Human Chromosome 7

Sequence-Tagged Sites (STSs)

Our goal was to achieve better than 100-kb average STS spacing across the ~170-Mb chromosome 7. This required the development and mapping of at least 1700 STSs. However, we recognized that it was desirable to map a significantly larger number of STSs. As a result, we have developed a total of 2,478 chromosome 7 STSs, of which 2150 have thus far been mapped to YAC contigs.

In developing our set of STS-specific PCR assays, our efforts accounted for: (1) both DNA sequence generation and PCR primer design for roughly 66% of the STSs; (2) PCR primer design but not DNA sequence generation for roughly 17%; and (3) neither DNA sequence generation nor PCR primer design for roughly 17%. Most of the STSs in the second and third categories correspond to markers that serve to integrate our physical map with the genetic, RH, and transcript [i.e., gene/EST] maps. For STSs in the third category, the corresponding PCR assays were simply imported from other laboratories.

We intentionally used a variety of sources for generating the DNA sequences used for STS development. Of those STSs mapped to YAC contigs, the distribution was as follows:

Random Sequence	26%
YAC Insert Ends	37%
Genetic (Microsatellite) Markers	20%
Genes/ESTs	17%

Of note, the majority of the STSs corresponding to ESTs were generated from a set of chromosome 7-enriched direct selection cDNA libraries that we developed.

For organizational simplicity, all of our STSs are named with the prefix 'sWSS' followed by an unique number. Information on all STSs is available in the STS Division of GenBank (dbSTS) at the National Center for Biotechnology Information (NCBI) and the Genome Database (GDB).

Comments, suggestions and problems to bioinformatics@nhgri.nih.gov

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