CARD15 in inflammatory bowel disease and Crohn''s disease phenotypes: An association study and pooled analysis

BACKGROUND: Three major polymorphisms of the Caspase-Activation Recruitment Domain containing protein 15 gene have been described to be associated with Crohn's disease. Genotype-phenotype studies reported in literature provide conflicting data on disease localisation and behaviour. We investigated the relation of Caspase-Activation Recruitment Domain containing protein 15 with inflammatory bowel disease and Crohn's disease phenotypic characteristics in a large Dutch cohort and performed a pooled analysis on inflammatory bowel disease patients and Crohn's disease phenotypic characteristics reported in association studies. METHODS: We genotyped 781 cases and 315 controls for the R702W, G908R and 1007fsinsC variants and for six microsatellite markers in and close to Caspase-Activation Recruitment Domain containing protein 15. In the pooled analysis data of 7201 inflammatory bowel disease patients and 3720 controls from 20 studies were included. RESULTS: Association was found for Crohn's disease with R702W and 1007fsinsC, including several disease characteristics, and not for ulcerative colitis. In the pooled analysis all three common Caspase-Activation Recruitment Domain containing protein 15 variants showed strong association with Crohn's disease (p<0.00001; odds ratio varying from 3.0 for single heterozygotes to 14.7 for compound heterozygotes) and not with ulcerative colitis. Phenotype analysis showed association with small bowel involvement, stricturing and penetrating disease. CONCLUSION: Caspase-Activation Recruitment Domain containing protein 15 is associated with Crohn's disease and not with ulcerative colitis. All three common Crohn's disease-associated variants are associated with small bowel involvement, the G908R and 1007fsinsC alleles also being associated with a complicated disease course.     

Association analyses of DNA methyltransferase-1 (<Emphasis Type="Italic">DNMT1</Emphasis>) polymorphisms with systemic lupus erythematosus

The etiology of systemic lupus erythematosus (SLE) is very complex, and genetic factors appear to play a significant role in susceptibility to SLE, in determining the disease expression, and in the autoantibody profiles of individuals with SLE. DNA methyltransferase-1 (DNMT1) is a major enzyme that determines genomic methylation patterns and both maintains methyltransferase and exhibits de novo DNA methylation activity in vivo. In order to clarify the association of DNMT1 polymorphisms with SLE, we scrutinized the genetic polymorphisms in exons and their boundaries of DNMT1, including the –1,500 bp promoter region, by direct sequencing in 24 Korean individuals. Twenty-nine sequence variants were identified: two in 5UTR, six in exons, and 21 in introns. Eight of these polymorphisms were selected for a larger-scale genotyping (n=680) by considering their allele frequencies, haplotype-tagging status, and linkage disequilibrium coefficiencies (LDs) among polymorphisms. The associations between DNMT1 polymorphisms and the clinical profiles of SLE were analyzed. No significant associations with the risk of SLE were detected. However, further analyses of association with autoantibody production among SLE patients revealed that one nonsynonymous SNP, +14463G>C (V120L) in exon 4, was weakly associated with an increased risk of anti-La antibody production (P=0.04), although the significance could not be retained after correction of multiple tests. The DNMT1 variations and haplotypes clarified in this study would provide valuable information for future genetic studies of other autoimmune diseases.     

Interferon-gamma receptor 1 promoter polymorphisms: population distribution and functional implications

Different polymorphisms have been described in the minimal promoter region (MPR) of the interferon-gamma receptor 1 (IFNGR1), a molecule that plays a critical role in mycobacterial control. We sequenced the IFNGR1 MPR from African American, Caucasian and Korean controls, and from mycobacteria-infected patients. Six different single nucleotide polymorphisms (SNPs) were detected in the IFNGR1 MPR. The three ethnic groups showed different SNP distribution patterns, but no significant differences were detected between mycobacterial cases and controls. Two polymorphisms were found in all populations (G-611A, T-56C). We cloned the four allelic variants (var) of haplotype G-611A/T-56C into a luciferase reporter vector and determined their promoter activity. Polymorphisms at position -611 had a stronger effect on the promoter activity than those at position -56, and constructs carrying G-611 produced a stronger promoter activity than -611A constructs. The IFNGR1 MPR is a polymorphic region with at least two SNPs influencing its activity, but these are not associated with increased mycobacterial susceptibility.     

