目的 建立依赖切口酶Nt.BstNBI的等温全基因组扩增体系,并对该体系的微量生物物证STR分型效能进行验证.方法 选用切口酶Nt.BstNBI(识别序列为GAGTC)和等温扩增的聚合酶Bst,建立切口酶依赖的扩增体系(NDA).对DNA样本进行NDA并纯化NDA产物,对NDA前后的样本进行复合扩增和毛细管电泳,检测该方法 的有效性、灵敏性.结果 007标准品12个常染色体基因座的扩增效率提高2倍以上,灵敏度约为3 pg/μL;19个Y染色体个基因座的扩增效率提高 2 倍以上,灵敏度约为 6 pg/μL.8 个人血样本扩增效率提高 2 倍以上的常染色体基因座与 007 标准品一致.结论 本文建立的NDA体系准确性好,能够对包含特定侧翼序列的STR基因座进行有效的线性扩增,对法医微量生物物证的高效扩增检测具有重要意义.

Rwanda is one of the smallest countries of Africa, where forensic genetic studies are rarely being conducted and very few DNA databases have been developed. Short tandem repeats (STRs) polymorphisms were investigated in 505 unrelated Rwandese by using the HUMDNA TYPING (Yanhuang) Kit. The following STRs were targeted: D3S1358, D13S317, D7S820, D16S539, SE33, D10S1248, D5S818, D21S11, TPOX, D1S1656, D6S1043, D19S433, D22S1045, D8S1179, Penta E, D2S441, D12S391, D2S1338, vWA, Penta D, TH01, D18S51, CSF1PO and FGA. The purpose of this study was to elucidate the genetic diversity and explore the potential of applying these 24 STR in 505 Rwandan population in forensics. A total of 360 alleles, with corresponding allele frequencies in the range from 0.001 to 0.442, were found in the Rwandan population. SE33 presented the highest polymorphism (PIC=0.921) among these 24 loci, whereas D13S317 presented the lowest one (PIC=0.671). No deviation from the Hardy-Weinberg equilibrium was observed for any of the 24 loci. The forensic parameters, including the combined power of discrimination (PD and the combined exclusion power, have demonstrated that this panel of 24 STRs is highly informative and useful for forensic applications such as individuals' identification and paternity tests. Additionally, the genetic distances between Rwanda population and other 24 published populations were calculated based on 8 overlapping loci with the polygenetic tree revealing significant clusters in the populations associated with their geographic locations and their historical relationship.

As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.

目的 验证炎黄Y染色体分型系统FGI 27Y试剂盒的性能并分析其法医学参数,评价其法医学应用价值.方法 按照我国公共安全行业标准GA/T 815-2009《法庭科学人类荧光标记STR复合扩增检测试剂质量基本要求》,对FGI 27Y试剂盒进行灵敏度、混合样本、种属特异性等测试.并利用FGI 27Y试剂盒对269份中国汉族男性无关个体血卡进行检测,统计27个STR基因座的等位基因频率、基因多样性及单倍型多样性参数.同时查阅文献,收集不同人群的STR数据,与本文的汉族群体STR数据进行比较分析,统计群体遗传距离FST矩阵.结果 FGI 27Y在DNA模板量低至0.0625ng或大量女性DNA(男性与女性1∶300混合)条件下仍然能获得男性DNA的完整分型结果.且在男性混合样本(1∶9和9∶1)中,等位基因检出率达到88％以上.27个Y-STR的基因多样性在0.4058 ～ 0.8973,单倍型多样性值为1.利用FST矩阵分析可得,不同人种间的遗传距离均较远,而相同人种间的遗传距离相对较近.结论 炎黄Y染色体分型系统FGI 27Y试剂盒满足GA/T815-2009《法庭科学人类荧光标记STR复合扩增检测试剂质量基本要求》,可用于Y-STR数据库建设以及男性家系排查.

