Effects of cutoff thresholds for minor allele frequencies on HapMap resolution: A real dataset-based evaluation of the Chinese Han and Tibetan populations

Genomic variation is the genetic basis of phenotypic diversity among individuals, including variation in disease susceptibility and drug response. The greatest promise of the International HapMap is to provide roadmaps for identifying genetic variants predisposing to complex diseases. Single nucleotide polymorphism （SNP） is the fundamental element of the HapMap. Allele frequency of SNPs is one of the major factors affecting the resulting HapMap, being the factor upon which linkage disequilibrium （LD） is calculated, haplotypes are constructed, and tagging SNPs （tagSNPs） are selected. The cutoff thresholds for the frequency of minor alleles used in the making of the map therefore have profound effects on the resolution of that map. To date most researchers have adopted their own cutoff thresh- olds, and there has been little real dataset-based evaluation of the effects of different cutoff thresholds on HapMap resolution. In an attempt to assess the implications of different cutoff values, we analyzed our own data for the centromeric genes on Chromosome 15 in Chinese Han and Tibetan populations, with respect to minor allele frequency cutoff values of 〉0.01 （0.01 group）, 〉0.05 （0.05 group）, and 〉0.10 （0.10 group）, and constructed HapMaps from each of the datasets. The resolution, study power and cost-effectiveness for each of the maps were compared. Our results show that the 0.01 threshold provides the greatest power （P= 0.019 in Han and P= 0.029 in Tibetan for 0.01 vs. 0.05 threshold） and de- tects most population-specific haploypes （P= 0.012 for 0.01 vs. 0.05 threshold）. However, in the regions studied, the 0.05 cutoff threshold did not significantly increase power above the 0.10 threshold （P = 0.191 in Han; 1.000 in Tibetans）, and did not improve resolution over the 0.10 value for population- specific haplotypes （P= 0.592） neither. Furthermore the 0.05 and 0.10 values produced the same figures for tagging efficiency, LD block number, LD length, study power and cost-savings in the Tibetan population. These results suggest that a lower cutoff value is more appropriate for studies in which population-specific haplotypes are crucial, and that the most appropriate cutoff value may differ between populations. Due to the limited genes studied in this project more studies should be conducted to further address this important issue.     

台湾海区斜带石斑鱼群体遗传学的等位酶研究

应用聚丙烯酰胺凝胶和淀粉凝胶技术对台湾海区斜带石斑鱼的遗传结构和遗传多样性水平进行了等位酶分析。对18种酶系统共27个等位酶基因座位的检测表明。ADH—l、ODH-2、FDH-1和Est-3等5个基因座位具多态性，其群体的多态位点百分率P为18．5％。有效等位基因平均数Ne为1．185，平均杂合度的观测值Ho为0．0469，预期值He为0．0662，反映了该群体的遗传多样性水平在鱼类中处于中等程度，而其Hardy-Weinberg遗传偏离指数(D)为-0．246，表明该群体仍存在着明显的杂合子缺失现象，相对于捕捞压力，海岸线的工程改造是对其资源的更主要威胁。     

中国：发现4个人类新等位基因

浙江省血液中心近日宣布，该机构成功发现了4个人类HLA新等位基因。这是继2004年9月，该中心发现2个HLA等位基因以来的又一科研新发现。     

白化黑线仓鼠的遗传学研究──I、异构蛋白及同工酶醋纤膜电泳结果观察

利用生化电泳技术对白化黑线仓鼠、驯育中的黑线仓鼠、野牛黑线仓鼠的九种异构蛋白及同工酶进行了醋酸纤维素膜电泳，以观察它们在生化基因位点上有何差别及基因频率分布。结果表明，这三种类型的黑线仓鼠电泳带型单一，看不出像小鼠那样有两种或两种以上的多态性，且电泳迁移率完全一致。从生化标记基因方面提供了该动物基因单一性的又一证据．     

等位基因分离定律的计算机模拟

利用Visual Basic语言面向对象的程序设计,实现对盂德尔的遗传规律——等位基因分离规律的计算机模拟,使抽象的遗传过程成为具体、可视,为遗传学的教学和科研与计算机应用的结合作了有益的探索．     

青岛近海毛蚶群体等位基因酶遗传变异

采用淀粉凝胶电泳技术研究了青岛近海毛蚶自然群体的等痊基因酶遗传变异。在十二种等位基因酶中共检测到了二十七个基因座位，多态位点比例为５１．８５％，位点有效等位基因数分布从１．０３０．．．２．５７，位点杂合度观察值分布为０．０２９．．．０．６１２，在六个基因座位上存在相当明显的杂合子缺失现象。文中讨论了杂合子缺失的原因。     

基因增强将成奥运制胜法宝?

与普通人相比,奥运选手可能跑得更快、跳得更高、举得更重,当然,很多奥运选手的奖牌都是由艰苦的训练以及无数泪水和汗水凝聚而成,但是,有些选手也拥有一些不劳而获的优势:那就是合适的正确的基因。合适的基因成为制胜法宝设在波士顿的优越风险管理公司的一名常务董事史蒂夫·格兰斯和他的同事胡安·恩里克斯7月18日在英     

AT1R基因A1166C多态性与新疆哈萨克族原发性高血压的相关性

采用病例对照的研究方法,选择200例哈萨克族EH患者做病例组,220例血压正常哈萨克族人群做为对照组,用多聚酶链式反应法及限制性片段长度多态性技术(PCR-RFLP),对两组人群外周血白细胞DNA进行AT-1R基因A1166C多态性进行基因型检测,探讨了新疆哈萨克族人群EH与血管紧张素Ⅱ1型受体基因(AT1R)A1166C多态性之间的相关性.结果表明:AA、AC和CC基因型及A/C等位基因在EH群和对照人群中分布无差异,男、女不同性别的患者间C等位基因的分布无差异.这显示AT-1R基因A1166C分子变异与新疆哈萨克族EH的发病无相关关系.     

Fine mapping and cloning of MT1,a novel allele of D10

Rice tillering is an important determinant for grain production.To investigate the mechanism of tillering,we characterized a multiple tillering mutant (mt1) identified from the japonica variety,Zhonghua 11,treated with EMS.This mutant exhibits advanced tillering development and dwarfed compared with wild-type plants.Genetic analysis and fine gene mapping indicated that the mt1 mutant was controlled by a recessive gene,residing on a 29-kb window on AP003376 of chromosome 1.One putative gene in this region,encoding a carotenoid cleavage dioxygenase 8 (CCD8),was allelic to D10.The mt1 mutant phenotype was complemented by introduction of wild-type MT1,and knockdown of MT1 in wild-type rice mimicked the mutant phenotype.Real-time PCR analysis indicated that the MT1 gene is expressed highly in stems and at a low level in axillary buds,panicles,leaves,and roots.In addition,MT1 expression is clearly under feedback regulation.     

结瘤和非结瘤近等位基因品系大豆地上部生长性状

采用田间试验方法,以结瘤和非结瘤的近等位基因大豆品系为研究对象,研究了在当地常规施肥管理条件下结瘤和非结瘤品系大豆叶面积、亚表层栅栏细胞数和细胞大小的表现型。结果表明,结瘤品系大豆叶质量比非结瘤品系大,而叶面积却较低。各品种叶片亚表层栅栏组织细胞数也表现出与叶面积相同的规律,而细胞大小却表现为结瘤品系较非结瘤品系细胞大。说明结瘤品系叶面积较小是由于细胞数量减少所致,而不是由细胞大小引起的。图5,参7。