Genetic variants in the CPNE5 gene are associated with alcohol dependence and obesity in Caucasian populations

Alcohol addiction may increase the risk of obesity due to shared genetic components. The Copine V (CPNE5) gene is involved in Ca²⁺ binding and may play an important role in the development of the central nervous system. This study tested the genetic associations of 77 single-nucleotide polymorphisms (SNPs) within the CPNE5 gene with alcohol dependence (AD) and obesity using a Caucasian sample – The Study of Addiction – Genetics and Environment (SAGE) sample (1066 AD cases and 1278 non-AD controls, 422 obese cases and 1395 non-obese controls). The Marshfield sample (1442 obese cases and 2122 non-obese controls) was used for replication of obesity. Multiple logistic regression analysis was performed using the PLINK software. In the SAGE sample, we identified 10 SNPs associated with AD and 17 SNPs associated with obesity (p < 0.05). Interestingly, 6 SNPs (rs9986517, rs9470387, rs3213534, rs10456444, rs3752482, and rs9470386) were associated with both AD (OR = 0.77, 0.77, 0.83, 0.84, 0.79 and 1.14, respectively; p = 9.72 × 10⁻⁵, 1.1 × 10⁻⁴, 4.09 × 10⁻³, 5.26 × 10⁻³, 1.59 × 10⁻², and 3.81 × 10⁻², respectively) and obesity (OR = 0.77, 0.77, 0.78, 0.77, 0.68 and 1.18, respectively; p = 2.74 × 10⁻³, 2.69 × 10⁻³, 2.45 × 10⁻³, 1.01 × 10⁻³, 5.18 × 10⁻³ and 3.85 × 10⁻², respectively). In the Marshfield sample, rs3752480 was associated with obesity (p = 0.0379). In addition, four SNPs (rs9986517, rs10456444, rs7763347 and rs4714010) showed associations with obesity in the meta-analysis using both samples (p = 0.00493, 0.0274, 0.00346, and 0.0141, respectively). These findings provide the first evidence of common genetic variants in the CPNE5 gene influencing both the AD and obesity; and will serve as a resource for replication in other populations.     

Distribution of HLA-A, -B and -DRB1 antigenic groups and haplotypes from the Brazilian bone marrow donor registry (REDOME)

To improve assistance for patients awaiting a bone marrow transplant from an unrelated donor, it is important to genetically characterize the Brazilian volunteer bone marrow donors registry (REDOME). Our objective was to describe the antigenic groups and haplotype frequencies of HLA-A, HLA-B and HLA-DRB1 in the five regions of Brazil and by self-reported ethnicity groups using the REDOME data. Our study included 3,038,286 individuals. HLA antigenic groups and haplotype frequencies were estimated using an Expectation-Maximization (EM) algorithm. All described HLA-A*, HLA-B* and HLA-DRB1* groups were identified in this study. A*02 (25.9%), B*35 (11.8%) and DRB1*13 (13.4%) are the most frequent antigenic groups in REDOME, and the A*01-B*08-DRB1*03 haplotype is the most frequent in the registry. The antigenic group and haplotype frequency data obtained in this study could be helpful for national donor recruitment strategies across the country.     

High-resolution HLA-A,HLA-B,and HLA-DRB1 haplotype frequencies from the French Bone Marrow Donor Registry

We have estimated human leukocyte antigen (HLA) haplotype frequencies using the maximum likelihood mode, which accommodates typing ambiguities. The results of the frequency distribution of the 7015 haplotypes obtained are presented here. These include a total of 114 HLA-A, 185 HLA-B, and 76 HLA-DRB1 unique alleles at each locus. Across all populations, although the most common individual HLA alleles were HLA-A¹02:01 (29.0%), HLA-B¹07:02 (11.4%), and HLA-DRB1¹07:01 (15.9%), the most frequent haplotype was found to be HLA-A¹01:01∼B¹08:01∼DRB1¹03:01.     

BRCA1 and BRCA2 Mutations in Ethnic Lebanese Arab Women With High Hereditary Risk Breast Cancer

Purpose.

Breast cancer is the most common malignancy among women in Lebanon and in Arab countries, with 50% of cases presenting before the age of 50 years.

Methods.