以短串联重复序列（short tandem repeats, STR）和性别基因为基础的动物分型系统,不仅能提供重要的分子遗传标记信息,还能有效地解决动物个体识别和亲缘关系难题。为建立家鸽（Columba livia domestica）短串联重复序列与染色体螺旋蛋白基因（chromobox-helicase-DNA binding gene, CHD）复合扩增检测体系,并评估其法医学应用价值,本研究采用六色荧光标记复合扩增方法,选取了CliμD11、PG4、PG1、PG2、CliμT02、CliμD17、CliμD35、CliμT17、CliμD16、PIGN04、CliμD32、PIGN57、PIGN26、PG5、PG6、CliμD19、PIGN12、PIGN15、PIGN10和性别鉴定基因CHD,共计20个基因位点。结果显示,本研究建立的家鸽复合扩增体系的分型结果稳定、图谱清晰,241只家鸽的羽毛样本检测全部稳定可靠;检测灵敏度高达0.0625 ng;与其他物种对比扩增,表现出高度的种属特异性;对19个STR位点的等位基因在232只家鸽群体中的统计分析表明,本研究所选取的STR位点均可用于家鸽的个体识别和亲子鉴定。本研究最终成功建立的稳定性好、灵敏度高、种属特异性强的家鸽STR位点复合扩增检测体系,是目前已知位点数最多的家鸽检测体系,也是国内相关研究的首次报道,为家鸽的个体识别和亲子鉴定提供了分子鉴定基础。

Background: The domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection have led to dramatic phenotypic purification and intermediate breeds for the high-quality production of dairy, cashmere wool, and meat. Genomic resequencing provides a powerful means for the direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication. Results: Here, we report our effort to define such variations based on data from domestic goat breeds (Capra aegagrus hircus; five each) selected for dairy, cashmere, and meat production in reference to their wild ancestors, the Sindh ibex (Capra aegagrus blythi; two) and the Markhor (Capra falconeri; two). Using similar to 24 million high-quality single nucleotide polymorphisms (SNPs), similar to 1.9 million insertions/deletions, and 2,317 copy number variations, we define SNP-desert-associated genes (SAGs), domestic-associated genes (DAGs), and trait-associated genes (TAGs) and attempt to associate them with quantitative trait loci (QTL), domestication, and agronomic traits. A greater majority of SAGs shared by all domestic breeds are classified into Gene Ontology categories of metabolism and cell cycle. DAGs, together with some SAGs, are most relevant to behavior, immunity, and trait specificity. Whereas, TAGs such as growth differentiation factor 5 and fibroblast growth factor 5 for bone and hair growth, respectively, appear to be directly involved in growth regulation. Conclusions: When investigating the divergence of Capra populations, the sequence variations and candidate function-associated genes we have identified provide valuable molecular markers for trait-driven genetic mapping and breeding.

Background:DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data.Findings:We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF.Conclusions:BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

Whole-genome shotgun (WGS) sequencing has become a routine method in genome research over the past decade. However, the assembly of highly polymorphic regions in WGS projects remains a challenge, especially for large genomes. Employing BAC library constructing, PCR screening and Sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. As one of the most highly polymorphic regions, the major histocompatibility complex (MHC) plays a central role in the adaptive immunity of all jawed vertebrates. In this study, we introduced an efficient procedure based on recombination screening and short-reads assembly. With this procedure, we constructed a high quality 488-kb region of crested ibis MHC that consists of 3 superscaffolds and contains 50 genes. Our sequence showed comparable quality (97.29% identity) to traditional Sanger assembly, while the workload was reduced almost 7 times. Comparative study revealed distinctive features of crested ibis by exhibiting the COL11A2-BLA-BLB-BRD2 cluster and presenting both ADPRH and odorant receptor (OR) gene in the MHC region. Furthermore, the conservation of the BF-TAP1-TAP2 structure in crested ibis and other vertebrate lineages is interesting in light of the hypothesis that coevolution of functionally related genes in the primordial MHC is responsible for the appearance of the antigen presentation pathways at the birth of the adaptive immune system.

