Relevant bibliographies by topics / Somatic amplification

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Somatic amplification'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Somatic amplification"

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Barsky, A. J., J. D. Goodson, R. S. Lane, and P. D. Cleary. "The amplification of somatic symptoms." Psychosomatic Medicine 50, no. 5 (September 1988): 510–19. http://dx.doi.org/10.1097/00006842-198809000-00007.

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McKenzie, Kirsten J., Ellen Poliakoff, Stephen Puntis, Adam Lawrence, Richard J. Brown, and Donna M. Lloyd. "Investigations into visually-induced somatic amplification." Seeing and Perceiving 25 (2012): 165. http://dx.doi.org/10.1163/187847612x647955.

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Studies into tactile detection have found that a simultaneous light stimulus affects judgments of the presence or absence of a near threshold tactile stimulus, leading to higher numbers of false alarms, whereby participants report feeling a touch in the absence of a stimulus, as well as modest improvements in tactile sensitivity (Lloydet al., 2008; McKenzieet al., 2010, 2012). Anecdotally, the reported intensity of the bi-modal stimuli was also enhanced — an effect that was investigated in the current studies. In Experiment 1 participants discriminated between ‘weak’ and ‘strong’ tactile stimuli, which were accompanied by a light flash on 50% of trials. We observed a bias towards classifying light-present vibrations as ‘strong’ regardless of signal strength, as well as some evidence for improved accuracy in discrimination. In Experiment 2, participants gave a subjective intensity rating on a 6-point scale, which showed an increase in magnitude ratings for both ‘weak’ and ‘strong’ vibrotactile stimuli when the light was present. This shows that a simultaneous light can both improve tactile discrimination and lead to both types of tactile stimulus being rated as stronger. Primary somatosensory cortex may underlie these effects, as it receives direct projections from visual cortex and indirect projections from association areas of the brain. However, it is as yet unclear whether or not these effects are due to the same underlying mechanism, or at which processing stage they occur. Therefore, we are currently exploring the neural underpinnings of this amplification effect using both fMRI and EEG.
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Ramel, C., H. Cederberg, J. Magnusson, E. Vogel, A. T. Natarajan, L. H. Mullender, J. M. Nivard, et al. "Somatic recombination, gene amplification and cancer." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 353, no. 1-2 (June 1996): 85–107. http://dx.doi.org/10.1016/0027-5107(95)00243-x.

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Kosturek, Anna, Robert J. Gregory, Anthony J. Sousou, and Paula Trief. "Alexithymia and Somatic Amplification in Chronic Pain." Psychosomatics 39, no. 5 (September 1998): 399–404. http://dx.doi.org/10.1016/s0033-3182(98)71298-8.

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Minarikova, Petra, Lucie Benesova, Tereza Halkova, Barbora Belsanova, Inna Tuckova, Frantisek Belina, Ladislav Dusek, Miroslav Zavoral, and Marek Minarik. "Prognostic Importance of Cell Cycle Regulators Cyclin D1 (CCND1) and Cyclin-Dependent Kinase Inhibitor 1B (CDKN1B/p27) in Sporadic Gastric Cancers." Gastroenterology Research and Practice 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/9408190.

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Background. Gastric cancer is known for a notable variety in the course of the disease. Clinical factors, such as tumor stage, grade, and localization, are key in patient survival. It is expected that molecular factors such as somatic mutations and gene amplifications are also underlying tumor biological behavior and may serve as factors for prognosis estimation.Aim. The purpose of this study was to examine gene amplifications from a panel of genes to uncover potential prognostic marker candidates.Methods. A panel of gene amplifications including 71 genes was tested by multiplex ligation-dependent probe amplification (MLPA) technique in 76 gastric cancer samples from a Caucasian population. The correlation of gene amplification status with patient survival was determined by the Kaplan-Meier method.Results. The amplification of two cell cycle regulators,CCND1andCDKN1B, was identified to have a negative prognostic role. The medial survival of patients with gastric cancer displaying amplification compared to patients without amplification was 192 versus 725 days forCCND1(P=0.0012) and 165 versus 611 days forCDKN1B(P=0.0098).Conclusion. Gene amplifications ofCCND1andCDKN1Bare potential candidates to serve as prognostic markers for the stratification of patients based on the estimate of survival in the management of gastric cancer patients.
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Wang, X., X. Li, L. Zhang, S. H. Wong, M. H. T. Wang, G. Tse, R. Z. W. Dai, et al. "Oncogenes expand during evolution to withstand somatic amplification." Annals of Oncology 29, no. 11 (November 2018): 2254–60. http://dx.doi.org/10.1093/annonc/mdy397.

