An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number

2015 ◽  
pp. 402-412 ◽  
Author(s):  
Jun Zhou ◽  
Yu Lin ◽  
William Hoskins ◽  
Jijun Tang
Keyword(s):  
Phylogenetic Analysis ◽  
Tumor Progression ◽  
Copy Number ◽  
Iterative Approach

Reduced mitochondrial DNA copy number is correlated with tumor progression and prognosis in Chinese breast cancer patients

IUBMB Life ◽  
2007 ◽  
Vol 59 (7) ◽  
pp. 450-457 ◽  
Author(s):  
Man Yu ◽  
Yunli Zhou ◽  
Yurong Shi ◽  
Liansheng Ning ◽  
Yi Yang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mitochondrial Dna ◽  
Tumor Progression ◽  
Cancer Patients ◽  
Copy Number ◽  
Breast Cancer Patients ◽  
Dna Copy Number ◽  
Mitochondrial Dna Copy Number

Identification of mariner-like elements in Sitodiplosis mosellana (Diptera: Cecidomyiidae)

2006 ◽  
Vol 138 (2) ◽  
pp. 138-146 ◽  
Author(s):  
O. Mittapalli ◽  
R.H. Shukle ◽  
I.L. Wise
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Blot Analysis ◽  
Copy Number ◽  
Southern Blot Analysis ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Degenerate Pcr ◽  
Sitodiplosis Mosellana ◽  
Wheat Midge

AbstractMariner-like element sequences were recovered from the genome of the orange wheat midge, Sitodiplosis mosellana (Géhin), with degenerate PCR primers designed to conserved regions of mariner transposases. The deduced amino acid sequences of the mariner-like transposases from S. mosellana showed 67% to 78% identity with the peptide sequences of other mariner transposases. A phylogenetic analysis revealed that the mariner-like elements from S. mosellana grouped in the mauritiana subfamily of mariner transposons. Results from Southern blot analysis suggest mariner-like elements are at a moderate copy number in the genome of S. mosellana.

A case of hepatitis B virus infection in Eritrean Diciotti migrant: phylogenetic analysis and ‘mirror effect’

2019 ◽  
Vol 14 (8) ◽  
pp. 509-514
Author(s):  
Giancarlo Ceccarelli ◽  
Eleonora Cella ◽  
Serena Vita ◽  
Alessia Lai ◽  
Erika Ebranati ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Copy Number ◽  
Mirror Effect ◽  
Hepatitis B Virus Infection ◽  
Migrant Population ◽  
Hbv Genotype ◽  
B Virus ◽  
Epidemiological Approach

A case of hepatitis B virus (HBV) infection in an Eritrean migrant was described to provide an epidemiological approach based on phylogenetic analysis useful in developing countries with lacking information. Migrant, positive for HBsAg and HBeAg, carried HBV at high copy number. A sequence of HBV HBsAg region was used for phylogenetic relationships and genetic variability investigation. In the phylogenetic tree, the sequence corresponded to D2 HBV genotype and the cluster root dated 7 years ago. These data compared with the date of landing in Italy, suggest that he was infected at least 7 years before his arrival. This approach by ‘mirror effect’ allows the reconstruction of HBV epidemiology in the country of origin, analyzing the migrant population in the host country.

scholarly journals Genes with Relevance for Early to Late Progression of Colon Carcinoma Based on Combined Genomic and Transcriptomic Information from the Same Patients

2010 ◽  
Vol 9 ◽  
pp. CIN.S4545 ◽  
Author(s):  
Kristina K. Lagerstedt ◽  
Erik Kristiansson ◽  
Christina Lönnroth ◽  
Marianne Andersson ◽  
Britt-Marie IresjÖ ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Tumor Progression ◽  
Cancer Progression ◽  
Copy Number ◽  
Dna Copy Number ◽  
Colon Cancer Progression ◽  
Dna Alterations ◽  
Copy Number Changes ◽  
Dukes C

Background Genetic and epigenetic alterations in colorectal cancer are numerous. However, it is difficult to judge whether such changes are primary or secondary to the appearance and progression of tumors. Therefore, the aim of the present study was to identify altered DNA regions with significant covariation to transcription alterations along colon cancer progression. Methods Tumor and normal colon tissue were obtained at primary operations from 24 patients selected by chance. DNA, RNA and microRNAs were extracted from the same biopsy material in all individuals and analyzed by oligo-nucleotide array-based comparative genomic hybridization (CGH), mRNA- and microRNA oligo-arrays. Statistical analyses were performed to assess statistical interactions (correlations, co-variations) between DNA copy number changes and significant alterations in gene and microRNA expression using appropriate parametric and non-parametric statistics. Results Main DNA alterations were located on chromosome 7, 8, 13 and 20. Tumor DNA copy number gain increased with tumor progression, significantly related to increased gene expression. Copy number loss was not observed in Dukes A tumors. There was no significant relationship between expressed genes and tumor progression across Dukes A–D tumors; and no relationship between tumor stage and the number of microRNAs with significantly altered expression. Interaction analyses identified overall 41 genes, which discriminated early Dukes A plus B tumors from late Dukes C plus D tumor; 28 of these genes remained with correlations between genomic and transcriptomic alterations in Dukes C plus D tumors and 17 in Dukes D. One microRNA (microR-663) showed interactions with DNA alterations in all Dukes A-D tumors. Conclusions Our modeling confirms that colon cancer progression is related to genomic instability and altered gene expression. However, early invasive tumor growth seemed rather related to transcriptomic alterations, where changes in microRNA may be an early phenomenon, and less to DNA copy number changes.

