Abstract:
:Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilization of a CGH has been limited by the lack of well characterized, high-resolution clone sets optimized for consistent performance in aCGH assays and specifically designed analytic software. We have assembled a set of approximately 4100 publicly available human bacterial artificial chromosome (BAC) clones evenly spaced at approximately 1-Mb resolution across the genome, which includes direct coverage of approximately 400 known cancer genes. This aCGH-optimized clone set was compiled from five existing sets, experimentally refined, and supplemented for higher resolution and enhancing mapping capabilities. This clone set is associated with a public online resource containing detailed clone mapping data, protocols for the construction and use of arrays, and a suite of analytical software tools designed specifically for aCGH analysis. These resources should greatly facilitate the use of aCGH in gene discovery.
journal_name
Genome Resjournal_title
Genome researchauthors
Greshock J,Naylor TL,Margolin A,Diskin S,Cleaver SH,Futreal PA,deJong PJ,Zhao S,Liebman M,Weber BLdoi
10.1101/gr.1847304subject
Has Abstractpub_date
2004-01-01 00:00:00pages
179-87issue
1eissn
1088-9051issn
1549-5469pii
1847304journal_volume
14pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.211201.116
更新日期:2017-01-01 00:00:00
abstract::Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1940604
更新日期:2004-04-01 00:00:00
abstract::Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.263202.120
更新日期:2021-01-19 00:00:00
abstract::High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration ra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.121095.111
更新日期:2011-09-01 00:00:00
abstract::Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191098.115
更新日期:2015-10-01 00:00:00
abstract::Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each indi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.246934.118
更新日期:2020-02-01 00:00:00
abstract::Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.175240.114
更新日期:2015-03-01 00:00:00
abstract::We have identified three new families of insulin homologs in Caenorhabditis elegans. In two of these families, concerted mutations suggest that an additional disulfide bond links B and A domains, and that the A-domain internal disulfide bond is substituted by a hydrophobic interaction. Homology modeling remarkably con...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.4.348
更新日期:1998-04-01 00:00:00
abstract::Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combinat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.200840.115
更新日期:2016-05-01 00:00:00
abstract::Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.128652.111
更新日期:2012-03-01 00:00:00
abstract::Elucidating the pathophysiology and molecular attributes of common disorders as well as developing targeted and effective treatments hinges on the study of the relevant cell type and tissues. Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diab...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.150706.112
更新日期:2013-09-01 00:00:00
abstract::Nutrient availability profoundly influences gene expression. Many animal genes encode multiple transcript isoforms, yet the effect of nutrient availability on transcript isoform expression has not been studied in genome-wide fashion. When Caenorhabditis elegans larvae hatch without food, they arrest development in the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.133587.111
更新日期:2012-10-01 00:00:00
abstract::We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying various publicly available expression data sets we conclude that enrichment of clusters for biological function is, in g...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.397002
更新日期:2002-10-01 00:00:00
abstract::Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.8.747
更新日期:1996-08-01 00:00:00
abstract::The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1555203
更新日期:2003-08-01 00:00:00
abstract::Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription facto...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.130682.111
更新日期:2012-04-01 00:00:00
abstract::The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a develo...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5155706
更新日期:2007-04-01 00:00:00
abstract::Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challen...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.231183.117
更新日期:2018-09-01 00:00:00
abstract::Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relati...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6073107
更新日期:2007-06-01 00:00:00
abstract::Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.12.1245
更新日期:1998-12-01 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 prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.10.1022
更新日期:1998-10-01 00:00:00
abstract::Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems biology. Because interactions among modules can give rise to higher-level properties that are essential to cellular function, a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3847105
更新日期:2005-09-01 00:00:00
abstract::Loss of heterozygosity (LOH) and copy number alteration (CNA) feature prominently in the somatic genomic landscape of tumors. As such, karyotypic aberrations in cancer genomes have been studied extensively to discover novel oncogenes and tumor-suppressor genes. Advances in sequencing technology have enabled the cost-e...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.137570.112
更新日期:2012-10-01 00:00:00
abstract::In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in the Escherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecula...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.611403
更新日期:2003-04-01 00:00:00
abstract::Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212696.116
更新日期:2017-06-01 00:00:00
abstract::To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.520702
更新日期:2002-11-01 00:00:00
abstract::Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212316.116
更新日期:2017-01-01 00:00:00
abstract::Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.217331.116
更新日期:2017-08-01 00:00:00
abstract::Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting tha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.168963.113
更新日期:2014-09-01 00:00:00