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Berezovsky, A. D., A. Transou, S. Irtenkauf, L. Poisson, K. Hank Wu, T. Mikkelsen, and A. deCarvalho. "P11.54 Identification of PDGFRA and MYC(N) as somatic driver genes in Glioblastoma." Neuro-Oncology 21, Supplement_3 (August 2019): iii55—iii56. http://dx.doi.org/10.1093/neuonc/noz126.200.

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Abstract BACKGROUND Somatic oncogene amplification happens frequently in glioblastoma (GBM). The second most frequently amplified gene encoding receptor tyrosine kinases in GBMs is platelet derived growth factor alpha (PDGFRA) (15%). In contrast, MYC and MYCN amplification occurs in 1.6% and 2.9%, respectively. Our goal was to characterize the role of PDGFRɑ and Myc in GBM. MATERIAL AND METHODS Neurosphere cultures were implanted in cohorts of 10–15 nude mice. 5 PDX lines, presenting median survival of 29–59 days were classified as short survivors, and 5 lines with median survival between 104–134 days classified as long survivors. Total RNA was extracted from PDX terminal tumors (3 biological replicates) and sequenced in a paired-end read format. Mouse reads were filtered out using Xenome. MYC and PDGFRA expression patterns were analyzed in tissue microarrays representing duplicated samples from 40 glioma neurosphere-derived PDX lines by IHC (1 anaplastic oligodendroglioma, 8 recurrent GBM with 2 newly diagnosed/recurrent pairs). Normalized staining intensity (MI) and area (A) were quantified using Fiji/ImageJ. RESULTS PDGFRA, MYC, MYCN gene amplifications were represented in a molecularly diverse panel of GBM patient-derived cancer stem-like cells (CSC) and orthotopic mouse xenografts (PDX). Transforming to a normal distribution (log10), 4/13 of cell lines had a PDGFRA mRNA expression (RPKM) higher than 1.5. Similarly, one PDX line had a staining index of greater than 10, 11 (27.5%) had an index between 5–10. The range of intra-tumoral variance, represented by standard deviation, was 0.09–24.25 highlighting the heterogeneity of PDGFRɑ expression. PDGFRɑ phosphorylation (Y754) did not differ between 8 cell lines cultured in NMGF, but deviated in alternate medias without growth factors, supplemented with FBS. In comparison, MYC(N) mRNA expression is only elevated in the context of a known amplification. Furthermore, a a MYC activity signature consisting of 18 target genes was only evident in the 5 amplified CSC lines. Taking advantage of genomic heterogeneity, we have isolated subclones lacking PDGFRA amplification from a PDGFRA amplified GBM CSC. The absence of PDGFRA amplification reduced the self-renewal potential to 37% of the PDGFRA amplified cell population (p=0.001) in clone 1 and 57% in clone 2 (p=0.013). Pertaining to determinants of in vivo survival, MYC was altered in 80% of short survivors (2/5 MYC, 2/5 MYCN amplification) and in 0% of long survivors. Myc signature was highly correlated with in vivo survival (Pearsons’ corr. = -0.77) and MYC gene expression was correlated with in vivo TMZ resistance (corr. = 0.7). CONCLUSION These results suggest that PDGFRɑ expression and activity can occur in the absence of gene amplification, while Myc activity is dependent on gene amplification. Both oncogenes drive oncogenic pathways that should be explored as therapeutic targets.
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Raikar, S. V., C. Bryant, R. Braun, A. J. Conner, and M. C. Christey. "Whole genome amplification from plant cell colonies of somatic hybrids using strand displacement amplification." Plant Biotechnology Reports 1, no. 3 (July 12, 2007): 175–77. http://dx.doi.org/10.1007/s11816-007-0026-3.

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Brocca, Ginevra, Beatrice Poncina, Alessandro Sammarco, Laura Cavicchioli, and Massimo Castagnaro. "KIT Somatic Mutations and Immunohistochemical Expression in Canine Oral Melanoma." Animals 10, no. 12 (December 10, 2020): 2370. http://dx.doi.org/10.3390/ani10122370.

