurodegeneration as there is a well-established genetic link between the MAPT gene locus and tauopathies, a diverse group of neurodegenerative dementias and movement disorders. The genomic architecture in the region spanning the MAPT locus contains a ~1.8 Mb block of linkage disequilibrium characterized by two major haplotypes: H1 and H2. Recent studies have established strong genetic association between the MAPT locus and neurodegenerative disease and uncovered haplotype-specific differences in expression and alternative splicing of MAPT transcripts. Integrating genetic association data and gene expression data to understand how non-coding genetic variation at a gene locus affects gene expression and leads to susceptibility to disease is a high priority in disease genetics, and the MAPT locus provides an excellent paradigm for this. In the absence of protein-coding changes caused by haplotype sequence variation, altered levels of protein expression or altered ratios of isoform expression are excellent candidate mechanisms to link the MAPT genetic disease association with biological function. The use of novel transgenic and endogenous genetic models are required to understand the role of MAPT sequence variation in mechanisms of disease susceptibility.

Genetically Distinct Subsets within ANCA-Associated Vasculitis

BackgroundAntineutrophil cytoplasmic antibody (ANCA)–associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener's granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis.MethodsA genomewide association study was performed in a discovery cohort of 1233 U.K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria.ResultsWe found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti–proteinase 3 ANCA was associated with HLA-DP and the genes encoding α1-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P=6.2×10−89, P=5.6×10−12, and P=2.6×10−7, respectively). Anti–myeloperoxidase ANCA was associated with HLA-DQ (P=2.1×10−8).ConclusionsThis study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA–associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA–associated vasculitis and myeloperoxidase ANCA–associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.)

Genetic association study of UCMA/GRP and OPTN genes (PDB6 locus) with Paget's disease of bone

We performed a genetic association study of rare variants and single nucleotide polymorphisms (SNPs) of UCMA/GRP and OPTN genes, in French-Canadian patients with Paget's disease of bone (PDB) and in healthy controls from the same population. We reproduced the variant found in the UCMA/GRP basal promoter and tested its functionality using in vitro transient transfection assays. Interestingly, this SNP rs17152980 appears to affect the transcription level of UCMA/GRP. In addition, we have identified five rare genetic variants in UCMA/GRP gene, four of them being population-specific, although none were found to be associated with PDB. Six Tag SNPs of UCMA/GRP gene were associated with PDB, particularly the SNP rs17152980 (uncorrected P=3.8×10−3), although not significant after Bonferroni's correction. More importantly, we replicated the strong and statistically significant genetic association of two SNPs of the OPTN gene, the rs1561570 (uncorrected P=5.7×10−7) and the rs2095388 (uncorrected P=4.9×10−3), with PDB. In addition, we identified a very rare variant found to be located close to the basal promoter of the OPTN gene, at −232bp from its distal transcription start site. Furthermore, depending on the type of allele present (G or A), the binding of several important nuclear factors such as the vitamin D or the retinoic acid receptors is predicted to be altered at this position, suggesting a significant effect in the regulation of transcription of the OPTN gene. In conclusion, we identified a functional SNP located in the basal promoter of the UCMA/GRP gene which provided a weak genetic association with PDB. In addition, we replicated the strong genetic association of two already known SNPs of the OPTN gene, with PDB in a founder effect population. We also identified a very rare variant in the promoter of OPTN, and through bioinformatic analysis, identified putative transcription factor binding sites likely to affect OPTN gene transcription.

