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Medical Oncology

, 33:38 | Cite as

Identification of allelic expression imbalance genes in human hepatocellular carcinoma through massively parallel DNA and RNA sequencing

  • Qiudao Wang
  • Yan An
  • Qing Yuan
  • Yao Qi
  • Ying Ou
  • Junhui Chen
  • Jian HuangEmail author
Original Paper

Abstract

Hepatocellular carcinoma (HCC) is a common malignant tumor worldwide. The prognosis and treatment of this disease have changed little in recent decades because the mechanisms underlying most events of this disease remain obscure. Allelic variation of gene expression is associated with many important biological processes, which provide a new perspective to understand HCC pathogenesis at the molecular level. To identify allelic expression imbalance (AEI) genes in HCCs, we developed a computational method that considered accurate mapping and vigorous AEI detection using paired DNA-seq and RNA-seq data. We analyzed the DNA-seq and RNA-seq data derived from two HCC samples and two cell lines. By applying a strict criterion, a total of 203 tumor-specific AEI genes were identified with high confidence, and several genes have been reported to be associated with the migration or proliferation of cancer cells, such as the genes RELN and DHRS3. In addition, we also found some novel AEI genes in HCCs, such as HNRNPR and PTAFR. Our study provides new insight into AEI events that may contribute to understanding gene expression regulation, cell proliferation and migration, and tumorigenesis.

Keywords

Allelic expression imbalance Hepatocellular carcinoma DNA-seq RNA-seq Cancer Tumor-specific AEI gene 

Abbreviations

HCC

Hepatocellular carcinoma

AEI

Allelic expression imbalance

HOM

One site is homozygous

NO

Not tumor-specific AEI site

gDNA

Genomic DNA

cDNA

Complementary DNA

Notes

Acknowledgments

This work was supported by Grants from the National High Technology Research and Development Program of China (2012AA02A205), the National Natural Science Foundation of China (81472639 and 81272306), the Shanghai Commission for Science and Technology (15431902900), and the Program of Shenzhen Science Technology and Innovation Committee (JCYJ20130329171031740, CXZZ20130515163643, and JCYJ20120831144704366).

Complaince with ethical standards

Conflicts of interest

The authors disclose no potential conflicts of interest.

Supplementary material

12032_2016_751_MOESM1_ESM.xlsx (32 kb)
Supplementary material 1 (XLSX 31 kb)

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Qiudao Wang
    • 1
    • 2
  • Yan An
    • 1
  • Qing Yuan
    • 2
  • Yao Qi
    • 2
  • Ying Ou
    • 2
  • Junhui Chen
    • 5
  • Jian Huang
    • 1
    • 2
    • 3
    • 4
    Email author
  1. 1.Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
  2. 2.National Engineering Center for Biochip at ShanghaiShanghaiChina
  3. 3.Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s HospitalGuangdong Medical CollegeShenzhenChina
  4. 4.Shanghai-MOST Key Laboratory for Disease and Health GenomicsChinese National Human Genome CenterShanghaiChina
  5. 5.Peking University Shenzhen HospitalShenzhenChina

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