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Canine oral melanoma (COM) is an aggressive neoplasm with a low response to therapies, sharing similarities with human mucosal melanomas. In the latter, significant alterations of the proto-oncogene KIT have been shown, while in COMs only its exon 11 has been adequately investigated. In this study, 14 formalin-fixed, paraffin-embedded COMs were selected considering the following inclusion criteria: unequivocal diagnosis, presence of healthy tissue, and a known amplification status of the gene KIT (seven samples affected and seven non-affected by amplification). The DNA was extracted and KIT target exons 13, 17, and 18 were amplified by PCR and sequenced. Immunohistochemistry (IHC) for KIT and Ki67 was performed, and a quantitative index was calculated for each protein. PCR amplification and sequencing was successful in 97.62% of cases, and no single nucleotide polymorphism (SNP) was detected in any of the exons examined, similarly to exon 11 in other studies. The immunolabeling of KIT was positive in 84.6% of the samples with a mean value of 3.1 cells in positive cases, yet there was no correlation with aberration status. Our findings confirm the hypothesis that SNPs are not a frequent event in KIT activation in COMs, with the pathway activation relying mainly on amplification.
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Joyce, Bryan S., and Pablo A. Tarazaga. "A study of active artificial hair cell models inspired by outer hair cell somatic motility." Journal of Intelligent Material Systems and Structures 28, no. 6 (July 28, 2016): 811–23. http://dx.doi.org/10.1177/1045389x16657425.

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The cochlea displays an important, nonlinear amplification of sound-induced oscillations. In mammals, this amplification is largely powered by the somatic motility of the outer hair cells. The resulting cochlear amplifier has three important characteristics useful for hearing: an amplification of responses from low sound pressures, an improvement in frequency selectivity, and an ability to transduce a broad range of sound pressure levels. These useful features can be incorporated into designs for active artificial hair cells, bio-inspired sensors for use as microphones, accelerometers, or other dynamic sensors. The sensor consists of a cantilever beam with piezoelectric actuators. A feedback controller applies a voltage to the actuators to mimic the outer hair cells’ somatic motility. This article describes three control laws for an active artificial hair cell inspired by models of the outer hair cells’ somatic motility. The first control law is based on a phenomenological model of the cochlea while the second and third models incorporate physiological aspects of the biological cochlea to further improve sensor performance. Simulations show that these models qualitatively reproduce the key aspects of the mammalian cochlea, namely, amplification of oscillations from weak stimuli, higher quality factors, and a wider input dynamic range.
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Dissertations / Theses on the topic "Somatic amplification"

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Hall, Katharyn. "The role of somatic amplification in physical symptom reporting." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/the-role-of-somatic-amplification-in-physical-symptom-reporting(ce112c8e-ee8b-47c9-97e6-0d37bc9dc608).html.

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Despite their apparent ubiquity across healthcare settings medically unexplained symptoms (MUS) remain poorly understood. Theoretical models have proposed several different ways in which altered sensory and perceptual processes may contribute to the development and/or maintenance of MUS. The narrative review presented in Chapter 1 explores sensory and perceptual processes relevant to MUS and physical symptom reporting in general and considers whether current empirical findings lend support to a particular model or hypothesis. One conclusion of the review is that there is a paucity of research using objective methods to measure the putative role of somatic amplification during the perception of physical symptoms, and the influence of negative affect on this process. To address this shortfall, Chapter 2 presents an original study that attempts to test the effect of negative affect on somatic amplification, using a novel paradigm derived from signal detection theory (SDT), the somatic signal discrimination task (SSDiT). On the SSDiT, subjects are required to discriminate between a series of 'weak' and 'strong' vibrations. Nonclinical 'high' and 'low' symptom reporters completed this task prior to and following either a neutral or negative mood induction. Contrary to expectation, there was limited support for differences between symptom reporting groups on the SSDiT task at baseline. However, there was some suggestion that highs and lows may drift differentially on this task over time, such that lows showed a tendency to become more conservative than highs over time. Potential implications for theoretical models are discussed.Finally, Chapter 3 presents a critical evaluation in which the literature review and empirical study are placed within a wider context, allowing implications of the research process as a whole to be drawn out further. This chapter also identifies potential directions for future research, discusses limitations of the present thesis and offers personal reflections about the research process as a whole. This thesis follows the paper-based format, such that Chapters 1 and 2 are formatted as stand-alone papers considered suitable for publication, prepared in accordance with submission requirements for Clinical Psychology Review (Chapter 1) and Journal of Abnormal Psychology respectively (Chapter 2; see Appendix 1 for submission guidelines).
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Jiao, Xiang. "Somatic Mutations in Breast Cancer Genomes : Discovery and Validation of Breast Cancer Genes." Doctoral thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-182319.

