Haplotype analysis of the 4p16.3 region in Portuguese families with Huntington's disease

Huntington's disease (HD) is a neurodegenerative disorder characterized by involuntary choreic movements, cognitive impairment, and behavioral changes, caused by the expansion of an unstable CAG repeat in HTT. We characterized the genetic diversity of the HD mutation by performing an extensive haplotype analysis of ～1Mb region flanking HTT in over 300 HD families of Portuguese origin. We observed that haplotype A, marked by HTT delta2642, was enriched in HD chromosomes and carried the two largest expansions reported in the Portuguese population. However, the most frequent HD haplotype B carried one of the largest (+12 CAGs) expansions, which resulted in an allele class change to full penetrance. Despite having a normal CAG distribution skewed to the higher end of the range, these two core haplotypes had similar expanded CAG repeat sizes compared to the other major core haplotypes (C and D) and there was no statistical difference in transmitted repeat instability across haplotypes. We observed a diversity of HTT region haplotypes in both normal and expanded chromosomes, representative of more than one ancestral chromosome underlying HD in Portugal, where multiple independent events on distinct chromosome 4 haplotypes have given rise to expansion into the pathogenic range. © 2015 Wiley Periodicals, Inc.     

我国云南、海南恶性疟原虫顶端膜抗原1基因结构域Ⅲ多态性分析

目的 分析中国云南、海南两省恶性疟原虫顶端膜抗原1(apical membrane antigen 1,AMA-1)(Ⅲ)多态性.方法 收集海南、云南感染恶性疟原虫患者的血液187份,提取血样基因组DNA.设计两对引物扩增AMA-1(Ⅲ)基因,将PCR产物进行测序,分析其单倍型多样性.结果 187份样品中的AMA-1(Ⅲ)基因有23种单倍型,云南株有21种,海南株7种,海南有2种单倍型未在云南株中发现,云南株单倍型多样性高于海南株.AMA-1(Ⅲ)基因有9个多态位点,云南株有3份样品451位氨基酸残基的同义突变,云南、海南这些位点每种突变出现的比例不同.结论 恶性疟原虫AMA-1(Ⅲ)基因多态性在云南、海南两省各有其特点,对此结构域的群体遗传多样性分析可为针对此区域疟疾疫苗的设计提供有价值的信息.     

先天性巨结肠与RET基因多态性和单倍型的关系

目的 研究先天性巨结肠与RET基因多态性的关系,进一步推断主要的先天性巨结肠相关单倍型,并分析浙江汉族人群RET基因单核苷酸多态性的分布特点.方法 采集2005年至2007年浙江大学医学院附属儿童医院收治的123例汉族先天性巨结肠患儿以及194例健康体检儿童的外周血,并提取DNA.根据选取的RET基因单核苷酸多态性合成引物,行PCR扩增,经2%琼脂糖电泳证实PCR产物后,将PCR产物进一步纯化、测序.采用PHASE软件计算单倍型频率.将健康儿童RET基因各位点等位基因频率与文献和数据库已有的其他种族资料进行比较.RET基因和先天性巨结肠间关系的分析采用x2检验,以比值比及95%可信区间表示.结果 RET基因-5G＞A、-1A＞C、c135G＞A、c2307T＞G 4个位点的少见基因型AA、CC、AA、GG在先天性巨结肠患儿中的频率显著高于健康儿童(x2=57.775,20.469,57.040,38.869,P＜0.05).RET基因-5A、-1C、c135A、c2307G在先天性巨结肠患儿中等位基因频率显著高于健康儿童(x2=85.114,53.117,77.005,70.161,P＜0.05).RET基因各位点等位基因频率在不同类型先天性巨结肠间的差异无统计学意义(x2=0.048,0.265,0.395,0.027,P＞0.05).RET基因4个位点单倍型中ACAG占先天性巨结肠患儿的75.2%,显著高于健康儿童的38.7%(x2=62.776,P＜0.05).本组健康儿童RET基因-5A、c135A和c2307G位点的少见等位基因频率明显高于欧洲高加索人和非洲约鲁巴人(P＜0.05).结论 RET基因-5G＞A、-1A＞C、c135G＞A、c2307T＞G 4个位点多态性与浙江汉族人群先天性巨结肠发病明显相关,但与先天性巨结肠类型无关.RET基因4个位点单倍型中ACAG是浙江汉族人群的先天性巨结肠相关核心单倍型.浙江汉族人群的RET基因-5、c135和c2307位点的少见等位基因频率显著高于欧洲高加索人和非洲约鲁巴人.     