Gender-specific haplotype association of collagen α2 (XI) gene in ossification of the posterior longitudinal ligament of the spine

Among Japanese, ossification of the posterior longitudinal ligament of the spine (OPLL) is a leading cause of myelopathy, showing ectopic bone formation in the paravertebral ligament. We have provided genetic evidence that the collagen α2 (XI) (COL11A2) locus of chromosome 6 constitutes susceptibility for OPLL. Five distinct single nucleotide polymorphisms (SNPs), identified in COL11A2, were combined to construct possible haplotypes by the use of a maximum likelihood program. Estimated haplotype frequency was compared in OPLL patients and non-OPLL controls. We report a gender-specific association of the COL11A2 haplotype with OPLL. The frequency of the most commonly observed haplotype was significantly higher in male patients (P = 0.0003) compared with controls, but not in female patients (P = 0.21). OPLL is predominantly observed in males, with a prevalence ratio of 2 : 1, and our gender-specific associations indicate that genetic factors involving COL11A2 play a specific role in the etiology of OPLL exclusively in males. Received: September 5, 2000 / Accepted: October 2, 2000     

Rapid DNA haplotyping using a multiplex heteroduplex approach: Application to duchenne muscular dystrophy carrier testing

A new strategy has been developed for rapid haplotype analysis based on an initial multiplex amplification of several polymorphic sites, followed by heteroduplex detection. Heteroduplexes formed between two different alleles are detected because they migrate differently than the corresponding homoduplexes in Hydrolink-MDE gel. This simple, rapid method does not depend on specific sequences such as restriction enzyme sites or CA boxes and does not require the use of isotope. This approach has been tested using commonly occurring polymorphisms spanning the dystrophin gene as a model. We describe the use of the method to assign the carrier status of females in Duchenne muscular dystrophy (DMD) pedigrees. The method may be used for other genetic diseases when mutations are unknown or there are few dinucleotide markers in the gene proximity, and for the identification of haplotype backgrounds of mutant alleles. © 1995 Wiley-Liss, Inc.     

潮汕地区汉族人群9个新Y-STR基因座多态性研究

目的 分析9个新Y染色体短串联重复序列(Y short tandem repeats,Y-STR)基因座的序列结构,及其在潮汕地区汉族人群中的遗传多态性分布,评价其法医学应用价值.方法 应用PCR反应,对潮汕地区汉族159名无关男性个体的血样进行基因分型,采用直接计数法计算9个Y-STR基因座的等位基因频率和单体型频率.结果 9个Y-STR基因座(DYS522、DYS549、DYS556、DYS565、DYS568、DYS570、DYS594、DYS593、DYS588)均为单拷贝,并分别检测出7、5、5、4、6、9、4、4、8个等位基因,基因多样性(gene diversity,GD)在0.1434～0.7994间;共检出136种单体型;累计单体型GD值为0.997.另对30个2代父子家系调查显示:同一家系成员9个Y-STR基因座单体型一致,未观察到基因突变.结论 9个Y-STR基因座具有较高的鉴别效能,适合作为法医学应用的遗传标记.     

Haplotype analysis in gelsoiin-related amyloidosis reveals independent origin of identical mutation (G654A) of gelsolin in Finland and Japan

Familial amyloidosis, Finnish type (FAF) (gelsolin-related amyloidosis) is an autosomal dominant form of systemic amyloidosis characterized by corneal lattice dystrophy and peripheral polyneuropathy. The accumulating protein in FAF consists of fragments of gelsolin, an actin-modulating protein. The gelsolin mutation G654A has been found in both Finnish and Japanese patients. To study the origin of the gelsolin mutation in these patients we performed haplotype analysis in 10 Finnish and 2 Japanese FAF families. Poymorphic DNA markers GSN, D9S103, AFMa061xd9, and AFMa139xb9 revealed a uniform disease haplotype in all the disease-associated chromosomes of the Finnish FAF families, which was different from the one observed in the Japanese families. The present results and the previously detected gelsolin mutation G654T in Czech and Danish FAF patients suggest that nucle otide 654 may represent a mutation hot spot in the gelsolin gene. The DNA markers studied here will be useful in future genealogical analyses of FAF. © 1995 Wiley-Liss, Inc.     

Forensic characteristics and phylogenetic analysis of 23 Y-STR loci in the Miao population from Guizhou province,southwest China

Background: Investigation of haplotype/allele frequency data of Y-STR loci in ethnically diverse populations is essential for forensic reference database construction and genetic application. However, the population genetic characteristics of the Chinese Miao minority from Guizhou Province remain uncharacterised.

Aim: To assess forensic characteristics for 23 Y-Chromosomal STR loci in Guizhou Miao and explore population genetic relationships with geographically neighbouring populations.

Subjects and methods: Twenty-three Y-Chromosomal STRs were genotyped using the Powerplex^® Y23 system in 103 unrelated Chinese Miao males from Guizhou Province, southwest China. Haplotypes and forensic parameters were obtained. Population relationships of Guizhou Miao with others were revealed using AMOVA and an MDS plot.

