Comparative Genomic Tools for Exploring the Human Genome

2003 ◽  
Vol 68 (0) ◽  
pp. 283-292 ◽  
Author(s):  
I. OVCHARENKO ◽  
G.G. LOOTS
Keyword(s):  
Human Genome ◽  
Comparative Genomic ◽  
Genomic Tools

scholarly journals Recent Advances in Medicago truncatula Genomics

2008 ◽  
Vol 2008 ◽  
pp. 1-11 ◽  
Author(s):  
Jean-Michel Ané ◽  
Hongyan Zhu ◽  
Julia Frugoli
Keyword(s):  
Medicago Truncatula ◽  
Human Population ◽  
Lotus Japonicus ◽  
Model Systems ◽  
Biological Information ◽  
Comparative Genomic ◽  
Legume Nodulation ◽  
Symbiotic Interactions ◽  
Genomic Tools ◽  
Consistent Increase

Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodulation, these two models are now widely used in a variety of biological fields from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed.

scholarly journals Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution

2019 ◽  
Author(s):  
Christian D. Huber ◽  
Bernard Y. Kim ◽  
Kirk E. Lohmueller
Keyword(s):  
Human Genome ◽  
Population Genetic ◽  
Purifying Selection ◽  
Tree Size ◽  
Genetic Models ◽  
Comparative Genomic ◽  
Mammalian Evolution ◽  
High Turnover ◽  
Functional Elements ◽  
Optimal Tree

AbstractComparative genomic approaches have been used to identify sites where mutations are under purifying selection and of functional consequence by searching for sequences that are conserved across distantly related species. However, the performance of these approaches has not been rigorously evaluated under population genetic models. Further, short-lived functional elements may not leave a footprint of sequence conservation across many species. Here, we use simulations to study how one measure of conservation, the GERP score, relates to the strength of selection (Nes). We show that the GERP score is related to the strength of purifying selection. However, changes in selection coefficients or functional elements over time (i.e. functional turnover) can strongly affect the GERP distribution, leading to unexpected relationships between GERP and Nes. Further, we show that for functional elements that have a high turnover rate, the optimal tree size is not necessarily the largest possible tree, and more turnover reduces the optimal tree size. Finally, we use the distribution of GERP scores across the human genome to compare models with and without turnover of sites where mutations under purifying selection. We show that mutations in 4.51% of the noncoding human genome are under purifying selection and that most of this sequence has likely experienced changes in selection coefficients throughout mammalian evolution.

scholarly journals Dcode.org anthology of comparative genomic tools

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W56-W64 ◽  
Author(s):  
G. G. Loots ◽  
I. Ovcharenko
Keyword(s):  
Comparative Genomic ◽  
Genomic Tools

scholarly journals panModule: detecting conserved modules in the variable regions of a pangenome graph

2021 ◽  
Author(s):  
Adelme Bazin ◽  
Claudine Medigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Original Method ◽  
Comparative Genomic ◽  
Phylogenetic Groups ◽  
Variable Regions ◽  
Microbial Genomes ◽  
As Species ◽  
Genomic Tools ◽  
Strain Adaptation ◽  
Synteny Blocks ◽  
Genomic Regions

The recent years have seen the rise of pangenomes as comparative genomic tools to better understand the evolution of gene content among microbial genomes in close phylogenetic groups such as species. While the core or persistent genome is often well-known as it includes essential or ubiquitous genes, the variable genome is usually less characterized and includes many genes with unknown functions even among the most studied organisms. It gathers important genes for strain adaptation that are acquired by horizontal gene transfer. Here, we introduce panModule, an original method to identify conserved modules in pangenome graphs built from thousands of microbial genomes. These modules correspond to synteny blocks composed of consecutive genes that are conserved in a subset of the compared strains. Identifying conserved modules can provide insights on genes involved in the same functional processes, and as such is a very helpful tool to facilitate the understanding of genomic regions with complex evolutionary histories. The panModule method was benchmarked on a curated dataset of conserved modules in Escherichia coli genomes. Its use was illustrated through a study of a high pathogenicity island in Klebsiella pneumoniae that allowed a better understanding of this region. panModule is freely available and accessible through the PPanGGOLiN software suite (https://github.com/labgem/PPanGGOLiN).

scholarly journals Genome-wide approaches and technologies to assess human variation

2013 ◽  
Author(s):  
Claudia Gonzaga-Jauregui
Keyword(s):  
Human Genome ◽  
Genetic Disorders ◽  
Copy Number Variants ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Genomic Technologies ◽  
Genome Wide ◽  
Genome Analyses ◽  
Next Generation Sequencing Ngs

