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Genome
About: Genome is a research topic. Over the lifetime, 74231 publications have been published within this topic receiving 3819713 citations.
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TL;DR: A new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions is reported, which will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.
Abstract: Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes. Here we report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. Notably, we estimate that typical individuals are hemizygous for roughly 30-50 deletions larger than 5 kb, totaling around 550-750 kb of euchromatic sequence across their genomes. The detected deletions span a total of 267 known and predicted genes. Overall, however, the deleted regions are relatively gene-poor, consistent with the action of purifying selection against deletions. Deletion polymorphisms may well have an important role in the genetics of complex traits; however, they are not directly observed in most current gene mapping studies. Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.
702 citations
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TL;DR: Observations suggest that the mechanisms of replication, transcription, processing, and translation in mitochondria are highly conserved throughout higher vertebrates.
702 citations
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TL;DR: The use of complete-genome sequencing in the characterization of spontaneously arising mutations in the yeast Saccharomyces cerevisiae yields numerous unexpected findings, in particular a very high rate of point mutation and skewed distribution of base-substitution types in the mitochondrion and segmental duplication and deletion in the nuclear genome.
Abstract: The mutation process ultimately defines the genetic features of all populations and, hence, has a bearing on a wide range of issues involving evolutionary genetics, inheritance, and genetic disorders, including the predisposition to cancer. Nevertheless, formidable technical barriers have constrained our understanding of the rate at which mutations arise and the molecular spectrum of their effects. Here, we report on the use of complete-genome sequencing in the characterization of spontaneously arising mutations in the yeast Saccharomyces cerevisiae. Our results confirm some findings previously obtained by indirect methods but also yield numerous unexpected findings, in particular a very high rate of point mutation and skewed distribution of base-substitution types in the mitochondrion, a very high rate of segmental duplication and deletion in the nuclear genome, and substantial deviations in the mutational profile among various model organisms.
702 citations
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TL;DR: The genome sequence of Atlantic cod is presented, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates.
Abstract: The genome of the Atlantic cod has been sequenced, and genomic analysis reveals an immune system that differs significantly from that in other vertebrates. The major histocompatibility complex (MHC) II has been lost, as have some other genes that are essential for MHC II function. But there is an expansion in the number of MHC I genes and a unique composition for its toll-like receptor family. These compensatory changes in both adaptive and innate immunity mean that cod is no more susceptible to disease than most other vertebrates. These findings challenge current models of vertebrate immune evolution, and may facilitate the development of targeted vaccines for disease management in aquaculture. Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture1,2. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates3,4, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions5. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
702 citations
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National Institute of Genetics1, Nippon Telegraph and Telephone2, Osaka University3, Novartis4, University of Iowa5, Rockefeller University6, University of Milan7, Keio University8, University of Maryland, Baltimore9, University of California, Berkeley10, Tokai University11, J. Craig Venter Institute12, National Institutes of Health13, Stanford University14, Lawrence Berkeley National Laboratory15, University of Tokyo16, Harvard University17, University of Queensland18, University of Cambridge19, AREA Science Park20, University of Pennsylvania21, Roswell Park Cancer Institute22, National Cancer Research Institute23, University of Tsukuba24, University of California, San Diego25, Massachusetts Institute of Technology26, Wellcome Trust27
TL;DR: The first RIKEN clone collection is described, which is one of the largest described for any organism and analysis of these cDNAs extends known gene families and identifies new ones.
Abstract: The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.
700 citations