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- Jaffe, David B., et al.
(författare)
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Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
- 2003
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 13:1, s. 91-96
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Tidskriftsartikel (refereegranskat)abstract
- We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).
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| 2. |
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| 3. |
- Lindblad-Toh, Kerstin
(författare)
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Three's company
- 2004
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 428:6982, s. 475-476
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Yuan, Q.-P., et al.
(författare)
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A cloning strategy for identification of genes containing trinucleotide repeat expansions
- 2001
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Ingår i: International Journal of Molecular Medicine. - : Spandidos Publications. - 1107-3756 .- 1791-244X. ; 8:4, s. 427-431
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Tidskriftsartikel (refereegranskat)abstract
- Until today, nineteen trinucleotide repeat expansions larger than forty repeat copies have been found in the human genome. Of these, the CAG/CTG repeat is predominant motif with twelve loci identified, ten of which have been associated with the development of neurodegenerative diseases. We have developed a cloning approach which isolates disease genes containing trinucleotide repeat expansions. The method is based on size separation of genomic fragments, followed by subcloning and library hybridization with an oligonucleotide probe. Fractions and clones containing expanded repeats are identified by the repeat expansion detection (RED) method throughout the cloning procedure. Large family materials are not required and as little as 10 microg genomic DNA from a single individual is sufficient for this method. Using this strategy we have cloned two DNA fragments containing expanded repeats from two unrelated patients with a clinical diagnosis of cerebellar ataxia. Sequencing of the two fragments showed sequence identities with two disease genes, the Huntington gene and the ataxin 3 gene, respectively. The method should be adaptable to the cloning of any long repeat motif in any species. Furthermore the experimental steps can be performed in less than a month, making it very effective and time efficient to disease gene identification.
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| 5. |
- Yuan, Qiu-Ping, et al.
(författare)
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Repeat Expansion Detection (RED) and the RED Cloning Strategy
- 2003
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Ingår i: Neurogenetics. - Totowa : Humana Press. ; 217, s. 51-60
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Bokkapitel (refereegranskat)abstract
- Trinucleotide repeat sequences are present at approx 30,000-40,000 loci in the human genome (1). The majority of these repeats are below 35 copies and are stably transmitted. However, unstable trinucleotide repeat expansions at some loci have been found to be the causal mutation for nearly 20 genetic neurodegenerative disorders in human (2–4). Most of these disorders occur at repeat lengths above 35 copies, with a tendency towards further expansion upon successive transmissions. An inverse correlation between the repeat length and disease severity/earlier age of onset, known as anticipation, has been observed in most of the families transmitting such types of diseases, suggesting that the length change of the repeats may play a role in the manifestation of anticipation. Only three motifs, CAG/CTG, CGG/CCG, and GAA/TTC, of the 10 possible trinucleotide repeat permutations have so far been associated with human disease. It remains possible that other disease phenotypes are caused by expansions of any repeat motif at any repeat containing locus. We have established a repeat detection and gene-isolation system, which allows identification of a repeat-containing gene within a couple of months.
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