Between 2009 and 2012, 250 Lebanese women with breast cancer who were considered to be at high risk of carrying BRCA1 or BRCA2 mutations because of presentation at young age and/or positive family history (FH) of breast or ovarian cancer were recruited. Clinical data were analyzed statistically. Coding exons and intron-exon boundaries of BRCA1 and BRCA2 were sequenced from peripheral blood DNA. All patients were tested for BRCA1 rearrangements using multiplex ligation-dependent probe amplification (MLPA). BRCA2 MLPA was done in selected cases.

Results.

Overall, 14 of 250 patients (5.6%) carried a deleterious BRCA mutation (7 BRCA1, 7 BRCA2) and 31 (12.4%) carried a variant of uncertain significance. Eight of 74 patients (10.8%) aged ≤40 years with positive FH and only 1 of 74 patients (1.4%) aged ≤40 years without FH had a mutated BRCA. Four of 75 patients (5.3%) aged 41–50 years with FH had a deleterious mutation. Only 1 of 27 patients aged >50 years at diagnosis had a BRCA mutation. All seven patients with BRCA1 mutations had grade 3 infiltrating ductal carcinoma and triple-negative breast cancer. Nine BRCA1 and 17 BRCA2 common haplotypes were observed.

Conclusion.

Prevalence of deleterious BRCA mutations is lower than expected and does not support the hypothesis that BRCA mutations alone cause the observed high percentage of breast cancer in young women of Lebanese and Arab descent. Studies to search for other genetic mutations are recommended.     

慢性萎缩性胃炎和胃腺癌肿瘤坏死因子微卫星遗传易感性研究

目的 探讨中国湖北地区汉族人群中肿瘤坏死因子（TNF）a,TNFb和TNFc微卫星多态性分布，分析其与慢性萎缩性胃炎和胃腺癌的相关性。方法 应用PCR结合变性聚丙烯酰胺凝胶高压电泳和AgNO3染色，对164例健康者，53例慢性萎缩性胃炎和56例胃腺癌患者的TNFa,TNFb和TNFc微卫星进行分型，并将PCR产物克隆及测序鉴定。结果 慢性萎缩性胃炎中的TNFa10基因频率为19．81％，显著高于正常人中的11．84％（P．04）。进一步分析显示TNFa10等位基因与患者的年龄，性别,黏膜萎缩程度，肠上皮化生等无关。TNFa6b5c1单倍体纯合子在胃腺癌中的频率为1．79％，显著低于正常人中的15．85％（P＝0．006）。克隆测序发现，相同TNFa等位基因包含的（AC／GT）重复序列拷贝数与国外文献报道中不一致。结论 TNFa等位基因的定义内涵尚需进一步确定。TNFa10等位基因与慢性萎缩性胃炎的易感性相关，TNFa6b5c1单倍体纯合子在慢性萎缩性胃炎至胃腺癌移行过程中发挥其抵抗作用。     

Interleukin-37 gene polymorphism and susceptibility to pulmonary tuberculosis among Iraqi patients

BackgroundControl of tuberculosis (TB) depends on a balance between host's immune factors and bacterial evasion strategies. Interleukin-37 (IL-37) is among the immunomodulatory factors that have been proposed to influence susceptibility to tuberculosis.MethodsA case–control study was conducted on 105 patients with pulmonary TB (37 active, 41 multi-drug resistant and 27 relapse) and 79 healthy controls to determine serum levels and single nucleotide polymorphisms (SNPs) of IL-37. The IL-37 level was assessed with an enzyme-linked immunosorbent kit, while DNA-sequencing was used to detect SNPs in the promoter region of IL37 gene.Results: Median level of IL-37 was markedly increased in serum of TB patients compared to controls (325.0 vs. 169.1 pg/mL; p < 0.001). This increase was universally determined in subgroups of patients distributed according to gender, age groups, and clinical type of disease, while no significant differences were found between the subgroups in patients or controls. Analysis of receiver operating characteristic curve confirmed these findings and IL-37 occupied a very good area under the curve, which was 0.816 (95% CI = 0.744–0.888; p < 0.001). At a cut-off value of 185.6 pg/mL, the sensitivity and specificity of IL-37 were 81.0 and 82.3%, respectively. Of the nine detected SNPs (rs2466449 G/A, rs2466450 A/G, rs2723168 G/A, rs3811042 G/A, rs3811045 T/C, rs3811046 G/T, rs3811047 A/G, rs3811048 G/A and rs200782323 G/A), only rs3811048 showed a significant association with TB; the G allele showed a significantly decreased frequency in TB patients compared to controls (25.2 vs. 44.9%; OR = 0.41; p < 0.001). It was possible to assign five haplotypes, and three showed significant differences between patients and controls. Frequency of haplotype A-A-G-A-C-T-G-A-G (0.331 vs. 0.213; OR = 2.10; p = 0.015) was significantly increased in TB patients compared to controls. On the contrary, frequencies of haplotypes A-A-G-A-C-T-G-G-G (0.029 vs. 0.116; OR = 0.24; p = 0.01) and A-A-G-G-T-G-A-G-G (0.140 vs. 0.275; OR = 0.45; p = 0.015) were significantly decreased in patients.ConclusionsIL-37 was up-regulated in the serum of TB patients irrespective of their gender, age or clinical type of disease. SNPs in the promoter region of IL37 gene were proposed to be associated with susceptibility to TB.     