Recent advances in the genetics and immunology of Stevens-Johnson syndrome and toxic epidermal necrosis

Stevens-Johnson syndrome (SJS) and toxic epidermal necrosis (TEN) are rare but life-threatening severe cutaneous adverse reactions (SCARs), which are majorly (65-75%) induced by a variety of drugs. SJS/TEN could be recognized as SCARs or drug immune reactions, if the reactions are elicited by drugs. The recent studies suggested that SJS/TEN is a specific immune reaction initiated by the cytotoxic T lymphocytes (CTLs) via human leukocyte antigens (HLAs)-restricted pathway. The patho-mechanism involving HLA-restricted presentation of a drug or its metabolites for T-cell activation is supported by the findings of strong genetic associations with HLA alleles (e.g. HLA-B*15:02 and carbamazepine-SJS/TEN, and HLA-B*58:01 and allopurinol-SJS/TEN). However, the genetic associations of SJS/TEN or drug induced cutaneous immune reactions are complex, which are drug specific and ethnicity specific. The genetic polymorphisms and diversity of HLA alleles may provide different binding affinities for drug antigens to launch the activation of specific CTLs responses, further leading to the unique clinical manifestations in SJS/TEN. Fas-FasL and perforin/granzyme B have been advocated mediating the epidermal necrosis in SJS/TEN. Our recent study showed that granulysin, a cytotoxic protein produced by CTLs or natural killer (NK) cells, is the key mediator for disseminated keratinocyte death in SJS/TEN. From the point of view of a physician, the profounder understanding of the genetic predisposition and patho-mechanism we discover, the better strategies for prevention, clinical management, and therapeutic methods of SJS/TEN we can develop in the near future.

Poster #108 THE INFLUENCE OF DISC1 SER704CYS POLYMORPHISM ON THE CORTICAL THICKNESS OF SALIENCE NETWORK (INSULA AND ANTERIOR CINGULATE) IN PSYCHOSIS