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Breast cancer is the most common cancer in women worldwide. However, the genetic alterations that lead to breast cancer are not fully understood. This thesis aims to identify novel genes of potential mechanistic, diagnostic or therapeutic interest in breast cancers by mutational analysis and whole-genome sequencing. In paper I, sequencing of 36 previously identified candidate genes in 96 breast tumors with patient-matched normal DNA determined the somatic mutation prevalence of these candidate genes and identified additional mutations in Notch, NF-κB, PI3K, and Hedgehog pathways as well as in processes mediating DNA methylation, RNA processing and calcium signaling. In paper II, comparison of massively parallel mate-pair sequencing results of a human genome before and after phi29-mediated multiple displacement amplification (MDA) revealed that MDA introduces structural alteration artifacts, with an emphasis on false positive inversions, and impairs the sensitivity to detect true inversions. Therefore, MDA has limited value in sample preparation for whole-genome sequencing for structural alteration detection. In paper III, massively parallel paired-end sequencing identified gene rearrangements in 15 hormone receptor negative breast cancers. Forty validated rearrangements were predicted to directly affect 30 genes, involved in epigenetic regulation, cell mitosis, signalling transduction and glycolytic flux. RNA interference-based assays revealed the potential roles in cell growth of some affected genes, among which DDX10 was implicated to be involved in apoptosis. In paper IV, a method for statistical evaluation of putative translocations detected by massively parallel paired-end sequencing was proposed. In an application of this method to analyse translocations detected by cancer genome deep paired-end sequencing, 76 putative translocations were classified into four categories, with the majority likely to be caused by mismapping due to repetitive regions. Taken together, this thesis provides insights into genes and pathways mutated in sporadic breast cancer genomes, which broaden our understanding of the genetic basis of breast cancer and may ultimately facilitate the diagnosis and treatment of this disease.
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SOARES, CARLOS R. J. "Sintese de prolactina humana em celulas de ovario de hamster chines (CHO)." reponame:Repositório Institucional do IPEN, 2000. http://repositorio.ipen.br:8080/xmlui/handle/123456789/10770.

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Tese (Doutoramento)
IPEN/T
Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN-SP
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Coker, Suzanne Patricia, and s. coker@cqu edu au. "A Positive Psychological Perspective of the Direct and Indirect Influences of Gender Role Schema and the Experience of Childhood Trauma on Psychological, Physical, and Social Well-Being in Adulthood." Central Queensland University. Department of Psychology and Sociology, 2007. http://library-resources.cqu.edu.au./thesis/adt-QCQU/public/adt-QCQU20071016.145424.

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This research assessed psychosocial and cognitive factors influencing well-being, utilising a positive psychological perspective. The theoretical framework of this research was provided by two of the sub-theories of Self-Determination Theory – Basic Needs Theory and Organismic Integration Theory – along with Gender Role Theory, and Beck’s Cognitive Triad, with each of these theories relating differentially to the concept of control or self-determination. More specifically, the current research examined the relationship between gender role schema and the experience of childhood trauma with psychological, physical, and social well-being in adults. Two studies were conducted. Study 1 employed a random sample of 410 participants from Central Queensland, Australia, to develop the World Beliefs Inventory (WBI). This 21-item inventory was developed to assess world beliefs, based on a translation of Aerts et al.’s (1994) philosophical conceptualisation of world beliefs into common terminology. Developing the WBI enabled the assessment of world beliefs, which along with beliefs about oneself (operationalised as perceived control), and the future (dispositional optimism) constitute Beck’s (1976) cognitive triad. Statistical analyses indicated that the inventory provided a good representation of the world beliefs construct, as well as possessing favourable concurrent validity (e.g., positive views regarding the nature of the world were associated with decreased frequency of depressive symptoms experienced, and greater general psychological health and self-esteem). Study 2 was designed to investigate the direct and indirect relationships between gender role schema (masculinity and femininity) and the experience of childhood trauma with psychological, physical, and social well-being, being mediated by (a) the satisfaction of the basic psychological needs for autonomy, competence, and relatedness, (b) beliefs about the world, oneself, and the future, (c) the self-regulation of withholding negative emotion (SRWNE), and (d) somatic amplification. Study 2 employed a separate random sample of 605 participants from Central Queensland. Psychological, physical, and social well-being were each assessed independently to determine whether patterns of significant relationships were similar or different across the different types of well-being. In order to test the theories underlying the structural models of well-being, five hierarchical models of each type of well-being were analysed and compared. Satisfaction of the basic psychological needs for autonomy, competence, and relatedness, and beliefs about the future (dispositional optimism) were found to play a role in the process via which masculinity, femininity, and the experience of childhood trauma influenced all three forms of well-being, while world beliefs were additionally found to influence social well-being, and the SRWNE additionally influenced physical well-being. Results therefore support Basic Needs Theory and provide partial support for Beck’s cognitive triad. They also provide evidence of the utility of the concept of the SRWNE, which was developed in accordance with Organismic Integration Theory.
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Raikar, S. V. "Protoplast fusion of Lolium perenne and Lotus corniculatus for gene introgression." Diss., Lincoln University, 2007. http://hdl.handle.net/10182/301.

