Development and validation of a scalable next-generation sequencing system for assessing recurrent somatic alterations in solid tumors
Jon SherlockScott A. TomlinsAndi K. CaniDaniel H. HovelsonKate RhodesGeoffrey BienJeoffrey SchagemanRajesh GottimukkalaSantoshi BandlaP. Stephen WilliamsBryan JohnsonSeth Sadis
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Solid tumor
Two transgenic cloned sheep from the same somatic cell line and two pregnant sheep,together with the somatic cell line,were genetically analyzed using 10 microsatellite markers from IASG.According to the data obtained in the current experiment,the RCP for cloned sheep and a donor for cloned somatic cell was 99.999%.The genotypes of cloned sheep were same as the donor cell,but different from the pregnant sheep.In conclusion,two cloned sheep were originally come from the donor.
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Somatic fusion
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Development of a ‘gonidialess’/‘somatic regenerator’ double mutant of Volvox carteri was analyzed with a number of cell-type-specific cDNA probes that had been identified in a previous study. Whereas in wild-type strains somatic cells and gonidia (asexual reproductive cells) constitute two distinct cell lineages, in this mutant all cells first differentiate as somatic cells and then redifferentiate as gonidia. During the initial period of somatic differentiation, we found that both gonidial and ‘early’ somatic transcripts were accumulated in the mutant, consistent with the idea that it is the regA gene product (which is defective in this mutant) that normally acts to suppress gonidial gene expression in somatic cells. Later in development, levels of early somatic transcripts fell abruptly, levels of the late somatic transcripts remained extremely low, and levels of gonidial transcripts rose as the cells redifferentiated. Thus it appears that in the mutant cells the gonidial program of development takes over and somatic differentiation is aborted before the stage at which late somatic genes are normally activated. These results provide molecular genetic support for a model which postulates that three types of genes (including the two that are defective in the strain studied here) are crucial for converting the sequential program of differentiation seen in more primitive volvocalean algae to the dichotomous program of germ-soma differentiation that occurs in wild-type V. carteri.
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Somatic fusion
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There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge.In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold.The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells.
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Human genetics
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Two groups of lethal mutations that are expressed only in somatic cells were isolated using the gonosomic selective method. The mutations tend to be organized in clusters along the sex chromosome. Analysis of mutation expression allowed to characterize the degree of changes in genetic diversity of somatic and germ lines in development; it is minimal in the III instar larvae and prepupae and maximal in the I and II instar larvae and pupae.
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SUMMARYBecause of the unique developmental features of higher plants, somatic mutations may enter the germline and be transmitted to the progeny. In the present review, the role of somatic mutations in higher plant evolution is documented by taking into account the following topics: somatic gene mutations and chromosome structural changes; aneusomaty; bud sports; periclinal chimeras; somatic chromosome doubling; virus infection; effects of environment and soil conditions; mutagenic plant products.
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The fusion of somatic cells offers unique prospects for combining plant species that cannot be crossed sexually. This review investigates the involvement and consequences for intergeneric somatic hybridization of various types of somatic incompatibility as a phenomenon analogous to incompatibility and incongruity in sexual crosses. From an extensive survey of the literature on plant as well as vertebrate somatic cell fusion, various intracellular processes have been identified and are discussed as operational sites for somatic incompatibility reactions that interfere with the regular development of somatic hybrid cells and plants. The structural and dynamic instability of chromosomes can explain why many intergeneric fusion products have failed to proliferate continuously. The great complexity of the processes involved in the morphological differentiation of a hybrid plant makes heavy demands on the timing and sychronization of regulatory signals, and thus provides sites of action for somatic incompatibility mechanisms. The enforced coesixtence, in a hybrid cell, of the genomes and the cytoplasmic genophores from the two parents suggests that somatic incompatibility also results from genome-plasmon interactions. Functional plant regeneration from hybrid cells unimpaired by somatic incompatibility is required for agricultural uses of somatic hybridization. In contrast, somatic-cell genetical studies on the complementation, expression, and regulation of cellular traits are possible with non-morphogenic lines, and investigations of the chromosomal assignment, linkage, and segregation of relevant genes actually depend upon somatic incompatibility operating in somatic hybrid cells. Various experimental constraints of previous studies of discussed, and areas have been suggested where future investigations are needed for a further analysis and a better understanding of the mechanisms underlying somatic incompatibility.
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A variety of in vivo mammalian test models are available for screening of chemicals for mutagenicity at the chromosomal level. These models have been grouped into those focusing on somatic cell effects and those dealing with germ cell effects. An analysis of available literature indicates that 76 compounds have been tested from chromosome effects in both somatic and germ cells. Of these, concordant results (positive-positive or negative-negative) were obtained with 58 compounds. Of the remaining 18 compounds with discordant results, all were positive in somatic cells, but negative in germ cell assays. These results suggest an inherent relative insensitivity of germ cells themselves to mutagenic chemicals. In the context of screening for safety evaluation purposes, this analysis suggests that a negative somatic-cell response can be taken as highly predictive of negative results in a germ cell assessment.
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