H-抗原缺乏分泌型个体FUT1及FUT2等位基因的分子基础

一例H-缺乏分泌型个体被发现。其血清学表现为：红细胞上无A、B、H抗原；唾液中有B、H抗原分泌；血清中检出了抗A抗体。推测其为类孟买OHmB型。在该个体FUT1等位基因编码区上发现两处单碱基突变（T460C、G1042A）。这两个点变异，将导致两个氨基酸的置换（Y154H、E348K）。同时也破坏了限制性内切酶RsaⅠ和AvaⅠ的作用部位。用PCR－RFLP法可检出此两种变异。用PCR－RFLP法证实，该个体为T460C、G1042A变异的纯合子。在136例随机个体中未能查出上述变异。将该FUT1基因转染COS－7细胞未能检出α2－FUT活性及证实H抗原的表达。该个体的FUT2基因与野生型一致。     

The structure, frequency, and forensic application of the STR locus D16S543 in the Japanese population

D16S543 is a complex STR locus consisting of five types of repeat units. The frequency distribution and genetic characteristics of this locus in Japanese were investigated using blood samples from 124 unrelated Japanese and 15 families. Alleles were detected using denatured polyacrylamide gels followed by automated analysis on an ABI 373 sequencer using Genescan software 672. Twenty-one alleles were identified, ranging in size from 281 to 489 bp. An allelic ladder containing the 21 alleles was constructed and used as a typing standard. The repeat unit arrays allowed the 21 alleles to be classified into three distinct groups, including alleles 1 to 7 in group I, alleles 8 to 14 in group II, and alleles 15 to 22 in group III. The alleles in group II were characterized by the insertion of one repeat unit of CAGG, one of AAAG, and three of AAGG, while the group III alleles differed from those of groups I and II by the insertion of a total of 32 repeat units ranging in 5 types. Within each group, the alleles differed from each other only in one 5' side tetranucleotide AAGG. The power of discrimination (Pd) and the estimated heterozygosity were calculated to be 0.989 and 0.934, respectively. Typing of this locus was successfully applied in four old forensic materials. The study presented herein demonstrates that D16S543 is a highly polymorphic and applicable locus in Japanese.     

Stressful life events and adolescent drug use: Moderating influences of the MAOA gene

Purpose

Though stressful life events appear to impact the likelihood and frequency of substance use among adolescents, these effects are often varied and inconsistent. We suggest that the polymorphic MAOA gene may be partially responsible for variable susceptibility to environmental pressures and substance use. More specifically, we hypothesize that adolescents possessing low activity alleles for the MAOA genotype are more likely to respond to stressful life experiences by initiating substance use.

Methods

The genetic subsample of the National Longitudinal Study of Adolescent Health was analyzed (2,574 adolescents) using logistic regression models for each gender. Respondents’ self-reports of eight key stressors were used to create a composite life stress scale which was allowed to interact with a variable that represented the number of low activity MAOA alleles.

Results

For males, a significant interaction emerged between stressful life experiences and the MAOA gene for alcohol (p = .029) and marijuana (p = .039) initiation. For females, the interaction was not significant in each model.

Conclusions

MAOA interacts with life stress to increase the likelihood of substance use initiation for males. Those with a low activity MAOA allele are more likely to initiate substance use than those with a high activity allele when exposed to stressful experiences.     

Analysis of AmpFlSTR MiniFiler™ loci and its forensic application

The allele frequencies of eight MiniFiler™ loci have been analyzed in 101 Japanese individuals living in Kanagawa with informed consent by means of ABI 310 Genetic Analyzer. A total of 7 alleles for D13S317, 8 alleles for D7S820, 11 alleles for D2S1338, 11 alleles for D21S11, 5 alleles for D16S539, 14 alleles for D18S51, 8 alleles for CSF1PO, and 13 alleles for FGA were observed. The polymorphic profiles of these MiniFiler™ loci in the present study were essentially the same as those obtained by using the AmpFlSTR^® Identifiler^® PCR Amplification kit. The combined matching probability of eight MiniFiler™ loci and cumulative probability of paternity exclusion were estimated as 1.97 × 10⁻¹⁰ and 0.9996, respectively. The MiniFiler™ kit was useful for individual identification in forensic analysis.     

Sequence variation of new alleles at the short tandem repeat D19S253 locus

This paper reports the sequences of two new alleles identified in a population database study on the short tandem repeat D19S253 locus. A Portuguese Caucasian population and a Portuguese African population were studied. Forty-four selected alleles were sequenced and 11 different alleles were found. All the sequenced alleles shown to possess a simple tetranucleotide GATA repeat region structure. The two new alleles, alleles 6 and 16, follow the simple repeat pattern. During paternity investigation casework, 1028 meiosis were analyzed and five isolated genetic incompatibilities detected. In one case, a non-detectable allele with the used set of primers could be the explanation. In the other four cases, single-step mutations could be considered. The mutation rate obtained for this locus was 3.89 x 10(-3).     

