DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

6. Targeted cDNA Sequencing

Kimberly Prichard, Susi Wachocki, Mira Dimitrijevic-Bussod, Mark Mundt, Judith Cohn, David Bruce, Cliff Han, Norman Doggett, Christa Prange, and Michael R. Altherr

Los Alamos National Laboratory, Los Alamos, NM 87545

ALTHERR@LANL.GOV

The sequencing of cDNAs that are co-linear to genomic sequencing targets adds considerable value to the information generated from both efforts. Through the use of sequence analysis tools, comparisons of these distinct data sets reveal details of gene organization, splice sites and, because the sequences are derived from different sources, gene based single nucleotide polymorphisms (SNPs). We intend to exploit gene predictions derived from genomic sequencing data to identify full-length cDNAs (from initiation codon to the poly adenylation site) for complete cDNA sequencing. We will use "overgo" probes to identify cDNAs corresponding to the gene predictions. We have chosen the strategy of cDNA insert concatenation as our sequencing method. To model this effort, we have embarked by sequencing the complete inserts of cDNAs from the IMAGE collection previously mapped to chromosomes 5, 16, and 19. Approximately, 1800 clones were identified for this effort. We used the Unigene database to identify cDNAs for which the sequence data was incomplete and to identify the largest predicted member of the clone set. These clones are undergoing concatenation cDNA sequencing. Subsequent analyses are being done to identify those coding sequences for which co-linear genomic sequence exists, to characterize their gene structure and to identify SNPs.

This work was supported by Los Alamos National Laboratory LDRD funds and by US DOE OBER under contract W-7405-Eng36.