The 1000 genomes project.
Next-generation DNA sequencers have advanced genomic research through more accurate, less costly and faster analyses, and enabled the development of novel applications. The technology will now be applied to a coordinated international effort to better understand the extent of human genetic variation and its relation to disease. The National Institutes of Health's 1000 Genomes Project will build upon the HapMap project (see IBO Ibo: see Igbo. 9/30/03) to map human genetic variants of common diseases with new levels of accuracy.
Using next-generation sequencing technologies, the Wellcome Trust The Wellcome Trust is a United Kingdom-based charity established in 1936 to administer the fortune of the American-born pharmaceutical magnate Sir Henry Wellcome. Its income was derived from what was originally called Burroughs Wellcome & Co, later renamed in the UK as the Sanger Institute The Wellcome Trust Sanger Institute (formerly the Sanger Centre) is a genome research centre in Cambridgeshire, England. It was set up in 1992 by the Wellcome Trust and the Medical Research Council, the purpose of which is stated on their website ( as "to further our , the Beijing Genomics Institute The Beijing Genomics Institute (BGI) was founded in 1998. It achieved international prominence as a center for sequencing the human genome. BGI completed one percent of the human genome for the Human Genome Project. Shenzhen (BGI BGI Barclays Global Investors
BGI Bainbridge Graduate Institute
BGI Bureau Gravimétrique International
BGI Borland Graphic Interface (File Name Extension)
BGI Bridgetown, Barbados - Grantley Adams International ) and three members of the National Human Genome The human genome is the genome of Homo sapiens, which is composed of 24 distinct pairs of chromosomes (22 autosomal + X + Y) with a total of approximately 3 billion DNA base pairs containing an estimated 20,000–25,000 genes. Research Institute's (NHGRI NHGRI National Human Genome Research Institute ) Large-Scale Sequencing Network--the Broad Institute of MIT MIT - Massachusetts Institute of Technology and Harvard, Washington University of Medicine and Baylor College of Medicine--will sequence the genomes of 1,000 individuals, at a cost of between $30 million and $50 million, to discover the structural variants present in 1% or greater of the population and present at 0.5% or lower in genes. Current plans call for the use of 454 Life Sciences' GS FLX FLX Finger Lakes (New York)
FLX Fort Lauderdale Executive (airport code)
FLX Federal Learning eXchange
FLX Flatfishes system and Illumina's Genome Analyzer.
Asked about the possible use of Applied Biosystems' SOLID platform and Helicos Biosciences' HeliScope system, Adam Felsenfeld, PhD, program director of the Large-Scale Sequencing Program at the NHGRI, told IBO, "as long as the quality, cost and throughput needs are met, the plan is agnostic about what platforms are used. The only instruments that appear to be able to meet the requirements along the given timeline, within the limits of our confidence and knowledge, are, right now, a combination of 454 and Solexa. SOLID is promising as well. Because of this agnostic approach, if other technologies become available that can do better, we encourage their use."
The Project's first phase will consist of three pilot projects. Two nuclear families will be sequenced at an average of 20 passes of each genome. This information will be used to determine how to identify sequence variants. The second pilot project will sequence 180 peoples' genomes at an average of two passes per genome to access low-coverage data. The third pilot will sequence the coding region of 1,000 genes in around 1,000 people. This information will be used to develop plans for cataloging the coding regions known as exons.
One of the project's goals is to learn how to most effectively employ next-generation sequencing technologies to determine structural variants, such as regulations, deletions and duplications. "The test of this project for the new platforms is only for two specific applications, namely, identifying variants within their haplotype haplotype /hap·lo·type/ (-tip) the group of alleles of linked genes, e.g., the HLA complex, contributed by either parent; the haploid genetic constitution contributed by either parent.
n. contexts to 1% throughout the genome and to 0.5% in exons," said Dr. Felsenfeld. "The former requires large amounts of data that is of a consistent, predictable quality, cost and throughput, to the extent that the data produced by multiple groups can be combined for specific analysis. The latter requires integration of exon Exon
In split genes, a portion that is included in the ribonucleic acid (RNA) transcript of a gene and survives processing of the RNA in the cell nucleus to become part of a spliced messenger RNA (mRNA) or structural RNA in the cell cytoplasm. capture methods with the new technologies to become robust." As a result, the Project is expected to advance the use of next-generation sequencing technologies. "Both [applications] will foster better understanding of instrument performance in true production mode, including a better understanding of data quality and quality requirements. In addition, both will foster the development of new tools for data analysis and deposition," he commented.
Among the specific technology challenges cited by a summary of a September 2007 workshop to plan the Project include common production and quality metrics, data quality and accuracy, use of paired-end reads, exon capture methods, determination of the frequency distribution of rare variants and information about the phasing and imputing of genotypes. According to the summary, the Sanger Institute will use 12 of its 25 Illumina Genome Analyzers for the project and BGI will use 5 of its 7 Genome Analyzers. Genotyping on Affymetrix and Illumina's SNP SNP Scottish National Party
Noun 1. SNP - (genetics) genetic variation in a DNA sequence that occurs when a single nucleotide in a genome is altered; SNPs are usually considered to be point mutations that have been evolutionarily microarrays will provide validation for sequenced data.
When asked about new Project funding for instrument purchases, Dr. Felsenfeld explained that the Project is being ftmded by previously approved monies for the sequencing centers. He said, "funds are not allocated for specific machine purchase in advance for this project, though some centers may use available funds for additional instruments."