s of the 3rd Biennial Schizophrenia International Research Conference / Schizophrenia Research 136, Supplement 1 (2012) S1–S375 S319 Poster #107 EVIDENCE OF AN ASSOCIATION BETWEEN DYSBINDIN GENE AND AGE AT ONSET IN SCHIZOPHRENIA Kyuyoung Lee1, Eunjeong Joo1, Yongsik Kim2 1Department of Neuropsychiatry, Eulji University School of Medicine, Eulji General Hospital, Seoul, Korea; 2Department of Psychiatry & Behavioral Science and Institute of Human Behavioral Medicine, Seoul National University College of Medicine, Seoul, Korea Background: The dysbindin gene (DTNBP1) is located in chromosome 6p22.3, one of the regions of positive linkage for schizophrenia. In particular, dysbindin protein has been found to play a role in the glutatmate neural transmission in the brain. A strong genetic association between DTNBP1 and schizophrenia has been replicated through many recent studies. However, we have not replicated positive association between DTNBP1 and schizophrenia in our Korean sample. Because schizophrenia has been regarded as a disease with a quite heterogeneous origin and evolvement, it is useful to categorize patients with schizophrenia into relatively homogeneous subsets based on clinical characteristics including age at onset (AAO). Therefore, we investigated the association between DTNBP1 and AAOof schizophrenia. Methods: We assessed age at first occurrence of positive psychotic symptomsof 197 patients with schizophrenia. Four SNPs, SNPA, P1763, P1320 and P1655 of DTNBP1 were genotyped. Results: In SNPA, the patients with AT (N=10) showed significant earlier AAO than those with AA (N=187) (p<0.0001). The patients with heterozygote for SNP P1763 (TG, N=40) or P1320 (CT, N=41) also showed significant earlier AAO than those with homozygote (P<0.0001, P<0.0001, respectively). However, in SNP P1655, there was no significant difference of AAO between genotypes. Discussion: In conclusion, although we were unable to support an association between DTNBP1 and schizophrenia, DTNBP1 might play a role in disease-modifying. However, considering the several limitations of this study, further research involving different polymorphisms in DTNBP1and various clinical subsets with sufficient numbers will be required to evaluate the contribution of DTNBP1 to schizophrenia. Poster #108 THE INFLUENCE OF DISC1 SER704CYS POLYMORPHISM ON THE CORTICAL THICKNESS OF SALIENCE NETWORK (INSULA AND ANTERIOR CINGULATE) IN PSYCHOSIS Lena Palaniyappan1, Vijender Balain1, Molly Simmonite1, Liam Carrol2, Peter McGuffin2, Katherine Aitchison2, Peter F. Liddle1 1Division of Psychiatry, University of Nottingham, Nottingham, England, United Kingdom; 2MRC SGDP, Institute of Psychiatry, Kings College, London, England, United Kingdom Background: Psychosis is characterized by significant reduction of grey matter in anterior cingulate cortex (ACC) and the insula. An emerging literature has demonstrated an association between the Disrupted-inSchizophrenia 1 (DISC1) gene and the development of cortical grey matter. Allelic variation at rs821616 (Ser704cys) has been associated with both structural and functional changes in psychosis. Our objective was to examine the relationship between grey matter reduction salience network sites (ACC/Insula) and Ser704cys variation in psychosis. Methods: High-resolution anatomical scans were obtained from 45 subjects (23 with psychosis and 22 healthy individuals with 10 cysteine carriers in each group). We employed cortical surface based analysis using Freesurfer (v5.0) to measure cortical thickness and surface area. Various cortical regions were parcellated using Destrieux atlas, and the regions constituting the insula (short and long gyri) and anterior cingulate were included for further analysis. Results: We detected a significant omnibus interaction effect between diagnostic status and genotype for cortical thickness (F(1,38)=5.071, p=0.03). Among cysteine non-carriers, a highly pronounced diagnostic difference was noted in the adjusted mean thickness (patients = 3.014mm, controls = 3.254mm, t=3.54, p=0.002). Such a diagnostic difference was not noted in cysteine carriers (patients = 3.122mm, controls = 3.139mm, t=0.23, p=0.83). Among patients, a significant difference was also noted between the two genetic groups in terms of levels of functioning measured using Social and Occupational Functioning Scale (total SOFAS score: cys non-carriers = 47.54; carriers = 59.10, F=6.07, p=0.02) and symptom burden measured using Signs and Symptoms in Psychotic Illness scale (total SSPI score: cys non-carriers = 13.46; carriers = 8.10, F=2.71, p=0.11). The polymorphism was not associated with effects on the cortical surface area of ACC/Insula. Discussion: Our findings suggest that morphometric changes associated with psychosis are influenced by the polymorphic variation in DISC1, which plays a cardinal role in regulating neuronal migration. The pathoplastic effect of DISC1 in psychosis is likely to be mediated by the structure of grey matter in the Salience Network. Poster #109 HISTORICAL STUDY OF INFLUENCE OF NON-GENETIC FACTORS ON TWIN CONCORDANCE FOR SCHIZOPHRENIA

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance.

Endogenous retrotransposons have caused extensive genomic variation within mammalian species, but the functional implications of such mobilization are mostly unknown. We mapped thousands of endogenous retrovirus (ERV) germline integrants in highly divergent, previously unsequenced mouse lineages, facilitating a comparison of gene expression in the presence or absence of local insertions. Polymorphic ERVs occur relatively infrequently in gene introns and are particularly depleted from genes involved in embryogenesis or that are highly expressed in embryonic stem cells. Their genomic distribution implies ongoing negative selection due to deleterious effects on gene expression and function. A polymorphic, intronic ERV at Slc15a2 triggers up to 49-fold increases in premature transcriptional termination and up to 39-fold reductions in full-length transcripts in adult mouse tissues, thereby disrupting protein expression and functional activity. Prematurely truncated transcripts also occur at Polr1a, Spon1, and up to ∼5% of other genes when intronic ERV polymorphisms are present. Analysis of expression quantitative trait loci (eQTLs) in recombinant BxD mouse strains demonstrated very strong genetic associations between the polymorphic ERV in cis and disrupted transcript levels. Premature polyadenylation is triggered at genomic distances up to >12.5 kb upstream of the ERV, both in cis and between alleles. The parent of origin of the ERV is associated with variable expression of nonterminated transcripts and differential DNA methylation at its 5′-long terminal repeat. This study defines an unexpectedly strong functional impact of ERVs in disrupting gene transcription at a distance and demonstrates that ongoing retrotransposition can contribute significantly to natural phenotypic diversity.

