Analysis of NAT2 point mutations with biological microchips

The NAT2 product, N-acetyltransferase 2, is involved in biotransformation and detoxification of several aromatic amines (in particular, 2-aminofluorene, 4-aminobiphenyl, and 4-naphthylamine), which are strongly mutagenic and carcinogenic, and acetylates some drugs, affecting their metabolism. A biological microchip was developed to detect 16 point mutations, which determine 36 alleles and 660 genotypes of NAT2. The genotypes can be divided into four groups according to the acetylator phenotype: groups with rapid (R/R), intermediate (R/S), or slow (S/S) acetylation and a group combining intermediate and slow alleles (“R/S or S/S”). The last group includes the alleles determined by combinations of seven mutations (191G/A, 282C/T, 341T/C, 481C/T, 590G/A, 803A/G, and 857G/A), whose cis or trans position is detectable by restriction enzyme analysis. The NAT2 genotype was unequivocally established for 37 out of 71 DNA specimens, while the other 34 specimens were characterized by more than two genotypes. By the acetylator phenotype, 16 out of the 34 genotypes were assigned to the group “R/S or S/S,” combining mutations 282C/T, 341T/C, 481C/T, 590G/A, and 803A/G. Thus, the biochip allows primary analysis of most NAT2 polymorphic substitutions, the acetylator genotype being important to know in predictive medicine and individualized therapy.     

Association of <Emphasis Type="Italic">NAT2</Emphasis> polymorphisms with susceptibility to psoriasis in the Moscow population

N-acetyltransferase 2 (NAT2) is a key enzyme of biotransformation phase II that metabolizes genotoxic compounds such as carcinogens and mutagens in different types of cells. A decreased NAT2 activity may correlate with sensitivity to harmful environmental factors, thus increasing susceptibility to different multifactorial diseases, including dermatologic conditions like psoriasis. A biochip developed in our lab to detect 17 NAT2 SNPs was tested on 279 clinical DNA samples from 180 patients with psoriasis and 99 healthy individuals, all residents of Moscow. Six polymorphisms that are most common in European populations (282C > T, 341T > C, 481C > T, 590G > A, 803A > G, and 857G > A) were detected. The NAT2 allele and genotype frequencies for individual SNPs did not differ between patients and healthy individuals. The frequency of the slow acetylation phenotype was increased in patients with type II psoriasis and in normosthenic patients as compared to controls (OR = 1.76, P = 0.177 and OR = 2.07, P = 0.050, respectively). Genotype 341C/C,481T/T,803G/G was significantly more frequent in patients who smoked at least one pack of cigarettes per day and in those who regularly consumed alcohol than in controls (OR = 7.42, P = 0.008 and OR = 106.11, P = 0.003, respectively). The frequency of genotype 341T/T, 481C/C, 590A/-, 803A/A was increased in patients with adverse reactions to medications (OR = 2.05, P = 0.099). Thus, our data suggest that some NAT2 genotypes in combination with certain lifestyles can be considered risk factors of psoriasis in the Moscow population.     

Analysis of point mutations of the BRCA1 gene by hybridization with hydrogel microarrays

BRCA1 mutations are associated with a higher risk of breast (BC) and ovarian cancer in women. Testing for such mutations allows BC prognosis, selection of an individual treatment strategy, and prevention of disease recurrence. Hybridization on a hydrogel microarray was developed for identifying point mutations in BRCA1. The microarray was designed to detect five-point mutations: 185delAG, 300T→G, 4153delA, 4158A→G, and 5382insC. The microarray was tested with 36 control specimens with known genotypes and used to examine 65 BC patients. The results demonstrated the advantage of employing the microarray in analyzing BRCA1 mutations.     

A simple method for genotyping the bovine growth hormone gene

An allele-specific polymerase chain reaction (PCR) amplification method was developed to determine the genotypes at the bovine growth hormone locus that result from two nucleotide substitutions in exon 5 of the gene. This method was a multiplex PCR (ASM–PCR) employing a common primer pair and two allele-specific reverse primers. The common primer pair was designed to amplify a target region containing two substitution points from the three variants of the bovine growth hormone gene. The allele-specific primers were designed to be mismatched with other genotypes at the 3' end of oligonucleotides. When the common and allele-specific reverse primers competed with each other, the shorter allele-specific fragments were amplified preferentially. Consequently, the PCR products of the variant-specific fragments were 347, 483 and 656 bp for alleles A, B and C, respectively, of the bovine growth hormone gene. Genotypes of the bovine growth hormone gene were easily identified by agarose gel electrophoresis of PCR products. The results suggested that this multiplex PCR method would be useful for identification of genetic variants caused by point mutations.     

