克罗恩病与肿瘤坏死因子超家族15基因的关系

目的 探讨中国人群中肿瘤坏死因子超家族15(TNFSF15)基因的多态性分布及其与克罗恩病(CD)的相关性.方法 飞行质谱法检测144例CD和500例正常对照者的TNFSF15基因多态性位点,分析基因多态性与CD发病及各临床表型的相关性.结果 在检测的5个SNF位点中,CD组和正常对照组间,有4个位点的基因型频率和等位基因频率存在差异,并且差异具有统计学意义(P<0.05).在构建的我国人群特有单倍型中,单倍型Haplotype 1在CD组中低于正常对照组(P<0.05),是CD的保护性单倍型.各CD临床表型与基因型见无明显相关(P>0.05).结论 TNFSF15基因的是我国CD的易感基因,在IBD的发病过程中具有重要作用.     

Detection of reciprocal quantitative trait loci for acute ethanol withdrawal and ethanol consumption in heterogeneous stock mice

Rationale  Previous studies have suggested that there is an inverse genetic relationship between ethanol consumption (two-bottle choice, continuous access) and ethanol withdrawal (e.g., Metten et al., Behav Brain Res 95:113–122, 1998a). Objectives  The current study used short-term selective breeding from heterogeneous stock (HS) animals to examine this relationship. The primary goal of the current study was to determine if reciprocal quantitative trait loci (QTLs) could be found in the selectively bred lines. The advantage of detecting QTLs in HS animals is that it is possible to extract a haplotype signature for the QTL, which in turn can be used to narrow the number of candidate genes generated from gene expression and sequence databases (see, e.g., Hitzemann et al., Mamm Genome 14:733–747, 2003). Results  Seven reciprocal QTLs were detected on chromosomes (Chr) 1 (two), 3, 6, 11, 16, and 17 that exceeded the nominal LOD threshold of 10; genetic drift, which occurs during selection, dramatically increases the LOD threshold. The proximal Chr 1 QTL was examined in some detail. The haplotype structure of the QTL was such that the LP/J allele was associated with low withdrawal and high consumption. The QTL appears to be located in a gene-poor region between 170 and 173 Mbp. Based on available sequence data, two plausible candidate genes emerge—Nos1ap and Atf6α. Conclusions  The data presented here confirm some aspects of the negative genetic relationship between acute ethanol withdrawal and ethanol consumption. The QTL data point to the potential involvement of NO signaling and/or the unfolded protein response. This study was supported in part by AA 10760, 11034, and 13484.     

Genetic risk factors for diabetic nephropathy on chromosomes 6p and 7q identified by the set-association approach

Aims/hypothesis In the present study we investigated potential associations of a set of 45 single nucleotide polymorphisms (SNP) in 20 candidate genes on eight chromosomes with diabetic nephropathy (DN) in type 2 diabetes mellitus. We aimed to compare two methodological approaches suitable for analysing susceptibility to complex traits: single- and multi-locus analyses. Materials and methods The study comprised a total of 647 subjects in one of three groups: diabetes with or without DN, or no diabetes. Genotypes were detected by PCR-based methodology (PCR only, PCR plus RFLP, or allele-specific PCR). Haplotypes were inferred in silico. Set association (tested using SUMSTAT software) was used for multilocus analysis. Results After correction for multiple comparisons, only one SNP, in the gene encoding the receptor of advanced glycation end products, AGER 2184A/G (gene symbol formerly known as RAGE) showed a significant association with DN (p = 0.0006) in single-locus analysis. In multi-locus analysis, six SNPs exhibited a significant association with DN: four SNPs on chromosome 6p (AGER 2184A/G, LTA 252A/G, EDN1 8002G/A and AGER -429T/C) and two SNPs on chromosome 7q (NOS3 774C/T and NOS3 E298D), omnibus p = 0.033. Haplotype analysis revealed significant differences between DN and control groups in haplotype frequencies on chromosome 6 (p = 0.0002); however, there were no significant difference in the frequencies of the NOS3 haplotypes on chromosome 7. Logistic regression analysis identified SNPs AGER 2184A/G and NOS3 774C/T, together with diabetes duration and HbA_1c, as significant predictors of DN. Testing for interactions between SNPs on chromosomes 6 and 7 did not provide significant evidence for epistatic interaction. Conclusions/interpretation Using the set-association approach we identified significant associations of several SNPs on chromosomes 6 and 7 with DN. The single- and multi-locus analyses represent complementary methods. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorised users.     

Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area)

In this study, 20 Y-specific short tandem repeat (STR) loci (DYS434, Y-GATA-A10, Y-GATA-H4, DYS438, DYS439, DYS443, DYS444, DYS446, DYS447, DYS448, DYS456, DYS458, DYS460, DYS520, DYS531, DYS557, DYS622, DYS630, DYS635(Y-GATA-C4), and DYS709) were analyzed in 158 unrelated healthy men from southeast China by three fluorescence-labeled multiplex polymerase chain reaction systems. The Y-STR multiplexes developed have followed the published nomenclature and International Society for Forensic Genetics (ISFG) guidelines for STR analysis. Gene diversity ranged from 0.2506 at DYS434 to 0.8034 at DYS447. A total of 157 different haplotypes were observed, and among these, 156 were unique, while 1 was found two times. The haplotype diversity value calculated from all 20 loci combined was 0.9997, which is informative. Furthermore, 80 father–son pairs, previously confirmed by autosomal STR analysis, were typed using the same 20 Y-STR loci, and four mutation events were identified at the Y-GATA-H4, DYS439, DYS456, and DYS458 loci, giving an average mutation rate of 0.25% per locus per generation (95% confidence interval 0.09–0.54). These results including the haplotype data at 20 Y-STR loci would enrich Chinese genetic informational resources and provide useful information in forensic practice. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification and characterization of CFTR gene mutations in Indian CF patients

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study was performed on Indian CF patients (n = 50) to investigate the spectrum of mutations in the CFTR gene and their association with intragenic and extragenic marker haplotypes. We report identification of 14 previously known and eight novel mutations, namely 3986-3987delC, 876-6del4, 1792InsA, L69H, S158N, Q493L, I530L and E1329Q. The frequency of delta F508 was found to be 27%. Absolute linkage between delta F508 and the KM.19-GATT-TUB9-M470V-T854T haplotype (2-2-1-1-1) predicts a relatively recent appearance of delta F508 in Indian CF patients. Low frequency of delta F508 mutation and detection of eight novel and thirteen rare mutations reflect a heterogeneous spectrum of mutations in Indian CF patients. Failure to detect mutations in 34% of alleles indicates the possible presence of gross deletions involving one or more exons or may indicate the location of the molecular defects in either the noncoding parts of the gene or in the promoter region, which warrants analysis of those regions.     

一个中国汉族先天性附耳表型致病基因的定位研究

目的定位一个中国汉族先天性面部畸形家系附耳表型的致病基因。方法通过全基因组扫描、连锁分析和单体型分析用微卫星遗传标记在染色体区域定位致病基因。结果全基因组扫描和连锁分析发现,附耳的致病基因可能定位于d18s462～d18s70之间,遗传距离为6.00cM,LODZMAX=1.83（d18s462,θ=0.06）;或者d7s2546～d7s559之间,遗传距离为8.94cM,LODZMAX=2.74（d7s2546,θ=0.05）。再经过单体型分析将其致病基因定位在d7s2546～d7s550之间,遗传距离为5.38cM。结论这个中国汉族家系附耳表型的致病基因定位d7s2546～d7s550之间,在染色体的位置为7q36.1～q36.2。     

Diversity and prevalence of the C-terminal region of Plasmodium falciparum merozoite surface protein 1 in China