Current genome-wide technologies allow interrogation and exploration of the human genome as never before. Next-generation sequencing (NGS) technologies, along with high resolution Single Nucleotide Polymorphisms (SNP) arrays and array Comparative Genomic Hybrization (aCGH) enable assessment of human genome variation at the finest resolution from base pair changes such as simple nucleotide variants (SNVs) to large copy-number variants (CNVs). The application of these genomic technologies in the clinical setting has also enabled the molecular characterization of genetic disorders and the understanding of the biological functions of more genes in human development, disease, and health. In this review, the current approaches and platforms available for high-throughput human genome analyses, the steps involved in these different methodologies from sample preparation to data analysis, their applications, and limitations are summarized and discussed.

scholarly journals Overview of Genomic Tools for Circular Visualization in next-Generation Genomic Sequencing Era

2018 ◽  
Author(s):  
Alisha Parveen ◽  
Sukank Khurana ◽  
Abhishek Kumar
Keyword(s):  
Human Genome ◽  
Genome Sequencing ◽  
Genomic Sequencing ◽  
Next Generation ◽  
Sequencing Data ◽  
The Third ◽  
Genomic Tools ◽  
Rapid Changes ◽  
Human Genome Sequencing ◽  
Visualization Tools

After human genome sequencing and rapid changes in genome sequencing methods, we have entered in the era of rapidly accumulating genome-sequencing data. This has poses development of several types of methods for representing results of genome sequencing data. Circular genome visualizations tools are also critical in this area as they provide rapid interpretation and simple visualization of overall data. In the last 15 years, we have seen rapid changes in circular visualization tools after the development of the circos tool with 1–2 tools published per year. Herein we have summarized and revisited all these tools until the third quarter of 2018. 

Array-CGH Analysis of T-ALL Patients and Cell Lines.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4469-4469
Author(s):  
Idoya Lahortiga ◽  
Carlos Graux ◽  
Nicole Mentens ◽  
Katrien Van Roosbroeck ◽  
Kim De Keersmaecker ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Human Genome ◽  
Cell Lines ◽  
Tyrosine Kinases ◽  
Array Cgh ◽  
Genetic Alterations ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Protein Tyrosine ◽  
A Genome

Abstract Background Molecular analysis of T-cell acute lymphoblastic leukemia (T-ALL) has provided evidence that a stepwise alteration of at least four specific pathways is required during transformation of thymocytes to leukemic T-cells. Genetic alterations in hematopoietic precursor cells lead to loss of cell cycle control, impaired differentiation, proliferation and survival advantages, and unlimited self-renewal capacity. These defects include inactivation of CDKN2A (P16) present in 96 % of the patients, deregulated expression of transcription factors, and mutation of NOTCH1 in 56% of patients. However, the molecular lesions leading to the proliferative and survival advantages of T-ALL cells are less well characterized, remaining unknown in 80 % of the T-ALLs. Aims Our aim was to set up a genome-wide analysis of T-ALL in order to detect cryptic deletions and amplifications, with a special focus on the 90 protein tyrosine kinase genes present in the human genome. Methods We used the array-CGH (micro-array comparative genomic hybridization) technology with slides containing genomic BAC probes spaced every 1 Mb over the human genome. An additional 480 probes were added covering the genomic locations of each of the 90 protein tyrosine kinases genes. A total of 27 T-ALL cases and 12 cell lines were included in the study. Results An interstitial deletion on chromosome 9p24 directly upstream of JAK2 was identified in one patient. The deletion was confirmed by FISH. Quantitative PCR (qPCR) analyses indicated that the deletion was 700 kb in size including exons 1–4 of JAK2. In two cell lines, deletions affecting ALK and ERBB4 were detected. Molecular analyses to characterize the possible presence of fusion transcripts involving tyrosine kinases are in progress. We did not detected other rearrangements involving tyrosine kinase genes in neither of the 26 other T-ALL cases nor in the 10 cell lines, indicating that cryptic deletions or amplifications involving tyrosine kinase genes are relatively rare in T-ALL. The most frequent aberration was the deletion of CDKN2A (16/27 cases and 9/12 cell lines) ranging from only one clone to almost the complete 9p arm. MYB duplication was found in two cases and 4 cell lines, and was confirmed by qPCR and FISH analysis. Two of the 4 cell lines had overexpression of MYB detected by qPCR, which can interfere with apoptosis enhancing the survival of the cells, as has been previously described. PTEN deletion was present in one case and one cell line. Other unbalanced aberrations of various size were detected: del (2p) in 5/12 cell lines, del (5q) in 1/27 samples and 4/12 cell lines, del(6q) in 3/27 samples and 2/12 cell lines, or del(9p) in 5/27 samples and 4/12 cell lines. Some of these rearrangements were not observed by standard cytogenetics. Strikingly, cell lines had significantly more chromosomal abnormalities than primary T-ALL cases. Conclusions We detected a novel cryptic rearrangement of JAK2 in one T-ALL case, and duplication of MYB in two T-ALL cases (2/27; 7.5%) and four cell lines (4/12; 33%). Our results suggest that cryptic deletions or amplifications involving tyrosine kinase genes are relatively rare in T-ALL.

