Abstract:
:We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between individuals. We then expand these matches using dynamic programming to identify long, nearly identical segmental sharing that is indicative of relatedness. We use GERMLINE to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals. We verify that GERMLINE is in concordance with other methods when they can process the data, and also facilitates analysis of larger scale studies. We bolster these results by demonstrating novel applications of precise analysis of hidden relatedness for (1) identification and resolution of phasing errors and (2) exposing polymorphic deletions that are otherwise challenging to detect. This finding is supported by concordance of detected deletions with other evidence from independent databases and statistical analyses of fluorescence intensity not used by GERMLINE.
journal_name
Genome Resjournal_title
Genome researchauthors
Gusev A,Lowe JK,Stoffel M,Daly MJ,Altshuler D,Breslow JL,Friedman JM,Pe'er Idoi
10.1101/gr.081398.108subject
Has Abstractpub_date
2009-02-01 00:00:00pages
318-26issue
2eissn
1088-9051issn
1549-5469pii
gr.081398.108journal_volume
19pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.4.511
更新日期:2000-04-01 00:00:00
abstract::Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the p...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.6902
更新日期:2002-05-01 00:00:00
abstract::The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.129460.111
更新日期:2012-04-01 00:00:00
abstract::Large-scale gene expression studies and genomic sequencing projects are providing vast amounts of information that can be used to identify or predict cellular regulatory processes. Genes can be clustered on the basis of the similarity of their expression profiles or function and these clusters are likely to contain ge...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.148301
更新日期:2001-01-01 00:00:00
abstract::Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.178855.114
更新日期:2015-01-01 00:00:00
abstract::High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.225276.117
更新日期:2018-05-01 00:00:00
abstract::During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.096297.109
更新日期:2009-12-01 00:00:00
abstract::We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.226602
更新日期:2002-07-01 00:00:00
abstract::Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a g...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.053678.106
更新日期:2008-09-01 00:00:00
abstract::Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVista, for high-throughput discovery of cis-regulatory elements that combines clustering of predicted transcription factor binding sites (TFBSs) a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.225502
更新日期:2002-05-01 00:00:00
abstract::In the attempt to understand human variation and the genetic basis of complex disease, a tremendous number of single nucleotide polymorphisms (SNPs) have been discovered and deposited into NCBI's dbSNP public database. More than 2.7 million SNPs in the database have genotype information. This data provides an invaluab...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4297805
更新日期:2005-11-01 00:00:00
abstract::Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single-cell sequencing, which is not scalable and could be biased ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.202903.115
更新日期:2016-11-01 00:00:00
abstract::Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2001604
更新日期:2004-04-01 00:00:00
abstract::Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cepha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.073676.107
更新日期:2008-07-01 00:00:00
abstract::A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 geneticall...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.8.1115
更新日期:2000-08-01 00:00:00
abstract::A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perfor...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.9.901
更新日期:1998-09-01 00:00:00
abstract::Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5016106
更新日期:2006-07-01 00:00:00
abstract::Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.235820.118
更新日期:2018-12-01 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
abstract::An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying transcription regulation, i.e., (1) the identification of common transcriptional regulators of a set of coexpressed genes; (...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4303406
更新日期:2006-03-01 00:00:00
abstract::Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:1999-03-01 00:00:00
abstract::Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.193763.115
更新日期:2016-02-01 00:00:00
abstract::Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7105007
更新日期:2007-12-01 00:00:00
abstract::Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome seque...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3002305
更新日期:2005-01-01 00:00:00
abstract::Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.083089.108
更新日期:2008-12-01 00:00:00
abstract::After completion of the Schizosaccharomyces pombe genome sequence, we have carried out a pilot gene deletion project to assess the feasibility of a genome-wide deletion project and to estimate the percentage of essential genes. Using a PCR-based gene deletion procedure, we investigated 100 genes within a 253-kb region...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.636103
更新日期:2003-03-01 00:00:00
abstract::It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can exp...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2800104
更新日期:2004-12-01 00:00:00
abstract::Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212563.116
更新日期:2017-03-01 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::Thousands of long noncoding RNAs (lncRNAs) have been found in vertebrate animals, a few of which have known biological roles. To better understand the genomics and features of lncRNAs in invertebrates, we used available RNA-seq, poly(A)-site, and ribosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140475.112
更新日期:2012-12-01 00:00:00