Malaria continues to be a significant health concern for regions of southeastern Asia. Scientists have focused much effort on the development and regional testing of a vaccine against the most virulent of the pathogens that cause the disease, Plasmodium falciparum. The 19 kDa COOH-terminal region of the merozoite surface protein 1 (PfMSP1-19) is considered to be a potentially important component of a malaria vaccine and yet, to date, there is little data from China with regard to Pfmsp1-19 diversity. We have collected samples from 300 individuals diagnosed with P. falciparum infections from Yunnan and Hainan provinces - two potential vaccine trial sites in China. We determined the sequence of DNA encoding PfMSP1-19 for each. We identified seven polymorphic positions; varying arrangements of which accounted for 10 distinct Pfmsp1-19 haplotypes. Four haplotypes, however, represented more than 93% of the total. Differences in the prevalence of haplotypes between Yunnan and Hainan provinces were observed, even though the distribution of haplotypes in Yunnan province seemed to be very similar to those reported for Vietnam and Thailand. These results provide necessary information for the design of a major human vaccine trial as well as a basis for subsequent interpretations of the results. On broader scale, the data should complement the existing database on the prevalence and distribution of Pfmsp1-19 haplotypes and therefore have potential use in the design of PfMSP1-19-based polyvalent vaccines for use in Southeastern Asian countries.     

Benign adult familial myoclonic epilepsy (BAFME): evidence of an extended founder haplotype on chromosome 2p11.1-q12.2 in five Italian families

Benign adult familial myoclonic epilepsy (BAFME or FAME) is an autosomal dominant condition, characterized by shivering-like tremors of cortical origin, myoclonus, and epilepsy. Linkage to chromosomes 2p11.1-q12.2 and 8q23.1-q24.11 has been reported in Japanese and Italian families, respectively. We aimed to determine whether a common founder haplotype was shared by five BAFME families from southern Italy and attempted preliminary genotype-phenotype correlation analyses. Five Italian BAFME families were identified. One family has not been previously reported. DNA from 53 affected individuals was genotyped with highly polymorphic microsatellite markers spanning chromosomes 2p11.1-q12.2 and 8q23.1-q24.11. Multipoint linkage analysis was performed using LINKMAP 5.1 software assuming an autosomal dominant trait with 0.99 penetrance and frequency of 0.001. Significant linkage was found on chromosome 2p11.1-q12.2 and a maximum cumulative lod score of 18.5 was found for markers D2S2161 and D2S388. The haplotype "5332" of adjacent markers D2S388, D2S2216, D2S113, and D2S2175 segregates with the disease in all families indicating that the same mutation inherited from a common ancestor segregates in these families. Preliminary genotype-phenotype showed that patients carrying the disease haplotype show minor clinical differences, suggesting that expressivity of the founder mutation is not markedly influenced by other factors. The identification of causative mutations in BAFME requires an extensive and collaborative screening effort.     

Estrogen receptor alpha haplotypes and breast cancer risk in older Caucasian women

Life-long exposure to estrogen is an established risk factor for breast cancer development. The underlying mechanism has been suggested to be the binding of estrogen-to-estrogen receptors in mammary tissue, which in turn promotes the proliferation and differentiation of breast tissue. Polymorphisms and haplotypes in estrogen receptor alpha (ESR1) have been reportedly associated with breast cancer risk; however, the results are not fully consistent. In this study, we investigated breast cancer risk associated with genotypes and haplotypes resulting from four ESR1 single nucleotide polymorphisms (SNPs), rs746432, rs2234693, rs9340799, and rs1801132. Genotyping has been performed on 393 breast cancer cases and 790 randomly selected controls in 1,183 Caucasian women over age 65 from the Study of Osteoporotic Fractures (SOF). We observed an allelic protective effect for SNP rs9340799 with an estimated odds ratio (OR) of 0.82 (95% CI = 0.68–1.00; P = 0.04) after adjustment for age, BMI and hip BMD. A protective effect of this SNP has been reported before in several different studies. We did not replicate the previously reported C–C–A–G haplotype association to breast cancer—the C–C–A–G haplotype from these SNPs was rare in this study (estimated frequency below 0.001% in cases and controls). No other statistically significant associations were observed between ESR1 haplotypes from the same four SNPs and the risk of breast cancer in older Caucasian women.