FXYD2 mRNA expression represents a new independent factor that affects survival of glioma patients and predicts chemosensitivity of patients to temozolomide

Purpose Glioma is the most common primary intracranial tumor. Owing to the poor prognosis associated with high-grade gliomas, there is an urgent need to identify biomarkers related to prognosis and treatment sensitivity. Here, we analyze the expression of FXYD2 mRNA in gliomas, and explore its clinical prognostic value and significance in this disease. Methods Clinical features, FXYD2 mRNA expression levels, and survival data were analyzed for 516 glioma patients from the Chinese Glioma Genome Map Project, 481 from the cancer genome map datbase and 268 from the molecular braintumor database. The expression patterns for FXYD2 mRNA were compared using the chi-square test, and overall survival (OS) of glioma patients was evaluated according to FXYD2 mRNA expression levels. The factors affecting glioma survival were evaluated by Cox univariate and multivariate regression analysis. Results FXYD2 mRNA expression was related to the grade of gliomas. The higher the level, the lower the expression. Meanwhile related to the pathological classification of gliomas. Oligodendroglioma, IDH-mutant and 1p/19q-codeleted was higher than Astrocytoma, IDH-mutant, higher than Glioblastoma, IDH-wildtype. Moreover, temozolomide (TMZ) chemotherapy was found to be an independent factor affecting survival in patients with high FXYD2 mRNA expression, but not in patients with low expression. Conclusion FXYD2 mRNA expression represents a new independent factor affecting the survival of glioma patients and may serve as an independent prognostic indicator to predict the sensitivity of gliomas to TMZ.

Genes Associated with Prognosis of Hepatocellular Carcinoma

Background: Hepatocellular carcinoma (HCC) is the foremost common malignant liver malady within the world. In any case, the unthinking relationship between each quality and the signaling pathway remains vague. In this think about, we pointed to explain the potential center candidate genes and pathways for HCC. Methods: The GSE41804, GSE62232 and GSE65372 expression profiles cover 139 tumors and 46 non tumors and can be downloaded from the Gene Expression Integrated Database (GEO). Furthermore, we also downloaded the RNA arrangement information set of liver cancer from the cancer genome map (TCGA) database. Then use the online database David 6.8 The Kyoto Encyclopedia of Genes and Genomic Pathways. The protein-protein interaction organized complexes of these Differentially expressed genes (DEGs) were developed by utilizing cytokeratin program, atomic complex discovery plug-in and online database STRING. Results: To begin with, we identified 84 abnormally expressed genes (39 upregulation genes and 45 downregulation genes) that were abnormally expressed in both the Earth synthetic orbit and the TCGA dataset. In expansion, 10 center qualities were recognized: CCNB1, CCNA2, NCAPG, AURKA, ASPM, TOP2A, DLGAP5, NUSAP1, NUF2 and RACGAP1. At long last, the by and large survival examination and relationship examination were performed for these qualities. Conclusions: These discoveries recommend that center qualities and pathways recognized through bioinformatics examination can incredibly enhance our understanding of HCC improvement and repeat. In expansion, these candidate qualities and pathways may be restorative targets for HCC treatment.

Comprehensive Analysis of the Expression Characteristics of the Enhancer of the Zeste Homolog 2 Gene in Pan-Cancer

Although more and more studies have shown that EZH2 was closely related to human cancer, no pan-cancer analysis is available. Therefore, we summarized and analyzed the potential carcinogenic effect of EZH2 for the first time based on TCGA (cancer genome map) datasets. EZH2 is expressed highly in most tumors and there is a significant correlation between the EZH2 expression and the prognosis of patients. We observed the increased phosphorylation levels of T487 in breast cancer, colon cancer, UCEC, and LUAD. The expression of EZH2 was associated with the CD8+, tregs, macrophage, and cancer-associated fibroblast infiltration in some tumors. In addition, the cell cycle and cellular biology were involved in the functional mechanisms of EZH2. Our study summarized and analyzed the carcinogenic effect of EZH2 in different tumors comprehensively and provided a theoretical basis for targeting EZH2 therapy.

The Potential and Analysis of ctDNA Sequencing in Hepatocellular Carcinoma

Background: The Genome map of hepatocellular carcinoma (HCC) is complex. We used the next generation of targeted sequencing technology to decipher the mutations in patients with liver cancerMethods: The circulating tumor cell DNA (ctDNA) of 10 patients with hepatocellular carcinoma (Including 8 cases of primary hepatocellular carcinoma and 2 cases of metastatic hepatocellular carcinoma) were sequenced. We used SAMtools to detect and screen single nucleotide polymorphism (SNP) and insertion deletion (INDEL) mutations, and ANNOVAR to annotate the structure and function of the detected mutations.Results: Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples showed 8950 single nucleotide variations (SNVS) mutations and 70 INDELS. The most common mutation gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, we authenticated 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 patients with HCC.Conclusion: Our research provides the gene mutation map of Chinese hepatocarcinoma patients, and enriches the understanding of the pathogenesis of HCC.