PowerPlex^TM16体系OL等位基因序列分析及命名探讨

目的观察中国汉族人群PowerPlexTM16体系STR基因座分型标准物外等位基因(OL等位基因)的序列组成,探讨其类型及命名。方法应用PowerPlexTM16体系和ABI377或3100遗传分析仪,对10071名中国汉族无关个体的血样DNA进行15个STR基因座的分型,筛选出OL等位基因样本;对该样本进行单基因座扩增、聚丙稀酰胺凝胶电泳、银染显色,获取等位基因条带并再次扩增和测序。结果在11个基因座检见OL等位基因,共32个,频率0.05‰￣4.02‰,各基因座OL等位基因数目1￣9个不等。按其组成分为四类:(1)重复单位完整重复,但重复次数在ladder范围外;(2)不完整重复;(3)侧翼序列个别碱基的插入或缺失;(4)较大片断的缺失。结论OL等位基因类型不一,既有重复次数的变化,也有侧翼序列或核心序列的变化,现有命名原则尚不能反映其组成类型。     

Variant alleles on the penta E locus in the PowerPlex 16 kit

Penta E in the PowerPlex 16 kit is a pentanucleotide tandem repeat marker located on Chromosome 15, containing an AAAGA repeat motif. Variant alleles (18.4 and 19.4) were found in the Japanese population. A sequence analysis revealed that both the variant alleles had a partial repeat motif of AAAA, resulting in one-base-shorter alleles compared to known alleles. Despite the relatively large amplicon sizes (379 to 474 bp) of Penta E, an accurate allele assignment can be reliably made by capillary electrophoresis. However, alleles differing in size by only one base (e.g., 18.4 and 19) were not separated and appeared as a single broad peak. The Genotyper software assigned one of the component alleles to this peak. Therefore, such broad peaks require careful interpretation so as to not overlook the other component allele contained by the peak. As an index to recognize a peak containing two alleles, the ratio of peak area to peak height was found to be useful.     

Mutation in Y STRs: Repeat motif gains vs. losses

Y chromosome specific short tandem repeats (Y-STRs) are widely used in population genetics and forensics. Since these markers do not recombine, mutation is the only source of diversity. The primary mutational mechanism leading to length changes in STRs is thought to be polymerase template slippage, and the most common change is the gain or the loss of one repeat motif. In this work, we aim to study 19 Y-STR alleles’ contraction and expansion. Alleles were grouped into tertiles: short (1^st tertile), intermediate (2^nd tertile) and long alleles (3^rd tertile). Significant differences between repeat gains and losses were found at four markers - DYS19, DYS439 for intermediate alleles, and DYS570 and DYS626 for long alleles. When the average number is computed for the pooled loci, for short alleles, the number of repeat motif gains is higher than of repeat losses, and the opposite happens for long alleles. For intermediate alleles, the proportion between the number of repeat gains and losses is close to one. Generally, the rate of expansion decreases from the first tertile to the third, and conversely, the rate of contraction increases from the first tertile to the third. The pooled loci tertiles’ mutation rate increases from short to long alleles. Our results demonstrate that the mutation direction and rate depend on alleles’ length. The longer the allele the greater the mutation and contraction rates.     

Hungarian population data of eight X-linked markers in four linkage groups

The X chromosomal STR markers DXS10135 and DXS8378 in linkage group 1, DXS7132 and DXS10074 in linkage group 2, HPRTB and DXS10101 in linkage group 3, and DXS10134 and DXS7423 in linkage group 4 were studied in the Hungarian population. After genotyping unrelated men (219) and women (165), forensic efficiency parameters were calculated. Deviations from Hardy-Weinberg equilibrium could not be detected. There were several microvariant and rare alleles were sequenced: four in locus DXS10135 (alleles 17.1, 18.1, 20.1 and 26.1), one in locus DXS10074 (alleles 11), three in locus DXS10101 (alleles 26, 34.2 and 35) and five in locus DXS10134 (alleles 35.3, 37.2, 38.2, 39.2, 41).     

Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing

A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testing were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA, vWA, TH01) is an extension of published work, whereas no extensive sequence information is available with respect to the D3S1358, CSF1PO, and TPOX loci. Sequencing of alleles at each locus has provided quantitative data with respect to the true nucleotide length of common alleles, and of alleles that vary in length from the common alleles. All alleles that were identified as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CSF1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tandem repeat is demonstrated at the FGA locus. Alleles in which the core tandem repeat is interrupted by a repeat unit of different sequence have a reduced percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particular locus, and methods used to interpret amplification imbalance of heterozygous alleles at a locus is also addressed.     

