Real-time or quantitative loop-mediated isothermal amplification (qLAMP) is a promising technique for the accurate detection of pathogens in organisms and the environment. Here we present a comparative study of the performance of six fluorescent intercalating dyes-SYTO-9, SYTO-13, SYTO-82, SYBR Green I, SYBR Gold, EvaGreen-in three different qLAMP model systems. SYTO-9 and SYTO-82, which had the best results, were used for additional enzyme and template titration studies. SYTO-82 demonstrated the best combination of time-to-threshold (Tt) and signal-to-noise ratio (SNR).

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At the moment, one of the actual trends in medical diagnostics is a development of methods for practical applications such as point-of-care testing, POCT or research tools, for example, whole genome amplification, WGA. All the techniques are based on using of specific DNA polymerases having strand displacement activity, high synthetic processivity, fidelity and, most significantly, tolerance to contaminants, appearing from analysed biological samples or collected under purification procedures. Here, we have designed a set of fusion enzymes based on catalytic domain of DNA polymerase I from Geobacillus sp. 777 with DNA-binding domain of DNA ligase Pyrococcus abyssi and Sto7d protein from Sulfolobus tokodaii, analogue of Sso7d. Designed chimeric DNA polymerases DBD-Gss, Sto-Gss and Gss-Sto exhibited the same level of thermal stability, thermal transferase activity and fidelity as native Gss; however, the processivity was increased up to 3-fold, leading to about 4-fold of DNA product in WGA which is much more exiting. The attachment of DNA-binding proteins enhanced the inhibitor tolerance of chimeric polymerases in loop-mediated isothermal amplification to several of the most common DNA sample contaminants—urea and whole blood, heparin, ethylenediaminetetraacetic acid, NaCl, ethanol. Therefore, chimeric Bst-like Gss-polymerase will be promising tool for both WGA and POCT due to increased processivity and inhibitor tolerance.

A comparative analysis of the genetic diversity of ancient and modern sheep can shed light on the origin of these animals and their distribution as well as help to evaluate the role of humans at each formation stage of different sheep breeds. Here we isolated ancient DNA and performed sequencing of the mitochondrial DNA D-loop from 17 sheep bone remains (~4000-1000 years old) found in the archaeological complexes in the south of Altai (Western Siberia). The length of the sequences obtained ranged between 318 and 586 bp. The haplotype diversity and nucleotide diversity were 0.801 ± 0.081 and 0.0096 ± 0.0014 respectively. The average number of nucleotide differences was ~3.1. Nucleotide sequence analysis revealed that 15 specimens were nested within previously described A,B,C,D and E lineages and that two specimens had a basal position relative to the rest of the analyzed samples. A relatively high diversity of sheep haplotypes, including the presence of two basal haplotypes, indicates that the Altai region may have been a transport route of human migration. Further ancient DNA analysis of other specimens and deeper genome sequencing of samples with novel haplotypes is needed to better understand the demographic history of sheep in Southern Siberia.

It has been suggested that DNA hypomethylation because of poorer effectiveness of the 5,10-methylenetetrahydrofolate reductase (MTHFR) enzyme induces muscular growth. We hypothesised that the common, functional 1298A>C polymorphism in the MTHFR gene is associated with athletic status. To test this hypothesis, we investigated the distribution of the 1298A>C variant in Polish (n = 302) and Russian (n = 842) athletes divided into four groups: endurance, strength-endurance, sprint-strength and strength-endurance, as well as in 1540 control participants. We found different genotypes (the AC heterozygote advantage) and allele distributions among sprint-strength athletes and strength athletes than the groups of sedentary controls for each nationality. In the combined study, the allelic frequencies for the 1298C variant were 35.6% in sprint-strength athletes (OR 1.18 [1.02-1.36], P = 0.024 vs. controls) and 38.6% in strength athletes (OR 1.34 [1.10-1.64], P = 0.003 vs. controls). The results of the initial and repetition studies as well as the combined analysis suggest that the functional 1298A>C polymorphism in the MTHFR gene is associated with athletic status. The presence of the C allele seems to be beneficial in sprint-strength and strength athletes. It needs to be established whether and to what extent this effect is mediated by alteration in DNA methylation status.