HiCancer: accurate and complete cancer genome phasing with Hi-C reads

Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.

Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

Background: Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge.Results: A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligos were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3, and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1, and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary, and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of chromosomes.Conclusions: The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

Comparative Chloroplast Genome Analysis and Evolutionary Relationships in Some Species of Asclepiadeae, Apocynaceae

Background: Comparative study of the complete chloroplast genomes of some species in the Subtribe Asclepiadeae was conducted to evaluate the variations and similarities between the species and to resolve the phylogenetic relationship within the subtribe. P. tomentosa has been used for medicinal uses in Saudi Arabia, Middle East, Africa and Brazil. It is used often in cosmetics and tanning industries, although it’s very well utilized as a traditional medicine in many civilizations.Methods: The genomes were compared using Mvista Bioinformatics tools to evaluate the inverted repeats (IR), large single copy (LSC) and small single copy (SSC) regions and also the border junctions were visualized with IR scope to express the expansion and contraction of the circular genome structure. While SSR markers were determined using the Reputer program, the genome map was done using OGDRAW (OrganellarGenomeDRAW).Result: Observed variations of the Mvista alignments is mainly at the coding regions of the sequences, while IR borders were varied at the SSC region of A. nivea genome; with ycf1 and rps19 due to evolutionary events. The genome sizes of C. procera are 166,010 bp, P. tomentosa 164,213bp, A. nivea 161,592 bp and C. wilfordii 161,180 bp. GC contents of A. nivea, C. wilfordii and P. tomentosa are 38% respectively; while C. procera is the least with 37%.; total SSR markers as well as the circular genome map were presented in this study.

Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

Background: Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut. Thus, the identification of chromosomal variants in peanut remains a challenge, owing to a lack of efficient chromosomal markers. Results: A total 114 new oligo probes were developed, based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligos were classified into 28 types, based on their positions, and overlapping signals in chromosomes. For each oligo types, a single and representative oligos was selected and modified with 6-carboxyfluorescein (FAM) and 6-carboxytetramethylrhodamine (TAMRA). Based on these 28 probes, a new multiplex #3 cocktail was developed with FAM-modified TIF-439, TIF-185-1, TIF-134-3, and TIF-165-3, and TAMRA-modified Ipa-1162, Ipa-1137, DP-1, and DP-5. This cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of peanut induced by radiation. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, and intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the other 15 were extensively mapped in the pericentric regions of chromosomes. Conclusions: The development of new oligo probes provides effective tools, which can be used to distinguish various chromosomes of peanut. Physical mapping reveals the genomic organization of repetitive oligos in peanut chromosomes by FISH. Following comparisons with their positions in the reference sequences, a genome map-based karyotype was established and used for the identification of chromosome variations in peanut.

Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut

Background Chromosomal structural variants are important materials for crop breeding and genetic research. Oligo fluorescence in situ hybridization (oligo FISH) is a useful tool for the identification of chromosomal structural variants. Results We developed 114 new repetitive oligos based on genome-wide tandem repeats (TRs) using genomic reference sequences of the cultivar Tifrunner and the diploid species Arachis ipaensis by bioinformatics and FISH. These oligo probes were positioned and classified into 28 types. Signals produced by representative probes from eight types were in the secondary constriction, middle arm, and terminal regions; signals of four probe types were on the B subgenome; and one probe being able to produce signals on only one pair of chromosomes could be used to recognize a special genome or chromosomes of peanut. Based on new and previous oligo probes, we developed a cocktail Multiplex #3 including FAM modified TIF-439, TIF-185-1, TIF-134-3, TIF-165-3, and TAMRA modified Ipa-1162, Ipa-1137, DP-1, and DP-5, which combined with the total genomic DNA of A. duranensis and A. ipaensis probes, and 45S rDNA and 5S rDNA probes to establish a karyotype associated with the genome map of peanut and identify 14 chromosomal structural variants. Conclusions The new oligo probes are useful and convenient for distinguishing peanut chromosomes or specific segments of peanut chromosomes. Comparisons of oligo sites in the karyotype and chromosome plots of electronic location revealed the characteristics of repeated sequences, and showed that the assembly of repeated sequence in peanut genomic reference sequence was incomplete. We therefor demonstrated the great potentials of the new oligo probes in facilitating chromosome identification and characterization, and provided novel materials for further study and genetic improvement of peanut.