Abstract:
:In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggregation Consortium (ExAC) data to show that sample size and ratio interact to influence the number of these singletons identified in a cohort. These interactions are different across ancestries and can lead to the same number of identified singletons in both Europeans and non-Europeans without an equal number of samples. We conclude that there is a need to account for the ancestry-specific influence of demography on genomic architecture and rare variant analysis in order to address inequalities in medical genomic analysis.The authors of the original article were invited to submit a response, but declined to do so. Please see related Open Letter: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1016-y.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Kessler MD,O'Connor TDdoi
10.1186/s13059-017-1172-8subject
Has Abstractpub_date
2017-02-27 00:00:00pages
42issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-017-1172-8journal_volume
18pub_type
评论,信件相关文献
GENOME BIOLOGY文献大全abstract::Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-4-109
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1701-8
更新日期:2019-05-20 00:00:00
abstract::A report on the 64th annual American Society of Human Genetics meeting held in San Diego, USA, 18-22 October, 2014. ...
journal_title:Genome biology
pub_type:
doi:10.1186/s13059-014-0562-4
更新日期:2014-12-17 00:00:00
abstract:BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...
journal_title:Genome biology
pub_type: 杂志文章,随机对照试验
doi:10.1186/gb-2013-14-4-r34
更新日期:2013-04-29 00:00:00
abstract:BACKGROUND:Processed copies of genes (retrogenes) are duplicate genes that originated through the reverse-transcription of a host transcript and insertion in the genome. This type of gene duplication, as any other, could be a source of new genes and functions. Using whole genome sequence data for 12 Drosophila species,...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-1-r11
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/PREACCEPT-1067113631444973
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0655-8
更新日期:2015-04-30 00:00:00
abstract::A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb4179
更新日期:2014-01-01 00:00:00
abstract::A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2008-9-2-302
更新日期:2008-01-01 00:00:00
abstract::Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2000-1-3-reviews0003
更新日期:2000-01-01 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:BACKGROUND:The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1173-7
更新日期:2017-03-10 00:00:00
abstract::We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-12-research0081
更新日期:2002-01-01 00:00:00
abstract::A new study shows that genomic introgression between two Heliconius butterfly species is not solely confined to color pattern loci. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-016-0898-z
更新日期:2016-02-27 00:00:00
abstract::Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare o...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1538-6
更新日期:2018-10-08 00:00:00
abstract::CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single o...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02174-1
更新日期:2020-10-20 00:00:00
abstract::A central goal of biogerontology is to identify robust gene-expression biomarkers of aging. Here we develop a method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. Tested on Caenorhabditis elegans, our algorithm yields better biomar...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-2-r13
更新日期:2010-01-01 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:Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-1-r7
更新日期:2011-01-01 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:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1795-z
更新日期:2019-09-09 00:00:00
abstract:BACKGROUND:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-6-r79
更新日期:2014-06-19 00:00:00
abstract:BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-9-r180
更新日期:2007-01-01 00:00:00
abstract::Following publication of the original article [1], the authors reported the following errors. ...
journal_title:Genome biology
pub_type: 杂志文章,已发布勘误
doi:10.1186/s13059-019-1668-5
更新日期:2019-03-11 00:00:00
abstract::The majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. This large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct TIR-domain-containing (TNL) and CC-domain-containing (CNL) subfamilies. The...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-4-212
更新日期:2006-01-01 00:00:00
abstract::MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0500-5
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target gene...
journal_title:Genome biology
pub_type: 杂志文章,meta分析
doi:10.1186/gb-2004-5-9-r66
更新日期:2004-01-01 00:00:00
abstract::Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc http://mousecyc.jax.org. MouseCy...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-8-r84
更新日期:2009-01-01 00:00:00
abstract::mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-5-r90
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02131-y
更新日期:2020-09-07 00:00:00