Schizophrenia is a devastating psychiatric condition with high heritability. Replicating the specific genetic variants that increase susceptibility to schizophrenia in different populations is critical to better understand schizophrenia. CNNM2 and NT5C2 are genes recently identified as susceptibility genes for schizophrenia in Europeans, but the exact mechanism by which these genes confer risk for schizophrenia remains unknown. In this study, we examined the potential for genetic susceptibility to schizophrenia of a three-gene cluster region, AS3MT-CNNM2-NT5C2. We implemented a two-stage strategy to conduct association analyses of the targeted regions with schizophrenia. A total of 8218 individuals were recruited, and 45 pre-selected single nucleotide polymorphisms (SNPs) were genotyped. Both single-marker and haplotype-based analyses were conducted in addition to imputation analysis to increase the coverage of our genetic markers. Two SNPs, rs11191419 (OR=1.24, P=7.28×10(-5)) and rs11191514 (OR=1.24, P=0.0003), with significant independent effects were identified. These results were supported by the data from both the discovery and validation stages. Further haplotype and imputation analyses also validated these results, and bioinformatics analyses indicated that CALHM1, which is located approximately 630kb away from CNNM2, might be a susceptible gene for schizophrenia. Our results provide further support that AS3MT, CNNM2 and CALHM1 are involved with the etiology and pathogenesis of schizophrenia, suggesting these genes are potential targets of interest for the improvement of disease management and the development of novel pharmacological strategies.

Schizophrenia (SCZ) is a complex neuropsychiatric disorder with high heritability. Abnormal gene methylation was found to play a key role in the development of SCZ, suggesting that histone deacetylases (HDACs) may increase the expression of several key genes in the brain. However, recent studies evaluating the association between SCZ and genetic polymorphisms in histone deacetylase 3 (encoded by HDAC3) have shown conflicting results. In this study, we designed a two-stage case-control study to investigate the association of the HDAC3 with SCZ. Fourteen tag single nucleotide polymorphisms (SNPs) entirely covering the region of HDAC3 were analyzed in the testing group of 1,421 patients and 2,823 healthy controls, and the SNP rs14251 was found to be significant (and rs2530223 to be nominally significant). The significant result of rs14251 was successfully replicated in the validation group consisting of 896 cases and 1,815 healthy controls (P = 0.009276, OR = 1.219), and also confirmed by haplotype based analyses (rs976552-rs14251, global P < 0.001). To sum up, our results provide additional evidence that HDAC3 confers the increasing risk of SCZ susceptibility in Han Chinese individuals, suggesting this gene as a potential genetic modifier for SCZ development. © 2016 Wiley Periodicals, Inc.

SLC1A2 is reported to be responsible for the majority of glutamate uptake, which has a crucial role in neural development and synaptic plasticity, and a disturbance in glutamatergic transmission has been suggested to be involved in the pathophysiology of schizophrenia (SCZ) and cognition. To evaluate the relationship of common variants within SLC1A2 with SCZ and cognition in Han Chinese, 28 tag SNPs were genotyped in the discovery stage, which included 1117 cases and 2289 controls; significantly associated markers were genotyped in the replication stage with 2128 cases and 3865 controls. The rs4354668 SNP was identified to be significantly associated with SCZ in both datasets, and a similar pattern was also observed in the two-stage study on conducting imputation and haplotype association analyses. In addition, significant associations between the rs4354668 SNP and cognition were observed when processing the perseverative error of the Wisconsin Card Sorting Test in patients and controls. Our results provide supportive evidence for an effect of SLC1A2 on the etiology of SCZ, suggesting that genetic variation (rs4354668 and its haplotypes) in SLC1A2 may be involved in impaired executive function, which adds to the current body of knowledge regarding the risk of SCZ and the impairment of cognitive performance.

