Abstract:
:Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused by a heterozygous deletion of contiguous genes at 7q11.23 mediated by nonallelic homologous recombination (NAHR) between large flanking LCRs and facilitated by a structural variant of the region, a approximately 2-Mb paracentric inversion present in 20%-25% of WBS-transmitting progenitors. We now report that eight out of 180 (4.44%) WBS-transmitting progenitors are carriers of a CNV, displaying a chromosome with large deletion of LCRs. The prevalence of this CNV among control individuals and non-transmitting progenitors is much lower (1%, n=600), thus indicating that it is a predisposing factor for the WBS deletion (odds ratio 4.6-fold, P= 0.002). LCR duplications were found in 2.22% of WBS-transmitting progenitors but also in 1.16% of controls, which implies a non-statistically significant increase in WBS-transmitting progenitors. We have characterized the organization and breakpoints of these CNVs, encompassing approximately 100-300 kb of genomic DNA and containing several pseudogenes but no functional genes. Additional structural variants of the region have also been defined, all generated by NAHR between different blocks of segmental duplications. Our data further illustrate the highly dynamic structure of regions rich in segmental duplications, such as the WBS locus, and indicate that large CNVs can act as susceptibility alleles for disease-associated genomic rearrangements in the progeny.
journal_name
Genome Resjournal_title
Genome researchauthors
Cuscó I,Corominas R,Bayés M,Flores R,Rivera-Brugués N,Campuzano V,Pérez-Jurado LAdoi
10.1101/gr.073197.107subject
Has Abstractpub_date
2008-05-01 00:00:00pages
683-94issue
5eissn
1088-9051issn
1549-5469pii
gr.073197.107journal_volume
18pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.142661.112
更新日期:2013-01-01 00:00:00
abstract::While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.213959.116
更新日期:2017-05-01 00:00:00
abstract::The remarkable olfactory power of insect species is thought to be generated by a combinatorial action of two large protein families, G protein-coupled olfactory receptors (ORs) and odorant binding proteins (OBPs). In olfactory sensilla, OBPs deliver hydrophobic airborne molecules to ORs, but their expression in nonolf...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5075706
更新日期:2006-11-01 00:00:00
abstract::CRISPR/Cas9-mediated targeted mutagenesis allows efficient generation of loss-of-function alleles in zebrafish. To date, this technology has been primarily used to generate genetic knockout animals. Nevertheless, the study of the function of certain loci might require tight spatiotemporal control of gene inactivation....
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.196170.115
更新日期:2016-05-01 00:00:00
abstract::A machine that employs a novel reagent delivery technique for biomolecular synthesis has been developed. This machine separates the addressing of individual synthesis sites from the actual process of reagent delivery by using masks placed over the sites. Because of this separation, this machine is both cost-effective ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.359002
更新日期:2002-12-01 00:00:00
abstract::Recent studies have revealed that insertions and deletions (indels) are more different in their formation than previously assumed. What remains enigmatic is how the local DNA sequence context contributes to these differences. To investigate the relative impact of various molecular mechanisms to indel formation, we ana...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.088922.108
更新日期:2009-07-01 00:00:00
abstract::The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.8.842
更新日期:1998-08-01 00:00:00
abstract::The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.215186.116
更新日期:2017-07-01 00:00:00
abstract::The recent publication of the FANTOM mouse transcriptome has provided a unique opportunity to study the diversity of transcripts arising from a single gene locus. We have focused on the Gnas complex, as imprinting loci themselves provide unique insights into transcriptional regulation. Thirteen full-length cDNAs from ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.955503
更新日期:2003-06-01 00:00:00
abstract::We present a database of copy number variations (CNVs) detected in 2026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort, comprised mainly of Caucasians (65.2%) and African-Americans (34.2%), was analyzed for CNVs in a single study using a uniform array platform an...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.083501.108
更新日期:2009-09-01 00:00:00
abstract::MicroRNAs (miRNAs) are critical regulators of gene expression, and their role in a wide variety of biological processes, including host antimicrobial defense, is increasingly well described. Consistent with their diverse functional effects, miRNA expression is highly context dependent and shows marked changes upon cel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.161471.113
更新日期:2014-05-01 00:00:00
abstract::We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal change...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.828403
更新日期:2003-01-01 00:00:00
abstract::Careful titration of Vent polymerase activity allows efficient amplification of full-length plasmids (12 kb). The high processivity and fidelity of this enzyme made oligonucleotide-directed site-specific mutagenesis of plasmids a straight-forward process. Using only two primers, a mutagenic and a complementary, single...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5.4.404
更新日期:1995-11-01 00:00:00
abstract::DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212050.116
更新日期:2017-04-01 00:00:00
abstract::The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.174052.114
更新日期:2014-09-01 00:00:00
abstract::To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains....
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5302
更新日期:2002-04-01 00:00:00
abstract::A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.137430.112
更新日期:2012-12-01 00:00:00
abstract::A DNA mutation detection protocol able to identify and characterize a previously unknown change in a given sequence in a rapid, efficient, sensitive, and inexpensive manner is required to take advantage of the resources now available to researchers through the genome sequencing projects. We have developed a method bas...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.gr-1578r
更新日期:2002-09-01 00:00:00
abstract::Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds -- soon thousands -- of variable loci to in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.172901
更新日期:2001-03-01 00:00:00
abstract::Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.176586.114
更新日期:2014-12-01 00:00:00
abstract::The initial comparison of the human and chimpanzee genome sequences revealed 16 genomic regions with an unusually high density of rapidly evolving genes. One such region is the whey acidic protein (WAP) four-disulfide core domain locus (or WFDC locus), which contains 14 WFDC genes organized in two subloci on human chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6004607
更新日期:2007-03-01 00:00:00
abstract::Previously, we have described novel families of genes, warthog (wrt) and groundhog (grd), in Caenorhabditis elegans. They are related to Hedgehog (Hh) through the carboxy-terminal autoprocessing domain (called Hog or Hint). A comprehensive survey revealed 10 genes with Hog/Hint modules in C. elegans. Five of these are...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.9.10.909
更新日期:1999-10-01 00:00:00
abstract::CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.215160.116
更新日期:2017-07-01 00:00:00
abstract::Genomic structural variation (SV) is a major determinant for phenotypic variation. Although it has been extensively studied in humans, the nucleotide resolution structure of SVs within the widely used model organism Drosophila remains unknown. We report a highly accurate, densely validated map of unbalanced SVs compri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.142646.112
更新日期:2013-03-01 00:00:00
abstract::Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and co...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.185579.114
更新日期:2015-03-01 00:00:00
abstract::Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover rates and how these rates are integrated into cellular decisions. We decided to measure mRNA decay rates in two human ce...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1272403
更新日期:2003-08-01 00:00:00
abstract::The allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By app...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.230003.117
更新日期:2018-07-01 00:00:00
abstract::Dual channel imaging and warping of two-dimensional (2D) protein gels were used to visualize global changes of the gene expression patterns in growing Bacillus subtilis cells during entry into the stationary phase as triggered by glucose exhaustion. The 2D gels only depict single moments during the cells' growth cycle...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.905003
更新日期:2003-02-01 00:00:00
abstract::The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density oligonucleotide microarray to detect small-scale genomic deletions among 19 clinically and epidemiologically well-characterized isolates ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.166401
更新日期:2001-04-01 00:00:00
abstract::Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.240952.118
更新日期:2019-04-01 00:00:00