We propose to conduct high throughput Human DNA sequencing using novel automated instrumentation and deposit 370 Mb of Human sequence into GenBank. This instrumentation designed, developed and tested at the Stanford DNA Sequencing and Technology Center is ready for application at the 100 Mb per year level or greater. We will achieve substantial cost reduction through the use of this instrumentation and by combining the sequence finishing operation with DNA polymorphism detection. All exons, intron/exon boundaries, promoter regions, and regions recognized for biological activity will be scanned in 90 individuals representing the diverse U.S. population using comparative scanning with denaturing HPLC followed by sequencing of varients. The analogous regions in chimpanzee, gorilla, and orangutan will also be sequenced. We expect to identify 300,000 polymorphisms (mostly single nucleotide polymorphisms) in the 370 Mb of DNA giving one site on the average every 1.2kb. This combined approach of genomic sequencing and scanning for allelic variation will reduce the cost of first producing finished DNA sequencing followed by polymorphism detection. We project the average cost for producing both highly accurate DNA sequence and polymorphisms to be 0.20 dollars per base total cost. The establishment of highly accurate DNA sequence of less than one error in 10,000 bases and all of the common polymorphisms in the biologically important region will provide the best data to the medical community.