Connecting ncRNA Cigarette Smoking Studies with Tobacco Use Behaviors and Health Outcomes.

Connecting ncRNA Cigarette Smoking Studies with Tobacco Use Behaviors and Health Outcomes.

Sickle cell trait is not independently associated with susceptibility to end-stage renal disease in African Americans

Conflicting reports exist as to whether sickle cell trait is a risk factor for the progression of nephropathy. In order to determine whether African Americans with sickle cell trait are at increased risk for kidney disease, we assessed the genetic association between sickle cell trait and end-stage renal disease (ESRD). Hemoglobin S, non-muscle myosin heavy chain 9 (MYH9), and apolipoprotein L1 (APOL1) risk variants were genotyped in 3258 unrelated African Americans: 1085 with non-diabetic ESRD, 996 with type 2 diabetes-associated ESRD, and 1177 controls. Since APOL1 is strongly associated with ESRD in African Americans, interactions between APOL1 and MYH9 risk variants and hemoglobin S were assessed using case-only and case-control centered two-way logistic regression interaction analyses. The sickle cell trait genotype frequencies were 8.7% in non-diabetic ESRD, 7.1% in type 2 diabetes-ESRD, and 7.2% in controls. There was no age-, gender-, and admixture-adjusted significance for sickle cell trait association with non-diabetic ESRD (odds ratio 1.16); type 2 diabetes-ESRD (odds ratio 1.01); or all-cause ESRD (combined non-diabetic and type 2 diabetic-ESRD patients compared to the controls; odds ratio 1.05) in dominant models. In addition, no evidence of APOL1 or MYH9 interactions with sickle cell trait was detected. Hence, sickle cell trait is not associated with diabetic or non-diabetic ESRD in a large sample of African Americans.

Recent Progress in HIV-Associated Nephropathy

The classic kidney disease of HIV infection, HIV-associated nephropathy (HIVAN), is an aggressive form of collapsing focal segmental glomerulosclerosis with accompanying tubular and interstitial lesions. HIVAN was first described among African-Americans and Haitian immigrants with advanced HIV disease, an early suggestion of a strong genetic association. This genetic susceptibility was recently linked to polymorphisms on chromosome 22 in individuals of African descent. The association with advanced HIV infection and evidence from HIV-transgenic mice suggested the possibility that HIV directly infects the kidney and that specific HIV gene expression induces host cellular pathways that are responsible for HIVAN pathogenesis. Although combination antiretroviral therapy has substantially reduced the impact of HIVAN in the United States, continued growth of the HIV epidemic in susceptible African populations may have important public health implications. This article reviews recent progress in the pathogenesis and treatment of HIVAN and describes the changing epidemiology of HIV-related kidney disease.

Large-scale methylation domains mark a functional subset of neuronally expressed genes

DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks is poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters. However, it was recently shown that the IMR90 human fetal lung fibroblast cells have large regions of the genome with partially methylated domains (PMDs, <70% average methylation), in contrast to the rest of the genome which is in highly methylated domains (HMDs, >70% average methylation). Using bisulfite conversion followed by high-throughput sequencing (MethylC-seq), we discovered that human SH-SY5Y neuronal cells also contain PMDs. We developed a novel hidden Markov model (HMM) to computationally map the genomic locations of PMDs in both cell types and found that autosomal PMDs can be >9 Mb in length and cover 41% of the IMR90 genome and 19% of the SH-SY5Y genome. Genomic regions marked by cell line specific PMDs contain genes that are expressed in a tissue-specific manner, with PMDs being a mark of repressed transcription. Genes contained within N-HMDs (neuronal HMDs, defined as a PMD in IMR90 but HMD in SH-SY5Y) were significantly enriched for calcium signaling, synaptic transmission, and neuron differentiation functions. Autism candidate genes were enriched within PMDs and the largest PMD observed in SH-SY5Y cells marked a 10 Mb cluster of cadherin genes with strong genetic association to autism. Our results suggest that these large-scale methylation domain maps could be relevant to interpreting and directing future investigations into the elusive etiology of autism.

