Genotyping of hundreds of individuals from Kazakh population in Kazakhstan
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PROVIDER: PRJNA819402 | ENA |
REPOSITORIES: ENA
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Project description:Genotyping of hundreds of healthy individuals with Kazakh ethnicity as a reference cohort for further genetic investigations
2024-10-04 | GSE199322 | GEO
Project description:NGS and analysis of Kazakh genomes
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Project description:Artemia sp. Kazakhstan ARC1039 isolate:Kazakhstan ARC1039 Genome sequencing and assembly
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Project description:AIM:To study the genetic relationship of Kazakhs from East Kazakhstan to other Eurasian populations by examining paternal and maternal DNA lineages. METHODS:Whole blood samples were collected in 2010 from 160 unrelated healthy Kazakhs residing in East Kazakhstan. Genomic DNA was extracted with Wizard genomic DNA Purification Kit. Nucleotide sequence of hypervariable segment I of mitochondrial DNA (mtDNA) was determined and analyzed. Seventeen Y-short tandem repeat (STR) loci were studied in 67 samples with the AmpFiSTR Y-filer PCR Amplification Kit. In addition, mtDNA data for 2701 individuals and Y-STR data for 677 individuals were retrieved from the literature for comparison. RESULTS:There was a high degree of genetic differentiation on the level of mitochondrial DNA. The majority of maternal lineages belonged to haplogroups common in Central Asia. In contrast, Y-STR data showed very low genetic diversity, with the relative frequency of the predominant haplotype of 0.612. CONCLUSION:The results revealed different migration patterns in the population sample, showing there had been more migration among women. mtDNA genetic diversity in this population was equivalent to that in other Central Asian populations. Genetic evidence suggests the existence of a single paternal founder lineage in the population of East Kazakhstan, which is consistent with verbal genealogical data of the local tribes.
| S-EPMC3583390 | biostudies-literature
Project description:Investigate long non-coding RNA (lncRNA) expression characteristics in the peripheral blood lymphocytes of Xinjiang Kazakh people with essential hypertension.
2023-06-10 | GSE234085 | GEO
Project description:Introduction:ABO blood group genotyping is a new technology in hematology that helps prevent adverse transfusion reactions in patients. Identification of antigens on the surface of red blood cells is based on serology; however, genotyping employs a different strategy and is aimed directly at genes that determine the surface proteins. ABO blood group genotyping by real-time PCR has several crucial advantages over other PCR-based techniques, such as high rapidity and reliability of analysis. The purpose of this study was to examine nucleotide substitutions differences by blood types using a PCR-based method on Kazakh blood donors. Methods:The study was approved by the Ethics Committee of the National Center for Biotechnology. Venous blood samples from 369 healthy Kazakh blood donors, whose blood types had been determined by serological methods, were collected after obtaining informed consent. The phenotypes of the samples included blood group A (n = 99), B (n = 93), O (n = 132), and AB (n = 45). Genomic DNA was extracted using a salting-out method. PCR products of ABO gene were sequenced on an ABI 3730xl DNA analyzer (Applied Biosystems). The resulting nucleotide sequences were compared and aligned against reference sequence NM_020469.2. Real-time PCR analysis was performed on CFX96 Touch™ Real-Time PCR Detection System (BioRad). Results:Direct sequencing of ABO gene in 369 samples revealed that the vast majority of nucleotide substitutions that change the ABO phenotype were limited to exons 6 and 7 of the ABO gene at positions 261, 467, 657, 796, 803, 930 and 1,060. However, genotyping of only three of them (261, 796 and 803) resulted in identification of major ABO genotypes in the Kazakh population. As a result, TaqMan probe based real-time PCR assay for the specific detection of genotypes 261, 796 and 803 was developed. The assay did not take into account several other mutations that may affect the determination of blood group, because they have a low occurrence rate and therefore have not been found in the population sample. Conclusion:Real-time PCR based method for fast and reliable ABO genotyping was developed. This assay may be used as a complement to classic serological blood typing.
| S-EPMC5960945 | biostudies-literature
Project description:GeneSeek HD Bovine 77k Genotyping array is used to estimate population structure and ancestry of bovine and evaluate loci responsible for complex traits. Further, copy number variation of bovine can be estimated by GeneSeek HD Bovine 77k Genotyping array. Here, we estimate population structure and ancestry of Qinchuan cattle.
2017-06-15 | GSE100038 | GEO
Project description:Esophageal squamous cell carcinoma (ESCC) is characterized as a metabolic disorder characterized by lipid metabolic reprogramming. To investigate the regional characteristics of ESCC patients in Xinjiang Province, China, and lipid metabolism, in this study, we described the characteristics of the serum lipid composition in Kazakh ESCC patients by performing an integrated analysis of the transcriptome and lipidomic data. Serum samples from 30 Kazakh ESCC patients and 30 healthy individuals were subjected to targeted lipid metabolomics analysis via UPLC‒MS/MS, while 3 tumor samples and matched adjacent normal tissues from 30 ESCC patients were subjected to transcriptome analysis. Compared with those in the healthy group, we observed obvious changes in the serum lipid subclass content, chain length and unsaturation in the ESCC patients. Integrated lipidomic and transcriptomic analyses revealed that unsaturated fatty acid biosynthesis, fatty acid metabolism, lipid degradation, cholesterol metabolism and the AMPK signaling pathway were enriched in tumor tissues. In addition, RT–qPCR results demonstrated that genes closely related to these pathways were differentially expressed between the ESCC group and the healthy control group. Considering the key role of AMPK in lipid metabolism, we conducted a targeted lipid metabolomics analysis on AMPK-knockdown esophageal cancer cells by UPLC‒MS/MS. These findings suggested that AMPK might be correlated with lipid metabolism in Kazakh ESCC patients, identifying potential therapeutic targets of AMPK and other lipid metabolism-related markers against the progression of ESCC.
2024-01-17 | GSE253171 | GEO
Project description:We performed genotyping of Neuroblastoma Primary tumors using Illumina HumanHap 550 - v1,v3,v3duo and 610 Quad genotyping beadchips.
2011-09-15 | GSE19385 | GEO
Project description:Ovis aries strain:kazakh sheep Transcriptome or Gene expression
| PRJNA79013 | ENA