Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel

Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the ‘NAME’ panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs.     

Epithelial ovarian cancer risk: A review of the current genetic landscape

Ovarian cancer is the fourth most common cause of cancer-related death in women in the developed world, and one of the most heritable cancers. One of the most significant risk factors for epithelial ovarian cancer (EOC) is a family history of breast and/or ovarian cancer. Combined risk factors can be used in models to stratify risk of EOC, and aid in decisions regarding risk-reduction strategies. Germline pathogenic variants in EOC susceptibility genes including those involved in homologous recombination and mismatch repair pathways are present in approximately 22% to 25% of EOC. These genes are associated with an estimated lifetime risk of EOC of 13% to 60% for BRCA1 variants and 10% to 25% for BRCA2 variants, with lower risks associated with remaining genes. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) thought to explain an additional 6.4% of the familial risk of ovarian cancer, with 34 susceptibility loci identified to date. However, an unknown proportion of the genetic component of EOC risk remains unexplained. This review comprises an overview of individual genes and SNPs suspected to contribute to risk of EOC, and discusses use of a polygenic risk score to predict individual cancer risk more accurately.     

女孩雌激素受体基因6号内含子区域两个新SNPs位点报道

目的：在女性性早熟患儿中检测雌激素受体基因6号外显子及内含子基因序列可能存在的突变。方法：PCR扩增雌激素受体基因6号外显子及内含子，对扩增产物进行DNA序列分析。结果：在6号内含子一侧，发现两个100％连锁的单核苷酸多态性(SNPs)，分别为．53G—67A和53T—67G。结论：这一对单核苷酸多态性并不引起氨基酸的替代，与女孩性早熟的发生也无关，但是否和其他疾病有连锁关系尚待进一步探讨。     

Single nucleotide polymorphisms in the protamine-1 and -2 genes of fertile and infertile human male populations

Although various genetic factors have been implicated in human male infertility, the causative genes for the different types of idiopathic male infertility have not been elucidated. Protamines, which are the major DNA-binding proteins in the sperm nucleus, package the DNA into the sperm head. Analysis of the human protamine-1 (PRM1) and -2 (PRM2) gene sequences in 226 sterile male patients and in 270 proven-fertile male volunteers revealed four single nucleotide polymorphisms (SNPs) in the PRM1 coding region, which did not cause any amino acid substitutions, and one SNP in the PRM2 gene, which produced translation termination. We also observed one SNP in the 3' non-coding region of the PRM1 gene, and two SNPs within the intron of the PRM2 gene. The prevalence of these SNPs was similar in both infertile patients and in proven-fertile volunteers, except that the c248t alteration in the PRM2 gene induced a nonsense codon under conditions of heterozygosity in one infertile patient. Although the PRM1 and PRM2 genes are highly conserved, the single SNP in the PRM2 gene that induces translation termination may result in male infertility due to haploinsufficiency of PRM2.     

Human arylhydrocarbon receptor repressor (AHRR) gene: genomic structure and analysis of polymorphism in endometriosis

The diversity of biological effects resulting from exposure to dioxin may reflect the ability of this environmental pollutant to alter gene expression by binding to the arylhydrocarbon receptor (AHR) gene and related genes. AHR function may be regulated by structural variations in AHR itself, in the AHR repressor (AHRR), in the AHR nuclear translocator (ARNT), or in AHR target molecules such as cytochrome P-4501A1 (CYP1A1) and glutathione S-transferase. Analysis of the genomic organization of AHRR revealed an open reading frame consisting of a 2094-bp mRNA encoded by ten exons. We found one novel polymorphism, a substitution of Ala by Pro at codon 185 (GCC to CCC), in exon 5 of the AHRR gene; among 108 healthy unrelated Japanese women, genotypes Ala/Ala, Ala/Pro, and Pro/Pro were represented, respectively, by 20 (18.5%), 49 (45.4%), and 39 (36.1%) individuals. We did not detect previously published polymorphisms of ARNT (D511N) or the CYP1A1 promoter (G-469A and C-459T) in our subjects, suggesting that these polymorphisms are rare in the Japanese population. No association was found between uterine endometriosis and any polymorphisms in the AHRR, AHR, ARNT, or CYP1A1 genes analyzed in the present study. Received: January 24, 2001 / Accepted: March 1, 2001     

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     

Confirmation of genetic variants associated with lethal prostate cancer in a cohort of men from hereditary prostate cancer families