Schizophrenia (SCZ) is a complex psychiatric disorder that is strongly influenced by a genetic component. Recent studies suggested that histone deacetylases (HDACs) might increase the expression of several key genes in the brain and may also be associated with susceptibility to SCZ. Among human HDACs, HDAC2 is a critical modulator of gene regulation. Here, we designed a two-stage case–control study to thoroughly examine the association between the HDAC2 gene and SCZ. A total of 19 common single-nucleotide polymorphisms (SNPs) in the region of the HDAC2 gene were analyzed in the test group of 1430 patients and 2862 matched healthy controls. A comparison of the genotype and allele frequencies of the SNPs between cases and controls revealed that three SNPs, rs13212283, rs6568819 and rs9488289, were nominally associated with SCZ. However, we failed to observe any association between these SNPs and SCZ in the validation group consisting of 896 cases and 1815 matched healthy controls. Furthermore, haplotypic analysis also confirmed the negative results. Our results provide preliminary evidence that HDAC2 may not confer susceptibility to SCZ in Han Chinese. Additional genetic studies from a large population are required to obtain more conclusive results.

NOTCH4 regulates signaling pathways associated with neuronal maturation, a process involved in the development and patterning of the central nervous system. TheNOTCH4gene has also been identified as a possible susceptibility gene for schizophrenia (SCZ). The objective of this study was to examine the relationship betweenNOTCH4polymorphisms and SCZ in the Chinese Han population. The rs2071287 and rs204993 polymorphisms of theNOTCH4gene were analyzed in 443 patients with SCZ and 628 controls of Han Chinese descent. Single SNP allele-, genotype-, and gender-specific associations were analyzed using different models (i.e., additive, dominant, and recessive models). This association study revealed that the rs204993 polymorphism is significantly associated with susceptibility for SCZ and that the AA genotype of rs204993 is associated with a higher risk for SCZ (P=0.027; OR = 1.460; 95% CI, 1.043–2.054). Our data are consistent with those obtained in previous studies that suggested that rs204993 is associated with SCZ and that the AA genotype of rs204993 demonstrates a higher risk. Further large-scale association analyses in Han Chinese populations are warranted.

Osteoporosis is a systemic skeletal disorder characterized by reduced bone mineral density (BMD) and disrupted bone architecture, predisposing the patient to increased fracture risk. Evidence from early genetic epidemiological studies has indicated a major role for genetics in the development of osteoporosis and the variation in BMD. In this study, we focused on two key genes in the endochondral ossification pathway, IBSP and PTHLH. Over 9,000 postmenopausal Han Chinese women were recruited, and 54 SNPs were genotyped. Two significant SNPs within IBSP, rs1054627 and rs17013181, were associated with BMD and postmenopausal osteoporosis by the two-stage strategy, and rs17013181 was also significantly associated with serum IBSP levels. Moreover, one haplotype (rs12425376-rs10843047-rs42294) covering the 5' end of PTHLH was associated with postmenopausal osteoporosis. Our results provide evidence for the association of these two key endochondral ossification pathway genes with BMD and osteoporosis in postmenopausal Han Chinese women. Combined with previous findings, we provide evidence that a particular SNP in IBSP has an allele-specific effect on mRNA levels, which would, in turn, reflect serum IBSP levels.

Schizophrenia (SCZ) is a severe and debilitating mental disorder, and the specific genetic factors that underlie the risk for SCZ remain elusive. The autism susceptibility candidate 2 (AUTS2) gene has been reported to be associated with autism, suicide, alcohol consumption, and heroin dependence. We hypothesized that AUTS2 might be associated with SCZ. In the present study, three polymorphisms (rs6943555, rs7459368, and rs9886351) in the AUTS2 gene were genotyped in 410 patients with SCZ and 435 controls using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forced PCR-RFLP methods. We detected an association between SCZ and the rs6943555 genotype distribution (odds ratio (OR) = 1.363, 95% confidence interval (CI): 0.848–2.191, p = 0.001). The association remained significant after adjusting for gender, and a significant effect (p = 0.001) was observed among the females. In the present study, rs6943555 was determined to be associated with female SCZ. Our results confirm previous reports which have suggested that rs6943555 might elucidate the pathogenesis of schizophrenia and play an important role in its etiology.