Physical Map and Overlapping Cosmid Set for Human 

 Chromosome 11 



(Jlen A. Evans, Kathy A. Lewis, Gary Hennanson, Kathryn C. Evans, Jun Zhao, 



Kimball O. Pomeroy, Carlisle P. Landel, David McElligott. Mary Saleh, James 



Eubanks, Daniel Kaufman, Ken D. Pischel, Shizhong Chen, Joseph Trotter, Reece Hart, 



and Grai Andreason 



Molecular Genetics Laboratory, The Salk Institute for Biological Studies, La Jolla, 



CA 92037 



(619)453-4100. ext. 279 



The mission of The Salk Institute is to apply concepts and techniques of modem 

 biology to the solution of human medical problems. Human genome research at The 

 Salk Institute was initiated in 1988 with the support of the Department of Energy 

 (DOE), under the direction of Dr. Glen A. Evans. The recently established Center for 

 Human Genome Research, a closely integrated research group at The Salk Institute, is 

 working in collaboration with several DOE national laboratories within a highly focused 

 program to produce a continuous physical map and overlapping cosmid set for human 

 chromosome 1 1. Inherent in this approach is strong involvement in the development of 

 novel techniques and strategies for genome analysis. 



In the past two years, researchers at The Salk histitute's Center for Human Genome 

 Research have made considerable progress in the development of new cloning 

 methodologies and techniques for genomic analysis and in using these approaches to 

 construct a physical map of human chromosome 1 1 . Extending over about 148 mb, 

 chromosome 1 1 represents about 4.2% of the human genome. We have constructed, 

 as a pilot project, an initial small set of cosmid clones in a specialized cosmid vector, 

 sCos- 1 , that allows the rapid detemiination of overlapping sequences in the collection 

 through the synthesis of directional RNA probes. Over 1000 cosmids mapping in the 

 region from 1 lql2 to 1 Iqter have been isolated from a cosmid library constructed from 

 a somatic cell hybrid containing a portion of human chromosome 1 1 in a mouse MEL 

 cell background. These cosmids have been organized in a 36-X-36 array on a 

 nitrocellulose filter: using a novel strategy of overlap determination — referred to as 

 multiplex mapping — that uses pools of clones, we detected 1099 pairs of linked clones 

 in the collection. These pairs have been assembled into 315 predicted cosmid contigs, 

 which are now undergoing analysis by restriction mapping. 



Using a laboratory robot, we also devised techniques for automated preparation of 

 cosmid DNA and for restriction analysis. Each of the clones for four rare restriction 

 enzymes — Nor I, BssH II, Sfi I, and Sac II — have been mapped, and over 150 Not-l- 

 containing linking clones and 37 putative ///w/TI-tiny-fragment (HTF) islands have 

 been identified. This automated system is now being used to complete the restriction 

 mapping of the entire collection of cosmids. 



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