Abstract：
BACKGROUND:Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotypes and could have clinical applications. RESULTS:Here, penalized regression models are used to develop DNAm predictors for ten modifiable health and lifestyle factors in a cohort of 5087 individuals. Using an independent test cohort comprising 895 individuals, the proportion of phenotypic variance explained in each trait is examined for DNAm-based and genetic predictors. Receiver operator characteristic curves are generated to investigate the predictive performance of DNAm-based predictors, using dichotomized phenotypes. The relationship between DNAm scores and all-cause mortality (n = 212 events) is assessed via Cox proportional hazards models. DNAm predictors for smoking, alcohol, education, and waist-to-hip ratio are shown to predict mortality in multivariate models. The predictors show moderate discrimination of obesity, alcohol consumption, and HDL cholesterol. There is excellent discrimination of current smoking status, poorer discrimination of college-educated individuals and those with high total cholesterol, LDL with remnant cholesterol, and total:HDL cholesterol ratios. CONCLUSIONS:DNAm predictors correlate with lifestyle factors that are associated with health and mortality. They may supplement DNAm-based predictors of age to identify the lifestyle profiles of individuals and predict disease risk.
journal_name
Genome Bioljournal_title
Genome biologyauthors
McCartney DL,Hillary RF,Stevenson AJ,Ritchie SJ,Walker RM,Zhang Q,Morris SW,Bermingham ML,Campbell A,Murray AD,Whalley HC,Gale CR,Porteous DJ,Haley CS,McRae AF,Wray NR,Visscher PM,McIntosh AM,Evans KL,Deary IJ,Mardoi
10.1186/s13059-018-1514-1subject
Has Abstractpub_date
2018-09-27 00:00:00pages
136issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-018-1514-1journal_volume
19pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract：:Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus cluste...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2004-5-11-r94
更新日期：2004-01-01 00:00:00
abstract：:We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1517-y
更新日期：2018-09-25 00:00:00
abstract：:Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...
journal_title：Genome biology
pub_type： 历史文章,杂志文章,评审
doi：10.1186/s13059-015-0866-z
更新日期：2016-01-11 00:00:00
abstract：:The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask. ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-7-113
更新日期：2003-01-01 00:00:00
abstract：:A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1502-5
更新日期：2018-08-14 00:00:00
abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...
journal_title：Genome biology
pub_type： 评论,信件
doi：10.1186/s13059-015-0709-y
更新日期：2015-07-11 00:00:00
abstract：:Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1610-2
更新日期：2018-12-22 00:00:00
abstract：BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the a...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-4-research0019
更新日期：2002-01-01 00:00:00
abstract：BACKGROUND:Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first com...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-11-r74
更新日期：2003-01-01 00:00:00
abstract：BACKGROUND:Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged dev...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-10-r216
更新日期：2007-01-01 00:00:00
abstract：:The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots. ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-020-02212-y
更新日期：2020-12-08 00:00:00
abstract：:We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-020-02051-x
更新日期：2020-06-16 00:00:00
abstract：BACKGROUND:Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains ma...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-2-r10
更新日期：2003-01-01 00:00:00
abstract：BACKGROUND:Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to obtain and study. We have used gene-expression analysis and polymorphism screening to study molecular senescence of the retina and...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2005-6-6-r48
更新日期：2005-01-01 00:00:00
abstract：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-020-01988-3
更新日期：2020-03-17 00:00:00
abstract：BACKGROUND:Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2008-9-3-r48
更新日期：2008-01-01 00:00:00
abstract：BACKGROUND:Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-016-1080-3
更新日期：2016-10-28 00:00:00
abstract：:How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1618-7
更新日期：2019-01-08 00:00:00
abstract：:The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2004-6-1-r8
更新日期：2005-01-01 00:00:00
abstract：:The functional annotation of proteins identified in genome sequencing projects is based on similarities to homologs in the databases. As a result of the possible strategies for divergent evolution, homologous enzymes frequently do not catalyze the same reaction, and we conclude that assignment of function from sequenc...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2000-1-5-reviews0005
更新日期：2000-01-01 00:00:00
abstract：:Protein kinases with a conserved catalytic domain make up one of the largest 'superfamilies' of eukaryotic proteins and play many key roles in biology and disease. Efforts to identify and classify all the members of the eukaryotic protein kinase superfamily have recently culminated in the mining of essentially complet...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-5-111
更新日期：2003-01-01 00:00:00
abstract：:Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, i...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-4-comment2004
更新日期：2002-01-01 00:00:00
abstract：BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1512-3
更新日期：2018-09-14 00:00:00
abstract：BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-019-1744-x
更新日期：2019-07-12 00:00:00
abstract：:Repeated DNA elements and region-specific protein modifications combine within chromosomes to form a transcriptionally silent chromatin structure called heterochromatin. Recent work in the fission yeast Schizosaccharomyces pombe reveals that RNA is also an integral component of silent heterochromatin, providing a new ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2002-3-12-reviews1035
更新日期：2002-01-01 00:00:00
abstract：:Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. We have developed the uncorrelated shrunken centroid (USC) and error-weighted, uncorrelated shrunken centroid (EWUSC) algorithms...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2003-4-12-r83
更新日期：2003-01-01 00:00:00
abstract：:We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-017-1380-2
更新日期：2018-01-17 00:00:00
abstract：BACKGROUND:Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-10-r222
更新日期：2007-01-01 00:00:00
abstract：:The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2006-7-11-r111
更新日期：2006-01-01 00:00:00
abstract：BACKGROUND:Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases an...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-017-1147-9
更新日期：2017-01-30 00:00:00
