Table 1 - uploaded by Denis O Fesenko
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Single-nucleotide polymorphism among the AB0 gene alleles. Allele A is conventionally regarded wild-type. The number of position corresponds to the nucleotide posi- tion in the gene sequence
Contexts in source publication
Context 1
... was isolated using the Wizard kit (Promega, United States). Alleles A , B , 0 1 , 0 1v , and 0 2 of the AB0 gene were determined on the basis of positions in exons 6 and 7 of this gene ( Table 1). The sequences of oligonucleotide probes were selected using the Ensembl nucleotide sequence data- base (www.ensembl.org) ...
Context 2
... demonstrate the algorithm of genotyping, let us analyze the hybridization map of the microchip shown in Fig. 1d. For the AB0 gene, the presence of the fluo- rescent signal in the two lower wells in the first row is indicative of deletion 261G in the homozygous state, which rules out all alleles except for 0 1 and 0 1 v (see Table 1). The presence of the signal in both upper and lower wells at positions 297 and 646 is indicative of the heterozygous state and the simultaneous presence of alleles 0 1 and 0 1 v . ...
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... Therefore, genetic methods intended for gleaning non-genetic search information about the offender helpful in narrowing a circle of suspects should be highlighted. There are methods for blood group determination [1][2][3][4][5] , prediction of iris, hair and skin [6][7][8] colour, biogeographical ancestry 9 , etc. We hope that predicting paternal ethnicity by Y-SNP genotyping can be one such search tool. ...
A biochip Ycore10 has been developed which allows identification of the following SNP mar-kers of Y haplogroups: M130 (C), M145 (DE), P257 (G), M69 (H), U179 (I), M304 (J), M185 (L), M231 (N), M175 (O) and P224 (R). The biochip can be used in determination of paternal ethnicity of offenders in the complex ethnic milieu of Russia. The sensitivity limit of the biochip-based assay was 31 pg of DNA template. Ycore10 genotyping was successfully performed with a range of male DNA concentrations (0.5-300 ng). Alto-gether 89 samples were genotyped and the following haplogroups were detected: C (2), DE (10), G (6), H (2), I (20), J (6), L (1), N (17), O (2), R (22). In one sample the ancestral alleles were detected for all ten biallelic markers. This tool is feasible for genotyping of mixed and degraded samples.
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A method for fluorescently labeled single-stranded DNA (ssDNA) production during single-stage polymerase chain reaction (PCR)
for subsequent hybridization on a biochip was described. This approach, whose efficiency was confirmed in the case of DARC gene, is considered as an alternative to two-stage nested PCR, consisting of two separate reactions: symmetric and asymmetric.
Implementation of PCR in a single stage was achieved due to the use of a truncated excess primer in the second stage that
does not anneal on the matrix during the cycles of symmetric stage of PCR and that enters the reaction after decrease of the
annealing temperature in asymmetric stage. As a result, high efficiency of genotyping by means of hybridization on biochips
is maintained. The suggested approach will allow us to reduce the time, working hours, and risk of contamination when researching
biochips.
Keywordsproduction of ssDNA–biochips–single-stage nested PCR
... The 3 0 -end of each oligonucleotide carried a spacer with a free amino group, which was introduced during synthesis using 3 0 -amino-modifier C7 CPG 500 (Glen Research, Sterling, VA). The nucleotide sequences of immobilized oligonucleotides were published earlier (Glotov et al., 2005; Kozhekbaeva et al., 2007; Gra et al., 2008; Nasedkina et al., 2008). Biochips were prepared by photo-inducible copolymerization of oligonucleotides and components of polyacrylamide gel, as described previously (Rubina et al., 2004). ...
... The less frequent allele observed was *04, which appeared in 4.4% (3.0%–6.2%). When the four polymorphic sites (261 G>del, 297 A>G, 646 T>A, and 657 C>T) in 6 and 7 exons of the AB0 gene had been analyzed, five groups of alleles were identified: A, B, 0 1 , 0 1v , and 0 2 (Nasedkina et al., 2008 ...
