HIVID: an efficient method to detect HBV integration using low coverage sequencing.
Genomics
; 102(4): 338-44, 2013 Oct.
Article
en En
| MEDLINE
| ID: mdl-23867110
ABSTRACT
We reported HIVID (high-throughput Viral Integration Detection), a novel experimental and computational method to detect the location of Hepatitis B Virus (HBV) integration breakpoints in Hepatocellular Carcinoma (HCC) genome. In this method, the fragments with HBV sequence were enriched by a set of HBV probes and then processed to high-throughput sequencing. In order to evaluate the performance of HIVID, we compared the results of HIVID with that of whole genome sequencing method (WGS) in 28 HCC tumors. We detected a total of 246 HBV integration breakpoints in HCC genome, 113 out of which were within 400bp upstream or downstream of 125 breakpoints identified by WGS method, covering 89.3% (125/140) of total breakpoints. The integration was located in the gene TERT, MLL4, and CCNE1. In addition, we discovered 133 novel breakpoints missed by WGS method, with 66.7% (10/15) of validation rate. Our study shows HIVID is a cost-effective methodology with high specificity and sensitivity to identify viral integration in human genome.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Virus de la Hepatitis B
/
Integración Viral
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Carcinoma Hepatocelular
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Secuenciación de Nucleótidos de Alto Rendimiento
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Neoplasias Hepáticas
Límite:
Humans
País/Región como asunto:
Asia
Idioma:
En
Revista:
Genomics
Asunto de la revista:
GENETICA
Año:
2013
Tipo del documento:
Article
País de afiliación:
China