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Lolium perenne is one of the most important forage crops globally and in New Zealand. Lotus corniculatus is a dicotyledonous forage that contains valuable traits such as high levels of condensed tannins, increased digestibility, and high nitrogen fixing abilities. However, conventional breeding between these two forage crops is impossible due to their markedly different taxonomic origin. Protoplast fusion (somatic hybridisation) provides an opportunity for gene introgression between these two species. This thesis describes the somatic hybridisation, the regeneration and the molecular analysis of the putative somatic hybrid plants obtained between L. perenne and L. corniculatus. Callus and cell suspensions of different cultivars of L. perenne were established from immature embryos and plants were regenerated from the callus. Of the 10 cultivars screened, cultivars Bronsyn and Canon had the highest percentage of callus induction at 36% each on 5 mg/L 2,4-D. Removal of the palea and lemma which form the seed coat was found to increase callus induction ability of the embryos. Plant regeneration from the callus was achieved when the callus was plated on LS medium supplemented with plant growth regulators at different concentrations. Variable responses to shoot regeneration was observed between the different cultivars with the cv Kingston having the lowest frequency of shoot formation (12%). Different factors affecting the protoplast isolation of L. perenne were investigated. The highest protoplast yield of 10×10⁶ g⁻¹FW was obtained when cell suspensions were used as the tissue source, with enzyme combination 'A' (Cellulase Onozuka RS 2%, Macerozyme R-10 1%, Driselase 0.5%, Pectolyase 0.2%), for 6 h incubation period in 0.6 M mannitol. Development of microcolonies was only achieved when protoplasts were plated on nitrocellulose membrane with a L. perenne feeder layer on PEL medium. All the shoots regenerated from the protoplast-derived calli were albino shoots. The highest protoplast yield (7×10⁶ g⁻¹FW) of L. corniculatus was achieved from cotyledons also with enzyme combination 'A' (Cellulase Onozuka RS 2%, Macerozyme R-10 1%, Driselase 0.5%, Pectolyase 0.2%), for 6 h incubation period in 0.6 M mannitol. The highest plating efficiency for L. corniculatus of 1.57 % was achieved when protoplasts were plated on nitrocellulose membrane with a L. perenne feeder layer on PEL medium. The highest frequency of shoot regeneration (46%) was achieved when calli were plated on LS medium with NAA (0.1 mg/L) and BA (0.1 mg/L). Protoplast fusion between L. perenne and L. corniculatus was performed using the asymmetric somatic hybridisation technique using PEG as the fusogen. L. perenne protoplasts were treated with 0.1 mM IOA for 15 min and L. corniculatus protoplasts were treated with UV at 0.15 J/cm² for 10 min. Various parameters affecting the fusion percentage were investigated. Successful fusions were obtained when the fusions were conducted on a plastic surface with 35% PEG (3350 MW) for 25 min duration, followed by 100 mM calcium chloride treatment for 25 min. A total of 14 putative fusion colonies were recovered. Shoots were regenerated from 8 fusion colonies. Unexpectedly, the regenerated putative hybrid plants resembled L. corniculatus plants. The flow cytometric profile of the putative somatic hybrids resembled that of L. corniculatus. Molecular analysis using SD-AFLP, SCARs and Lolium specific chloroplast microsatellite markers suggest that the putative somatic hybrids could be L. corniculatus escapes from the asymmetric protoplast fusion process. This thesis details a novel Whole Genome Amplification technique for plants using Strand Displacement Amplification technique.
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Bianchi, Joy J. "Origin of somatic mutations in lymphoid cancers : role of the V(D)J recombinase Breakage-fusion-bridge events trigger complex genome rearrangements and amplifications in developmentally arrested T cell lymphomas End donation errors at antigen receptor loci trigger genome-wide instability in ATM-deficient T cell lymphomas." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCB057.

