Genome-wide identification of somatic aberrations from paired normal-tumor samples.
Genomic copy number alteration and allelic imbalance are distinct features of cancer cells, and recent advances in the genotyping technology have greatly boosted the research in the cancer genome. However, the complicated nature of tumor usually hampers the dissection of the SNP arrays. In this study, we describe a bioinformatic tool, named GIANT, for genome-wide identification of somatic aberrations from paired normal-tumor samples measured with SNP arrays. By efficiently incorporating genotype information of matched normal sample, it accurately detects different types of aberrations in cancer genome, even for aneuploid tumor samples with severe normal cell contamination. Furthermore, it allows for discovery of recurrent aberrations with critical biological properties in tumorigenesis by using statistical significance test. We demonstrate the superior performance of the proposed method on various datasets including tumor replicate pairs, simulated SNP arrays and dilution series of normal-cancer cell lines. Results show that GIANT has the potential to detect the genomic aberration even when the cancer cell proportion is as low as 5∼10%. Application on a large number of paired tumor samples delivers a genome-wide profile of the statistical significance of the various aberrations, including amplification, deletion and LOH. We believe that GIANT represents a powerful bioinformatic tool for interpreting the complex genomic aberration, and thus assisting both academic study and the clinical treatment of cancer.
Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, China ; School of Information Science and Technology, University of Science and Technology of China, Hefei, China.
Ao
A
Li
School of Information Science and Technology, University of Science and Technology of China, Hefei, China.
Yuanning
Y
Liu
School of Public Health, Anhui Medical University, Hefei, China.
Qihong
Q
Zhao
School of Information Science and Technology, University of Science and Technology of China, Hefei, China.
Huanqing
H
Feng
Seidman Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, United States of America.
Lyndsay
L
Harris
Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, China ; School of Information Science and Technology, University of Science and Technology of China, Hefei, China.
Minghui
M
Wang
D002460:Cell Line; D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*