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Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks.

ABSTRACT: The growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiation (HDIR) is well documented, the detrimental effects of LDIR is not well understood and has been a topic of much debate. Since little is known about the effects of LDIR, various kinds of wet-lab and computational analyses are required to advance knowledge in this domain. In this paper we carry out an "upside-down pyramid" form of systems biology analysis of microarray data. We characterised the global genomic response following 10 cGy (low dose) and 100 cGy (high dose) doses of X-ray ionising radiation at four time points by analysing the topology of gene coexpression networks. This study includes a rich experimental design and state-of-the-art computational systems biology methods of analysis to study the differences in the transcriptional response of skin cells exposed to low and high doses of radiation.Using this method we found important genes that have been linked to immune response, cell survival and apoptosis. Furthermore, we also were able to identify genes such as BRCA1, ABCA1, TNFRSF1B, MLLT11 that have been associated with various types of cancers. We were also able to detect many genes known to be associated with various medical conditions.Our method of applying network topological differences can aid in identifying the differences among similar (eg: radiation effect) yet very different biological conditions (eg: different dose and time) to generate testable hypotheses. This is the first study where a network level analysis was performed across two different radiation doses at various time points, thereby illustrating changes in the cellular response over time.

SUBMITTER: Ray M

PROVIDER: S-EPMC3443446 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature

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Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks.

Ray Monika M Yunis Reem R Chen Xiucui X Rocke David M DM

BMC genomics 20120517

<h4>Background</h4>The growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiation (HDIR) is well documented, the detrimental effects of LDIR is not well understood and has been a topic of much debate. Since little is known about the effects of LDIR, various kinds of wet-lab and computational analyses are required to advance knowledge in this domain. In this paper we carry out ...[more]

PMID: 22594378

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Project description:ObjectiveFew studies have explored the clinical feasibility of using deep-learning reconstruction to reduce the radiation dose of CT. We aimed to compare the image quality and lung nodule detectability between chest CT using a quarter of the low dose (QLD) reconstructed with vendor-agnostic deep-learning image reconstruction (DLIR) and conventional low-dose (LD) CT reconstructed with iterative reconstruction (IR).Materials and methodsWe retrospectively collected 100 patients (median age, 61 years [IQR, 53-70 years]) who received LDCT using a dual-source scanner, where total radiation was split into a 1:3 ratio. QLD CT was generated using a quarter dose and reconstructed with DLIR (QLD-DLIR), while LDCT images were generated using a full dose and reconstructed with IR (LD-IR). Three thoracic radiologists reviewed subjective noise, spatial resolution, and overall image quality, and image noise was measured in five areas. The radiologists were also asked to detect all Lung-RADS category 3 or 4 nodules, and their performance was evaluated using area under the jackknife free-response receiver operating characteristic curve (AUFROC).ResultsThe median effective dose was 0.16 (IQR, 0.14-0.18) mSv for QLD CT and 0.65 (IQR, 0.57-0.71) mSv for LDCT. The radiologists' evaluations showed no significant differences in subjective noise (QLD-DLIR vs. LD-IR, lung-window setting; 3.23 ± 0.19 vs. 3.27 ± 0.22; P = .11), spatial resolution (3.14 ± 0.28 vs. 3.16 ± 0.27; P = .12), and overall image quality (3.14 ± 0.21 vs. 3.17 ± 0.17; P = .15). QLD-DLIR demonstrated lower measured noise than LD-IR in most areas (P < .001 for all). No significant difference was found between QLD-DLIR and LD-IR for the sensitivity (76.4% vs. 72.2%; P = .35) or the AUFROCs (0.77 vs. 0.78; P = .68) in detecting Lung-RADS category 3 or 4 nodules. Under a noninferiority limit of -0.1, QLD-DLIR showed noninferior detection performance (95% CI for AUFROC difference, -0.04 to 0.06).ConclusionQLD-DLIR images showed comparable image quality and noninferior nodule detectability relative to LD-IR images.

Dataset Information

Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks.

Publications

Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks.

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