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Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.

ABSTRACT: Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P?=?0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P?=?0.0017) and are co-selected to present synergistic functions (P?

SUBMITTER: Galante PA 

PROVIDER: S-EPMC3152357 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.

Galante Pedro A F PA   Parmigiani Raphael B RB   Zhao Qi Q   Caballero Otávia L OL   de Souza Jorge E JE   Navarro Fábio C P FC   Gerber Alexandra L AL   Nicolás Marisa F MF   Salim Anna Christina M AC   Silva Ana Paula M AP   Edsall Lee L   Devalle Sylvie S   Almeida Luiz G LG   Ye Zhen Z   Kuan Samantha S   Pinheiro Daniel G DG   Tojal Israel I   Pedigoni Renato G RG   de Sousa Rodrigo G M A RG   Oliveira Thiago Y K TY   de Paula Marcelo G MG   Ohno-Machado Lucila L   Kirkness Ewen F EF   Levy Samuel S   da Silva Wilson A WA   Vasconcelos Ana Tereza R AT   Ren Bing B   Zago Marco Antonio MA   Strausberg Robert L RL   Simpson Andrew J G AJ   de Souza Sandro J SJ   Camargo Anamaria A AA  

Nucleic acids research 20110414 14

Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable  ...[more]

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