scholarly journals Overview of Genomic Tools for Circular Visualization in the Nextgeneration Genomic Sequencing Era

2019 ◽  
Vol 20 (2) ◽  
pp. 90-99 ◽  
Author(s):  
Alisha Parveen ◽  
Sukant Khurana ◽  
Abhishek Kumar
Keyword(s):  
Human Genome ◽  
Genome Sequencing ◽  
Genomic Sequencing ◽  
Sequencing Data ◽  
The Third ◽  
Genomic Tools ◽  
Genome Visualization ◽  
Rapid Changes ◽  
Human Genome Sequencing ◽  
Visualization Tools

After human genome sequencing and rapid changes in genome sequencing methods, we have entered into the era of rapidly accumulating genome-sequencing data. This has derived the development of several types of methods for representing results of genome sequencing data. Circular genome visualization tools are also critical in this area as they provide rapid interpretation and simple visualization of overall data. In the last 15 years, we have seen rapid changes in circular visualization tools after the development of the circos tool with 1-2 tools published per year. Herein we have summarized and revisited all these tools until the third quarter of 2018.

Array-Based Comparative Genomic Hybridization for Genome-Wide Analysis of DNA Copy Number in Myelodysplastic Syndromes.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3420-3420
Author(s):  
Masashi Sanada ◽  
Yasuhito Nanya ◽  
Akira Hangaishi ◽  
Noriko Hosoya ◽  
LiLi Wang ◽  
...  
Keyword(s):  
Human Genome ◽  
Tumor Cells ◽  
Copy Number ◽  
Large Scale ◽  
Array Cgh ◽  
Chromosomal Abnormalities ◽  
Comparative Genomic ◽  
Normal Cells ◽  
Genome Wide Analysis ◽  
Genome Wide

Abstract Myelodysplastic syndrome(MDS)is a clonal disorder of hematopoietic stem cells characterized by ineffective hematopoiesis and propensity to acute myeloid leukemias. The conversion of a normal stem cell into a preleukemic and ultimately leukemic state is thought to be a multistep process requiring accumulation of a number of genetic changes. Conventional cytogenetic analysis has disclosed a number of chromosome abnormalities common to MDS and provided valuable clues to characterize these genetic lesions, rarity of balanced translocations and relative predominance of unbalanced abnormalities in MDS, including gene deletions and amplifications. However conventional analytical methods provide only limited resolutions of analysis for identification of genetic gains and losses and prevent further molecular delineation of relevant genes to the pathogenesis of MDS.</PRE> Array-based comparative genomic hybridization (CGH) is a robust technique to enable rapid and comprehensive genome-wide analysis of genetic aberrations in cancers, in which differentially labeled DNAs from both tumor and normal samples are comparatively hybridized to a large number of genomic DNAs. In this study, we constructed a high-quality array-based CGH system for genome-wide analysis of chromosomal abnormalities to identify candidate target genes of MDS. Our whole genome arrays consisted of 3,300 BAC/PAC clones, thus having an average resolution of 1.0 Mb over the whole human genome. Each clone was amplified with degenerated oligonucleotide primed-PCR (DOP-PCR) and the amplified products were spotted in duplicate grids onto aminosilan-coated glass slides. For more high-resolution analysis, we employed the GeneChip Mapping 100k arrays (Affymetrix), originally developed for large-scale SNP typing, as a tool for detection of copy number changes in selected MDS cases. It contains 116,204 different SNPs on two separate arrays, covering the whole human genome with an average resolution of 21 kb. With this arrays DNA copy number’s changes could be estimated by comparing intensity of SNP signals of tumor cells with that of normal cells from the same patients. In addition, using paired samples from tumor cells and normal cells, large-scale LOH analysis became also possible.</PRE> In total, 54 MDS samples were analyzed using our array CGH system. In addition to large chromosomal changes, including loss of 5q, 7q, 13q, and 20q, and gain of the whole chromosome 8, a number of small, cryptic chromosomal abnormalities were identified that would escape from conventional cytogenetic detection. Many of these abnormalities were represented only by a single PAC/BAC clone. In several chromosome regions, including 3q13, 5p15, 13p33, and 20q12, there existed commonly deleted regions, which could be confirmed by FISH analysis. Similarly gains of genetic materials were found on 8p23 and 17p13. Several genes were identified within these regions that may be candidates for relevant genes to these genetic alterations. In conclusion, genome-profiling using array CGH techniques were highly useful tools for delineating the pathogenesis of MDS.</PRE>

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