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Large-scale genome-wide SnP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第4期25卷 324-340页

作者： natalia V.DEMEnTIEVA Yuri S.SHCHERBAkOV Olga I.STAnISHEVSkAYA Anatoly B.VAkHRAMEEV Tatiana A.LARkInA Artem P.DYSIn Olga A.nIkOLAEVA Anna E.RYABOVA Anastasiia I.AZOVTSEVA Olga V.MITROFAnOVA grigoriy.k.peglivany.n natalia R.REInBACH Darren k.GRIFFIn Michael n.ROMAnOV Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.k.Ernst Federal Research Centre for Animal Husbandry.Pushkin St.Petersburg196601Russia School of Biosciences University of KentCanterburyCT27NJUK L.k.Ernst Federal Research Center for Animal Husbandry DubrovitsyPodolskMoscow Oblast142132Russia

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse *** study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 *** populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,Uk,etc.),Asia(China),north America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60k single nucleotide polymorphism(SnP)chip,a bioinformatic analysis was carried *** included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population *** also included assessment of linkage disequilibrium and construction of phylogenetic *** multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each *** overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous *** a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry *** general,whole genome SnP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

关键词： Chicken genome diversity Single nucleotide polymorphism(SnP)analysis Gene pool Global ancestry Phylogeny Demographic history

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Spatiospectral transformation of noncollimated light beams diffracted by ultrasound in birefringent crystals

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Photonics Research 2021年第5期9卷 687-693页

作者： ALEXEY V.GOREVOY ALEXAnDER S.MACHIkHIn grigoriy n.MARTYnOV VITOLD E.POZHAR Laboratory of Acousto-optic Spectroscopy Scientific and Technological Center of Unique InstrumentationRussian Academy of SciencesMoscow 117342Russia

Spatiospectral structure of wave phase matching in birefringent crystals has a strong dependence on the geometry of the acousto-optic interaction and incident light spectrum. This dependence defines details of light beam profile transformation. It is especially important for imaging applications related to a large angular aperture and a wide spectral bandwidth of the incident light. In this paper, we demonstrate accurate three-dimensional plotting of a light transmission pattern without small birefringence approximation. The rather complicated shape of the phase-matching locus in the spatiospectral domain inevitably leads to residual spatially nonuniform chromatic aberrations in the spectral image. Theoretical consideration and computational modeling are confirmed by the experiments on Bragg diffraction in paratellurite crystal. The results are especially important for the development of acousto-optical imaging devices and laser beam shaping technologies.

关键词： spectral light matching

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Hereditary cancer syndromes

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World Journal of Clinical Oncology 2023年第2期14卷 40-68页

作者： Evgeny n Imyanitov Ekaterina S kuligina Anna P Sokolenko Evgeny n Suspitsin grigoriy A Yanus Aglaya G Iyevleva Alexandr O Ivantsov Svetlana n Aleksakhina Department of Tumor Growth Biology N.N.Petrov Institute of OncologySt.-Petersburg 197758Russia Department of Clinical Genetics St.-Petersburg Pediatric Medical UniversitySt.-Petersburg 194100Russia

Hereditary cancer syndromes(HCSs)are arguably the most frequent category of Mendelian genetic diseases,as at least 2%of presumably healthy subjects carry highly-penetrant tumor-predisposing pathogenic variants(PVs).Hereditary breast-ovarian cancer and Lynch syndrome make the highest contribution to cancer morbidity;in addition,there are several dozen less frequent types of familial *** development of the majority albeit not all hereditary malignancies involves two-hit mechanism,*** somatic inactivation of the remaining copy of the affected *** studies on cancer families suggested nearly fatal penetrance for the majority of HCS genes;however,population-based investigations and especially large-scale next-generation sequencing data sets demonstrate that the presence of some highly-penetrant PVs is often compatible with healthy *** cancer research initially focused mainly on cancer detection and *** studies identified multiple HCS-specific drug vulnerabilities,which translated into the development of highly efficient therapeutic options.

关键词： Hereditary cancer syndromes Germline pathogenic variants Cancer predisposition Cancer treatment next-generation sequencing

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Tumor irradiation may facilitate the detection of tumor-specific mutations in plasma

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World Journal of Clinical Oncology 2021年第12期12卷 1215-1226页

作者： Ekaterina kuligina Fedor Moiseyenko Sergey Belukhin Ekaterina Stepanova Maria Zakharova Vera Chernobrivtseva Ikram Aliev Tatiana Sharabura Vladimir Moiseyenko Svetlana Aleksakhina Tatiana Laidus Aleksandr Martianov Maksim kholmatov Aldon Whitehead grigoriy Yanus Evgeny Imyanitov Department of Tumor Biology N.N.Petrov Institute of OncologySt.-Petersburg 197758Russia Department of Medical Genetics St.-Petersburg Pediatric Medical UniversitySt.-Petersburg 194100Russia Department of Therapy City Cancer CenterSt.-Petersburg 197758Russia Department of Surgery City Cancer CenterSt.-Petersburg 197758Russia Department of Radiology City Cancer CenterSt.-Petersburg 197758Russia Internal Medicine Residency Program The University of Illinois College of MedicineChicagoIL 60612United States Department of Oncology I.I.Mechnikov Northwestern Medical UniversitySt.-Petersburg 191015Russia

BACkGROUnD The mutation-based analysis of circulating tumor DnA(ctDnA)is a promising diagnostic tool for clinical ***,it has low success rate because many cancer patients do not have detectable ctDnA in the *** To evaluate whether preoperative tumor irradiation results in a transient increase of plasma ctDnA concentration due to the induction of apoptosis in radiationexposed *** This study focused on patients with locally advanced rectal cancer,because preoperative tumor irradiation is a part of their standard treatment *** subjects,whose tumors contained kRAS,nRAS or BRAF mutations,donated serial blood samples 1 h prior to the first fraction of irradiation(at baseline),immediately after the first fraction(time 0),and 1,3,6,12,24,36,48,72 and 96 h after the first *** amount of mutated gene copies was measured by droplet digital *** Five out of nine patients were mutation-negative by ctDnA test at baseline;two of these subjects demonstrated an emergence of the mutated DnA copies in the bloodstream within the follow-up *** were 4 patients,who had detectable ctDnA in the plasma at the start of the experiment;three of them showed an evident treatment-induced increase of the content of mutated RAS/RAF *** Local tumor irradiation may facilitate the detection of tumor-specific DnA in the *** data justify further assessment of the clinical feasibility of irradiation-assisted liquid biopsy.

关键词： Liquid biopsy Rectal cancer kRAS BRAF Mutations Tumor response Radiotherapy

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