Complement component C5a Promotes Expression of IL-22 and IL-17 from Human T cells and its Implication in Age-related Macular Degeneration

BackgroundAge related macular degeneration (AMD) is the leading cause of irreversible blindness in elderly populations worldwide. Inflammation, among many factors, has been suggested to play an important role in AMD pathogenesis. Recent studies have demonstrated a strong genetic association between AMD and complement factor H (CFH), the down-regulatory factor of complement activation. Elevated levels of complement activating molecules including complement component 5a (C5a) have been found in the serum of AMD patients. Our aim is to study whether C5a can impact human T cells and its implication in AMD.MethodsHuman peripheral blood mononuclear cells (PBMCs) were isolated from the blood of exudative form of AMD patients using a Ficoll gradient centrifugation protocol. Intracellular staining and enzyme-linked immunosorbent assays were used to measure protein expression. Apoptotic cells were detected by staining of cells with the annexin-V and TUNEL technology and analyzed by a FACS Caliber flow cytometer. SNP genotyping was analyzed by TaqMan genotyping assay using the Real-time PCR system 7500.ResultsWe show that C5a promotes interleukin (IL)-22 and IL-17 expression by human CD4+ T cells. This effect is dependent on B7, IL-1β and IL-6 expression from monocytes. We have also found that C5a could protect human CD4+ cells from undergoing apoptosis. Importantly, consistent with a role of C5a in promoting IL-22 and IL-17 expression, significant elevation in IL-22 and IL-17 levels was found in AMD patients as compared to non-AMD controls.ConclusionsOur results support the notion that C5a may be one of the factors contributing to the elevated serum IL-22 and IL-17 levels in AMD patients. The possible involvement of IL-22 and IL-17 in the inflammation that contributes to AMD may herald a new approach to treat AMD.

Interstitial Lung Disease in Gefitinib-Treated Japanese Patients with Non-Small-Cell Lung Cancer: Genome-Wide Analysis of Genetic Data

To investigate potential relationships between SNPs and acute interstitial lung disease (ILD) events in Japanese non-small-cell lung cancer patients receiving gefitinib. Japanese non-small-cell lung cancer patients treated with gefitinib from a prospective pharmacoepidemiological cohort with a nested case-control study component ('CCS'; 52 ILD cases, 139 controls) and a retrospective study (28 ILD cases, 55 controls) were genotyped for nearly 500,000 SNPs. Associations between genotype and ILD were evaluated using Fisher's exact test and logistic regression modeling, and false discovery rate analysis was used to adjust for the large number of statistical tests. The CCS data provided some false discovery rate evidence that the significance of top-ranking SNPs exceeded levels expected by chance, suggesting some genuine associations. However, replication analyses using retrospective study data were not supportive and there was little evidence of strong genetic associations from a combined analysis. Adjustment of CCS analyses for clinical variables provided little additional convincing evidence. Significant gene-gene interactions between SNP pairs using CCS data were not confirmed in retrospective study replication analyses. Although it is not possible to exclude genetic influences in ILD etiology, common sequence variation is unlikely to explain a major component of ILD risk. Our top results may provide a useful hypothesis-generating starting point for further research.

