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
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
evaluated ...
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
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 the
range ...
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
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-density SN...
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
Genome Research - Tập 16 Số 1 - Trang 123-131 - 2006
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 described a prot...
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
Exploring Expression Data: Identification and Analysis of Coexpressed Genes
Genome Research - Tập 9 Số 11 - Trang 1106-1115 - 1999
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
grouping g...
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
Genome Research - Tập 22 Số 7 - Trang 1197-1211 - 2012
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 lung adeno...
The Nuclear Receptor Superfamily Has Undergone Extensive Proliferation and Diversification in Nematodes
Genome Research - Tập 9 Số 2 - Trang 103-120 - 1999
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 sequence from the
related nematode Caenorh...
Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
Genome Research - Tập 18 Số 3 - Trang 343-358 - 2008
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
sequences of t...
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
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 to affect...
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