广西梧州籍汉族α-地中海贫血患者HLA-A、B等位基因多态性及单倍型分析

目的分析广西梧州籍汉族α-地中海贫血患者人类白细胞抗原（HLA）-A、B在高分辨基因分型水平上的等位基因多态性和单倍型的分布特征。方法采用聚合酶链反应-直接测序分型法（PCR-SBT）,对广西梧州籍汉族117例α-地中海贫血患者的HLA-A、B位点进行高分辨基因分型,用直接计数法计算等位基因频率,应用Arlequin V3.5软件,以最大似然法分析单倍型频率。结果在117例α-地中海贫血患者中共检出高分辨HLA-A等位基因17个,HLA-B等位基因33个。A位点等位基因频率最高的是A＊11：01（27.35%）,B位点等位基因频率最高的是B＊40：01（15.38%）和B＊46：01（14.96%）。频率最高的HLA-A-B单倍型有A＊33：03-B＊58：01（11.49%）、A＊02：07-B＊46：01（8.33%）、A＊11：01-B＊40：01（6.34%）。连锁不平衡最显著的单倍型是A＊33：03-B＊58：01、A＊02：07-B＊46：01、A＊74：02-B＊51：01、A＊02：03-B＊38：02、A＊11：02-B＊27：04。结论广西梧州籍汉族α-地中海贫血患者HLA-A、B等位基因具有较高的多态性,其双座位单倍型具有地区性遗传特征。     

A Novel Approach to Rapid Determination of βS‐Globin Haplotypes: Sequencing of the Aγ‐IVS‐II Region

β‐Globin gene cluster haplotypes were originally determined by restriction endonuclease mapping with Southern blots of polymorphic sites around the gene cluster. Over the years, haplotyping has been found to be useful, not only in population genetics but also in predicting the severity of hemoglobinopathies such as sickle cell disease. The sickle mutation occurs on five distinct haplotypes. The hitherto used methods are cumbersome and time‐consuming, making haplotype determination a tedious procedure. We report our experience with a novel, rapid approach to haplotyping based on sequence polymorphisms in the ^Aγ‐IVS‐II region. We provide an algorithm that allows rapid assignment of the four African haplotypes carrying the sickle mutation.     

The β-GLobin Gene Haplotypes Associated With Hb D-Los Angeles [β121(GH4)Glu→Gln] in Western Iran

Hb D-Los Angeles is characterized by the substitution of glutamine for glutamic acid at position 121 of the β-globin chain. The present investigation is the first study on the β-globin gene haplotypes associated with β-D-Los Angeles in Western Iran. Thirty two individuals from 11 unrelated families from Western Iran were studied. The Hb D-Los Angeles status of all cases was confirmed using polymerase chain reaction (PCR) followed by digestion with EcoRI. The haplotype of the β‐globin gene cluster was determined by a PCR-RFLP (restriction fragment length polymorphism) procedure. The haplotype background of the β^A chromosomes was also determined in 35 normal subjects from the same geographic region. The β-globin gene haplotype analysis demonstrated that all β-D-Los Angeles genes (23 genes) were in linkage disequilibrium with haplotype I [+????++]. Among the 70 β^A chromosomes, 30 chromosomes (42.9%) were associated with haplotype I. The present study indicates the unicentric origin of the β-D-Los Angeles gene in Western Iran. It seems that this mutation may have occurred at the same chromosomal background common in the local population.