Integrated genomics approach to identify biologically relevant alterations in fewer samples

BMC Genomics

Research Article

Pawan Upadhyay¹  Ankita Singh¹  Madhur Shetty¹  Ninad Oak¹  Amit Dutt¹  Mayur Tanna¹  Manoj Ramteke¹  Pratik Chandrani¹  Gorantala Venkata Raghuram¹  Prajish Iyer¹  Rohan Chaubal¹  Sudeep Gupta² 

[1] Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, 410210, Navi Mumbai, Maharashtra, India;Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, Maharashtra, India;

关键词: Exome Sequencing;    Transcriptome Sequencing;    Copy Number Analysis;    Altered Copy Number;    Relevant Alteration;   

DOI  :  10.1186/s12864-015-2138-4

 received in 2015-08-13, accepted in 2015-10-23,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundSeveral statistical tools have been developed to identify genes mutated at rates significantly higher than background, indicative of positive selection, involving large sample cohort studies. However, studies involving smaller sample sizes are inherently restrictive due to their limited statistical power to identify low frequency genetic variations.ResultsWe performed an integrated characterization of copy number, mutation and expression analyses of four head and neck cancer cell lines - NT8e, OT9, AW13516 and AW8507-- by applying a filtering strategy to prioritize for genes affected by two or more alterations within or across the cell lines. Besides identifying TP53, PTEN, HRAS and MET as major altered HNSCC hallmark genes, this analysis uncovered 34 novel candidate genes altered. Of these, we find a heterozygous truncating mutation in Nuclear receptor binding protein, NRBP1 pseudokinase gene, identical to as reported in other cancers, is oncogenic when ectopically expressed in NIH-3 T3 cells. Knockdown of NRBP1 in an oral carcinoma cell line bearing NRBP1 mutation inhibit transformation and survival of the cells.ConclusionsIn overall, we present the first comprehensive genomic characterization of four head and neck cancer cell lines established from Indian patients. We also demonstrate the ability of integrated analysis to uncover biologically important genetic variation in studies involving fewer or rare clinical specimens.

【 授权许可】

CC BY   
© Chandrani et al. 2015