A common functional variant of endoplasmic reticulum aminopeptidase 2 (ERAP2) that reduces major histocompatibility complex class I expression is not associated with ankylosing spondylitis

Sir, The strong genetic association between AS and HLA-B27 has defied explanation for nearly 40 years. However, the additional discovery of a strong association between AS and ERAP1 (endoplasmic reticulum aminopeptidase 1), a gene that almost certainly operates in the trimming of peptides for optimal binding to MHC class I molecules, has rekindled hopes of rapid advances in this field [1]. It has been suggested that another aminopeptidase, endoplasmic reticulum aminopeptidase 2 (ERAP2), may act in concert with ERAP1, trimming residues inefficiently removed by ERAP1 [2]. The association described recently between ERAP2 and Crohn’s disease, which shares many clinical and genetic overlaps with AS [3], suggests that ERAP2 is worthy of further study in AS. An experiment of nature allows us to do this relatively simply. ERAP2 has evolved under balancing selection, similar to the MHC, and includes a high-frequency variant (∼50%) that influences antigen presentation [4]. A single nucleotide polymorphism (SNP), rs2248374 (A to G), located within the 5′ canonical splice site of exon 10, results in an alternatively spliced ERAP2 mRNA that is degraded by nonsense-mediated decay (NMD). Homozygosity for the minor G allele (carried by ∼25% of the population) results in failure to express ERAP2 protein; in turn this genotype is also associated with reduced surface MHC Class I expression on human B cells [4]. Such a dramatic phenotypic effect provides a great opportunity for studying the potential role of ERAP2 in AS, analogous to using a knockout model. We therefore specifically tested for differences in frequency of rs2248374 in 470 sporadic AS cases and 420 healthy, ethnically matched blood donors to determine whether this functionally important variant is implicated in AS. All patients were Caucasians, of UK origin and fulfilled the modified New York criteria for AS. Eighty-four per cent of the AS patients were HLA-B27 positive. All patients gave informed consent and ethical approval was obtained (Multicentre Research Ethics Committee 98/5/23). Genotyping involved restriction fragment length polymorphism (RFLP) analysis of PCR products performed under standard conditions. Primers (forward 5′-GCATCCATGGCTAATGTGCR and reverse 5′-GTTGTGGGAAAGCCGAACTA) amplified a 370-bp product that, in the presence of the G allele, was digested to 214 and 156 bp products by HphI. Genotype and allele frequencies in AS cases and controls were compared using the Cochrane–Armitage test of trend and the chi-squared test, respectively. This study had 80% power under a log-additive model to detect an odds ratio (OR) of 1.3 with a population risk of AS of 0.04% and a risk allele frequency of 46% (frequency in our controls) at a significance level of 0.05. There were no significant differences between allele or genotype frequencies in AS cases and controls at rs2248374 (Table 1). Additionally, due to the potential functional significance of homozygosity at the minor G allele (i.e. no functional ERAP2 protein), we also compared the frequency of GG homozygotes in AS cases and controls, but these proved almost identical again (Table 1). Table 1 Genotypes, minor allele frequency (MAF), OR, 95% CI and P-value for the ERAP2 SNP rs2248374 The association between ERAP1 and AS is the second only to HLA-B27, but formal testing for additional association with the neighbouring gene, ERAP2, had not been previously undertaken. A study of familial AS that typed one marker within ERAP2 reported that an ERAP1/ERAP2 haplotype was over-represented in affected family members [5]. However, such studies are frequently confounded by linkage disequilibrium effects. If genetic variation at ERAP2 were to play a role in susceptibility to AS, then a dramatic loss-of-function variant, such as rs2248374, would appear to be a prime candidate for the ‘causal variant’ at this locus. However, we have now excluded any significant effect arising from this important functional ERAP2 variant. Nonetheless, the possibility of other associations between ERAP2 and AS has not been excluded by this study. This could be done only by systematic mapping of the gene with tagging SNPs in a very large sample after controlling for the significant linkage disequilibrium between ERAP1 and ERAP2 would this be achievable. Our study was insufficiently powered to do this.

