scholarly journals BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data

2020 ◽  
Author(s):  
Dengwei Zhang ◽  
Hai-Xi Sun ◽  
Ziheng Zhou ◽  
Xiaosen Jiang ◽  
Dongsheng Chen ◽  
...  
Keyword(s):  
Birth Defects ◽  
Birth Defect ◽  
High Throughput Sequencing ◽  
Infant Health ◽  
Data Sets ◽  
Omics Data ◽  
Related Data ◽  
Circulating Free Dna ◽  
The World ◽  
Next Generation Sequencing Ngs

ABSTRACTBirth defect, not only poses a major challenge for infant health but also attracts the attention of countless people in the world. Chromosome abnormality directly results in diverse birth defects which are generally deleterious and even lethal. Therefore, gaining molecular regulatory insights into these diseases is important and necessary for effective prenatal screening. Recently, with the advance of next-generation sequencing (NGS) techniques, a myriad of treatises and data associated with these diseases are now constantly produced from different laboratories across the world. To meet the increasing requirements for birth-related data resources, we developed a birth defect multi-omics database (BDdb), freely accessible at http://t21omics.cngb.org and consisting of multi-omics data, circulating free DNA (cfDNA) data, as well as diseases biomarkers. Omics data sets from 138 GSE samples, 5271 GSM samples and 328 entries, and more than 2000 biomarkers of 22 birth-defect diseases in 5 different species were integrated into BDdb, which provides a user-friendly interface for searching, browsing and downloading selected data. Additionally, we re-analyzed and normalized the raw data so that users can also customize the analysis using the data generated from different sources or different High-Throughput Sequencing (HTS) methods. To our knowledge, BDdb is the first comprehensive database associated with birth-defect-related diseases. which would benefit the diagnosis and prevention of birth defects.

scholarly journals BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dengwei Zhang ◽  
Si Zhou ◽  
Ziheng Zhou ◽  
Xiaosen Jiang ◽  
Dongsheng Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Birth Defects ◽  
Birth Defect ◽  
Infant Health ◽  
Expression Patterns ◽  
Gene Expression Omnibus ◽  
Omics Data ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Underlying Mechanisms ◽  
User Friendly

Abstract Background Birth defects pose a major challenge to infant health. Thus far, however, the causes of most birth defects remain cryptic. Over the past few decades, considerable effort has been expended on disclosing the underlying mechanisms related to birth defects, yielding myriad treatises and data. To meet the increasing requirements for data resources, we developed a freely accessible birth defect multi-omics database (BDdb, http://t21omics.cngb.org) consisting of multi-omics data and potential disease biomarkers. Results In total, omics datasets from 136 Gene Expression Omnibus (GEO) Series records, including 5245 samples, as well as 869 biomarkers of 22 birth defects in six different species, were integrated into the BDdb. The database provides a user-friendly interface for searching, browsing, and downloading data of interest. The BDdb also enables users to explore the correlations among different sequencing methods, such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) from different studies, to obtain the information on gene expression patterns from diverse aspects. Conclusion To the best of our knowledge, the BDdb is the first comprehensive database associated with birth defects, which should benefit the diagnosis and prevention of birth defects.

scholarly journals Integrated Genome Browser: visual analytics platform for genomics

2015 ◽  
Author(s):  
Nowlan H. Freese ◽  
David C. Norris ◽  
Ann E. Loraine
Keyword(s):  
Open Source ◽  
Visual Analytics ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Genomic Data ◽  
Genome Browser ◽  
Data Availability ◽  
Data Sets ◽  
Related Data ◽  
Genome Scale

Motivation: Genome browsers that support fast navigation and interactive visual analytics can help scientists achieve deeper insight into large-scale genomic data sets more quickly, thus accelerating the discovery process. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Results: Here we describe multiple updates to IGB, including all-new capability to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of data sets from RNA-Seq, ChIP-Seq, and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related data sets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation, and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. Availability: IGB is open source and is freely available from http://bioviz.org/igb.

