Abstract
The interrelationship among genetic variations between the developing process of carcinoma and the order of occurrence has not been completely understood. Interpreting the mechanisms of copy number variation (CNV) is absolutely necessary for understanding the etiology of genetic disorders. Oncogenetic tree is a special phylogenetic tree inferential pictorial representation of oncogenesis. In our present study, we constructed oncogenetic tree to imitate the occurrence of genetic and cytogenetic alterations in human breast cancer. The oncogenetic tree model was built on CNV of ErbB2, AKT2, KRAS, PIK3CA, PTEN, and CCND1 genes in 963 cases of tumors with sequencing and CNA data of human breast cancer from TCGA. Results from the oncogenetic tree model indicate that ErbB2 copy number variation is the frequent early event of human breast cancer. The oncogenetic tree model based on the phylogenetic tree is a type of mathematical model that may eventually provide a better way to understand the process of oncogenesis.
Highlights
Copy number variations (CNVs) are a form of structural genetic alterations contributed to the initiation and progression of breast cancer
Distinct CNV patterns have been reported in breast cancer subgroups, which are correlated to different stages of cancer progression [2]
Important copy number variations were selected by searching the key words “copy number alterations”, “CNAS”, “breast cancer”, “deletion”, and “amplification” in Online Mendelian Inheritance in Man (OMIM), and candidate alteration biomarkers for breast cancer were chosen as ErbB2, AKT2, KRAS, PIK3CA, PTEN, and CCND1, whose copy number alterations we supposed would play a key role in the development of breast cancer based upon literature research
Summary
Copy number variations (CNVs) are a form of structural genetic alterations contributed to the initiation and progression of breast cancer They are an underlying cause of the cancer cell population adaption by affecting cell evolution including proliferation, fitness, and clonal selection [1]. Besides its application to depict the evolutionary descent of different species or organisms from the same ancestor, it is widely used in cancer study to reveal the phylogenetic relationships of tumor subclones during cell evolution. Based on the assumption that each of the subclones derived from a parental cell population carries all its alterations and acquires additional ones, phylogenetic tree describes this linear cancer genome evolution by constructing an oncogenetic tree representing common sequences of genetic events in tumor progression. Various bioinformatics software programs have been proposed for the construction of oncogenetic tree including TrAp [4] and oncotree [5]
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