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Les cancers lymphoïdes présentent fréquemment des aberrations chromosomiques. Dans les lymphocytes, cette instabilité génomique peut découler d'une activité anormale de la recombinase V(D)J (i.e. RAG endonuclease), alors que des facteurs de réponse aux dommages à l'ADN (DDR), tels que les protéines Ataxia-telangiectasia mutated (ATM) et p53, sont connus pour empêcher l'apparition de réarrangements chromosomiques et la lymphomagénèse. Le but de ma thèse fut de tester la contribution relative de ces facteurs dans l'émergence des mutations somatiques dans le génome des lymphomes. Pour ce faire, j'ai réalisé du séquençage génome et transcriptome entier de différents lymphomes, issus de modèles murins génétiquement modifiés pour lesquels les activités RAG et DDR étaient altérées. Lors d'une première étude, j'ai identifié des lésions génomiques spécifiques et récurrentes, causées par l'activité « off-target » de RAG et, de manière plus surprenante, un pattern de réarrangements anormaux survenant en l'absence de RAG. J'ai mis en évidence un mécanisme de « Breakage-Fusion-Bridge », en l'absence de RAG, entrainant l'instabilité et l'amplification d'une région génomique s'étendant sur plusieurs mégabases. Plus encore, j'ai également montré que cette amplification mène à son tour à la surexpression de multiples gènes connus ou candidats dans le cancer et se retrouve dans un sous-groupe de leucémies humaines. Afin de rétablir la différentiation des cellules T, bloquée en l'absence des RAG, j'ai utilisé un autre modèle murin exprimant un récepteur des cellules T (TCR) transgéniques. Ce travail a permis de montrer que le stade du développement et l'activité RAG tous les deux déterminent le paysage génomique des lymphomes T et guident la transformation maligne des cellules à travers différentes voies oncogéniques. De plus, j'ai également réalisé la première étude génome entier de lymphomes T déficients pour ATM et ai identifié un nombre important d'anomalies dans ces tumeurs, présentes aux loci des récepteurs aux antigènes mais aussi à des positions ectopiques. Mes résultats suggèrent, qu'en l'absence d'ATM, les cassures de l'ADN induites par les RAG (non réparées ou résolues de manière anormales) déclenchent une instabilité massive au niveau des loci des récepteurs aux antigènes. Cette instabilité se propage ensuite ailleurs dans le génome et affecte des gènes du cancer. De manière plus générale, ma thèse approfondie la compréhension des mécanismes générant des mutations somatiques dans les cancers lymphoïdes, suite à des défauts de recombinaison V(D)J ou de DDR
Lymphoid cancers frequently harbor chromosomal aberrations. Abnormal V(D)J recombinase (i.e RAG endonuclease) activity is thought to promote genomic instability in lymphocytes, while DNA damage response (DDR) factors such as Ataxia-telangiectasia mutated (ATM) and p53 have been shown to suppress aberrant chromosomal rearrangements and lymphomagenesis. During my thesis, to test the relative contribution of these factors in shaping the pattern of somatic mutations in lymphoma genome, I performed whole genome and transcriptome sequencing of several genetically modified mouse lymphoma models in which the activities of RAG and DDR were perturbed. In a first study, I have identified specific recurrent genomic lesions caused by off-target RAG activity and, more surprisingly, a unique pattern of aberrant rearrangements occurring in the absence of RAG. I provided evidence that, in the absence of RAG, Breakage-Fusion-Bridge triggers instability and amplification of a genomic region of several megabases leading to the overexpression of multiple known and putative cancer genes. Importantly, I also showed that this region is found amplified in a subset of human leukemia. Using additional animal models in which blocked T cell differentiation due to the absence of RAG was rescued by the expression of a transgenic T cell receptor, I could demonstrate that both developmental stage and RAG activity determine T cell lymphoma genome landscapes and mediate malignant transformation through distinct oncogenic paths. In addition, I have established the first genome-wide analysis of ATM-deficient T-cell lymphomas and identified a high number of aberrations localized at antigen receptor loci and ectopic locations in these tumors. My results suggest that, in the absence of ATM, aberrantly resolved RAG-induced DNA breaks at antigen receptor loci trigger massive complex rearrangements spreading to ectopic locations and affecting cancer genes. Overall, my studies provide new insights into the mechanisms of somatic mutations arising in lymphoid cancers in the context of aberrant V(D)J recombination and DDR
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Books on the topic "Somatic amplification"

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Williams, Charlotte. The effects of somatic amplification on understanding of medical terminology & utilisaion of the health care system. 1997.