Novel Visualization of Large Health Related Data Sets

2015 ◽  
Author(s):  
William E. Hammond ◽  
Vivian L. West ◽  
David Borland ◽  
Igor Akushevich ◽  
Eugenia M. Heinz
Keyword(s):  
Data Sets ◽  
Related Data ◽  
Health Related

scholarly journals Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 794
Author(s):  
Cullen Horstmann ◽  
Victoria Davenport ◽  
Min Zhang ◽  
Alyse Peters ◽  
Kyoungtae Kim
Keyword(s):  
Carbon Nanotubes ◽  
Quantum Dots ◽  
High Throughput Sequencing ◽  
The Body ◽  
Rna Seq ◽  
Mechanisms Of Toxicity ◽  
Promising Tool ◽  
Engineered Nanomaterial ◽  
Next Generation Sequencing Ngs ◽  
Transcriptomic Changes

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

scholarly journals Periconceptional folic acid intake in Northwest Russia: a birth registry study

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
V A Postoev ◽  
L I Menshikova ◽  
A A Usynina ◽  
A M Grjibovski ◽  
J O Odland
Keyword(s):  
Folic Acid ◽  
Birth Defects ◽  
Birth Defect ◽  
Demographic Factors ◽  
Folic Acid Supplementation ◽  
Demographic Characteristics ◽  
Prenatal Counseling ◽  
Folic Acid Intake ◽  
Birth Registry ◽  
Socio Demographic Factors

Abstract Introduction Periconceptional use of folic acid supplementation is an evidence-based measure of birth defects prevention. The study was aimed to assess effect of periconceptual use of folic acid on birth defect prevalence in Arkhangelsk county and to investigate socio-demographic factors, which are associated with adherence to this preventive measure. Methods A registry-based study was conducted with data from the Arkhangelsk County Birth Registry for 2012-2015. The study population included 57084 pregnancies to calculate the proportion of women taking folic acid and 53340 pregnancy outcomes without missing data to analyze related socio-demographic characteristics. Results The proportion of women followed a folic acid supplementation before pregnancy was 1.3% (95% CI: 1.2-1.4), during pregnancy - 55.8% (95%CI: 54.6-56.4). Such women had less risk to deliver a newborn with any birth defects (OR = 0,84, 95%CI: 0,75 - 0,95). Considering birth defects prevalence of 38,6 per 1000 newborns in Arkhangelsk county, number needed to prevent one case of birth defect was 142,9. Based on multivariate analysis, nulliparous married women with higher education, aged 30 or more, had a higher chance to use folic acid before and during pregnancy. The history of spontaneous abortion in the mother's medical history and the first pregnancy were negatively associated with the probability of folic acid intake both before and during pregnancy. Conclusions The compliance to periconceptional intake of folic acid among women in the region was low. A level of compliance was associated with such socio-demographic factors as age, education, marital status, gravidity and parity. The findings have direct applications in improving prenatal care in Arkhangelsk county and establishing targets for prenatal counseling. Key messages A level of compliance to primary prevention of birth defects is associated with such socio-demographic factors as age, education, marital status, gravidity and parity. Prenatal counseling in terms of birth defects prevention should be based on socio-demographic characteristics of pregnant women.

Belief Movement, Uncertainty Reduction, and Rational Updating*

2021 ◽  
Author(s):  
Ned Augenblick ◽  
Matthew Rabin
Keyword(s):  
Statistical Tests ◽  
Uncertainty Reduction ◽  
The State ◽  
Data Sets ◽  
New Information ◽  
The World ◽  
Core Concepts ◽  
Market Beliefs ◽  
Over Time

Abstract When a Bayesian learns new information and changes her beliefs, she must on average become concomitantly more certain about the state of the world. Consequently, it is rare for a Bayesian to frequently shift beliefs substantially while remaining relatively uncertain, or, conversely, become very confident with relatively little belief movement. We formalize this intuition by developing specific measures of movement and uncertainty reduction given a Bayesian’s changing beliefs over time, showing that these measures are equal in expectation and creating consequent statistical tests for Bayesianess. We then show connections between these two core concepts and four common psychological biases, suggesting that the test might be particularly good at detecting these biases. We provide support for this conclusion by simulating the performance of our test and other martingale tests. Finally, we apply our test to data sets of individual, algorithmic, and market beliefs.