生长激素基因多态性与山羊体重性状的关系

以鲁北白山羊、波尔山羊以及波尔山羊与鲁北白山羊的杂交一代、回交一代共计224只山羊为材料,根据山羊生长激素基因5′调控区的序列(GenBank登录号:D00476)设计两对引物,用PCRSSCP法进行多态性分析。多态性片段的纯合基因型经克隆测序,发现共有5处突变。对突变位点产生的不同基因型与体重、体尺性状进行分析表明:第一对引物扩增片段波尔山羊AA型个体的初生重、周岁重显著高于BB型和AB型(P<0.05);杂交一代中断奶重、周岁重也以AA型偏高,但不同基因型间的差异均不显著(P>0.05);而鲁北白山羊BB基因型的体重相对于另外两种基因型的偏低,且断奶重的差异达到显著水平(P<0.05)。第二对引物扩增片段不同基因型对体重、体尺没有显著影响。由此初步推断生长激素基因可能是影响山羊体重性状的主基因或与主基因相连锁,可以用该位点对山羊体重性状进行标记辅助选择。     

Association of permanent arterial hypertension with the renin-angiotensin and kinin-bradykinin system genes in children

A new approach, based on scoring, was proposed for a more objective estimation of the contribution of several genetic variants to a multifactorial disease. Two variants of the approach—genotype scoring and unfavorable factor scoring—were tested by analyzing the polymorphisms of REN (I9–83G>A), AGT (M235T), ACE (I/D), AGTR1 (1166A>C), ATGR2 (3123C>A), and BKR2 (?58T>C and I/D) in children with arterial hypertension (AH). Each of the two variants reported that the genes of the renin-angiotensin and kinin-brady-kinin systems play an important role in permanent AH in girls.     

Development and multiplexing of microsatellite markers using pyrosequencing in the clonal plant Comarum palustre (Rosaceae)

Microsatellites represent one of the most commonly used genetic markers for population genetic studies. Traditionally, their development is quite time consuming, requiring construction of a genomic library enriched for repeated motifs. Using pyrosequencing, a fast and cost-effective new generation sequencing technique, we produced 24,340,862 bases in 63,860 short fragment reads, including 1170 dinucleotide motifs with a minimum of six repeats and 1383 trinucleotide motifs with a minimum of four repeats for the Marsh Cinquefoil, Comarum palustre L., an endangered marsh pioneer species. We selected 58 loci with SSR (Short Sequence Repeat) segments (at least 10 repeats) for a preliminary screening. Out of them, we screened 29 loci on a capillary sequencer after ligation in a vector and PCR using T7 forward primer labelled with FAM fluorescent dye and the specific unlabeled reverse primers. This procedure allowed us to screen large number of candidate loci with the same labelled primer and unlabelled specific primers. Finally, we characterized 20 polymorphic microsatellite markers, nine dinucleotides and 11 trinucleotides. We used these markers to assess genetic diversity and clonal structure in two Belgian populations. All loci showed a maximum of two alleles per individual, suggesting that they are from a diploid genome. One genet was detected in a newly extending population while 53 different genets in a long-term ecologically managed population. The number of alleles per locus ranged from 6 to 14 in this old population with an expected heterozygosity, ranging from 0.5964 to 0.8278. These preliminary results show a genet size up to 7.2 m.     

Genetic polymorphism of GST, NAT2, and MTRR and susceptibility to childhood acute leukemia

Polymorphisms of xenobiotic-metabolizing genes correlate with hereditary predisposition to neoplasia in some cases. The frequencies of polymorphisms of xenobiotic-metabolizing genes were determined in 332 children with acute lymphoblastic leukemia, 71 children with acute myelogenous leukemia, and 490 healthy donors by allele-specific hybridization on a biochip. The frequencies of the GSTT1 null genotype and the GSTT1/GSTM1 double null genotype were significantly increased in children with acute leukemia as compared to healthy donors (OR = 1.9, P = 4.7E-5, and OR = 3.1, P = 2.5E-8, respectively). The frequency of NAT2 genotype 341T/T, 481C/C, 590G/G was increased 1.8-fold in children with acute leukemia as compared to healthy controls (P = 0.026). Analysis of gene-gene interactions showed that the combination of NAT2 genotype 341T/T, 481C/C, 590G/G with the GSTT1 and/or GSTM1 null genotypes was significantly more frequent in patients with acute leukemia than in the population control. In addition, the frequency of MTRR genotype 66G/G was reduced in girls with acute leukemia as compared to healthy female donors (OR = 0.50, P = 0.0015). The GSTT1 and/or GSTM1 null genotypes combined with MTRR genotype 66A/-were considered to be a risk factor for acute leukemia in girls. Thus, the polymorphisms of GSTT1, GSTM1, NAT2, and MTRR proved to influence the risk of childhood acute leukemia in residents of European Russia.     

