Pooled genomic indexing of rhesus macaque
- Aleksandar Milosavljevic1,4,
- Ronald A. Harris1,
- Erica J. Sodergren1,
- Andrew R. Jackson1,
- Ken J. Kalafus1,
- Anne Hodgson1,
- Andrew Cree1,
- Weilie Dai1,
- Miklos Csuros2,
- Baoli Zhu3,
- Pieter J. de Jong3,
- George M. Weinstock1, and
- Richard A. Gibbs1
- 1 Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- 2 Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- 3 Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
Abstract
Pooled genomic indexing (PGI) is a method for mapping collections of bacterial artificial chromosome (BAC) clones between species by using a combination of clone pooling and DNA sequencing. PGI has been used to map a total of 3858 BAC clones covering ∼24% of the rhesus macaque (Macaca mulatta) genome onto 4178 homologous loci in the human genome. A number of intrachromosomal rearrangements were detected by mapping multiple segments within the individual rhesus BACs onto multiple disjoined loci in the human genome. Transversal pooling designs involving shuffled BAC arrays were employed for robust mapping even with modest DNA sequence read coverage. A further innovation, short-tag pooled genomic indexing (ST-PGI), was also introduced to further improve the economy of mapping by sequencing multiple, short, mapable tags within a single sequencing reaction.
Footnotes
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[Supplemental material is available online at www.genome.org and www.genboree.org.]
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3162505.
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↵4 Corresponding author. E-mail amilosav{at}bcm.tmc.edu; fax (713) 798-4373.
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- Accepted October 13, 2004.
- Received August 17, 2004.
- Cold Spring Harbor Laboratory Press