scholarly journals Identification of alterations in DNA copy number in host stromal cells during tumor progression

2006 ◽  
Vol 103 (52) ◽  
pp. 19848-19853 ◽  
Author(s):  
R. J. Pelham ◽  
L. Rodgers ◽  
I. Hall ◽  
R. Lucito ◽  
K. C. Q. Nguyen ◽  
...  
Keyword(s):  
Tumor Progression ◽  
Stromal Cells ◽  
Copy Number ◽  
Dna Copy Number

scholarly journals Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome

2015 ◽  
Vol 112 (46) ◽  
pp. 14343-14347 ◽  
Author(s):  
Mizue Anda ◽  
Yoshiyuki Ohtsubo ◽  
Takashi Okubo ◽  
Masayuki Sugawara ◽  
Yuji Nagata ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Protein Synthesis ◽  
Ribosomal Rna ◽  
Genome Analysis ◽  
Copy Number ◽  
High Copy Number ◽  
Functional Importance ◽  
Small Plasmid ◽  
Main Chromosome ◽  
Bacterial Clade

rRNA is essential for life because of its functional importance in protein synthesis. The rRNA (rrn) operon encoding 16S, 23S, and 5S rRNAs is located on the “main” chromosome in all bacteria documented to date and is frequently used as a marker of chromosomes. Here, our genome analysis of a plant-associated alphaproteobacterium,Aureimonassp. AU20, indicates that this strain has its solerrnoperon on a small (9.4 kb), high-copy-number replicon. We designated this unusual replicon carrying therrnoperon on the background of anrrn-lacking chromosome (RLC) as therrn-plasmid. Four of 12 strains close to AU20 also had this RLC/rrn-plasmid organization. Phylogenetic analysis showed that those strains having the RLC/rrn-plasmid organization represented one clade within the genusAureimonas. Our finding introduces a previously unaddressed viewpoint into studies of genetics, genomics, and evolution in microbiology and biology in general.

Assessing intratumor heterogeneity and evolutionary distance in exome sequencing of colon cancer.

2016 ◽  
Vol 34 (4_suppl) ◽  
pp. 590-590
Author(s):  
Ulrich Popper ◽  
Holger Rumpold
Keyword(s):  
Colon Cancer ◽  
Phylogenetic Analysis ◽  
Exome Sequencing ◽  
Copy Number ◽  
Distance Measure ◽  
Copy Number Variants ◽  
Evolutionary Process ◽  
Evolutionary Distance ◽  
Intratumor Heterogeneity ◽  
Tumor Biopsy

590 Background: Carcinogenesis is considered to be an evolutionary process by natural selection of cell clones which have acquired advantageous heritable characteristics. This adaption process, which resembles Darwin’s evolutionary theory, has also been suggested as a potential mechanism promoting resistance to anti-cancer treatment. Methods: We performed whole exome sequencing of four colon cancers at five morphologically different loci of the primary tumor tissue. To investigate intratumor heterogeneity we conducted structural variant analysis, copy number analysis and ploidy profiling. We propose an evolutionary distance of the tumor samples based on a distance function in copy number space. Results: Copy number and phylogenetic analysis demonstrated substantial intratumor heterogeneity, with all 20 samples (5 loci for 4 tumors) possessing a unique copy number profile. Our analysis further revealed cancer-specific, tumor-specific and locus-specific copy number variants. We found that at least one copy of 18q, including the genes DCC and SMAD4, as well as 8p, carrying the CSMD1 gene, was missing in all tumors. Additionally, gains of chromosome 7,8q, 13q, 20q and losses of 4q and 21q were frequent. Using our distance measure in copy number space, phylogenetic analysis grouped together the five loci of one tumor and showed their evolutionary branching. We found that our distance measure in copy number space is superior to a distance measure in SNV space for colon cancer. Conclusions: Our analysis reveals that the landscape of the tumor genome cannot be captured by single tumor-biopsy, which is one of the challenges to personalized-medicine as heterogeneity can lead to therapeutic failures. However, there can be characteristics of the tumor genomes that are stable across samples which can potentially be used as biomarkers. Nonetheless variability of copy number profiles of colorectal cancers might suggest a personalized therapy.

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