The short tandem repeat locus VWF2 in Intron 40 of the von Willebrand factor gene consists of two polymorphic sub-loci

This study describes the complex nucleotide sequence structure of the TCTA short tandem repeat (STR) locus, VWF2. Eight alleles of VWF2 were observed in a population of 116 unrelated Caucasian individuals. The alleles ranged in size from 150 to 178 base pairs (bp). Sequence analysis of the isolated alleles revealed two polymorphic regions that were named sub-loci VWF2-a and VWF2-b. VWF2-a is located at the 5' end of the conventional locus, whilst VWF2-b is located at the 3' end. The two sub-loci are joined by a 30-nucleotide non-polymorphic sequence which contains two additional TCTA motif repeats. A semi-nested polymerase chain reaction (PCR) was designed to amplify the VWF2-b region in conjunction with the standard VWF2 amplification. This new amplification method enabled a higher level of allele discrimination than could be achieved by assigning alleles according to size. A cohort of 99 unrelated individuals was tested with this method. VWF2-a expressed five different alleles ranging from zero motif repeats to four motif repeats, while VWF2-b alleles ranged from 8 to 14 motif repeats. Allelic configuration based on the VWF2-a and VWF2-b sub-alleles revealed 23 unique configurations out of a possible 31 for the original eight VWF2 alleles. In conclusion, the VWF2 is a highly polymorphic STR locus with potential application for forensic and parentage testing.     

Allelic structure and distribution of two STR loci, D8S580 and D22S442, in the Japanese population

The allelic frequency and structural characteristics of two STR loci D8S580 and D22S442 were investigated using blood samples from 143 unrelated healthy Japanese individuals. Thirty-eight alleles in D8S580 locus and 13 alleles in D22S442 locus were identified. The discrimination power, heterozygosity, and the polymorphic information content of those loci displayed high values (0.98, 0.88, and 0.87 in D8S580 and 0.97, 0.86 and 0.85 in D22S442), and their frequency distributions met Hardy-Weinberg equilibrium expectations. The allelic pattern of D8S580 was complex and differentiated into three groups (group I: alleles 184-194bp; group II: alleles 203-223, 235, 239, 243, 252 and 255bp; group III: alleles 227-286bp). Most of their alleles contained five categories of repeat units (A: aaaag; B: aaag; C: aagg; D: caag; E: agaa). On the other hand, D22S442 contained only two types of repeat units (A: agga; B: aggg). The present study, hence, proves that both D8S580 and D22S442 are highly polymorphic and represent stable genetic markers applicable to forensic investigations.     

Sequence polymorphisms at the DXS6789, DXS8377 and DXS101 loci in three Asian populations

Sequence analyses of X-chromosomal short tandem repeats, DXS6789, DXS8377 and DXS101 were performed for representatives of 3 Asian populations: 130 Japanese, 61 Bangladeshi and 89 Indonesian males. At DXS6789, the sequence polymorphism was found in 7 alleles in the Japanese, 3 in the Bangladeshis and 3 in the Indonesians. At DXS8377, the sequence polymorphism was found in 13 alleles in the Japanese, 9 in the Bangladeshis and in all alleles identified in the Indonesians. At DXS101, the sequence polymorphism was found in 7 alleles in the Japanese, 9 in the Bangladeshis and 8 in the Indonesians. Because sequence polymorphisms were found in most of the alleles at the DXS6789, DXS8377 and DXS101 loci, it was concluded that sequencing was essential for identifying the alleles at these loci in all 3 Asian populations.     

PowerPlex~(TM) 16体系在中国人群中罕见等位基因及其类型

目的 分析PowerPlexTM 16体系基因座在中国人群中的罕见等位基因及其类型。方法 应用PCR-STR和DNA序列分析技术,对4650个无关个体在15个STR基因座中的罕见等位基因进行检测。结果 在PowerPlexTM16体系中的D7S820、D16S539、Penta E基因座,检测到2种类型的罕见等位基因,而TH01、D21S11、D5S818、D13S317、Penta D、D8S1179、TPOX、FGA基因座检测出1种类型。其等位基因频率均较低(0.215‰-7.097‰)。结论 超出ladder范围的罕见等位基因序列比相邻等位基因增加(或减少)1个或数个重复单位,因碱基的插入或缺失的罕见等位基因出现在两等位基因之间。     

Further alleles of phosphoglucomutase in human semen detected by isoelectric focusing

A technique for identifying further alleles of PGM1 in human semen detected by isoelectric focusing has been described. A survey of 100 semen samples has shown that there was close agreement between the observed and expected gene frequencies of these new alleles on the basis that there were four common alleles determined by the PGM1 locus and not two as originally proposed [1,2]. The use of these new genetic variatns of PGM will considerably enhance the investigation of semen stains in forensic science.     