中国汉蒙两族人群MTHFR基因热敏感性多态性分布的比较

为比较中国蒙汉两族人群MTHFR基因第677位核苷酸多态性的分布情况,获得该位点多态性的群体遗传学数据,本研究应用PCR扩增技术, 其扩增产物用限制性核酸内切酶Hinf I消化后进行非变性聚丙烯酰胺凝胶电泳,分析蒙汉族人群中MTHFR基因第677位核苷酸基因型（野生型、杂合型和突变纯合型）的分布频率。结果表明,蒙族人群基因型构成以野生型为主,占45.6％,突变杂合型占39.2％,突变纯合型仅占15.2％,汉族人群基因型构成以突变杂合型为主,占55.7％,野生型仅占17.9％,突变纯合型占26.4％,明显高于蒙族人群。经χ2检验,两组基因型构成比具有显著性差异（P<0.001）;蒙族人群MTHFR 677T等位基因频率为34.8％,经u检验显著低于汉族人群（54.2％）的频率。据此认为,中国蒙族人群MTHFR热敏感性基因突变频率显著低于汉族人群,提示该基因多态性分布在中国不同民族人群中存在差异。 Abstract：The purpose of this study is to compare the genetic polymorphism distribution of the 677th nucleotide of MTHFR between the Mongolian population and the Hans of China,and to obtain the population genetic data of this polymorphism.Using PCR－RFLP method,the authors analyzed the genotypes of the 677th nucleotide of MTHFR in Mongolians and Hans.Results show that in Mongolian population,the proportion of wild type is 45.6％,proportion of heterozygotes is 39.2％ and that of homozygotes is 15.2％; While in Hans,proportions are wild type 17.9％,heterozygotes 55.7％ and homozygotes 26.4％.The ratios of genotypes are significantly different between Mongolian and Han populations(χ2－test,P<0.001).The 677th allele frequency in Mongolians is 34.8％,lower than that in Hans(54.2％,u－test,P<0.001).This suggests that the mutant MTHFR gene frequency is significantly higher in the Han population than in the Mongolian population in China.     

1 + 1 = 3: Development and Validation of a SNP-Based Algorithm to Identify Genetic Contributions from Three Distinct Inbred Mouse Strains

State-of-the-art, genome-wide assessment of mouse genetic background uses single nucleotide polymorphism (SNP) PCR. As SNP analysis can use multiplex testing, it is amenable to high-throughput analysis and is the preferred method for shared resource facilities that offer genetic background assessment of mouse genomes. However, a typical individual SNP query yields only two alleles (A vs. B), limiting the application of this methodology to distinguishing contributions from no more than two inbred mouse strains. By contrast, simple sequence length polymorphism (SSLP) analysis yields multiple alleles but is not amenable to high-throughput testing. We sought to devise a SNP-based technique to identify donor strain origins when three distinct mouse strains potentially contribute to the genetic makeup of an individual mouse. A computational approach was used to devise a three-strain analysis (3SA) algorithm that would permit identification of three genetic backgrounds while still using a binary-output SNP platform. A panel of 15 mosaic mice with contributions from BALB/c, C57Bl/6, and DBA/2 genetic backgrounds was bred and analyzed using a genome-wide SNP panel using 1449 markers. The 3SA algorithm was applied and then validated using SSLP. The 3SA algorithm assigned 85% of 1449 SNPs as informative for the C57Bl/6, BALB/c, or DBA/2 backgrounds, respectively. Testing the panel of 15 F2 mice, the 3SA algorithm predicted donor strain origins genome-wide. Donor strain origins predicted by the 3SA algorithm correlated perfectly with results from individual SSLP markers located on five different chromosomes (n=70 tests). We have established and validated an analysis algorithm based on binary SNP data that can successfully identify the donor strain origins of chromosomal regions in mice that are bred from three distinct inbred mouse strains.     

