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Vol. 11, Issue 10, 1619-1623, October 2001

PERSPECTIVE
A Clone-Array Pooled Shotgun Strategy for Sequencing Large Genomes

Wei-Wen Cai,1,2 Rui Chen,1,2 Richard A. Gibbs,1,2,5 and Allan Bradley1,3,4

1 Department of Molecular and Human Genetics, 2 Human Genome Sequencing Center, and 3 Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA

A simplified strategy for sequencing large genomes is proposed. Clone-Array Pooled Shotgun Sequencing (CAPSS) is based on pooling rows and columns of arrayed genomic clones, for shotgun library construction. Random sequences are accumulated, and the data are processed by sequential comparison of rows and columns to assemble the sequence of clones at points of intersection. Compared with either a clone-by-clone approach or whole-genome shotgun sequencing, CAPSS requires relatively few library constructions and only minimal computational power for a complete genome assembly. The strategy is suitable for sequencing large genomes for which there are no sequence-ready maps, but for which relatively high resolution STS maps and highly redundant BAC libraries are available. It is immediately applicable to the sequencing of mouse, rat, zebrafish, and other important genomes, and can be managed in a cooperative fashion to take advantage of a distributed international DNA sequencing capacity.

4 Present address: Sanger Centre, Hinxton, UK.

5 Corresponding author.

11:1619-1623 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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