cDNA Sequencing Program

Internal

Transcript Database

The Baylor College of Medicine Human Genome Sequencing Center's (Baylor HGSC) Concatenation cDNA Sequencing (CCS) program is supported by funding from the Department of Energy (DOE) and the National Institute of Health (NIH). NIH funding is through the National Cancer Institiute (NCI) and the NCI-Federick Cancer Research and Development Program. The Baylor HGSC-CCS is actively participating in the Mammalian Gene Collection (MGC) project.

The main objective of the CCS program is to generate full length cDNA clones from various species including mouse, human and rat. Research efforts have focused on four main areas:

cDNA library construction

improvement of the CCS bench procedures

improved informatics

production of cDNA data

1) Library construction has been developed following the methods of the RIKEN group in Japan using the "CAP-TRAP" method. Libraries are being generated from human, mouse and rat tissue.

2) Improved CCS library techniques now allow routine production of CCS libraries of ~100 cDNA clones (total length 200-250 kb) that perform as well as the equivalent shotgun sequencing libraries from human genomic DNA clones.

3) New informatics tools allow simplified processing of data in the CCS pipeline. Clone selection is simplified by the use of an internal website which displays database blast searches generated from each EST, complete with a compilation of sequence homology results. The preexisting Baylor HGSC informatics tools facilitate sequence tracking and reporting.

As a modification to P. Green's PHRAP program, a technique has been developed for automated preprocessing of CCS reads before assembly in PHRAP. An improved to expedite the database submission process enables the annotator to select appropriate annotation features using an internal website tool.

4) The Human Transcript Database (HTD) is a curated for information related to RNA molecules that have been sequenced. The goal of the HTD is to provide a clone-based platform that represents as many of the transcripts that have been sequenced as possible. As the focus of the HTD is on complete or nearly complete sequences, EST sequence information has been excluded.

Conditions for use

Pediatric Leukemias
with Judith Margolin, MD, Texas Children's Hospital
Primary cancer tissues (not cell lines) are used to avoid the sequencing of expressed genes that may be related to growth in culture, but not to the histology of the tumor.

LN-CIB
with Claudio Schneider, PhD, LN CIB

Human Reproductive Tissue
with Aleks Rajikovic, MD, PhD., Baylor College of Medicine

	Andersson, B. Wentland, M.A. Ricafrente, J.Y. Liu, W. Gibbs, R.A.(1996) A "Double Adaptor" Method for Improved Shotgun Library Construction. Anal. Biochem. 236: 107-113. Abstract Andersson, B. Lu, J. Shen, Y. Wentland, M.A. Gibbs, R.A. (1997) Simultaneous Shotgun Sequencing of Multiple cDNA Clones. J. Sequencing and Mapping. 7: 63-70. Abstract Yu, W. Andersson, B. Worley, K. Muzny, D.M. Ding, Y. Liu, W. Ricafrente, J.Y. Wentland, M.A. Lennon, G. Gibbs, R.A. (1997) Large-Scale Concatenation cDNA Sequencing. Genome Research 7: 353-358. Abstract Bouck, J. McLeod M.P. Worley, K. Gibbs, R.A. (2000) The Human Transcript Database: A Catalogue of Full Length cDNAs. Bioinformatics 2000 16: 176-177. Abstract


	All finished data sent to GenBank should be cited according to GenBank's guidelines. The image of cDNA included above was provided for our use by the DOE Human Genome Project.