Development and evaluation of a multiplex PCR for simultaneous detection of five foodborne pathogens

Aims: To develop a rapid multiplex PCR method for simultaneous detection of five major foodborne pathogens (Staphylococcus aureus, Listeria monocytogenes, Escherichia coli O157:H7, Salmonella Enteritidis and Shigella flexneri, respectively). Methods and Results: Amplification by PCR was optimized to obtain high efficiency. Sensitivity and specificity assays were investigated by testing different strains. With a multipathogen enrichment, multiplex PCR assay was able to simultaneously detect all of the five organisms in artificially contaminated pork samples. The developed method was further applied to retail meat samples, of which 80% were found to be positive for one or more of these five organisms. All the samples were confirmed by traditional culture methods for each individual species. Conclusions: This study reported a rapid multiplex PCR assay using five primers sets for detection of multiple pathogens. Higher consistency was obtained between the results of multiplex PCR and traditional culture methods. Significance and Impact of the Study: This work has developed a reliable, useful and cost‐effective multiplex PCR method. The assay performed equally as well as the traditional cultural method and facilitated the sensitive detection both in artificially contaminated and naturally contaminated samples.     

Structure of Amylase Genes in Populations of Pacific Cupped Oyster (Crassostrea gigas): Tissue Expression and Allelic Polymorphism

Using the previously determined complementary DNA Sequence of Crassostrea gigas amylase (Y08370), we designed several oligonucleotide primers and used them with polymerase chain reaction (PCR) technology to characterize oyster amylase gene sequences. Two genes encoding 2 different amylases were characterized and sequenced. The 2 genes are similarly organized with 8 exons and 7 introns. Intron insertions are found at the same location in the 2 genes. Sizes and nucleotide sequences are different for the different introns inside each gene and different for the corresponding introns in the 2 genes. Comparing the 2 genes, around 10% of the nucleotides are different along the exons, and comparing the 2 deduced protein sequences, a mean value of 10.4% of amino acids are changed. Genes A and B encode mature proteins of, respectively, 500 and 499 amino acids, which present 94% similarity. A microsatellite (TC₃₇) that constitutes the largest part of intron 4 of gene A has been used as a polymorphic marker. A method consisting of a PCR step followed by EcoRI digestion of the obtained fragments was used to observe polymorphism in these 2 genes. Six and 4 alleles for genes A and B, respectively, have been sequenced, leading to a maximum of 2.9% base change. The 2 genes are ubiquitously expressed in the different digestive tissues with quantitative differences. Gene A is strongly expressed in the digestive gland and at a lower level in stomach, while gene B is preferentially expressed in the labial palps. The microsatellite repeat was used in the analysis of 4 populations of Crassostrea gigas from the French Atlantic coast. A high level of polymorphism observed with 30 different alleles of gene A inside the populations should allow their characterization using the mean value of the microsatellite allelic distribution. These populations showed a low level of differentiation (F _st between 0 and 0.011); however, the population of Bonne Anse appeared to be distinguished from the other populations.     

Development and multiplex PCR amplification of new microsatellite markers for the freshwater fish,ayu (Plecoglossus altivelis)

Multiplex polymerase chain reaction (PCR) technique has recently been applied to gain many advantages in molecular genetics. The present study focused on the development of 15 new microsatellite markers with multiplex PCR systems in ayu, Plecoglossus altivelis, an important freshwater fish in Japan. All loci were followed Mendelian inheritance in 27 F1 progeny except for the one locus. The number of alleles per locus ranged from nine to 44 and the observed heterozygosities ranged from 0.680 to 0.980 in 50 unrelated individuals. The results indicate that these new microsatellite markers are useful for studies of linkage mapping and population genetics for the species.     

Polymorphic microsatellite markers for the human oomycete pathogen Pythium insidiosum

We describe the development and characterization of microsatellite loci from the human oomycete pathogen Pythium insidiosum. Nine of 15 microsatellite loci were shown to be appropriate for population genetic study. All loci were polymorphic with observed heterozygosities ranging from 0.241 to 0.912 and from five to 18 alleles per locus among 65 individuals in Thailand. These markers are being used to ascertain multilocus genotypes for molecular epidemiological and population genetic analyses of this little known human pathogen.     