Mutation in the STR locus D21S1 1 of father causing allele mismatch in the child

We analyzed a case of paternity dispute with 15 autosomal STR loci and found a mismatch in one of the alleles of the locus D21S11 in the child. The composition of the alleles of this locus in the mother, suspicious father, and child were 29/32, 29/29, and 29/30, respectively. The combined paternity index (2.4 x 10(10)) and paternity probability (0.9999) suggest that the suspicious father is the biological father of the child. Further analysis of 6 Y chromosome STR loci revealed matching of all the Y chromosomal alleles of the child with that of the suspicious father. Since there was a perfect match of all the paternal alleles inherited (15 autosomal and 6 Y chromosomal) in the child with that of the suspicious father except the allele D21S11, it is suggested that this might be a case of mutation. Cloning and sequencing of all the alleles of the locus D21S11 of the suspicious father, mother, and the child helped in determining that the suspicious father contributed the mutated allele.     

Allelic distribution of four tetranucleotide repeat loci (D3S1358, D18S51, D19S253, and FGA) in a population from Porto (North Portugal)

Allele frequencies for four short tandem repeat loci were determined in a population sample from Porto (North Portugal), using the polymerase chain reaction (PCR), in order to investigate possible genetic differences between populations from the center and north of Portugal. After denaturing PAGE electrophoresis, nine alleles were identified for D3S1358 (n = 256), 13 alleles for D18S51 (n = 235), 10 alleles for D19S253 (n = 238), and 15 alleles for FGA (n = 181). No deviations from Hardy-Weinberg equilibrium were found. The allele frequencies observed are similar to those of the Portuguese population compared except for the D3S1358 system.     

Allelic frequencies for the HLA-DQA1, D1S80, HUMTHO1, HUMTPOX, HUMCSF1PO and HUMVWA loci in Cantabria (middle north Spain)

Allele frequencies for six DNA polymorphisms have been studied in a population sample from Cantabria (middle north Spain) using the polymerase chain reaction. The HLA-DQA1 locus was analyzed by the reverse dot-blot technique and the other five by polyacrylamide gel electrophoresis followed by silver staining. Six alleles were found for HLA-DQA1. 15 alleles for D1S80, 6 alleles for HUMTHO1 and HUMCSF1PO, 7 for HUMTPOX and 8 alleles for HUMVWA. The 21 repeat allele in HUMVWA had not previously been reported in a Spanish population. The genotype distributions met Hardy-Weinberg expectations for all the systems and some statistical parameters of forensic interest were calculated. Comparisons with other populations revealed significant differences for HLA-DQA1, HUMVWA and HUMTHO1, with interracial differences being more pronounced than between Spanish populations. The HUMVWA system showed the highest forensic efficiency of the six polymorphisms studied.     

Inclusion Probabilities and Dropout

Abstract: Recent discussions on a forensic discussion group highlighted the prevalence of a practice in the application of inclusion probabilities when dropout is possible that is of significant concern. In such cases, there appears to be an unpublished practice of calculation of an inclusion probability only for those loci at which the profile of interest (hereafter the suspect) is fully included among the alleles present in the crime scene sample and to omit those loci at which the suspect has alleles that are not fully represented among the alleles in the mixture. The danger is that this approach may produce apparently strong evidence against a surprisingly large fraction of noncontributors. In this paper, the risk associated with the approach of ignoring loci with discordant alleles is assessed by simulation.     

广州地区汉族人群Y染色体多个STR位点的研究

为建立一套高度多态且实用性强的Ｙ－ＳＴＲｓ标记系统,本文用ＰＣＲ结合银染显色技术研究了１１１例广州汉族男性ＤＹＳ１９、ＤＹＳ３８９Ⅰ／Ⅱ、ＤＹＳ３９０等位基因及单倍型分布状况。结果显示：广州地区汉族男性ＤＹＳ１９位点有Ａ１、Ａ２、Ａ３、Ａ４、Ａ５五种等位基因,出现频率分别为１８．９％、３６．０％、３６．０％、７．２％、１．８％;ＤＹＳ３８９Ⅰ位点有Ｂ１、Ｂ２、Ｂ３、Ｂ４四种等位基因,出现频率分别为６．３％、５２．２％、１７．１％、２４．３％;ＤＹＳ３８９Ⅱ位点有Ｃ１、Ｃ２、Ｃ３、Ｃ４、Ｃ５五种等位基因,出现频率分别为１１．７％、３８．７％、２２．５％、１７．１％、９．９％,ＤＹＳ３９０位点有Ｄ１、Ｄ２、Ｄ３、Ｄ４、Ｄ５五种等位基因,出现频率分别为２．７％、９．９％、４６．８％、２７．９％、１２．６％;χ２检验表明上述各等位基因分布存在明显的地域差异。此外,还观察到７２种由上述座位共同构成的单倍型,单倍型多样性达０．９８０,表明该系统具有较强的个体识别能力