βS-Globin Gene Cluster Haplotypes in the West Bank of Palestine

Sickle cell disease is an inherited autosomal recessive disorder of the β-globin chain. In Palestine it is accompanied by a low level of Hb F (mean 5.14%) and a severe clinical presentation. In this study, 59 Palestinian patients, homozygotes for Hb S were studied for their haplotype background. Eight polymorphic sites in the β-globin gene cluster were examined. The Benin haplotype was predominant with a frequency of 88.1%, followed by a frequency of 5.1%?for the Bantu haplotype. One chromosome was found to carry the Cameroon haplotype (0.85%). Three atypical haplotypes were also found (5.95%). Heterogeneity was observed in Hb F production, ranging between 1.5 and 17.0%, whereas the ^Gγ ratio was homogeneous among all haplotypes with a normal amount of about 41%. Our results are in agreement with previous reports of the Benin haplotype origin in the Mediterranean.     

Genetic association of single nucleotide polymorphisms in endonuclease G-like 1 gene with type 2 diabetes in a Japanese population

Aims/hypothesis In order to identify type 2 diabetes disease susceptibility gene(s) in a Japanese population, we applied a region-wide case–control association test to the 20.4 Mb region between D3S1293 and D3S2319 on chromosome 3p24.3-22.1, supported by linkage to type 2 diabetes and its related traits in Japanese and multiple populations. Materials and methods We performed a two-stage association test using 1,762 Japanese persons with 485 gene-centric, evenly spaced, common single nucleotide polymorphism (SNP) markers with minor allele frequency >0.1. For mouse studies, total RNA was extracted from various organs of BKS.Cg-+Lepr ^db /+Lepr ^db and control mice, and from MIN6, NIH3T3 and C2C12 cell lines. Results We detected a landmark SNP375 (A/G) (rs2051211, p = 0.000046, odds ratio = 1.33, 95% CI 1.16–1.53) in intron 5 of the endonuclease G-like 1 (ENDOGL1) gene. Systematic dense SNPs approach identified a susceptibility linkage disequilibrium (LD) block of 116.5 kb by |D′|, an LD units map and a critical region of 2.1 kb by r ² in ENDOGL1. A haplotype-based association test showed that an at-risk haplotype is associated with disease status (p = 0.00001). The expression of ENDOGL1 was rather ubiquitous with relatively abundant expression in the brain and also in a pancreatic islet beta cell line. Mouse Endogl1 expression increased in pancreatic islets of hyperglycaemic BKS.Cg-+Lepr ^db /+Lepr ^db mice compared with that in control mice. Conclusions/interpretation Based on the population genetics, fine mapping of LD block and haplotype analysis, we conclude that ENDOGL1 is a candidate disease-susceptibility gene for type 2 diabetes in a Japanese population. Further analysis in a larger sample size is required to substantiate this conclusion. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorised users.     

Founder Effect in Different European Countries for the Recurrent P392L SQSTM1 Mutation in Paget’s Disease of Bone

Paget's Disease of Bone (PDB) is one of the most frequent metabolic bone diseases, affecting 1-5% of Western populations older than 55 years. Mutations in the sequestosome1 (SQSTM1) gene cause PDB in about one-third of familial PDB cases and in 2.4-9.3% of nonfamilial PDB cases, with the 1215C-->T (P392L) mutation being the most frequent one. We investigated whether a founder effect of the P392L SQSTM1 mutation was present in Belgian (n = 233), Dutch (n = 82), and Spanish (n = 64) patients without a PDB family history. First, direct sequencing analysis of exon 8 in these three populations showed that the P392L mutation occurred in 17 Belgian patients (7.3%), three Dutch patients without a family history (3.7%), and two Dutch patients with a family history. In the Spanish population, 15.6% of patients (n = 10) had the P392L mutation, including one homozygous mutant. This is by far the highest mutation frequency of all populations investigated so far. Next, we examined the genetic background of 33 mutated chromosomes by analyzing haplotypes. We genotyped four single-nucleotide polymorphisms (SNPs) in exon 6 and the 3'-untranslated region of SQSTM1 (rs4935C/T, rs4797G/A, rs10277T/C, and rs1065154G/T) and used software programs WHAP and PHASE to reconstruct haplotypes. Finally, allele-specific primers allowed us to assign the mutation to one of the two haplotypes from each individual. Sequencing results revealed that all 33 P392L mutations were on the CGTG (H2) haplotype. The chance to obtain this result due to 33 independent mutation events is 3.97 x 10(-14), providing strong evidence for a founder effect of the P392L SQSTM1 mutation in Belgian, Dutch, and Spanish patients with PDB.     