利用SRAP和ISSR建立快速鉴定灵芝属菌株的SCAR标记

根据ERIC聚类分析的结果,把152株灵芝属菌株(包括128株来自中国的栽培菌株及24株国外菌株)建成48个DNA池。用SRAP和ISSR引物对48个DNA池进行扩增,筛选获得4个特异性标记,回收特异性条带,经克隆测序后设计了4对SCAR引物,并通过SCAR-PCR扩增验证,从而将SRAP标记和ISSR标记均成功地转化为特异性和稳定性更好的SCAR标记;将得到的4个SCAR标记在构成DNA池的152个菌株上验证,并建立多重PCR体系,最终证实了SCAR特异标记在菌株快速检测鉴定中的可行性和可靠性。     

Heterogeneity of HLA-G Genes Identified by Polymerase Chain Reaction/Single Strand Conformational Polymorphism (PCR/SSCP)

A genomic HLA-G clone named 7.0E was isolated from a Japanese placenta. The deduced amino acid sequence of the 7.0E was identical to two HLA-G genomic clones and two cDNA clones previously described. The DNA sequences of α1 and α2 domains of the HLA-G gene from 5 cell lines also encoded the same amino acids. However, a 14 bp insertion, ATTTGTTCATGCCT, was present in the 3′ untranslated region of 7.0E compared with the originally described HLA-G clone (HLA 6.0). Polymerase chain reaction (PCR)/single strand conformational polymorphism (SSCP) analysis of exon 8 allowed the HLA-G gene to be classified into two alternative types, G6.0 and 7.0 E, those correlated to the absence or the presence of the 14 bp stretch. Each group had minor sequence variant(s), and the alleles of the 7.0E-type were more heterogeneous than those of the G6.0- type. The 14 bp deletion is present only in the G6.0-type of HLA-G alleles among HLA class I genes. Thus it was suggested that G6.0 alleles were generated after diversification of the HLA-G.     

Development and multiplexing of microsatellite markers in the polyploid perennial herb, Menyanthes trifoliata (Menyanthaceae)

• Premise of the study: We developed microsatellite primers to investigate genetic diversity and population genetic structure of the endangered herb Menyanthes trifoliata. • Methods and Results: Using the microsatellite-enriched library method, we identified 10 primer pairs in M. trifoliata. The primers amplified nine di- and one tri-nucleotide repeats with 4–13 alleles per locus in two Belgian populations. • Conclusions: The results indicate that these markers offer an appropriate amount of variation to investigate genetic diversity, pollen dispersal (through paternity inference), and other conservation issues.     

Molecular Characterization of Human Rotavirus VP4 Genes by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism Assay

A restriction fragment length polymorphism (RFLP) assay was developed to examine the genetic variability and similarity of the VP4 genes of human rotaviruses. The VP4 genes of 14 human rotavirus strains, including VP4 serotype P1A strains (Wa, P, VA70), serotype P1B strain (DS-1), serotype P2 strains (M37, 1076, McN, ST3) and serotype P3 strains (AU-1, AU228, K8, PA151, PCP5, MZ58), and those of 2 feline strains (FRV-1 and Cat2) were reverse-transcribed and amplified by the polymerase chain reaction (PCR). The amplified VP4 cDNAs were then digested with a panel of restriction endonucleases (HindIII, NruI, HaeIII, and EcoRI), resulting in the identification of at least one enzyme with which digestion produced an RFLP profile specific for a particular P serotype. Of interest was the presence of two distinct RFLP patterns within the serotype P3 VP4 genes: one corresponding to the VP4 gene carried by the members of the AU-1 genogroup and the other corresponding to the VP4 genes carried by naturally-occurring reassortants between members of the AU-1 and other genogroups.     

3种贝类原虫多重荧光定量PCR方法的建立

目的:建立能够同时检测单孢子虫、派琴虫和折光马尔太虫的三重荧光定量PCR方法。方法:根据基因库中单孢子虫、派琴虫和折光马尔太虫的基因序列,设计3对特异性引物和3条用不同荧光基团标记的TaqMan探针,对反应条件和试剂浓度进行优化,建立能够同时检测单孢子虫、派琴虫和折光马尔太虫的三重荧光定量PCR方法。结果:该方法对单孢子虫、派琴虫和折光马尔太虫的检测敏感性分别达到40、400和40个模板拷贝数;此外抗干扰能力强,对单孢子虫、派琴虫和折光马尔太虫不同模板浓度进行组合,仍可有效地同时检测这3种原虫,对嗜水气单胞菌、荧光假单胞菌、副溶血弧菌、溶藻弧菌、河弧菌和拟态弧菌等病原体的检测结果均为阴性。结论:建立的单孢子虫、派琴虫和折光马尔太虫多重荧光定量PCR具有特异、敏感、快速、定量和重复性好等优点,可用于临床上单孢子虫、派琴虫和折光马尔太虫感染的检测。