Multi-susceptibility genes associated with the risk of the development stages of esophageal squamous cell cancer in Feicheng County

BackgroundThe purpose of this study was to evaluate the association of multi-genotype polymorphisms with the stepwise progression of esophageal squamous cell cancer (ESCC) and the possibility of predicting those at higher risk.MethodsA total of 1,004 subjects were recruited from Feicheng County, China, between Jan. 2004 and Dec. 2007 and examined by endoscopy for esophageal lesions. These subjects included 270 patients with basal cell hyperplasia (BCH), 262 patients with esophageal squamous cell dysplasia (ESCD), 226 patients with ESCC, and 246 controls with Lugol-voiding area but diagnosed as having normal esophageal squamous epithelial cells by histopathology. The genotypes for CYP2E1 G1259C, hOGG1 C326G, MTHFR C677T, MPO G463A, and ALDH2 allele genes were identified in blood samples collected from all participants.ResultsThe alleles ALDH2 and MTHFR C677T were critical for determining individual susceptibility to esophageal cancer. Compared to the ALDH 1*1 genotype, the ALDH 2*2 genotype was significantly associated with increased risks of BCH, ESCD, and ESCC. However, the TT genotype of MTHFR C677T only increased the risk of ESCC. Further analysis revealed that the combination of the high-risk genotypes 2*2/1*2 of ALDH 2 and TT/TC of MTHFR C677T increased the risk of BCH by 4.0 fold, of ESCD by 3.7 fold, and ESSC by 8.72 fold. The generalized odds ratio (ORG) of the two combined genotypes was 1.83 (95%CI: 1.55-2.16), indicating a strong genetic association with the risk of carcinogenic progression in the esophagus.ConclusionsThe study demonstrated that the genotypes ALDH2*2 and MTHFR 677TT conferred elevated risk for developing esophageal carcinoma and that the two susceptibility genotypes combined to synergistically increase the risk.

A study of HLA class I and class II 4-digit allele level in Stevens-Johnson syndrome and toxic epidermal necrolysis

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are represented by rare but life-threatening cutaneous adverse reactions to different drugs. Previous studies have found that in a Han Chinese population from Taiwan and other Asian Countries, a strong genetic association between HLA-class I alleles (B*15:02, B*58:01) and SJS and TEN was induced by carbamazepine and allopurinol, respectively. To identify genetic markers that covered the MHC region, we carried out a case-control association enrolling 20 Caucasian patients with SJS/TEN. Our patient series included 10 cases related to paracetamol, 7 to allopurinol and 3 to different drugs (plaquenil, itraconazol, nabumetone). Healthy controls were represented by 115 Caucasian bone marrow or stem cell donors. The HLA-A*, B*, C*, DRB1*, DQB1*, DQA1* and DPB1* genotyping were determined. The frequencies of HLA-A*33:03 as well as C*03:02 and C*08:01 were significantly higher in SJS/TEN patient subgroup showing allopurinol drug-induced severe cutaneous adverse reactions (SCAR) as compared to controls (28.6% vs 0%, P=0.00002, Pc=0.0011; 28.6% vs 0%, P=0.00002, Pc=0.001; 28.6% vs 0%, P=0.00002, Pc=0.001, respectively). In the same subgroup the frequencies of B*58:01, DRB1*15:02 and DRB1*13:02 alleles, although considerably higher than in control group (42.8% vs 5.2%, P=0.003; 28.6% vs 1.7%, P=0.005; 28.6% vs 3.5%, P=0.037, respectively), appeared no more statistically different after P correction (Pc=0.248; Pc=0.29; Pc=1.00, respectively). In addition, in 10 of the 20 SJS/TEN patient subgroup with paracetamol-induced SCAR no statistically significant association with HLA alleles could be found. However, in the same SJS/TEN patient subgroup showing allopurinol drug-induced SCAR, haplotype analysis indicated that B*58:01, DRB1*13:02 and DRB1*15:02 alleles, that in a single allele analysis lost statistical significance after P correction, may still confer susceptibility, because the B*58:01-DRB1*13:02 and DRB1*15:02-DQB1*05:02 are positively associated with the disease (14.2% vs 0.43%, P= 0.00001, Pc=0.00028; 14.2% vs 0.43%, P=0.00001, Pc=0.00028, respectively). Our results show that in contrast to SCAR-related to paracetamol, where HLA alleles do not appear to be involved, HLA molecules behave as a strong risk factor for SCAR-related to allopurinol even when a limited number of patients are considered.

