Ionising radiation and genetic risks. XVI. A genome-based framework for risk estimation in the light of recent advances in genome research

2010 ◽  
Vol 87 (2) ◽  
pp. 161-178 ◽  
Author(s):  
Krishnaswami Sankaranarayanan ◽  
Hooshang Nikjoo
Keyword(s):  
Risk Estimation ◽  
Ionising Radiation ◽  
Genome Research ◽  
Recent Advances ◽  
A Genome ◽  
Genetic Risks

scholarly journals GSER (a Genome Size Estimator using R): a pipeline for quality assessment of sequenced genome libraries through genome size estimation

2021 ◽  
Vol 11 (4) ◽  
pp. 20200077 ◽  
Author(s):  
Braulio Valdebenito-Maturana ◽  
Gonzalo Riadi
Keyword(s):  
Quality Control ◽  
Quality Assessment ◽  
Genome Size ◽  
De Novo ◽  
Second Step ◽  
Size Estimation ◽  
Genome Research ◽  
A Genome ◽  
The Relationship ◽  
Assembly Software

The first step in any genome research after obtaining the read data is to perform a due quality control of the sequenced reads. In a de novo genome assembly project, the second step is to estimate two important features, the genome size and ‘best k -mer’, to start the assembly tests with different de novo assembly software and its parameters. However, the quality control of the sequenced genome libraries as a whole, instead of focusing on the reads only, is frequently overlooked and realized to be important only when the assembly tests did not render the expected results. We have developed GSER, a Genome Size Estimator using R, a pipeline to evaluate the relationship between k -mers and genome size, as a means for quality assessment of the sequenced genome libraries. GSER generates a set of charts that allow the analyst to evaluate the library datasets before starting the assembly. The script which runs the pipeline can be downloaded from http://www.mobilomics.org/GSER/downloads or http://github.com/mobilomics/GSER .

scholarly journals Epigenetic regulation and epigenomic landscape in rice

2016 ◽  
Vol 3 (3) ◽  
pp. 309-327 ◽  
Author(s):  
Xian Deng ◽  
Xianwei Song ◽  
Liya Wei ◽  
Chunyan Liu ◽  
Xiaofeng Cao
Keyword(s):  
Epigenetic Regulation ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Food Crop ◽  
Recent Advances ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Epigenetic Regulators ◽  
Complex Genome

Abstract Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.

scholarly journals Exposure to low-dose ionising radiation from cardiac catheterisation and risk of cancer: the COCCINELLE study cohort profile

BMJ Open ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. e048576
Author(s):  
Kossi Dovene Abalo ◽  
Sophie Malekzadeh-Milani ◽  
Sébastien Hascoët ◽  
Serge Dreuil ◽  
Tiphaine Feuillet ◽  
...  
Keyword(s):  
Low Dose ◽  
Risk Estimation ◽  
Ionising Radiation ◽  
Cardiac Catheterisation ◽  
Response Analysis ◽  
Study Cohort ◽  
Red Bone Marrow ◽  
Cns Tumours ◽  
Set Up ◽  
Risk Of Cancer

PurposeThe COCCINELLE study is a nationwide retrospective French cohort set up to evaluate the risk of cancer in patients who undergone cardiac catheterisation (CC) procedures for diagnosis or treatment of congenital heart disease during childhood.ParticipantsChildren who undergone CC procedures from 1 January 2000 to 31 December 2013, before the age of 16 in one of the 15 paediatric cardiology departments which perform paediatric CC in mainland France were included. The follow-up started at the date of the first recorded CC procedure until the exit date, that is, the date of death, the date of first cancer diagnosis, the date of the 18th birthday or the 31 December 2015, whichever occurred first. The cohort was linked to the National Childhood Cancer Registry to identify patients diagnosed with cancer and with the French National Directory for the Identification of Natural Persons to retrieve the patients’ vital status.Findings to dateA total of 17 104 children were included in the cohort and followed for 110 335 person-years, with 22 227 CC procedures collected. Among the patients, 81.6% received only one procedure. Fifty-nine cancer cases were observed in the cohort. Standardised incidence ratios (SIRs) were increased for all-cancer (SIR=3.8, 95% CI: 2.9 to 4.9), leukaemia (SIR=3.3, 95% CI: 2.0 to 5.4), lymphoma (SIR=14.9, 95% CI: 9.9 to 22.5) and solid cancers excluding central nervous system (CNS) tumours (SIR=3.3, 95% CI: 2.0 to 5.5) compared with the general population.Future plansDose reconstruction is currently underway to estimate individual cumulative doses absorbed to relevant organs, including red bone marrow and brain for respectively haematologic disorders and CNS tumours risk estimation. A dose–response analysis will be conducted with consideration to confounding factors such as age at exposure, gender, predisposing factors to cancer and other sources of medical diagnostic low-dose ionising radiation.

Sign in / Sign up

Export Citation Format

Share Document