Chromosome 7 accounts for approximately 5% of the human genome. It is estimated to be 136 centiMorgans (cM) in length and contains 170 million basepairs (170 Mb) of DNA. We are mapping and sequencing two targets along chromosome-7, one at 7q31.3, and the other at 7p14. Both are targets with little prior characterization other than the STS map, and as such, are representative of the bulk of the human genome.

Our starting point is Eric Green’s STS-content map of the chromosome. We believe that this map is superior to most other physical maps, for two reasons. First, the STSs are reliably ordered to a length scale of 88 kbp, comparable to the 79 kbp average spacing between adjacent STSs. Second, 57% of the mapped YAC clones are derived from a chromosome-specific YAC library prepared from a monochromosome hybrid [Green, et al. 1995. Genomics 25, 170-183. A human chromosome 7 yeast artificial chromosome (YAC) resource: construction, characterization, and screening]. These YACs have proven to be very stable, with only 10% to 15% re-arrangements detected over the course of the STS-content map construction. In contrast, CEPH mega-YACs displayed a chimerism rate of over 50% along this same chromosome.

Initially, YACs were subcloned into cosmids and restriction-mapped by the Multiple-Complete-Digest method. To protect against YAC re-arrangements that might not have been detected at the STS level, we required that every sequenced loci be validated by two different YACs (or BACs in regions that are poorly represented by YACs). Every YAC was mapped independently, and the resultant maps were expected to agree completely in all overlapping regions. After the MCD maps were completed and connected, a tiling path was selected and the tiling path cosmids were sequenced by a Shotgun Sequencing Strategy that employs M13 templates. Complete agreement between the finished sequence and the original MCD map was expected. More recently, we began to sequence BACs directly screened against the STS map. We are currently working to integrate the display of these various maps.

This project has also been tracking the agreement between overlapping cosmids that were independently sequenced and finished. This is a particularly powerful test of the accuracy of our sequence because all but one of the mapped YACs are derived from a monochromosome hybrid and, hence, exact agreement is expected.