Drosophila Duplication 20091218
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ABSTRACT:
PROVIDER: PRJNA122357 | ENA |
REPOSITORIES: ENA
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Project description:In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls. The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)
2011-09-01 | GSE29260 | GEO
Project description:In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls. The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model) 14 lines were used in this study. Each line was represented by 3 array hybridizations, for a total of 42 hybridizations. DNA collected from 30 virgin females.
2011-08-31 | E-GEOD-29260 | biostudies-arrayexpress
Project description:Tandem duplication of carbapenemase genes amplifies the gene copy number and enhances carbapenem resistance. These amplifications are often heterogenous, transient, locate in plasmids, which often also contribute to heteroresistance. The duplication is especially important for low-hydrolysis activity enzymes, which is often overlooked or even under controversy. Here we reported an intrinsic oxacillinase duplication mediated by two neighbor ISAba1inserted in the same orientation. The duplication is relatively stable, located in chromosome, and the duplication times is up to twenty-five, much larger than previous reports. We provided genomic, transcriptomic, and proteomic evidence that the duplication resulted oxacillinase overproduction and thus contribute to carbapenem resistance. No other possible carbapenem resistance related changes (point mutations of oxaAb, disturbed expression of porin protein and efflux pump) were found during the duplication process. Furthermore, introducing oxaAb flanked by two ISAba1 to A. baumannii via plasmids, mimicked the in vivo duplication process under carbapenem stress. Taken together, ISAba1 mediated duplication of low activity intrinsic antibiotic hydrolysis enzymes could lead to antibiotic resistance for advanced-generation antibiotics.
2023-01-17 | PXD039528 |
Project description:Comparative genomic hybridization of strains PN1 (no duplication) and PN1400 (duplication in Chromosome 3)
2018-05-31 | GSE107099 | GEO
Project description:Detection of duplication polymorphisms in the Drosophila simulans genome
| PRJNA140263 | ENA
Project description:ADARp150 prohibits whole genome duplication
| PRJNA1090949 | ENA
Project description:D. yakuba, D. simulans, and D. melanogaster female gDNA hybridized with D. melanogaster male gDNA to assess aCGH as a means of identification of duplicated genes
2009-12-23 | GSE19584 | GEO
Project description:Down syndrome is characterized by trisomy 21 or partial duplication of chromosome 21. There have been extensive studies focusing on the identification of the Down Syndrome Critical Region (DSCR). Our case aims in providing evidence that duplication of 21q21.1-q21.2 is not included in the DSCR and that it has no clinical consequences on the phenotype. Due to missing the appropriate gestational age for serological screening, Non-Invasive Prenatal Testing (NIPT) analysis was performed for a pregnant woman with normal prenatal examinations at 22 weeks of gestation. The result of NIPT revealed a 5.8Mb maternally inherited duplication of 21q21.1-q21.2. To test whether the fetus also carried this duplication, ultrasound-guided amniocentesis was conducted and the result of chromosomal microarray analysis (CMA) with amniotic fluid showed a 6.7Mb duplication of 21q21.1-q21.2 (ranging from position 18,981,715 to 25,707,009) for the fetus. This partial duplication of 21q21.1-q21.2 for the fetus was maternally inherited. The pregnant woman and her family decided to continue the pregnancy after genetic counseling. This case clearly indicates that 21q21.1-q21.2 duplication is not included in the DSCR and most probably has no clinical consequences on the phenotype.
2021-06-05 | GSE176138 | GEO
Project description:Potocki-Shaffer syndrome (PSS) is a rare contiguous gene deletion syndrome marked by haploinsufficiency of genes in chromosomal region 11p11.2p12. Approximately 50 cases of PSS have been reported; however, a syndrome with a PSS-like clinical phenotype caused by 11p11.12p12 duplication has not yet been reported. We first report the 11p11.12p12 duplication in a family with intellectual disability and craniofacial anomalies. 11p11.12p12 duplication syndrome was identified by karyotype analysis. Next-generation sequencing (NGS) analysis clarified the location of the chromosomal variations, which was confirmed by chromosome microarray analysis (CMA). Whole-exome sequencing (WES) was performed to exclude single nucleotide variations (SNVs). The raw data of NGS analysis and WES have been submitted to SRA, the accession number is PRJNA713823.
2021-03-24 | GSE169469 | GEO