Germline genetic variants have been suggested as prognostic biomarkers for identifying patients at high risk for lethal prostate cancer (PCa). Validation studies have confirmed the association of several single nucleotide polymorphisms (SNPs) with fatal PCa, but whether these variants affect PCa‐specific mortality (PCSM) in patients with an inherited predisposition to PCa, based on familial history, is unknown. For this study, a cohort of 957 PCa patients from 270 hereditary prostate cancer families of European ancestry was genotyped for a panel of 22 PCSM‐associated SNPs. Death certificates were reviewed to confirm cause of death. Mixed‐effect Cox proportional hazards models were used to assess survival according to genotypes, accounting for relatedness and clinicopathological factors. Within this cohort, 98 PCa deaths were confirmed over an average follow‐up period of 12.7 years after diagnosis. Variant allele carriers for three SNPs had significantly altered risk for PCSM [rs635261 at RNASEL, hazard ratio (HR), 0.35, 95% CI, 0.18–0.66; p = 0.002; rs915927 in XRCC1, HR, 1.91, 95% CI, 1.21–3.02; p = 0.009; and rs2494750 at AKT1, HR, 0.45, 95% CI, 0.23–0.90; p = 0.016). These results confirm the association of genetic variation in three genes with PCa lethality in a cohort of men with an inherited susceptibility to the disease and provide validation evidence that germline SNPs provide prognostic information for PCa patients. Development of a panel of germline biomarkers with clinical utility for distinguishing patients at detection who have an increased risk for fatal PCa is warranted.     

NLRP3基因多态性与中国北方东部汉族人群帕金森病相关性研究

目的探讨Nod样受体家族蛋白3 (Nod-like receptor protein 3,NLRP3)rs4612666及rs7525979位点多态性与中国北方东部汉族人群帕金森病(Parkinson disease,PD)发病风险的相关性。方法采用病例对照研究,共招募400例PD患者(PD组)及400例健康对照者(对照组),应用聚合酶链反应-限制性片段长度多态性方法鉴定NLRP3基因SNPs位点rs4612666和rs7525979。结果 PD组rs4612666等位基因与对照组具有统计学差异,C等位基因频率低于对照组,降低发病风险(OR=0.794,95%CI:0.653～0.967,P=0.021),隐性遗传模型CC/TT+CT分布在PD组与对照组之间差异具有统计学意义(OR=0.667,95%CI:0.481～0.925,P=0.015)。亚组分析中,与对照组比较,女性PD组与早发型PD组等位基因分布差异具有统计学意义(P=0.003,P=0.018)。rs7525979位点的基因型分布和等位基因频率在PD组与对照组比较均无统计学差异(P>0.05)。结论在中国北方东部汉...     

ABCA3基因多态性与新生儿呼吸窘迫综合征易感性关系研究

目的：探讨ATP结合盒转运蛋白A3基因（ABCA3） rs13332514（C．1059G/A）、rs117515055（C．213C/T）两个多态性位点与陕西汉族人群新生儿呼吸窘迫综合征（ NRDS）的遗传易感性。方法用SNaPshot多重微测序技术检测60例陕西汉族NRDS患者和120名健康对照者 ABCA3基因 rs13332514（ C．1059G/A ）、rs117515055（ C．213C/T ）两个多态性位点。结果rs117515055位点有两种基因型,对其进行比较,发现T等位基因在病例组（5．1％）高于对照组（3．1％）,但是差异无统计学意义;rs13332514位点CC基因型频率及C等位基因频率在病例组高于对照组（50．8％vs44．1％,69．5％vs63．5％）,差异亦无统计学意义。结论 rs117515055位点的T等位基因及rs13332514位点的C等位基因可能与汉族人群的NRDS有关,还需扩大样本量做进一步研究。     

遗传易感因素与慢性乙型肝炎干扰素治疗反应的相关性

IFN-α以抗病毒及免疫调节双莺作用用于慢性乙型肝炎的治疗,对治疗反应的早期预测有利于治疗的持续.随着人类基因组学和蛋白质组学的研究进展,国内外对HBV感染发病及治疗反应遗传易感因素有较多报道,主要集中于抗病毒蛋白和免疫调节相关细胞因子的基因多态性.此文就遗传易感因素对IFN-α治疗慢性乙型肝炎疗效的影响作了综述.