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J Biomol Tech. 2010 September; 21(3 Suppl): S64.
PMCID: PMC2918141

Utilizing Fluidigm's Access Array Long-Range Capability and Roche 454 s Titanium Chemistry to Capture and Sequence the Epstein-Barr Virus (EBV) for Variant Detection

V. Lonsberry,2 C. Chang,2 S. Mbulaiteye,2 K. Bhatia,3 M. Yeager,2 Z. Deng,2 C. Matthews,2 S. Chanock,4 K. Yu,2 and A. Hildesheim2
1National Cancer Institute, Germantown, MD, United States;
2Division of Cancer Epidemiology and Genetics, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, United States;
3National Cancer Institute, Office of HIV and AIDS Malignancy, Bethesda, MD, United States;
4National Cancer Institute, Core Genotyping Facility, Gaithersburg, MD, United States

Abstract

RP-133

The ubiquitous nature of the EBV makes it a very attractive focus for genetic sequence analysis; moreover, identification of tumor-associated strains of EBV would have major public impact, especially in populations where EBV-associated Malignancies are endemic. The ability to capture and sequence the entire EBV virus from human DNA would enable researchers to vastly increase the breadth of knowledge of the virus's numerous variants. The EBV genome is 172Kb and the ability to multiplex and sequence the entire virus genome to a depth of 40 to 50x would allow significant variants to be readily identified. We have been able to target, amplify, and capture the entire EBV genome from human DNA samples prior to Roche 454 sequencing. Using key advantages (e.g. flexibility, sensitivity and time saving) of Fluidigm's Long-Range Access Array chips; we had captured the entire EBV genome from a multiple patient DNA samples in a matter of days. Data will be presented that will highlight the flexibility and capability of the long-range Access Array as well as the reduced time from DNA sample to full genome sequence generated from a 454 Titanium run. Funded by NCI Contract No. HHSN261200800001E


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