A truncated gene of DNA polymerase I from the thermophilic bacteria Geobacillus sp. 777 encoding a large fragment of enzyme (LF Gss pol) was cloned and sequenced. The resulting sequence is 1776-bp long and encodes a 592 aa protein with a predicted molecular mass of 69.8 kDa. Enzyme was overexpressed in E. coli, purified by metal-chelate chromatography, and biochemically characterized. The specific activity of LF Gss pol is 104,000 U/mg (one unit of enzyme was defined as the amount of enzyme that incorporated 10 nmol of dNTP into acid insoluble material in 30 min at 65 °C). The properties of LF Gss pol were compared to commercially available large fragments of DNA polymerase I from G. stearothermophilus (LF Bst pol) and Bacillus smithii (LF Bsm pol). Studied enzymes showed maximum activity at similar pH and concentrations of monovalent/divalent ions, whereas LF Gss pol and LF Bst pol were more thermostable than LF Bsm pol. LF Gss pol is more resistant to enzyme inhibitors (SYBR Green I, heparin, ethanol, urea, blood plasma) in comparison with LF Bst pol and LF Bsm pol. LF Gss pol is also suitable for loop-mediated isothermal amplification and whole genome amplification of human genomic DNA.

Background: This study is a first attempt to determine frequency of gBRCAm and share of sBRCAm in Russian ovarian cancer (OC) cancer patients (pts) using next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA). Russian population is known to have a sizable proportion of “frequent” germline mutations in BRCA genes, with occurrence in >2% of all BRCAm cases. Methods: 498 pts with primary serous and endometrioid OC were enrolled in noninterventional study OVATAR (NCT02122588). NGS testing of BRCAm in genomic DNA (gDNA) from leukocytes and primary tumor tissue was performed. MLPA assay for large rearrangements (LGR) was used on gDNA from leukocytes. Results: Interim analysis includes pairs of tumor and blood samples from 400 pts. The total rate of BRCA1/2 mutations was 35% (140/400 pts) including 29.8% (119/400) of germline mutations (gBRCAm) and 5.2% (21/400) of somatic mutations. Alterations reported hereby were either classified as deleterious/pathogenic in public databases, or identified as “likely pathogenic” (e.g., loss-of-function). VUS were not included. Frequent gBRCAm were detected in 49.3% of gBRCAm cases (69/140). BRCAm were counted as rare: in 30.7% (43/140) pts, including LGR in 3.6% (5/140) pts. sBRCAm: in 15% (21/140) pts. Although previously counted as frequent, 6174delT in BRCA2 was not detected. 4 pts carried pathogenic germline BRCA2 c.T5286G:p.Y1762* nonsense mutation, with prevalence 2.9% among BRCAm carriers, which makes it the new and only potential “hot-spot” in BRCA2 gene. Large deletions comprise 5% of all BRCAm and mostly occur in BRCA1 gene. Conclusion: The overall rate of both somatic and germline BRCA variations in Russian OC population is in line with global data, with high percent of 8 frequent gBRCAm (49.3%). Use of MLPA is limited by blood samples with low rate of germline LGR. NGS is becoming a method of choice to hit both small variations and LGR in BRCA genes. gene/mutation# of pts (n=140) and % of BRCAmgBRCAmFrequent mutations n=69 (49,3%)BRCA15382insC3726,4%4154delA75,0%2080delA64,3%C61G53,6%185delAG42,9%3819del532,1%3875del432,1%BRCA2T5286G (c.T5286G:p.Y1762*)42,9%Rare mutations n=43 (30,7%)BRCA12417,1%BRCA21913,6%Exons deletions n=7 (5%)BRCA164,3%BRCA210,7%sBRCAmn=21 (15%)BRCA1139,3%BRCA285,7% Citation Format: Alexandra Tyulyandina, Vera Gorbunova, Svetlana Khokhlova, Larisa Kolomiets, Maksim Filipenko, Evgeny Imyanitov, Irina Demidova, Yuri Moliaka, Nadezhda Cherdyntseva, Dmitriy Vodolajskiy, Ludmila Lyubchenko, Sergei Tjulandin, Ilya Tsimafeyeu, Olga Vedrova, Vera Karaseva, Sergei Andreev, Tatiana Kekeeva. Profile of BRCA1/BRCA2 mutations in Russian ovarian cancer population detected by NGS and MLPA analysis: Interim results of OVATAR study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1241.

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