Alzheimer Disease: Advances in Pathogenesis, Diagnosis, and Therapy

Alzheimer disease (AD)9, the most frequent cause of dementia in Western societies, affects approximately 5.5 million people in the US and more than 35 million people worldwide. Common symptoms of this disease include memory loss, confusion, irritability, and aggression. Normal bodily functions are progressively lost, with AD becoming fatal within 3 to 9 years after diagnosis. The major risk factor for AD is advanced age. After the age of 65 years, the incidence of AD doubles every 5 years. As the size of the elderly population increases, particularly the “baby boomers,” the prevalence will approach 30 to 60 million cases in the US alone by 2050. The pathogenesis of AD is not clear, but the major pathogenetic mechanisms that have been suggested include the accumulation of misfolded proteins in the aging brain, which causes oxidative and inflammatory damage, which in turn leads to energy failure and synaptic dysfunction. A very small proportion (<1%) of AD cases are familial with early onset, and such cases have been linked to mutations in genes encoding amyloid precursor protein (APP) and presenilins 1 and 2. There is also a strong genetic association between one variant of apolipoprotein E (apo E) and the risk for developing AD. Over the last 10 years, there has been increased interest in understanding the pathogenesis of this disease and in the development of new therapies. We interview 4 specialists and examine the latest advances in pathogenesis, diagnosis, and therapy for this debilitating disease. Can you summarize briefly some new insights into the pathogenesis of AD? JoAnne McLaurin: We have understood for years that the biggest risk factor for AD is aging. We are now starting to unravel the effects of aging on memory function and link this back to disease progression. New data have arisen that link …

Association with HLA DQ of early onset myasthenia gravis in Southeast Texas region of the United States

Forty-four Caucasian American myasthenia gravis (MG) patients from Southeast Texas underwent high resolution HLA DQ analysis. For the majority of patients who were late onset or male, no significant associations with DQ were observed. However, associations with DQ increased in female patients and early onset patients. At the allele level, DQB1 *0503, *0604, *0502 and *0402 collectively contributed to a positive association of the DQ locus with early onset MG (EOMG), while individually failing to show significant association. At DQ level, the novel haplotype DQA1*0401:DQB1*0201 was the primary factor in the association of combined DQ loci with early onset. In addition, *0104:*0503, *0102:*0604, *0102:*0502 and *0303:*0402 collectively contributed to the positive association of the haplotype loci. DR3-DQ2.5cis, a well known risk factor for MG in Western Eurasia, was not found associated with disease in any group. For typical EOMG [early onset, no thymoma, anti-acetylcholine receptor (AChR) antibody (Ab) positive] no association with DQA1 locus was found, however DQB1*0604 demonstrated an 'uncorrected' positive association. A few DQ haplotype (DQA1:DQB1) were positively associated with typical EOMG; a positive individual association for *0401:*0201 was complimented by the contributions of *0102:*0604 and *0303:*0402 haplotypes. A small minority of patients that were atypical and EOMG had a strong genetic association with DQA1*0104:DQB1*0503, the group included an anti-MuSK Ab positive and an anti-AChR negative patient. This report finds common ground with European studies regarding MuSK association; however similarities in association for typical early onset disease resembled HLA risk factors in East Asia and Southern Europe.