ABSTRACT
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between the NCBI human reference sequence and the HuRef assembly, and it enables the navigation of the HuRef genome in the context of HuRef, NCBI and Ensembl annotations. Single nucleotide polymorphisms, indels, inversions, structural and copy-number variations are shown in the context of existing functional annotations on either genome in the comparative view. Demonstrated here are some potential uses of the browser to enable a better understanding of individual human genetic variation. The browser provides full access to the underlying reads with sequence and quality information, the genome assembly and the evidence supporting the identification of DNA polymorphisms. The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at http://huref.jcvi.org.
Subject(s)
Databases, Nucleic Acid , Genetic Variation , Genome, Human , Genomics , Humans , Internet , SoftwareABSTRACT
Presented here is a genome sequence of an individual human. It was produced from approximately 32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2-206 bp), 292,102 heterozygous insertion/deletion events (indels)(1-571 bp), 559,473 homozygous indels (1-82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.
Subject(s)
Chromosome Mapping , Diploidy , Genome, Human , Sequence Analysis, DNA , Base Sequence , Chromosome Mapping/instrumentation , Chromosome Mapping/methods , Chromosomes, Human , Chromosomes, Human, Y/genetics , Gene Dosage , Genotype , Haplotypes , Human Genome Project , Humans , INDEL Mutation , In Situ Hybridization, Fluorescence , Male , Microarray Analysis , Middle Aged , Molecular Sequence Data , Pedigree , Phenotype , Polymorphism, Single Nucleotide , Reproducibility of Results , Sequence Analysis, DNA/instrumentation , Sequence Analysis, DNA/methodsABSTRACT
The systems biology revolution is proceeding along multiple pathways as different science agencies and the private sector have adopted strategies suited to their particular needs and cultures. To meet this challenge, the U.S. Department of Energy has developed the Genomes to Life (GTL) program. A central focus of GTL is environmental microbial biology as a way to approach global environmental problems, and its key goal is to achieve, over the next 10 to 20 years, a basic understanding of thousands of microbes and microbial systems in their native environments. This focus demands that we address huge gaps in knowledge, technology, computing, data storage and manipulation, and systems-level integration.