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Xenobiotic-metabolizing genes (e.g., Cytochromes P450, GST, NAT2, and NQO1), folate metabolism genes (e.g., MTHFR and MTRR), and major histocompatibility complex genes (e.g., HLA-DQA1) play multiple roles in the organism functioning. In addition, AB0 is the most clinically significant high-polymorphic gene in transfusion and transplantation medicine. Epidemiological data show that allele frequencies of these genes exhibit ethnic and geographic diversity. Besides, little is known about frequency distribution of the major polymorphic variants in native Russians. We developed biological microchips that allow us to analyze a spectrum of allelic variants in 12 different genes: CYP1A1, CYP2D6, CYP2C9, CYP2C19, GSTT1, GSTM1, MTHFR, MTRR, NQO1, NAT2, HLA-DQA1, and AB0. Using this composite methodological platform we have studied 352 DNA samples from healthy native Russian volunteers. The allelic frequencies of gene polymorphisms obtained are close to allelic frequencies observed in some European populations, as published earlier. These data were used in comparative studies to determine predisposition to tuberculosis, lymphoma, and leukemia in adults and to childhood acute leukemia. The HLA-DQA1 and AB0 allele frequencies were used to estimate forensic population parameters for these loci.
The efficiency of fluorescence DNA labeling was estimated for four fluorescent 2′-deoxyuridine 5′-triphosphate derivatives differing in the orientation of the main dye axis, which passes through the polymethine chain, relative to the linker connecting the dye to the nucleotide. To estimate the polymerase chain reaction (PCR) rate, real-time PCR was run with two commercial hot-start DNA polymerases possessing 5′→3′ exonuclease activity in the presence of an intercalating dye. The efficiency of the test compound incorporation in the PCR product was estimated via a quantitative analysis of the amplification product by agarose gel electrophoresis. The fluorescently labeled product was then hybridized on a biological microchip and the ratio of signals from perfect match and mismatch duplexes was determined. The incorporation efficiency and discrimination between perfect match and mismatch duplexes were found to depend on the relative orientation of the dye and the linker between the dye and pyrimidine base, as well as on the presence of hydrophilic groups in the dye. Compounds that are efficiently incorporated in a growing DNA strand and show a high specificity in hybridization analysis were identified using biochips.
The kinetics of DNA labeling during PCR using six fluorescent derivatives of 2′-deoxyuridine 5′-triphosphate has been studied. These compounds differ in their chemical structure, total electric charge and the length of the linker between a dye and the C5 position of a pyrimidine base. The efficiency of the incorporation of the fluorescent derivatives into a growing DNA chain by four commercially available Taq DNA polymerases with 5′→3′ exonuclease and hot start activity has been determined using real-time PCR with a TaqMan probe and the subsequent electrophoretic analysis of the reaction products. Modified deoxyuridines with a total positive or negative charge of the chromophore were practically not incorporated by Taq polymerases during PCR. The modified deoxyuridines with a neutral charge of the chromophore were effectively incorporated into DNA. The extended length of the linker between the pyrimidine base and the chromophore led to a lower PCR inhibition and a more effective inclusion of modified nucleotides in the growing DNA chain. This fact can be explained by the reduced steric effects that were caused by the dye. As a result, the most promising combinations of fluorescently labeled nucleotide and Taq polymerase have been chosen for further use in fluorescent DNA labeling.
The authors describe a domestically produced test-system for the determination of the AB0 blood type by means of the single nucleotide polymorphisms (SNP) analysis. The results of the trials indicate that the proposed test-system can be employed for the investigation of DNA specimens of individual origin obtained from any objects of expertise including micro-objects containing human nuclear DNA.
A method for genotyping of biological material for AB0, HLA-DQA1, and AMEL loci is described. The method utilizes allele-specific SNP typing with th e help of hydrogel biochip technology. Amplified
fluorescentlylabeled fragments of genes were hybridized with SNP-specific DNA probes immobilized on a biochip. The alleles
of the gene in a sample were determined according to the distribution of the fluorescent signal. The minimal amount of biological
material required for the assay is 100 pg of DNA. The biochip assay was used to analyze 442 DNA specimens of the Eastern Slavic
population of Russia and to determine the allelic frequencies of AB0 and HLA-DQA1 loci. The feasibility of genotyping the biological traces of investigative value, such as cigarette butts, sweat traces on
paper, and swabs of the lip of the glass, was demonstrated. This assay is applicable in forensic studies. The significance
of identification for the used loci is 99.6%.
Key wordsgenes-
AB0
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HLA-DQA1
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AMEL
-genotyping-biochip-forensic studies