Efficient High-throughput Techniques for the Analysis of Disease-Resistant Plant Varieties and Detection of Food Adulteration

2021 ◽  
Vol 23 ◽  
Author(s):  
Romesh Kumar Salgotra ◽  
Rafiq Ahmad Bhat ◽  
Deyue Yu ◽  
Javaid Akhter Bhat
Keyword(s):  
Multiplex Pcr ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Crop Improvement ◽  
Small Sample ◽  
Food Crops ◽  
Genomic Resources ◽  
Breeding Programmes ◽  
Next Generation Sequencing Ngs

Abstract: Over the past two decades, the advances in the next generation sequencing (NGS) platforms have led to the identification of numerous genes/QTLs at high-resolution for their potential use in crop improvement. The genomic resources generated through these high-throughput sequencing techniques have been efficiently used in screening of particular gene of interest particularly for numerous types of plant stresses and quality traits. Subsequently, the identified-markers linked to a particular trait have been used in marker-assisted backcross breeding (MABB) activities. Besides, these markers are also being used to catalogue the food crops for detection of adulteration to improve the quality of food. With the advancement of technologies, the genomic resources are originating with new markers; however, to use these markers efficiently in crop breeding, high-throughput techniques (HTT) such as multiplex PCR and capillary electrophoresis (CE) can be exploited. Robustness, ease of operation, good reproducibility and low cost are the main advantages of multiplex PCR and CE. The CE is capable of separating and characterizing proteins with simplicity, speed and small sample requirements. Keeping in view the availability of vast data generated through NGS techniques and development of numerous markers, there is a need to use these resources efficiently in crop improvement programmes. In summary, this review describes the use of molecular markers in the screening of resistance genes in breeding programmes and detection of adulterations in food crops using high-throughput techniques.

Pregnancy Experience after Delivery of a Child with a Major Birth Defect: A Population Study

PEDIATRICS ◽  
1995 ◽  
Vol 95 (1) ◽  
pp. 59-65
Author(s):  
Margarett K. Davis ◽  
Muin J. Khoury ◽  
J. David Erickson
Keyword(s):  
Birth Defects ◽  
Reproductive Behavior ◽  
Birth Defect ◽  
Large Population ◽  
Population Based ◽  
Subsequent Pregnancy ◽  
Pregnancy Rates ◽  
Wide Range ◽  
First Year Of Life ◽  
And Control

Objective. Data from a large population-based, case-control study were analyzed to determine whether women giving birth to children with major birth defects have different subsequent pregnancy patterns than those giving birth to live-born babies without defects. Other studies examining this phenomenon have been smaller, have not been population-based, or have not addressed the different effects that a wide range of major defects might have on mothers' subsequent pregnancy rates. Methods. Mothers of 4918 infants with major birth defects born from 1968 through 1980 in metropolitan Atlanta were compared with mothers of 3029 control infants, frequency-matched on birth year, birth hospital, and race. Results. The pregnancy rate in the first 3 years after the index birth was higher among case mothers (36%) than among control mothers (30%, P < .0001). This excess was seen for mothers of stillborn case infants (64%) and mothers of case infants who died in infancy (58%), but not for mothers of case infants who survived the first year of life (31%). Pregnancy rates varied by birth defect type. Maternal and infant factors varied among case and control subjects and influenced subsequent pregnancy rates. Conclusion. The reproductive behavior observed in this study supports the theory that mothers of nonsurviving children with birth defects compensate by acting to "replace" the lost child. Reproductive behavior was also strongly associated with having completed a previous pregnancy and by the type of birth defect.

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