Results: A total of 96 haplotypes were identified with overall haplotype diversity (HD) and discrimination capacity (DC) of 0.9985 and 0.9320, respectively. Genetic differentiation was observed with most of the comparison populations, prominently for Guizhou Shui.

Conclusion: The 23 Y-STR loci were highly polymorphic and discriminating in the Guizhou Miao population and could be used for forensic practice and population genetic studies. Population relationship analysis revealed Guizhou Miao had a close genetic relationship with geographically close Guizhou Gelao, as well as Han majorities derived from different regions.     

维生素D受体基因多态性与妊娠期糖尿病关系的病例对照研究

目的 探讨维生素D受体（VDR）基因多态性与妊娠期糖尿病（GDM）之间的关系,为GDM的机制研究提供线索与依据。方法 采用病例对照研究设计,以2012年3月1日至2014年7月30日在山西医科大学第一医院产科分娩的孕妇为研究对象,其中334例被诊断为GDM,按年龄、妊娠时间及居住地1∶1匹配相应健康对照。对研究对象进行DNA基因分型,剔除基因分型缺失率>10%者,最终323例病例和320例对照纳入研究。在共显性、显性、隐性和等位基因遗传模型下,通过非条件logistic回归分析VDR基因位点多态性和GDM之间的关系,并采用Haploview软件分析单倍型与GDM之间的关系。结果 在基因水平上,VDR基因与GDM发病风险有关（P<0.05）。在调整孕前BMI、糖尿病家族史后,rs7967152位点在共显性（AC vs. AA,OR=1.58,95%CI：1.13~2.21）、显性（AC+CC vs. AA,OR=1.58,95%CI：1.15~2.18）和等位基因（C vs. A,OR=1.41,95%CI：1.10~1.82）遗传模型下与GDM风险升高有关;rs2238140位点在共显性（AA vs. GG,OR=2.24,95%CI：1.19~4.20）、显性（GA+AA vs. GG,OR=1.48,95%CI：1.07~2.03）和等位基因（A vs. G,OR=1.43,95%CI：1.11~1.83）遗传模型下与GDM风险升高有关。在共显性和显性遗传模型下,孕妇携带rs2853564位点AG基因型、AG+GG基因型（OR=1.46,95%CI：1.04~2.05;OR=1.45,95%CI：1.05~2.00）与携带AA基因型相比,是GDM的危险因素;孕妇携带rs2853566位点AG基因型、AG+GG基因型（OR=1.43,95%CI：1.03~2.00;OR=1.41,95%CI：1.02~1.94）与携带AA基因型相比,是GDM的危险因素。在VDR基因内由rs1544410、rs7967152组成的单倍型区块,其GC单倍型与是GDM的危险因素（OR=1.50,95%CI：1.15~1.97）。结论 VDR基因rs7967152、rs2238140、rs2853564、rs2853566位点多态性和区块（rs1544410、rs7967152）GC单倍型与GDM的发病风险升高有关。     

XRCC1单核苷酸多态及单体型分布与乳腺癌的相关研究

目的：探讨X线交叉互补基因1（XRCC1）外显子C26304T、G27466A和G28152A三处最常见的单核苷酸多态性（single nucleotide polymorphism，SNP）与乳腺癌的关系。方法：以自然人群为基础的病例对照研究方法，对84例乳腺癌患者组和以1：3成组频数匹配原则获得的252例对照组进行研究，XRCC1 C26304T、G27466A和G28152A SNPs基因分型采用聚合酶链反应-限制性内切酶片段长度多态性（polymerase chain reaction—restriction fragment length polymorphism，PCR—RFLP）分析方法。单体型分布采用EH linkage software 1．2分析软件进行预测和比较。结果：乳腺癌患者组和对照组吸烟状况分布差异有显著性，病例组曾经或现在吸烟个体比例7．1％明显高于对照组2．0％（P〈0．05），性别、年龄、饮酒状况及一二级亲属家族恶性肿瘤史等基本特征因素分布差异均无显著性（P〉0．05）。C26304T、G27466A和G28152A SNPs多态基因型和多态等位基因分布在两组间分布差异均无显著性（P〉0．05）。经上述因素校正后，XRCC1 SNPs与乳腺癌发病没有显著相关关系（P〉0．05）。应用EH linkage software 1．2单体型分析软件显示，XRCC1 SNPs在各组内均存在连锁不平衡现象，CGG、CGA、CAG和TGG是最常见的4类单体型。单体型组间分布同样不存在显著性差异（P〉0．05）。结论：XRCC1 C26304T、G27466A和G28152A SNPs与乳腺癌的风险没有相关关系，各SNPs存在连锁不平衡现象，CGG、CGA、CAG和TGG是最常见的4类单体型。