Modification of primers for GRHPR genotyping: avoiding allele dropout by single nucleotide polymorphisms and homology sequence

Mutation of primer site for genotyping by polymerase chain reaction (PCR) may cause allele dropout and other genotyping failures. Primary hyperoxaluria type 2 (PH2) is a rare inherited disease caused by overproduction of endogenous oxalate due to mutations in the glyoxylate/hydroxypyruvate reductase (GRHPR) gene. Here, to avoid allele dropout and primer annealing to multiple sites, and given the discrepancy in intron length between GRHPR gene data, we updated the primers used in the sequence assay of the GRHPR gene. These redesigned primers show potential in reducing detection failure of GRHPR mutations. In addition, we performed a single nucleotide polymorphism (SNP) linkage analysis of the GRHPR gene using direct sequencing with PCR amplification of specific alleles (DS-PASA). Using this technique, we sequenced four common SNPs between intron E and exon 6, which show linkage disequilibrium (LD) consisting of three types of haplotypes, similar to data from the HapMap SNP database. This article directly relates to material presented at the 11th International Urolithiasis Symposium, Nice, 2–5 September 2008, from which the abstracts were published in the following issue of Urological Research: Urological Research (2008) 36:157–232. doi:.     

Comparisons of <Emphasis Type="Italic">CYP1A2</Emphasis> genetic polymorphisms,enzyme activity and the genotype-phenotype relationship in Swedes and Koreans

Objectives To investigate the CYP1A2 genotype-phenotype relationship and to compare CYP1A2 genetic polymorphisms and enzyme activity in terms of the effect of smoking and oral contraceptive (OC) use in Swedes and Koreans. Methods CYP1A2 enzyme activity was determined in 194 and 150 healthy Swedish and Korean subjects, respectively, on the basis of the 4-h plasma paraxanthine/caffeine (17X/137X) ratio determined using high-performance liquid chromatography. Genotyping for the −3860G>A, −2467delT, −739 T>G, −729 C>T, −163C>A and −3113A>G polymorphisms was performed by PCR-restriction fragment length polymorphism analysis. Results The mean 17X/137X ratio was 1.54-fold higher in Swedes than in Koreans (mean difference: 0.16; 95% CI of the mean difference: 0.12, 0.20; p < 0.0001). Smokers had a significantly higher 17X/137X ratio (higher CYP1A2 activity) than non-smokers, while Swedish OC users had a significantly lower 17X/137X ratio than non-users (mean difference: 0.31, 95% CI of the mean difference: 0.23, 0.39; p < 0.0001). No effect of gender differences on enzyme activity was observed. Four known (CYP1A2*1A, *1D, *1F, and *1L) and two novel haplotypes (CYP1A2*1V and CYP1A2*1W) were found. CYP1A2*1K was rare in Swedes and absent in Koreans. No significant genotype-phenotype relationship was observed, with the exception of CYP1A2*1F in Swedish smokers, where it was associated with higher enzyme inducibility (p = 0.02). Koreans displayed a significantly lower mean 17X/137X ratio than Swedes having the same CYP1A2 genotype, smoking habit and OC use. Conclusions We found significant differences in CYP1A2 enzyme activity between Swedes and Koreans that could not be explained by environmental factors or the CYP1A2 haplotypes examined, despite differences in allele frequencies. None of the investigated CYP1A2 haplotypes are critical in inducing variations in enzyme activity, with the exception of CYP1A2*1F.     

Potential impact of ABCB1 (p-glycoprotein) polymorphisms on avermectin toxicity in humans

Several members of the ATP binding cassette (ABC) transporter protein superfamily perform xenobiotic efflux functions in mammals, limiting gut absorption, mediating excretion, and controlling entry of a wide range of chemicals to sensitive compartments such as brain, testes and foetus. Perhaps the best characterised of these is p-glycoprotein (gene name ABCB1/MDR1), a barrier epithelia expressed protein with structurally diverse substrates, including the avermectin pesticides. In specific mouse and dog strains, ABCB1 mutations have been identified that result in loss of p-glycoprotein function in the blood brain barrier (BBB) and increased susceptibility to avermectin neurotoxicity. As yet no large rearrangements of the human ABCB1 gene analogous to those in the mouse and dog have been identified. However, numerous human ABCB1 single nucleotide polymorphisms (SNPs) have been identified, the allelic frequencies of which vary with ethnicity. There is no clear consensus on whether or not SNPs, or combinations of SNPs, reduce human p-glycoprotein functionality. However, recent in vivo human data indicate that the two commonest ABCB1 haplotypes both exhibit full BBB functionality. We discuss here the role of p-glycoprotein in limiting brain absorption of avermectin pesticides, as well as the potential impact of the reported functional effects and population frequencies of known ABCB1 polymorphisms on avermectin pesticide risk assessments.