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Book chapters on the topic "Somatic amplification"

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Schimke, Robert T. "Methotrexate Resistance, Gene Amplification, and Somatic Cell Heterogeneity." In The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 117–20. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-5466-3_12.

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Ozias-Akins, P., Z. Tabaeizadeh, D. R. Pring, and I. K. Vasil. "Mitochondrial DNA Amplification in Somatic Hybrid Cells of Grasses." In Progress in Plant Protoplast Research, 267–68. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-009-2788-9_96.

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Schimke, Robert T., David S. Roos, and Peter C. Brown. "[7] Amplification of genes in somatic mammalian cells." In Methods in Enzymology, 85–104. Elsevier, 1987. http://dx.doi.org/10.1016/s0076-6879(87)51010-2.

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"Probes, Allele Mutations, and Restriction Enzymes." In DNA Fingerprinting, edited by Lorne t. Kirby. Oxford University Press, 1993. http://dx.doi.org/10.1093/oso/9780716770015.003.0010.

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Positive identification is the ultimate objective of forensic analysis of blood and other tissue specimens. Nucleotide probes can be very effective tools for detecting genetic markers in this identification process. The genetic markers should be highly polymorphic; allelic variants should be easily and readily detectable; if amplification is required, the alleles should be efficiently amplified using PCR technology; and a statistically sound estimate of the population allele and genotype frequencies should be available. Probes are single-stranded fragments of DNA or RNA containing the complementary code for a specific sequence of genome bases. Probes available for DNA profile analysis will, no doubt, eventually number in the hundreds. Currently, the most valuable detect tandem repetitive sequence fragments either at a specific locus under high-stringency analysis conditions or at numerous loci under low-stringency conditions. Each locus consists of many possible alleles with frequencies that vary depending on the specific population. Other factors also enter into the selection of probes, including ease of amplification, stability, cross-reactivity, and general availability. Rate of allele mutation is also a prime consideration in probe selection. Mutation can be considered at two levels: as the basis for the large number of tandem repeat (VNTR) alleles formed during evolution and as a possible reason for spurious unassignable bands in typing analysis. Although highly unlikely, somatic mutations may be of concern in forensic testing if DNA from different tissues, such as blood and hair roots, are being matched. Germ line (gamete) mutations must be considered when parentage analyses are undertaken. These situations could give rise to false negative results and, therefore, false exclusions. Different considerations also apply for single versus multilocus probes. If a band that is not seen in the putative father is detected in an offspring, the man could incorrectly be excluded if the single-locus probe approach is used. This situation would necessitate testing with more than the usual four or five probes.
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Conference papers on the topic "Somatic amplification"

1

Kim, Duk Joong, David C. Mountain, Allyn E. Hubbard, Christopher A. Shera, and Elizabeth S. Olson. "How Much Do Somatic and Hair Bundle Motility Contribute to Cochlear Amplification?" In WHAT FIRE IS IN MINE EARS: PROGRESS IN AUDITORY BIOMECHANICS: Proceedings of the 11th International Mechanics of Hearing Workshop. AIP, 2011. http://dx.doi.org/10.1063/1.3658161.

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Vincent-Salomon, A., A. Ferrari, X. Pivot, G. Macgrogan, L. Arnould, I. Treilleux, G. Romieux, et al. "Abstract P6-07-13: New insights on HER2 amplification from the constitutional and somatic standpoints: Results from the ICGC and SIGNAL/Phare studies." In Abstracts: Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium; December 8-12, 2015; San Antonio, TX. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.sabcs15-p6-07-13.

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3

Okamoto, Wataru, Takeshi Kuwata, Shingo Matsumoto, Yoichi Naito, Hideaki Takahashi, Kohei Shitara, Yasutoshi Kuboki, et al. "Abstract 2208: Detection of somatic mutations and gene amplifications using amplicon sequencing with biopsy samples from patients with advanced gastric cancer." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-2208.

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