Genome Research

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Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
Genome Research - Tập 21 Số 12 - Trang 2004-2013 - 2011
Andreas Schlattl, Simon Anders, Sebastian M. Waszak, Wolfgang Huber, Jan O. Korbel
Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have ev...... hiện toàn bộ
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
Genome Research - Tập 21 Số 6 - Trang 974-984 - 2011
Alexej Abyzov, Alexander E. Urban, M Snyder, Mark Gerstein
Copy number variation (CNV) in the genome is a complex phenomenon, and not completely understood. We have developed a method, CNVnator, for CNV discovery and genotyping from read-depth (RD) analysis of personal genome sequencing. Our method is based on combining the established mean-shift approach with additional refinements (multiple-bandwidth partitioning and GC correction) to broaden th...... hiện toàn bộ
PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
Genome Research - Tập 17 Số 11 - Trang 1665-1674 - 2007
Kai Wang, Mingyao Li, Dexter Hadley, Rui Liu, Joseph Glessner, Struan F.A. Grant, Hákon Hákonarson, Maja Bućan
Comprehensive identification and cataloging of copy number variations (CNVs) is required to provide a complete view of human genetic variation. The resolution of CNV detection in previous experimental designs has been limited to tens or hundreds of kilobases. Here we present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs from Illumina high-de...... hiện toàn bộ
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
Genome Research - Tập 16 Số 1 - Trang 123-131 - 2006
Gregory E. Crawford, Ingeborg Holt, James R. Whittle, Bryn D. Webb, Denise S. Tai, Sean Davis, Elliott H. Margulies, YiDong Chen, John Bernat, David Ginsburg, Daixing Zhou, Shujun Luo, Thomas J. Vasicek, Mark J. Daly, Tyra G. Wolfsberg, Francis S. Collins
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear chromatin is a powerful and well-established method of identifying many different types of regulatory elements, but in the past it has been limited to analysis of single loci. We have recently describe...... hiện toàn bộ
Phylogeny of the Serpin Superfamily: Implications of Patterns of Amino Acid Conservation for Structure and Function
Genome Research - Tập 10 Số 12 - Trang 1845-1864 - 2000
James A. Irving, Robert N. Pike, Arthur M. Lesk, James C. Whisstock
Exploring Expression Data: Identification and Analysis of Coexpressed Genes
Genome Research - Tập 9 Số 11 - Trang 1106-1115 - 1999
Laurie J. Heyer, Semyon Kruglyak, Shibu Yooseph
Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of false positives, (2) a new clustering algorithm designed specifically for gr...... hiện toàn bộ
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
Genome Research - Tập 22 Số 7 - Trang 1197-1211 - 2012
Suhaida A. Selamat, Brian S. I. Chung, Luc Girard, Wei Zhang, Ying Zhang, Mihaela Campan, Kimberly D. Siegmund, Michael N. Koss, Jeffrey A. Hagen, Wan L. Lam, Stephen Lam, Adi F. Gazdar, Ite A. Laird–Offringa
Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma is its most common histological subtype. Clinical and molecular evidence indicates that lung adenocarcinoma is a heterogeneous disease, which has important implications for treatment. Here we performed genome-scale DNA methylation profiling using the Illumina Infinium HumanMethylation27 platform on 59 matched lu...... hiện toàn bộ
The Nuclear Receptor Superfamily Has Undergone Extensive Proliferation and Diversification in Nematodes
Genome Research - Tập 9 Số 2 - Trang 103-120 - 1999
Ann E. Sluder, Siuyien Wong Mathews, David W. Hough, Viravuth P. Yin, Claude V. Maina
The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequ...... hiện toàn bộ
Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
Genome Research - Tập 18 Số 3 - Trang 343-358 - 2008
Victoria P. Belancio, Dale J. Hedges, Prescott L. Deininger
Transposable elements (TEs) have shared an exceptionally long coexistence with their host organisms and have come to occupy a significant fraction of eukaryotic genomes. The bulk of the expansion occurring within mammalian genomes has arisen from the activity of type I retrotransposons, which amplify in a “copy-and-paste” fashion through an RNA intermediate. For better or worse, the sequen...... hiện toàn bộ
The Power of Association Studies to Detect the Contribution of Candidate Genetic Loci to Variation in Complex Traits
Genome Research - Tập 9 Số 8 - Trang 720-731 - 1999
Anthony D. Long, Charles H. Langley
The statistical power of five association study test statistics (two haplotype-based tests, two marker-based tests, and the Transmission Disequilibrium Test–Q5) to detect single nucleotide polymorphism (SNP)/phenotype associations in a linkage–disequilibrium-based candidate gene scan employing a number of SNPs is examined. Power is estimated as a function of realistic parameters expected t...... hiện toàn bộ
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